From af89ba8efd34000f7423075e114e2dc52cb2ae2d Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 29 Feb 2024 17:13:37 +1100 Subject: [PATCH 01/44] Switch to use auto-generated interfaces --- MANIFEST.in | 2 - README.md | 13 - README.rst | 46 + conftest.py | 16 +- docs/conf.py | 51 - docs/requirements.txt | 10 + .../.codespell-ignorewords | 2 + fileformats-medimage-mrtrix3-extras/.flake8 | 17 + fileformats-medimage-mrtrix3-extras/LICENSE | 91 + .../README.rst | 37 + .../conftest.py | 45 + .../extras/medimage_mrtrix3/__init__.py | 5 + .../extras/medimage_mrtrix3/_version.py | 16 + .../extras/medimage_mrtrix3/converters.py | 64 + .../extras/medimage_mrtrix3/gradients.py | 10 + .../extras/medimage_mrtrix3/image.py | 34 + .../medimage_mrtrix3/tests/test_converters.py | 17 + .../extras/medimage_mrtrix3/tracks.py | 39 + .../pyproject.toml | 88 + .../pytest.ini | 8 + .../.codespell-ignorewords | 2 + fileformats-medimage-mrtrix3/.flake8 | 16 + fileformats-medimage-mrtrix3/LICENSE | 91 + fileformats-medimage-mrtrix3/README.rst | 48 + fileformats-medimage-mrtrix3/conftest.py | 37 + .../fileformats/medimage_mrtrix3/__init__.py | 15 + .../fileformats/medimage_mrtrix3/_version.py | 16 + .../fileformats/medimage_mrtrix3/dwi.py | 46 + .../fileformats/medimage_mrtrix3/image.py | 121 ++ .../fileformats/medimage_mrtrix3/in_out.py | 60 + .../fileformats/medimage_mrtrix3/track.py | 9 + fileformats-medimage-mrtrix3/pyproject.toml | 83 + fileformats-medimage-mrtrix3/pytest.ini | 8 + generate.py | 372 ++++ pydra/tasks/mrtrix3/__init__.py | 5 +- pydra/tasks/mrtrix3/_version.py | 525 ----- pydra/tasks/mrtrix3/base.py | 53 - pydra/tasks/mrtrix3/conftest.py | 33 - pydra/tasks/mrtrix3/latest.py | 3 + pydra/tasks/mrtrix3/manual/mrcalc_.py | 308 +++ pydra/tasks/mrtrix3/tests/__init__.py | 0 pydra/tasks/mrtrix3/tests/data/test.bval | 0 pydra/tasks/mrtrix3/tests/data/test.bvec | 0 pydra/tasks/mrtrix3/tests/data/test_b0.gz | 0 pydra/tasks/mrtrix3/tests/data/test_dwi.mif | 0 .../tasks/mrtrix3/tests/data/test_dwi.nii.gz | 0 pydra/tasks/mrtrix3/tests/test_utils.py | 42 - pydra/tasks/mrtrix3/utils.py | 169 -- pyproject.toml | 80 +- setup.cfg | 70 - setup.py | 23 - versioneer.py | 1917 ----------------- 52 files changed, 1856 insertions(+), 2907 deletions(-) delete mode 100644 MANIFEST.in delete mode 100644 README.md create mode 100644 README.rst delete mode 100644 docs/conf.py create mode 100644 docs/requirements.txt create mode 100644 fileformats-medimage-mrtrix3-extras/.codespell-ignorewords create mode 100644 fileformats-medimage-mrtrix3-extras/.flake8 create mode 100644 fileformats-medimage-mrtrix3-extras/LICENSE create mode 100644 fileformats-medimage-mrtrix3-extras/README.rst create mode 100644 fileformats-medimage-mrtrix3-extras/conftest.py create mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/__init__.py create mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py create mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py create mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/gradients.py create mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py create mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py create mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py create mode 100644 fileformats-medimage-mrtrix3-extras/pyproject.toml create mode 100644 fileformats-medimage-mrtrix3-extras/pytest.ini create mode 100644 fileformats-medimage-mrtrix3/.codespell-ignorewords create mode 100644 fileformats-medimage-mrtrix3/.flake8 create mode 100644 fileformats-medimage-mrtrix3/LICENSE create mode 100644 fileformats-medimage-mrtrix3/README.rst create mode 100644 fileformats-medimage-mrtrix3/conftest.py create mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/__init__.py create mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py create mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/dwi.py create mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py create mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/in_out.py create mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/track.py create mode 100644 fileformats-medimage-mrtrix3/pyproject.toml create mode 100644 fileformats-medimage-mrtrix3/pytest.ini create mode 100755 generate.py delete mode 100644 pydra/tasks/mrtrix3/_version.py delete mode 100644 pydra/tasks/mrtrix3/base.py delete mode 100644 pydra/tasks/mrtrix3/conftest.py create mode 100644 pydra/tasks/mrtrix3/latest.py create mode 100644 pydra/tasks/mrtrix3/manual/mrcalc_.py delete mode 100644 pydra/tasks/mrtrix3/tests/__init__.py delete mode 100644 pydra/tasks/mrtrix3/tests/data/test.bval delete mode 100644 pydra/tasks/mrtrix3/tests/data/test.bvec delete mode 100644 pydra/tasks/mrtrix3/tests/data/test_b0.gz delete mode 100644 pydra/tasks/mrtrix3/tests/data/test_dwi.mif delete mode 100644 pydra/tasks/mrtrix3/tests/data/test_dwi.nii.gz delete mode 100644 pydra/tasks/mrtrix3/tests/test_utils.py delete mode 100644 pydra/tasks/mrtrix3/utils.py delete mode 100644 setup.cfg delete mode 100755 setup.py delete mode 100644 versioneer.py diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index d1565cf..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,2 +0,0 @@ -include versioneer.py -include pydra/tasks/mrtrix3/_version.py diff --git a/README.md b/README.md deleted file mode 100644 index 93972ca..0000000 --- a/README.md +++ /dev/null @@ -1,13 +0,0 @@ -# Pydra Tasks for mrtrix3 - -[![Python package](https://github.com/nipype/pydra-mrtrix3/actions/workflows/pythonpackage.yml/badge.svg)](https://github.com/nipype/pydra-mrtrix3/actions/workflows/pythonpackage.yml) - -## For developers - -Install repo in developer mode from the source directory. It is also useful to -install pre-commit to take care of styling via black: - -``` -pip install -e .[dev] -pre-commit install -``` diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..7f202c9 --- /dev/null +++ b/README.rst @@ -0,0 +1,46 @@ +============================== +Pydra task package for mrtrix3 +============================== + +.. image:: https://github.com/nipype/pydra-mrtrix3/actions/workflows/pythonpackage.yaml/badge.svg + :target: https://github.com/nipype/pydra-mrtrix3/actions/workflows/pythonpackage.yaml +.. image:: https://codecov.io/gh/nipype/pydra-mrtrix3/branch/main/graph/badge.svg?token=UIS0OGPST7 + :target: https://codecov.io/gh/nipype/pydra-mrtrix3 +.. image:: https://img.shields.io/pypi/pyversions/pydra-mrtrix3.svg + :target: https://pypi.python.org/pypi/pydra-mrtrix3/ + :alt: Supported Python versions +.. image:: https://img.shields.io/pypi/v/pydra-mrtrix3.svg + :target: https://pypi.python.org/pypi/pydra-mrtrix3/ + :alt: Latest Version + + +This package contains a collection of Pydra task interfaces for the mrtrix3 toolkit. + + +Generation of interfaces +------------------------ + +Task interfaces are automatically generated from the MRtrix3 source code using the +`generate.py` script, with the exception of a few interfaces that are manually +written. + +Developer installation +---------------------- + +First install the package in editable mode + +.. code-block:: + + $ pip install -e .[test] + +Then generate the automic interfaces using + +.. code-block:: + + $ python3 generate.py + +This package comes with a battery of automatically generated test modules. They can be launched using + +.. code-block:: + + $ pytest --doctest-modules pydra/tasks/* diff --git a/conftest.py b/conftest.py index d1f3394..f6c49a9 100644 --- a/conftest.py +++ b/conftest.py @@ -1,12 +1,20 @@ import os -import tempfile -from pathlib import Path import pytest +from pathlib import Path + +os.environ["PATH"] = ( + str(Path(__file__).parent.parent.parent / "bin") + ":" + os.environ["PATH"] +) +os.environ["MRTRIX_CLI_PARSE_ONLY"] = "0" @pytest.fixture -def work_dir(): - return Path(tempfile.mkdtemp()) +def cli_parse_only(): + os.environ["MRTRIX_CLI_PARSE_ONLY"] = "1" + # You can set more environment variables here if needed + yield + # Clean up or reset environment variables if necessary + del os.environ["MRTRIX_CLI_PARSE_ONLY"] # For debugging in IDE's don't catch raised exceptions and let the IDE diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index cc372d9..0000000 --- a/docs/conf.py +++ /dev/null @@ -1,51 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) - - -# -- Project information ----------------------------------------------------- - -project = "pydra-mrtrix3" -copyright = "2020, Xihe Xie" -author = "Xihe Xie" - - -# -- General configuration --------------------------------------------------- - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] - - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = "alabaster" - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..6743c88 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,10 @@ +black >=22.12.0 +click >=8.1.3 +tqdm +attrs >=23.1.0 +fileformats >= 0.8 +fileformats-extras >= 0.2.1 +fileformats-medimage >= 0.4.4 +fileformats-medimage-extras >= 0.1.5 +fileformats-medimage-mrtrix3 +fileformats-medimage-mrtrix3-extras diff --git a/fileformats-medimage-mrtrix3-extras/.codespell-ignorewords b/fileformats-medimage-mrtrix3-extras/.codespell-ignorewords new file mode 100644 index 0000000..cfcbff2 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/.codespell-ignorewords @@ -0,0 +1,2 @@ +nd +te diff --git a/fileformats-medimage-mrtrix3-extras/.flake8 b/fileformats-medimage-mrtrix3-extras/.flake8 new file mode 100644 index 0000000..52a9a16 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/.flake8 @@ -0,0 +1,17 @@ + +[flake8] +doctests = True +exclude = + **/__init__.py + *build/ + docs/sphinxext/ + docs/tools/ + docs/conf.py + fileformats/extras/mrtrix3/_version.py + versioneer.py + docs/source/conf.py +max-line-length = 88 +select = C,E,F,W,B,B950 +extend-ignore = E203,E501,E129 +per-file-ignores = + setup.py:F401 diff --git a/fileformats-medimage-mrtrix3-extras/LICENSE b/fileformats-medimage-mrtrix3-extras/LICENSE new file mode 100644 index 0000000..7ad7921 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/LICENSE @@ -0,0 +1,91 @@ +Creative Commons Attribution 4.0 International Public License +By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License ("Public License"). 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Please read the FAQ for more information about official translations. diff --git a/fileformats-medimage-mrtrix3-extras/README.rst b/fileformats-medimage-mrtrix3-extras/README.rst new file mode 100644 index 0000000..974c55c --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/README.rst @@ -0,0 +1,37 @@ +FileFormats-mrtrix3 Extras +========================== +.. image:: https://github.com/arcanaframework/fileformats-mrtrix3-extras/actions/workflows/tests.yml/badge.svg + :target: https://github.com/arcanaframework/fileformats-mrtrix3-extras/actions/workflows/tests.yml +.. image:: https://codecov.io/gh/arcanaframework/fileformats-mrtrix3-extras/branch/main/graph/badge.svg?token=UIS0OGPST7 + :target: https://codecov.io/gh/arcanaframework/fileformats-mrtrix3-extras +.. image:: https://img.shields.io/github/stars/ArcanaFramework/fileformats-mrtrix3-extras.svg + :alt: GitHub stars + :target: https://github.com/ArcanaFramework/fileformats-mrtrix3 +.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat + :target: https://arcanaframework.github.io/fileformats/ + :alt: Documentation Status + + +This is a extras module for the fileformats-mrtrix3 package, which provides +additional functionality to format classes (i.e. aside from basic identification and validation), such as +conversion tools, metadata parsers, test data generators, etc... + + +Quick Installation +------------------ + +This extension can be installed for Python 3 using *pip*:: + + $ pip3 install fileformats-mrtrix3-extras + +This will install the core package and any other dependencies + +License +------- + +This work is licensed under a +`Creative Commons Attribution 4.0 International License `_ + +.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png + :target: http://creativecommons.org/licenses/by/4.0/ + :alt: Creative Commons Attribution 4.0 International License diff --git a/fileformats-medimage-mrtrix3-extras/conftest.py b/fileformats-medimage-mrtrix3-extras/conftest.py new file mode 100644 index 0000000..c5f2809 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/conftest.py @@ -0,0 +1,45 @@ +import os +import logging +from pathlib import Path +import tempfile +import pytest +from fileformats.medimage import DicomDir + +# Set DEBUG logging for unittests + +log_level = logging.WARNING + +logger = logging.getLogger("fileformats") +logger.setLevel(log_level) + +sch = logging.StreamHandler() +sch.setLevel(log_level) +formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") +sch.setFormatter(formatter) +logger.addHandler(sch) + + +# For debugging in IDE's don't catch raised exceptions and let the IDE +# break at it +if os.getenv("_PYTEST_RAISE", "0") != "0": + + @pytest.hookimpl(tryfirst=True) + def pytest_exception_interact(call): + raise call.excinfo.value + + @pytest.hookimpl(tryfirst=True) + def pytest_internalerror(excinfo): + raise excinfo.value + + +@pytest.fixture +def work_dir(): + work_dir = tempfile.mkdtemp() + return Path(work_dir) + + +@pytest.fixture(scope="session") +def dummy_dwi_dicom(): + import medimages4tests.dummy.dicom.mri.dwi.siemens.skyra.syngo_d13c as module + + return DicomDir(module.get_image()) diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/__init__.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/__init__.py new file mode 100644 index 0000000..2b41e46 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/__init__.py @@ -0,0 +1,5 @@ +from ._version import __version__ +from . import image +from . import gradients +from . import tracks +from . import converters diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py new file mode 100644 index 0000000..491a473 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py @@ -0,0 +1,16 @@ +# file generated by setuptools_scm +# don't change, don't track in version control +TYPE_CHECKING = False +if TYPE_CHECKING: + from typing import Tuple, Union + VERSION_TUPLE = Tuple[Union[int, str], ...] +else: + VERSION_TUPLE = object + +version: str +__version__: str +__version_tuple__: VERSION_TUPLE +version_tuple: VERSION_TUPLE + +__version__ = version = '3.0.5.dev860+g59980ada3' +__version_tuple__ = version_tuple = (3, 0, 5, 'dev860', 'g59980ada3') diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py new file mode 100644 index 0000000..260d218 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py @@ -0,0 +1,64 @@ +from fileformats.core import hook +from fileformats.medimage.base import MedicalImage + +from fileformats.medimage_mrtrix3 import ( + ImageFormat as MrtrixImage, + ImageHeader as MrtrixImageHeader, +) + +try: + from pydra.tasks.mrtrix3.utils import MRConvert +except ImportError: + from pydra.tasks.mrtrix3.latest import mrconvert as MRConvert + + in_out_file_kwargs = {"in_file": "input", "out_file": "output"} +else: + in_out_file_kwargs = {} + + +@hook.converter( + source_format=MedicalImage, + target_format=MrtrixImage, + out_ext=MrtrixImage.ext, + **in_out_file_kwargs, +) +def mrconvert(name, out_ext: str, **kwargs): + """Initiate an MRConvert task with the output file extension set + + Parameters + ---------- + name : str + name of the converter task + out_ext : str + extension of the output file, used by MRConvert to determine the desired format + + Returns + ------- + pydra.ShellCommandTask + the converter task + """ + return MRConvert(name=name, out_file="out" + out_ext, **kwargs) + + +@hook.converter( + source_format=MedicalImage, + target_format=MrtrixImageHeader, + out_ext=MrtrixImageHeader.ext, + **in_out_file_kwargs, +) +def mrconvert2(name, out_ext: str, **kwargs): + """Initiate an MRConvert task with the output file extension set + + Parameters + ---------- + name : str + name of the converter task + out_ext : str + extension of the output file, used by MRConvert to determine the desired format + + Returns + ------- + pydra.ShellCommandTask + the converter task + """ + return MRConvert(name=name, out_file="out" + out_ext, **kwargs) diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/gradients.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/gradients.py new file mode 100644 index 0000000..4b9f9b5 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/gradients.py @@ -0,0 +1,10 @@ +import numpy as np +from fileformats.medimage import DwiEncoding +from fileformats.medimage_mrtrix3 import BFile + + +@DwiEncoding.read_array.register +def bfile_read_array(bfile: BFile) -> np.ndarray: + return np.asarray( + [[float(x) for x in ln.split()] for ln in bfile.read_contents().splitlines()] + ) diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py new file mode 100644 index 0000000..1d05734 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py @@ -0,0 +1,34 @@ +import os +from unittest import mock +import typing as ty +from pathlib import Path +import numpy as np +from random import Random +from medimages4tests.dummy.nifti import get_image as get_dummy_nifti +from fileformats.core import FileSet +from fileformats.medimage import MedicalImage, Nifti1 +from fileformats.medimage_mrtrix3 import ImageFormat + + +@FileSet.generate_sample_data.register +def generate_mrtrix_sample_data( + mif: ImageFormat, + dest_dir: Path, + seed: ty.Union[int, Random] = 0, + stem: ty.Optional[str] = None, +) -> ty.Iterable[Path]: + nifti = Nifti1(get_dummy_nifti(dest_dir / "nifti.nii")) + with mock.patch.dict(os.environ, {"MRTRIX_CLI_PARSE_ONLY": "0"}): + mif = ImageFormat.convert(nifti) + return mif.fspaths + + +@MedicalImage.read_array.register +def mrtrix_read_array(mif: ImageFormat) -> np.ndarray: + raise NotImplementedError( + "Need to work out how to use the metadata to read the array in the correct order" + ) + data = mif.read_contents(offset=mif.data_offset) + array = np.asarray(data) + data_array = array.reshape(mif.dims) + return data_array diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py new file mode 100644 index 0000000..cf85377 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py @@ -0,0 +1,17 @@ +from fileformats.medimage import NiftiBvec +from fileformats.medimage_mrtrix3 import ImageFormat, ImageHeader + + +# @pytest.mark.xfail(reason="not sure what the reason is at this stage, might be bug in Pydra") +def test_nifti_to_mrtrix(dummy_dwi_dicom): + nifti_fsgrad = NiftiBvec.convert(dummy_dwi_dicom) + ImageFormat.convert(nifti_fsgrad) + ImageHeader.convert(nifti_fsgrad) + + +def test_dicom_to_mrtrix_image(dummy_dwi_dicom): + ImageFormat.convert(dummy_dwi_dicom) + + +def test_dicom_to_mrtrix_image_header(dummy_dwi_dicom): + ImageHeader.convert(dummy_dwi_dicom) diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py new file mode 100644 index 0000000..2d2a866 --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py @@ -0,0 +1,39 @@ +import time +import struct +import math +from pathlib import Path +import typing as ty +from random import Random +from fileformats.core import FileSet +from fileformats.medimage_mrtrix3 import Tracks + + +@FileSet.generate_sample_data.register +def generate_tracks_sample_data( + tracks: Tracks, + dest_dir: Path, + seed: ty.Union[int, Random] = 0, + stem: ty.Optional[str] = None, +) -> ty.Iterable[Path]: + """Generate a tracks file with a single straight track of length 10""" + fspath = dest_dir / "tracks.tck" + timestamp = str(time.time() * 1e9 + time.process_time_ns()) + contents = f"""mrtrix tracks +datatype: Float32BE +timestamp: {timestamp} +count: 1 +total_count: 1 +file: . """ + byte_contents = contents.encode() + offset = len(byte_contents) + math.ceil(math.log10(len(byte_contents))) + 5 + byte_contents += str(offset).encode() + b"\nEND\n" + for i in range(10): + ib = i.to_bytes(32, "big") + byte_contents += ib + ib + ib + nan_bytes = struct.pack("!d", float("nan")) + inf_bytes = struct.pack("!d", float("inf")) + byte_contents += nan_bytes + nan_bytes + nan_bytes + byte_contents += inf_bytes + inf_bytes + inf_bytes + with open(fspath, "wb") as f: + f.write(byte_contents) + return [fspath] diff --git a/fileformats-medimage-mrtrix3-extras/pyproject.toml b/fileformats-medimage-mrtrix3-extras/pyproject.toml new file mode 100644 index 0000000..22a069d --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/pyproject.toml @@ -0,0 +1,88 @@ +[build-system] +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" + +[project] +name = "fileformats-medimage-mrtrix3-extras" +description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" +readme = "README.rst" +requires-python = ">=3.8" +dependencies = [ + "fileformats >= 0.8", + "fileformats-medimage-mrtrix3", + "pydra >= 0.22.0" +] +license = {file = "LICENSE"} +authors = [ + {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, +] +maintainers = [ + {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, +] +keywords = [ + "file formats", + "data", +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Environment :: Console", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Apache Software License", + "Operating System :: MacOS :: MacOS X", + "Operating System :: Microsoft :: Windows", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Topic :: Scientific/Engineering", +] +dynamic = ["version"] + +[project.optional-dependencies] +dev = [ + "black", + "pre-commit", + "codespell", + "flake8", + "flake8-pyproject", +] +test = [ + "pytest >=6.2.5", + "pytest-env>=0.6.2", + "pytest-cov>=2.12.1", + "medimages4tests", + "codecov", +] + +converters = [ +] + +[project.urls] +repository = "https://github.com/MRtrix3/mrtrix3" + +[tool.hatch.version] +source = "vcs" +raw-options = { root = "../../.." } + +[tool.hatch.build.hooks.vcs] +version-file = "fileformats/extras/medimage_mrtrix3/_version.py" + +[tool.hatch.build.targets.wheel] +packages = ["fileformats"] + +[tool.black] +target-version = ['py38'] +exclude = "fileformats/extras/medimage_mrtrix3/_version.py" + +[tool.codespell] +ignore-words = ".codespell-ignorewords" + +[tool.flake8] +doctests = true +per-file-ignores = [ + "__init__.py:F401" +] +max-line-length = 88 +select = "C,E,F,W,B,B950" +extend-ignore = ['E203', 'E501', 'E129'] diff --git a/fileformats-medimage-mrtrix3-extras/pytest.ini b/fileformats-medimage-mrtrix3-extras/pytest.ini new file mode 100644 index 0000000..790edbe --- /dev/null +++ b/fileformats-medimage-mrtrix3-extras/pytest.ini @@ -0,0 +1,8 @@ +[pytest] +#log_cli=true +#log_level=NOTSET +filterwarnings = + default::DeprecationWarning:__main__ + ignore::DeprecationWarning + ignore::_pytest.warning_types.PytestCollectionWarning + ignore::PendingDeprecationWarning diff --git a/fileformats-medimage-mrtrix3/.codespell-ignorewords b/fileformats-medimage-mrtrix3/.codespell-ignorewords new file mode 100644 index 0000000..cfcbff2 --- /dev/null +++ b/fileformats-medimage-mrtrix3/.codespell-ignorewords @@ -0,0 +1,2 @@ +nd +te diff --git a/fileformats-medimage-mrtrix3/.flake8 b/fileformats-medimage-mrtrix3/.flake8 new file mode 100644 index 0000000..6bda53a --- /dev/null +++ b/fileformats-medimage-mrtrix3/.flake8 @@ -0,0 +1,16 @@ + +[flake8] +doctests = True +exclude = + **/__init__.py + *build/ + docs/sphinxext/ + docs/tools/ + docs/conf.py + fileformats/mrtrix3/_version.py + docs/source/conf.py +max-line-length = 88 +select = C,E,F,W,B,B950 +extend-ignore = E203,E501,E129 +per-file-ignores = + setup.py:F401 diff --git a/fileformats-medimage-mrtrix3/LICENSE b/fileformats-medimage-mrtrix3/LICENSE new file mode 100644 index 0000000..7ad7921 --- /dev/null +++ b/fileformats-medimage-mrtrix3/LICENSE @@ -0,0 +1,91 @@ +Creative Commons Attribution 4.0 International Public License +By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License ("Public License"). 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For the avoidance of doubt, this paragraph does not form part of the public licenses. + +Creative Commons may be contacted at creativecommons.org. + +Additional languages available: العربية, čeština, Deutsch, Ελληνικά, Español, euskara, suomeksi, français, hrvatski, Bahasa Indonesia, italiano, 日本語, 한국어, Lietuvių, latviski, te reo Māori, Nederlands, norsk, polski, português, română, русский, Slovenščina, svenska, Türkçe, українська, 中文, 華語. Please read the FAQ for more information about official translations. diff --git a/fileformats-medimage-mrtrix3/README.rst b/fileformats-medimage-mrtrix3/README.rst new file mode 100644 index 0000000..db33314 --- /dev/null +++ b/fileformats-medimage-mrtrix3/README.rst @@ -0,0 +1,48 @@ +How to customise this template +============================== + +#. Name your repository with the name fileformats- +#. Rename the `fileformats/mrtrix3` directory to the name of the fileformats subpackage the extras are for +#. Search and replace "mrtrix3" with the name of the fileformats subpackage the extras are to be added +#. Replace name + email placeholders in `pyproject.toml` for developers and maintainers +#. Add the extension file-format classes +#. Ensure that all the extension file-format classes are imported into the extras package root, i.e. `fileformats/mrtrix3` +#. Delete these instructions + +... + +FileFormats Extension - mrtrix3 +==================================== +.. image:: https://github.com/arcanaframework/fileformats-mrtrix3/actions/workflows/tests.yml/badge.svg + :target: https://github.com/arcanaframework/fileformats-mrtrix3/actions/workflows/tests.yml +.. image:: https://codecov.io/gh/arcanaframework/fileformats-mrtrix3/branch/main/graph/badge.svg?token=UIS0OGPST7 + :target: https://codecov.io/gh/arcanaframework/fileformats-mrtrix3 +.. image:: https://img.shields.io/github/stars/ArcanaFramework/fileformats-mrtrix3.svg + :alt: GitHub stars + :target: https://github.com/ArcanaFramework/fileformats-mrtrix3 +.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat + :target: https://arcanaframework.github.io/fileformats/ + :alt: Documentation Status + +This is the "mrtrix3" extension module for the +[fileformats](https://github.com/ArcanaFramework/fileformats-core) package + + +Quick Installation +------------------ + +This extension can be installed for Python 3 using *pip*:: + + $ pip3 install fileformats-mrtrix3 + +This will install the core package and any other dependencies + +License +------- + +This work is licensed under a +`Creative Commons Attribution 4.0 International License `_ + +.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png + :target: http://creativecommons.org/licenses/by/4.0/ + :alt: Creative Commons Attribution 4.0 International License diff --git a/fileformats-medimage-mrtrix3/conftest.py b/fileformats-medimage-mrtrix3/conftest.py new file mode 100644 index 0000000..2a703c0 --- /dev/null +++ b/fileformats-medimage-mrtrix3/conftest.py @@ -0,0 +1,37 @@ +import os +import logging +from pathlib import Path +import tempfile +import pytest + +# Set DEBUG logging for unittests + +log_level = logging.WARNING + +logger = logging.getLogger("fileformats") +logger.setLevel(log_level) + +sch = logging.StreamHandler() +sch.setLevel(log_level) +formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") +sch.setFormatter(formatter) +logger.addHandler(sch) + + +# For debugging in IDE's don't catch raised exceptions and let the IDE +# break at it +if os.getenv("_PYTEST_RAISE", "0") != "0": + + @pytest.hookimpl(tryfirst=True) + def pytest_exception_interact(call): + raise call.excinfo.value + + @pytest.hookimpl(tryfirst=True) + def pytest_internalerror(excinfo): + raise excinfo.value + + +@pytest.fixture +def work_dir(): + work_dir = tempfile.mkdtemp() + return Path(work_dir) diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/__init__.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/__init__.py new file mode 100644 index 0000000..abd61f2 --- /dev/null +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/__init__.py @@ -0,0 +1,15 @@ +from ._version import __version__ + +from .image import ImageFormat, ImageFormatGz, ImageHeader, ImageDataFile +from .in_out import ImageIn, ImageOut +from .dwi import ( + BFile, + NiftiB, + NiftiGzB, + NiftiGzXB, + NiftiXB, + ImageFormatB, + ImageFormatGzB, + ImageHeaderB, +) +from .track import Tracks diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py new file mode 100644 index 0000000..491a473 --- /dev/null +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py @@ -0,0 +1,16 @@ +# file generated by setuptools_scm +# don't change, don't track in version control +TYPE_CHECKING = False +if TYPE_CHECKING: + from typing import Tuple, Union + VERSION_TUPLE = Tuple[Union[int, str], ...] +else: + VERSION_TUPLE = object + +version: str +__version__: str +__version_tuple__: VERSION_TUPLE +version_tuple: VERSION_TUPLE + +__version__ = version = '3.0.5.dev860+g59980ada3' +__version_tuple__ = version_tuple = (3, 0, 5, 'dev860', 'g59980ada3') diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/dwi.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/dwi.py new file mode 100644 index 0000000..74bbcff --- /dev/null +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/dwi.py @@ -0,0 +1,46 @@ +from fileformats.core import hook +from fileformats.core.mixin import WithAdjacentFiles +from fileformats.medimage import DwiEncoding, Nifti1, NiftiGz, NiftiX, NiftiGzX +from .image import ImageFormat, ImageHeader, ImageFormatGz + + +class BFile(DwiEncoding): + """MRtrix-style diffusion encoding, all in one file""" + + ext = ".b" + + +# NIfTI file format gzipped with BIDS side car +class WithBFile(WithAdjacentFiles): + @hook.required + @property + def encoding(self) -> BFile: + return BFile(self.select_by_ext(BFile)) + + +class NiftiB(WithBFile, Nifti1): + iana_mime = "application/x-nifti2+b" + + +class NiftiGzB(WithBFile, NiftiGz): + iana_mime = "application/x-nifti2+gzip.b" + + +class NiftiXB(WithBFile, NiftiX): + iana_mime = "application/x-nifti2+json.b" + + +class NiftiGzXB(WithBFile, NiftiGzX): + iana_mime = "application/x-nifti2+gzip.json.b" + + +class ImageFormatB(WithBFile, ImageFormat): + pass + + +class ImageFormatGzB(WithBFile, ImageFormatGz): + pass + + +class ImageHeaderB(WithBFile, ImageHeader): + pass diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py new file mode 100644 index 0000000..253c69a --- /dev/null +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py @@ -0,0 +1,121 @@ +import typing as ty +from pathlib import Path +from fileformats.core import hook +from fileformats.generic import File +from fileformats.application import Gzip +from fileformats.core.mixin import WithMagicNumber +from fileformats.core.exceptions import FormatMismatchError +import fileformats.medimage + + +class MultiLineMetadataValue(list): + pass + + +class BaseMrtrixImage(WithMagicNumber, fileformats.medimage.MedicalImage, File): + + magic_number = b"mrtrix image\n" + binary = True + + def read_metadata(self): + metadata = {} + with open(self.fspath, "rb") as f: + line = f.readline() + if line != self.magic_number: + raise FormatMismatchError( + f"Magic line {line} doesn't match reference {self.magic_number}" + ) + line = f.readline().decode("utf-8") + while line and line != "END\n": + key, value = line.split(": ", maxsplit=1) + if "," in value: + try: + value = [int(v) for v in value.split(",")] + except ValueError: + try: + value = [float(v) for v in value.split(",")] + except ValueError: + pass + else: + try: + value = int(value) + except ValueError: + try: + value = float(value) + except ValueError: + pass + if key in metadata: + if isinstance(metadata[key], MultiLineMetadataValue): + metadata[key].append(value) + else: + metadata[key] = MultiLineMetadataValue([metadata[key], value]) + else: + metadata[key] = value + line = f.readline().decode("utf-8") + return metadata + + @property + def data_fspath(self): + data_fspath = self.metadata["file"].split()[0] + if data_fspath == ".": + data_fspath = self.fspath + elif Path(data_fspath).parent == Path("."): + data_fspath = self.fspath.parent / data_fspath + else: + data_fspath = Path(data_fspath).relative_to(self.fspath.parent) + return data_fspath + + @property + def data_offset(self): + return int(self.metadata["file"].split()[1]) + + @property + def vox_sizes(self): + return self.metadata["vox"] + + @property + def dims(self): + return self.metadata["dim"] + + +class ImageFormat(BaseMrtrixImage): + + ext = ".mif" + + @hook.check + def check_data_file(self): + if self.data_fspath != self.fspath: + raise FormatMismatchError( + f"Data file ('{self.data_fspath}') is not set to the same file as header " + f"('{self.fspath}')" + ) + + @property + def data_file(self): + return self + + +class ImageFormatGz(Gzip[ImageFormat]): + + ext = ".mif.gz" + + +class ImageHeader(BaseMrtrixImage): + + ext = ".mih" + + @hook.required + @property + def data_file(self): + return ImageDataFile(self.data_fspath) + + def __attrs_post_init__(self): + if len(self.fspaths) == 1: + # add in data file if only header file is provided + self.fspaths |= set([BaseMrtrixImage(self.fspath).data_fspath]) + super().__attrs_post_init__() + + +class ImageDataFile(File): + + ext = ".dat" diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/in_out.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/in_out.py new file mode 100644 index 0000000..fd5ab7b --- /dev/null +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/in_out.py @@ -0,0 +1,60 @@ +import typing as ty +from fileformats.application import Dicom +from fileformats.medimage import ( + DicomDir, + NiftiGzX, + NiftiGz, + NiftiX, + Nifti1, + Nifti2, + Mgh, + MghGz, + Analyze, +) +from .image import ImageFormat, ImageHeader, ImageFormatGz +from .dwi import ( + NiftiB, + NiftiGzB, + NiftiGzXB, + NiftiXB, + ImageFormatB, + ImageFormatGzB, + ImageHeaderB, +) + + +ImageIn = ty.Union[ + ImageFormat, + ImageFormatGz, + ImageHeader, + ImageFormatB, + ImageFormatGzB, + ImageHeaderB, + Dicom, + DicomDir, + NiftiGzX, + NiftiGz, + NiftiX, + Nifti1, + Nifti2, + Mgh, + MghGz, + Analyze, +] + +ImageOut = ty.Union[ + ImageFormat, + ImageFormatGz, + ImageHeader, + ImageFormatB, + ImageFormatGzB, + ImageHeaderB, + NiftiGzX, + NiftiGz, + NiftiX, + Nifti1, + Nifti2, + Mgh, + MghGz, + Analyze, +] diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/track.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/track.py new file mode 100644 index 0000000..d1dee77 --- /dev/null +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/track.py @@ -0,0 +1,9 @@ +from fileformats.generic import File +from fileformats.core.mixin import WithMagicNumber + + +class Tracks(WithMagicNumber, File): + + ext = ".tck" + magic_number = b"mrtrix tracks\n" + binary = True diff --git a/fileformats-medimage-mrtrix3/pyproject.toml b/fileformats-medimage-mrtrix3/pyproject.toml new file mode 100644 index 0000000..352f651 --- /dev/null +++ b/fileformats-medimage-mrtrix3/pyproject.toml @@ -0,0 +1,83 @@ +[build-system] +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" + +[project] +name = "fileformats-medimage-mrtrix3" +description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" +readme = "README.rst" +requires-python = ">=3.8" +dependencies = [ + "fileformats >= 0.8.5", + "fileformats-medimage >= 0.4.4" +] +license = {file = "LICENSE"} +authors = [ + {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, +] +maintainers = [ + {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, +] # Ideally this would be the generic MRtrix developers authors list, but will leave it as me for now +keywords = [ + "file formats", + "data", +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Environment :: Console", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Apache Software License", + "Operating System :: MacOS :: MacOS X", + "Operating System :: Microsoft :: Windows", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Topic :: Scientific/Engineering", +] +dynamic = ["version"] + +[project.optional-dependencies] +dev = [ + "black", + "pre-commit", + "codespell", + "flake8", + "flake8-pyproject", +] +test = [ + "pytest >=6.2.5", + "pytest-env>=0.6.2", + "pytest-cov>=2.12.1", + "codecov", +] + +[project.urls] +repository = "https://github.com/MRtrix3/mrtrix3" + +[tool.hatch.version] +source = "vcs" +raw-options = { root = "../../.." } + +[tool.hatch.build.hooks.vcs] +version-file = "fileformats/medimage_mrtrix3/_version.py" + +[tool.hatch.build.targets.wheel] +packages = ["fileformats"] + +[tool.black] +target-version = ['py38'] +exclude = "fileformats/medimage_mrtrix3/_version.py" + +[tool.codespell] +ignore-words = ".codespell-ignorewords" + +[tool.flake8] +doctests = true +per-file-ignores = [ + "__init__.py:F401" +] +max-line-length = 88 +select = "C,E,F,W,B,B950" +extend-ignore = ['E203', 'E501', 'E129'] diff --git a/fileformats-medimage-mrtrix3/pytest.ini b/fileformats-medimage-mrtrix3/pytest.ini new file mode 100644 index 0000000..790edbe --- /dev/null +++ b/fileformats-medimage-mrtrix3/pytest.ini @@ -0,0 +1,8 @@ +[pytest] +#log_cli=true +#log_level=NOTSET +filterwarnings = + default::DeprecationWarning:__main__ + ignore::DeprecationWarning + ignore::_pytest.warning_types.PytestCollectionWarning + ignore::PendingDeprecationWarning diff --git a/generate.py b/generate.py new file mode 100755 index 0000000..3678335 --- /dev/null +++ b/generate.py @@ -0,0 +1,372 @@ +#!/usr/bin/env python3 +import os +import sys +import attrs +from pathlib import Path +import subprocess as sp +import typing as ty +from importlib import import_module +import logging +from traceback import format_exc +import re +from tqdm import tqdm +import click +import black.report +import black.parsing +from fileformats.core import FileSet +from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, ImageOut, Tracks +from pydra.engine.helpers import make_klass +from pydra.engine import specs + + +logger = logging.getLogger("pydra-auto-gen") + +# Ignore non-standard tools that will need to be added manually +IGNORE = [ + "blend", + "convert_bruker", + "gen_scheme", + "notfound", + "for_each", + "mrview", + "shview", +] + + +CMD_PREFIXES = [ + "fivett", + "afd", + "amp", + "connectome", + "dcm", + "dir", + "dwi", + "fixel", + "fod", + "label", + "mask", + "mesh", + "mr", + "mt", + "peaks", + "sh", + "tck", + "tensor", + "transform", + "tsf", + "voxel", + "vector", + "warp", + "response", +] + + +@click.command( + help="""Loops through all MRtrix commands to generate Pydra +(https://pydra.readthedocs.io) task interfaces for them + +CMD_DIR the command directory to list the commands from + +OUTPUT_DIR the output directory to write the generated files to + +MRTRIX_VERSION the version of MRTrix the commands are generated for +""" +) +@click.argument( + "cmd_dir", + type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path), +) +@click.argument("output_dir", type=click.Path(exists=False, path_type=Path)) +@click.argument("mrtrix_version", type=str) +@click.option( + "--log-errors/--raise-errors", + type=bool, + help="whether to log errors (and skip to the next tool) instead of raising them", +) +@click.option( + "--latest/--not-latest", + type=bool, + default=False, + help="whether to write 'latest' module", +) +@click.option( + "--log-level", + type=click.Choice(["debug", "info", "warning", "error", "critical"]), + default="warning", + help="logging level", +) +def auto_gen_mrtrix3_pydra( + cmd_dir: Path, + mrtrix_version: str, + output_dir: Path, + log_errors: bool, + latest: bool, + log_level: str, +): + + logging.basicConfig(level=getattr(logging, log_level.upper())) + + pkg_version = "v" + "_".join(mrtrix_version.split(".")[:2]) + + cmd_dir = cmd_dir.absolute() + + # Insert output dir to path so we can load the generated tasks in order to + # generate the tests + sys.path.insert(0, str(output_dir)) + + manual_cmds = [] + manual_path = output_dir / "pydra" / "tasks" / "mrtrix3" / "manual" + if manual_path.exists(): + for manual_file in manual_path.iterdir(): + manual_cmd = manual_file.stem[:-1] + if not manual_cmd.startswith(".") and not manual_cmd.startswith("__"): + manual_cmds.append(manual_cmd) + + cmds = [] + for cmd_name in tqdm( + sorted(os.listdir(cmd_dir)), + "generating Pydra interfaces for all MRtrix3 commands", + ): + if ( + cmd_name.startswith("_") + or "." in cmd_name + or cmd_name in IGNORE + or cmd_name in manual_cmds + ): + continue + cmd = [str(cmd_dir / cmd_name)] + cmds.extend( + auto_gen_cmd(cmd, cmd_name, output_dir, cmd_dir, log_errors, pkg_version) + ) + + # Write init + init_path = output_dir / "pydra" / "tasks" / "mrtrix3" / pkg_version / "__init__.py" + imports = "\n".join(f"from .{c}_ import {pascal_case_task_name(c)}" for c in cmds) + imports += "\n" + "\n".join( + f"from ..manual.{c}_ import {pascal_case_task_name(c)}" for c in manual_cmds + ) + init_path.write_text(f"# Auto-generated, do not edit\n\n{imports}\n") + + if latest: + latest_path = output_dir / "pydra" / "tasks" / "mrtrix3" / "latest.py" + latest_path.write_text( + f"# Auto-generated, do not edit\n\nfrom .{pkg_version} import *\n" + ) + print(f"Generated pydra.tasks.mrtrix3.{pkg_version} package") + + # Test out import + import_module(f"pydra.tasks.mrtrix3.{pkg_version}") + + +def auto_gen_cmd( + cmd: ty.List[str], + cmd_name: str, + output_dir: Path, + cmd_dir: Path, + log_errors: bool, + pkg_version: str, +) -> ty.List[str]: + base_cmd = str(cmd_dir / cmd[0]) + cmd = [base_cmd] + cmd[1:] + try: + code_str = sp.check_output(cmd + ["__print_usage_pydra__"]).decode("utf-8") + except sp.CalledProcessError: + if log_errors: + logger.error("Could not generate interface for '%s'", cmd_name) + logger.error(format_exc()) + return [] + else: + raise + + if re.match(r"(\w+,)+\w+", code_str): + sub_cmds = [] + for algorithm in code_str.split(","): + sub_cmds.extend( + auto_gen_cmd( + cmd + [algorithm], + f"{cmd_name}_{algorithm}", + output_dir, + cmd_dir, + log_errors, + pkg_version, + ) + ) + return sub_cmds + + # Since Python identifiers can't start with numbers we need to rename 5tt* + # with fivett* + if cmd_name.startswith("5tt"): + old_name = cmd_name + cmd_name = escape_cmd_name(cmd_name) + code_str = code_str.replace(f"class {old_name}", f"class {cmd_name}") + code_str = code_str.replace(f"{old_name}_input", f"{cmd_name}_input") + code_str = code_str.replace(f"{old_name}_output", f"{cmd_name}_output") + code_str = re.sub(r"(? str: + return cmd_name.replace("5tt", "fivett") + + +def pascal_case_task_name(cmd_name: str) -> str: + # convert to PascalCase + if cmd_name == "population_template": + return "PopulationTemplate" + try: + return "".join( + g.capitalize() + for g in re.match( + rf"({'|'.join(CMD_PREFIXES)}?)(2?)([^_]+)(_?)(.*)", cmd_name + ).groups() + ) + except AttributeError as e: + raise ValueError( + f"Could not convert {cmd_name} to PascalCase, please add its prefix to CMD_PREFIXES" + ) from e + + +if __name__ == "__main__": + from pathlib import Path + + script_dir = Path(__file__).parent + + mrtrix_version = sp.check_output( + "git describe --tags --abbrev=0", cwd=script_dir, shell=True + ).decode("utf-8") + + auto_gen_mrtrix3_pydra(sys.argv[1:]) diff --git a/pydra/tasks/mrtrix3/__init__.py b/pydra/tasks/mrtrix3/__init__.py index df2eb78..df4106e 100644 --- a/pydra/tasks/mrtrix3/__init__.py +++ b/pydra/tasks/mrtrix3/__init__.py @@ -2,7 +2,4 @@ >>> import pydra >>> import pydra.tasks.mrtrix3 """ -from ._version import get_versions - -__version__ = get_versions()["version"] -del get_versions +from ._version import __version__ diff --git a/pydra/tasks/mrtrix3/_version.py b/pydra/tasks/mrtrix3/_version.py deleted file mode 100644 index 309cdb6..0000000 --- a/pydra/tasks/mrtrix3/_version.py +++ /dev/null @@ -1,525 +0,0 @@ - -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.19 (https://github.com/python-versioneer/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "" - cfg.versionfile_source = "pydra/tasks/mrtrix3/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip().decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post0.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post0.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} diff --git a/pydra/tasks/mrtrix3/base.py b/pydra/tasks/mrtrix3/base.py deleted file mode 100644 index 89d909b..0000000 --- a/pydra/tasks/mrtrix3/base.py +++ /dev/null @@ -1,53 +0,0 @@ -import attr -import typing as ty -from pydra.engine.specs import ShellSpec, File - - -@attr.s(auto_attribs=True, kw_only=True) -class MRTrix3BaseSpec(ShellSpec): - """mrtrix3 command standard input specs - - includes: nthreads, grad_file, grad_fsl, force, quiet - """ - - # number of threads - nthreads: ty.Optional[int] = attr.ib( - default=None, - metadata={ - "help_string": "number of CPU threads to use for multi-threading", - "argstr": "-nthreads", - }, - ) - - # gradient files in mrtrix3 format - grad_file: File = attr.ib( - metadata={ - "help_string": "MRTrix3 format gradient file", - "argstr": "-grad", - "xor": "grad_fsl", - } - ) - - # gradient files in FSL format - grad_fsl: ty.List[File] = attr.ib( - metadata={ - "help_string": "FSL format gradient files [bvecs, bvals]", - "argstr": "-fslgrad", - "xor": "grad_file", - } - ) - - # force outputs - force: ty.Optional[bool] = attr.ib( - metadata={ - "help_string": "force & replace output if one already exists", - "argstr": "-force", - } - ) - - # progress & information messages - quiet: ty.Optional[bool] = attr.ib( - metadata={ - "help_string": "Whether to display progress and information messages", - "argstr": "-quiet", - } - ) diff --git a/pydra/tasks/mrtrix3/conftest.py b/pydra/tasks/mrtrix3/conftest.py deleted file mode 100644 index b121c79..0000000 --- a/pydra/tasks/mrtrix3/conftest.py +++ /dev/null @@ -1,33 +0,0 @@ -# Created from https://github.com/nipype/pydra-fsl/blob/master/pydra/tasks/fsl/conftest.py - -import os -import shutil -import pytest -import py.path as pp -from tempfile import mkdtemp - -TEST_DATADIR = os.path.realpath(os.path.join(os.path.dirname(__file__), "tests/data")) -temp_folder = mkdtemp() -data_dir = os.path.join(temp_folder, "data") -shutil.copytree(TEST_DATADIR, data_dir) - - -@pytest.fixture(autouse=True) -def _docdir(request): - doctest_plugin = request.config.pluginmanager.getplugin("doctest") - if isinstance(request.node, doctest_plugin.DoctestItem): - - # get the fixture dynamically by its name - tmpdir = pp.local(data_dir) - - # chdir only for duration of the test - with tmpdir.as_cwd(): - yield - - else: - # For normal tests, yield: - yield - - -def pytest_unconfigure(config): - shutil.rmtree(temp_folder) diff --git a/pydra/tasks/mrtrix3/latest.py b/pydra/tasks/mrtrix3/latest.py new file mode 100644 index 0000000..4b28d17 --- /dev/null +++ b/pydra/tasks/mrtrix3/latest.py @@ -0,0 +1,3 @@ +# Auto-generated, do not edit + +from .v3_0 import * diff --git a/pydra/tasks/mrtrix3/manual/mrcalc_.py b/pydra/tasks/mrtrix3/manual/mrcalc_.py new file mode 100644 index 0000000..aff91a9 --- /dev/null +++ b/pydra/tasks/mrtrix3/manual/mrcalc_.py @@ -0,0 +1,308 @@ +import typing as ty +from pathlib import Path # noqa: F401 +from enum import Enum +from fileformats.generic import File, Directory # noqa: F401 +from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks # noqa: F401 +from pydra.engine import specs, ShellCommandTask + + +class MrCalcOp(Enum): + abs = "abs" # return absolute value (magnitude) of real or complex number + neg = "neg" # negative value + add = "add" # add values + subtract = "subtract" # subtract values + multiply = "multiply" # multiply values + divide = "divide" # divide values + modulo = "modulo" # modulo operation + min = "min" # minimum value + max = "max" # maximum value + lt = "lt" # less than comparison + gt = "gt" # greater than comparison + le = "le" # less than or equal to comparison + ge = "ge" # greater than or equal to comparison + eq = "eq" # equal to comparison + neq = "neq" # not equal to comparison + if_ = "if" # if-else condition + replace = "replace" # replace values + sqrt = "sqrt" # square root + pow = "pow" # power operation + round = "round" # round to nearest integer + ceil = "ceil" # round up to nearest integer + floor = "floor" # round down to nearest integer + not_ = "not" # logical NOT operation + and_ = "and" # logical AND operation + or_ = "or" # logical OR operation + xor = "xor" # logical XOR operation + isnan = "isnan" # check if value is NaN + isinf = "isinf" # check if value is infinity + finite = "finite" # check if value is finite + complex = "complex" # convert to complex number + polar = "polar" # convert to polar coordinates + real = "real" # get real part of complex number + imag = "imag" # get imaginary part of complex number + phase = "phase" # get phase angle of complex number + conj = "conj" # complex conjugate + proj = "proj" # projection of complex number + exp = "exp" # exponential function + log = "log" # natural logarithm + log10 = "log10" # base-10 logarithm + cos = "cos" # cosine function + sin = "sin" # sine function + tan = "tan" # tangent function + acos = "acos" # arc cosine function + asin = "asin" # arc sine function + atan = "atan" # arc tangent function + cosh = "cosh" # hyperbolic cosine function + sinh = "sinh" # hyperbolic sine function + tanh = "tanh" # hyperbolic tangent function + acosh = "acosh" # inverse hyperbolic cosine function + asinh = "asinh" # inverse hyperbolic sine function + atanh = "atanh" # inverse hyperbolic tangent function + + +def operations_formatter( + operations: ty.List[ty.Tuple[ty.List[ty.Union[ImageIn, float]], MrCalcOp]] +): + return " ".join( + [ + f"{' '.join([str(i) for i in operands])} -{op.value}" + for operands, op in operations + ] + ) + + +input_fields = [ + # Arguments + ( + "operations", + ty.List[ty.Tuple[ty.List[ty.Union[ImageIn, float]], MrCalcOp]], + { + "argstr": "", + "sep": " ", + "position": 0, + "formatter": operations_formatter, + "help_string": """an input image, intensity value, or the special keywords 'rand' (random number between 0 and 1) or 'randn' (random number from unit std.dev. normal distribution) or the mathematical constants 'e' and 'pi'.""", + "mandatory": True, + }, + ), + ( + "output", + Path, + { + "argstr": "", + "position": -1, + "help_string": """the output image.""", + "output_file_template": "mrcalc_output.mif", + }, + ), + # Data type options Option Group + ( + "datatype", + str, + { + "argstr": "-datatype", + "help_string": "specify output image data type.", + "allowed_values": [ + "float16", + "float16", + "float16le", + "float16be", + "float32", + "float32le", + "float32be", + "float64", + "float64le", + "float64be", + "int64", + "uint64", + "int64le", + "uint64le", + "int64be", + "uint64be", + "int32", + "uint32", + "int32le", + "uint32le", + "int32be", + "uint32be", + "int16", + "uint16", + "int16le", + "uint16le", + "int16be", + "uint16be", + "cfloat16", + "cfloat16le", + "cfloat16be", + "cfloat32", + "cfloat32le", + "cfloat32be", + "cfloat64", + "cfloat64le", + "cfloat64be", + "int8", + "uint8", + "bit", + ], + }, + ), + # Standard options + ( + "info", + bool, + { + "argstr": "-info", + "help_string": """display information messages.""", + }, + ), + ( + "quiet", + bool, + { + "argstr": "-quiet", + "help_string": """do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.""", + }, + ), + ( + "debug", + bool, + { + "argstr": "-debug", + "help_string": """display debugging messages.""", + }, + ), + ( + "force", + bool, + { + "argstr": "-force", + "help_string": """force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).""", + }, + ), + ( + "nthreads", + int, + { + "argstr": "-nthreads", + "help_string": """use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).""", + }, + ), + ( + "config", + specs.MultiInputObj[ty.Tuple[str, str]], + { + "argstr": "-config", + "help_string": """temporarily set the value of an MRtrix config file entry.""", + }, + ), + ( + "help", + bool, + { + "argstr": "-help", + "help_string": """display this information page and exit.""", + }, + ), + ( + "version", + bool, + { + "argstr": "-version", + "help_string": """display version information and exit.""", + }, + ), +] + +MrCalcInputSpec = specs.SpecInfo( + name="mrcalc_input", fields=input_fields, bases=(specs.ShellSpec,) +) + + +output_fields = [ + ( + "output", + ImageOut, + { + "help_string": """the output image.""", + }, + ), +] +MrCalcOutputSpec = specs.SpecInfo( + name="mrcalc_output", fields=output_fields, bases=(specs.ShellOutSpec,) +) + + +class MrCalc(ShellCommandTask): + """This command will only compute per-voxel operations. Use 'mrmath' to compute summary statistics across images or along image axes. + + This command uses a stack-based syntax, with operators (specified using options) operating on the top-most entries (i.e. images or values) in the stack. Operands (values or images) are pushed onto the stack in the order they appear (as arguments) on the command-line, and operators (specified as options) operate on and consume the top-most entries in the stack, and push their output as a new entry on the stack. + + As an additional feature, this command will allow images with different dimensions to be processed, provided they satisfy the following conditions: for each axis, the dimensions match if they are the same size, or one of them has size one. In the latter case, the entire image will be replicated along that axis. This allows for example a 4D image of size [ X Y Z N ] to be added to a 3D image of size [ X Y Z ], as if it consisted of N copies of the 3D image along the 4th axis (the missing dimension is assumed to have size 1). Another example would a single-voxel 4D image of size [ 1 1 1 N ], multiplied by a 3D image of size [ X Y Z ], which would allow the creation of a 4D image where each volume consists of the 3D image scaled by the corresponding value for that volume in the single-voxel image. + + + Example usages + -------------- + + + Double the value stored in every voxel: + + `$ mrcalc a.mif 2 -mult r.mif` + + This performs the operation: r = 2*a for every voxel a,r in images a.mif and r.mif respectively. + + + A more complex example: + + `$ mrcalc a.mif -neg b.mif -div -exp 9.3 -mult r.mif` + + This performs the operation: r = 9.3*exp(-a/b) + + + Another complex example: + + `$ mrcalc a.mif b.mif -add c.mif d.mif -mult 4.2 -add -div r.mif` + + This performs: r = (a+b)/(c*d+4.2). + + + Rescale the densities in a SH l=0 image: + + `$ mrcalc ODF_CSF.mif 4 pi -mult -sqrt -div ODF_CSF_scaled.mif` + + This applies the spherical harmonic basis scaling factor: 1.0/sqrt(4*pi), such that a single-tissue voxel containing the same intensities as the response function of that tissue should contain the value 1.0. + + + References + ---------- + + Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137 + + + MRtrix + ------ + + Version:3.0.4-691-g05465c3c-dirty, built Sep 29 2023 + + Author: J-Donald Tournier (jdtournier@gmail.com) + + Copyright: Copyright (c) 2008-2023 the MRtrix3 contributors. + + This Source Code Form is subject to the terms of the Mozilla Public + License, v. 2.0. If a copy of the MPL was not distributed with this + file, You can obtain one at http://mozilla.org/MPL/2.0/. + + Covered Software is provided under this License on an "as is" + basis, without warranty of any kind, either expressed, implied, or + statutory, including, without limitation, warranties that the + Covered Software is free of defects, merchantable, fit for a + particular purpose or non-infringing. + See the Mozilla Public License v. 2.0 for more details. + + For more details, see http://www.mrtrix.org/. + """ + + Op = Operator = MrCalcOp + + executable = "mrcalc" + input_spec = MrCalcInputSpec + output_spec = MrCalcOutputSpec diff --git a/pydra/tasks/mrtrix3/tests/__init__.py b/pydra/tasks/mrtrix3/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/pydra/tasks/mrtrix3/tests/data/test.bval b/pydra/tasks/mrtrix3/tests/data/test.bval deleted file mode 100644 index e69de29..0000000 diff --git a/pydra/tasks/mrtrix3/tests/data/test.bvec b/pydra/tasks/mrtrix3/tests/data/test.bvec deleted file mode 100644 index e69de29..0000000 diff --git a/pydra/tasks/mrtrix3/tests/data/test_b0.gz b/pydra/tasks/mrtrix3/tests/data/test_b0.gz deleted file mode 100644 index e69de29..0000000 diff --git a/pydra/tasks/mrtrix3/tests/data/test_dwi.mif b/pydra/tasks/mrtrix3/tests/data/test_dwi.mif deleted file mode 100644 index e69de29..0000000 diff --git a/pydra/tasks/mrtrix3/tests/data/test_dwi.nii.gz b/pydra/tasks/mrtrix3/tests/data/test_dwi.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/pydra/tasks/mrtrix3/tests/test_utils.py b/pydra/tasks/mrtrix3/tests/test_utils.py deleted file mode 100644 index 6b5906f..0000000 --- a/pydra/tasks/mrtrix3/tests/test_utils.py +++ /dev/null @@ -1,42 +0,0 @@ -from pathlib import Path -import pytest -from pydra.tasks.mrtrix3.utils import MRConvert -from medimages4tests.dummy.dicom.mri.dwi.siemens.skyra.syngo_d13c import ( - get_image as get_dwi_dicom, -) -from medimages4tests.dummy.nifti import get_image as get_nifti - - -@pytest.fixture -def dwi_dicom_dataset(): - return get_dwi_dicom() - - -@pytest.fixture -def nifti_dataset(work_dir): - return get_nifti(work_dir / "nifti", compressed=True) - - -def test_mrconvert_default_out_file(nifti_dataset): - - task = MRConvert(in_file=nifti_dataset, axes=[0, 1, 2, -1]) - - result = task() - - assert Path(result.output.out_file).exists() - - -@pytest.mark.xfail( - reason=( - "Cannot pass input to input field with 'output_file_template' " - "https://github.com/nipype/pydra/pull/585 (or equivalent) is merged " - "into main branch" - ) -) -def test_mrconvert_explicit_out_file(dwi_dicom_dataset): - - task = MRConvert(in_file=dwi_dicom_dataset, out_file="test.nii.gz") - - result = task() - - assert Path(result.output.out_file).exists() diff --git a/pydra/tasks/mrtrix3/utils.py b/pydra/tasks/mrtrix3/utils.py deleted file mode 100644 index ba9de0b..0000000 --- a/pydra/tasks/mrtrix3/utils.py +++ /dev/null @@ -1,169 +0,0 @@ -import attr -import typing as ty -from pydra import ShellCommandTask -from pydra.engine.specs import SpecInfo, ShellOutSpec -from .base import MRTrix3BaseSpec - - -MRConvertInputSpec = SpecInfo( - name="MRConvertInputs", - fields=[ - ( - "in_file", - attr.ib( - type=str, - metadata={ - "argstr": "{in_file}", - "position": 1, - "help_string": "input image", - "mandatory": True, - }, - ), - ), - ( - "out_file", - attr.ib( - type=str, - metadata={ - "position": -1, - "argstr": "", - "help_string": "output image", - "output_file_template": "{in_file}_converted", - }, - ), - ), - ( - "coord", - attr.ib( - type=ty.Tuple[int, ty.Union[int, str]], - metadata={ - "sep": " ", - "argstr": "-coord", - "help_string": "extract data at the specific coordinatest", - }, - ), - ), - ( - "vox", - attr.ib( - type=ty.List[float], - metadata={ - "sep": ",", - "argstr": "-vox", - "help_string": "change the voxel dimensions", - }, - ), - ), - ( - "axes", - attr.ib( - type=ty.List[int], - metadata={ - "sep": ",", - "argstr": "-axes", - "help_string": "specify the axes that will be used", - }, - ), - ), - ( - "scaling", - attr.ib( - type=ty.List[float], - metadata={ - "sep": ",", - "argstr": "-scaling", - "help_string": "specify the data scaling parameter", - }, - ), - ), - ( - "export_grad", - attr.ib( - type=str, - metadata={ - "argstr": "-export_grad_mrtrix {export_grad}", - "help_string": "export gradient encodings in mrtrix3 file format", - "output_file_template": "{export_grad}", - }, - ), - ), - ( - "export_json", - attr.ib( - type=str, - metadata={ - "argstr": "-json_export {export_json}", - "help_string": "export image headet to JSON file", - "output_file_template": "{export_json}", - }, - ), - ), - # ( - # "export_grad_fsl", - # attr.ib( - # type=ty.Tuple[str, str], - # metadata={ - # "argstr": "-export_grad_fsl", - # "help_string": "export gradient encodings in FSL file format", - # "sep": " ", - # "output_file_template": "{in_file}_bvec {in_file}_bval", - # }, - # ) - # ) - ], - bases=(MRTrix3BaseSpec,), -) - -MRConvertOutputSpec = SpecInfo( - name="MRConvertOutputs", - fields=[], - bases=(ShellOutSpec,), -) - - -class MRConvert(ShellCommandTask): - """ - Example - ------ - - Convert NIfTI file with FSL-style gradient encoding files to - MRtrix Image Format with MRtrix-style gradient encoding files - - >>> task = MRConvert() - >>> task.inputs.in_file = "test_dwi.nii.gz" - >>> task.inputs.grad_fsl = ["test.bvec", "test.bval"] - >>> task.inputs.export_grad = "test.b" - >>> task.inputs.out_file = "test.mif" - >>> task.cmdline - 'mrconvert test_dwi.nii.gz -fslgrad test.bvec test.bval -export_grad_mrtrix test.b test.mif' - - Select the first volume from a diffusion-weighted dataset - - >>> task = MRConvert() - >>> task.inputs.in_file = "test_dwi.nii.gz" - >>> task.inputs.out_file = "vol.nii.gz" - >>> task.inputs.coord = [3, 0] - >>> task.cmdline - 'mrconvert test_dwi.nii.gz -coord 3 0 vol.nii.gz' - - Extend a 3D image to 4D by adding a singular dimension - - >>> task = MRConvert() - >>> task.inputs.in_file = "test_b0.nii.gz" - >>> task.inputs.out_file = "4d.nii.gz" - >>> task.inputs.axes = [0, 1, 2, -1] - >>> task.cmdline - 'mrconvert test_b0.nii.gz -axes 0,1,2,-1 4d.nii.gz' - - """ - - input_spec = MRConvertInputSpec - output_spec = MRConvertOutputSpec - executable = "mrconvert" - - # >>> task = MRConvert() - # >>> task.inputs.in_file = "test_dwi.mif" - # >>> task.inputs.export_grad_fsl = ("test.bvec", "test.bval") - # >>> task.inputs.out_file = "test.mif" - # >>> task.cmdline - # 'mrconvert test_dwi.mif -export_grad_fsl test.bvec test.bval test.mif' diff --git a/pyproject.toml b/pyproject.toml index f18a62b..b61a138 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,2 +1,80 @@ [build-system] -requires = ["setuptools==62", "wheel"] +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" + +[project] +name = "pydra-mrtrix3" +description = "pydra-mrtrix3 contains Pydra task specifications for MRtrix3 tools" +readme = "README.md" +requires-python = ">=3.8" +dependencies = [ + "pydra >=0.22", + "fileformats-medimage >=0.3.4"] +license = {file = "LICENCE.txt"} +authors = [ + {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, +] +maintainers = [ + {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, +] +keywords = ["pydra"] +classifiers = [ + "Development Status :: 2 - Pre-Alpha", + "Environment :: Console", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Apache Software License", + "Operating System :: MacOS :: MacOS X", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering", +] +dynamic = ["version"] + +[project.optional-dependencies] +dev = [ + "black", + "pre-commit", +] +doc = [ + "packaging", + "sphinx >=2.1.2", + "sphinx_rtd_theme", + "sphinxcontrib-apidoc ~=0.3.0", + "sphinxcontrib-napoleon", + "sphinxcontrib-versioning", +] +test = [ + "pytest >= 4.4.0", + "pytest-cov", + "pytest-env", + "pytest-xdist", + "pytest-rerunfailures", + "codecov", +] + +[tool.hatch.version] +source = "vcs" +raw-options = { root = "../../.." } + +[tool.hatch.build.hooks.vcs] +version-file = "pydra/tasks/mrtrix3/_version.py" + +[tool.hatch.build.targets.wheel] +packages = ["pydra"] +include-only = ["pydra/tasks/mrtrix3"] + +[tool.black] +target-version = ["py38"] +exclude = "_version.py" + +[tool.codespell] +ignore-words = ".codespell-ignorewords" + +[tool.flake8] +doctests = true +per-file-ignores = [ + "__init__.py:F401" +] +max-line-length = 88 +select = "C,E,F,W,B,B950" +extend-ignore = ['E203', 'E501', 'E129', 'W503'] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 100a2ad..0000000 --- a/setup.cfg +++ /dev/null @@ -1,70 +0,0 @@ -[metadata] -author = Nipype developers -author_email = neuroimaging@python.org -description = Pydra tasks for MRtrix3 -long_description = file:README.md -long_description_content_type = text/markdown; variant=CommonMark -license = Apache License, 2.0 -classifiers = - Development Status :: 3 - Alpha - Environment :: Console - Intended Audience :: Science/Research - License :: OSI Approved :: Apache Software License - Operating System :: MacOS :: MacOS X - Operating System :: POSIX :: Linux - Programming Language :: Python :: 3.7 - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3.9 - Topic :: Scientific/Engineering - -[options] -python_requires = >=3.7 -install_requires = - pydra >= 0.19 -packages = find_namespace: - -[options.packages.find] -include = - pydra.tasks.mrtrix3 - pydra.tasks.mrtrix3.* - -[options.extras_require] -doc = - packaging - sphinx >= 2.1.2 - sphinx_rtd_theme - sphinxcontrib-apidoc ~= 0.3.0 - sphinxcontrib-napoleon - sphinxcontrib-versioning -docs = - %(doc)s -test = - pytest >= 4.4.0 - pytest-cov - pytest-env - pytest-xdist - pytest-rerunfailures - medimages4tests >= 0.2 - codecov -tests = - %(test)s -dev = - %(test)s - black - pre-commit -all = - %(doc)s - %(dev)s - -[versioneer] -VCS = git -style = pep440 -versionfile_source = pydra/tasks/mrtrix3/_version.py -versionfile_build = pydra/tasks/mrtrix3/_version.py -tag_prefix = -parentdir_prefix = - - -[tool:pytest] -addopts = --doctest-modules --doctest-report ndiff -doctest_optionflags= NORMALIZE_WHITESPACE ELLIPSIS diff --git a/setup.py b/setup.py deleted file mode 100755 index a2d6461..0000000 --- a/setup.py +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env python -import sys - -from setuptools import setup -import versioneer - -SUBPACKAGE = "mrtrix3" - -# Give setuptools a hint to complain if it's too old a version -# 30.3.0 allows us to put most metadata in setup.cfg -# 40.1.0 enables the `find_namespace:` directive -# Should match pyproject.toml -SETUP_REQUIRES = ["setuptools >= 40.1.0"] -# This enables setuptools to install wheel on-the-fly -SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else [] - -if __name__ == "__main__": - setup( - name=f"pydra-{SUBPACKAGE}", - setup_requires=SETUP_REQUIRES, - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - ) diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index d5e0eb5..0000000 --- a/versioneer.py +++ /dev/null @@ -1,1917 +0,0 @@ -# Version: 0.19 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/python-versioneer/python-versioneer -* Brian Warner -* License: Public Domain -* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3 -* [![Latest Version][pypi-image]][pypi-url] -* [![Build Status][travis-image]][travis-url] - -This is a tool for managing a recorded version number in distutils-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -* `pip install versioneer` to somewhere in your $PATH -* add a `[versioneer]` section to your setup.cfg (see [Install](INSTALL.md)) -* run `versioneer install` in your source tree, commit the results -* Verify version information with `python setup.py version` - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes). - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/python-versioneer/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other languages) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg`, if necessary, to include any new configuration settings - indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - -## Similar projects - -* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time - dependency -* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of - versioneer - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg -[pypi-url]: https://pypi.python.org/pypi/versioneer/ -[travis-image]: -https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg -[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer - -""" - -import configparser -import errno -import json -import os -import re -import subprocess -import sys - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ( - "Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND')." - ) - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - me = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(me)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir: - print( - "Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py) - ) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise EnvironmentError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.ConfigParser() - with open(setup_cfg, "r") as f: - parser.read_file(f) - VCS = parser.get("versioneer", "VCS") # mandatory - - def get(parser, name): - if parser.has_option("versioneer", name): - return parser.get("versioneer", name) - return None - - cfg = VersioneerConfig() - cfg.VCS = VCS - cfg.style = get(parser, "style") or "" - cfg.versionfile_source = get(parser, "versionfile_source") - cfg.versionfile_build = get(parser, "versionfile_build") - cfg.tag_prefix = get(parser, "tag_prefix") - if cfg.tag_prefix in ("''", '""'): - cfg.tag_prefix = "" - cfg.parentdir_prefix = get(parser, "parentdir_prefix") - cfg.verbose = get(parser, "verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen( - [c] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - ) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip().decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -LONG_VERSION_PY[ - "git" -] = r''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.19 (https://github.com/python-versioneer/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = p.communicate()[0].strip().decode() - if p.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%%s*" %% tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], - cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post0.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post0.dev%%d" %% pieces["distance"] - else: - # exception #1 - rendered = "0.post0.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - "%s*" % tag_prefix, - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ - 0 - ].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(manifest_in, versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [manifest_in, versionfile_source] - if ipy: - files.append(ipy) - try: - me = __file__ - if me.endswith(".pyc") or me.endswith(".pyo"): - me = os.path.splitext(me)[0] + ".py" - versioneer_file = os.path.relpath(me) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - f = open(".gitattributes", "r") - for line in f.readlines(): - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - f.close() - except EnvironmentError: - pass - if not present: - f = open(".gitattributes", "a+") - f.write("%s export-subst\n" % versionfile_source) - f.close() - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.19) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except EnvironmentError: - raise NotThisMethod("unable to read _version.py") - mo = re.search( - r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - mo = re.search( - r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post0.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post0.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert ( - cfg.versionfile_source is not None - ), "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(cmdclass=None): - """Get the custom setuptools/distutils subclasses used by Versioneer. - - If the package uses a different cmdclass (e.g. one from numpy), it - should be provide as an argument. - """ - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - - cmds = {} if cmdclass is None else cmdclass.copy() - - # we add "version" to both distutils and setuptools - from distutils.core import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - - cmds["version"] = cmd_version - - # we override "build_py" in both distutils and setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # we override different "build_py" commands for both environments - if "build_py" in cmds: - _build_py = cmds["build_py"] - elif "setuptools" in sys.modules: - from setuptools.command.build_py import build_py as _build_py - else: - from distutils.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_py"] = cmd_build_py - - if "setuptools" in sys.modules: - from setuptools.command.build_ext import build_ext as _build_ext - else: - from distutils.command.build_ext import build_ext as _build_ext - - class cmd_build_ext(_build_ext): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_ext.run(self) - if self.inplace: - # build_ext --inplace will only build extensions in - # build/lib<..> dir with no _version.py to write to. - # As in place builds will already have a _version.py - # in the module dir, we do not need to write one. - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_ext"] = cmd_build_ext - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if "py2exe" in sys.modules: # py2exe enabled? - from py2exe.distutils_buildexe import py2exe as _py2exe - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["py2exe"] = cmd_py2exe - - # we override different "sdist" commands for both environments - if "sdist" in cmds: - _sdist = cmds["sdist"] - elif "setuptools" in sys.modules: - from setuptools.command.sdist import sdist as _sdist - else: - from distutils.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file( - target_versionfile, self._versioneer_generated_versions - ) - - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -INIT_PY_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - - -def do_setup(): - """Do main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except ( - EnvironmentError, - configparser.NoSectionError, - configparser.NoOptionError, - ) as e: - if isinstance(e, (EnvironmentError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except EnvironmentError: - old = "" - if INIT_PY_SNIPPET not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(INIT_PY_SNIPPET) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make sure both the top-level "versioneer.py" and versionfile_source - # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so - # they'll be copied into source distributions. Pip won't be able to - # install the package without this. - manifest_in = os.path.join(root, "MANIFEST.in") - simple_includes = set() - try: - with open(manifest_in, "r") as f: - for line in f: - if line.startswith("include "): - for include in line.split()[1:]: - simple_includes.add(include) - except EnvironmentError: - pass - # That doesn't cover everything MANIFEST.in can do - # (http://docs.python.org/2/distutils/sourcedist.html#commands), so - # it might give some false negatives. Appending redundant 'include' - # lines is safe, though. - if "versioneer.py" not in simple_includes: - print(" appending 'versioneer.py' to MANIFEST.in") - with open(manifest_in, "a") as f: - f.write("include versioneer.py\n") - else: - print(" 'versioneer.py' already in MANIFEST.in") - if cfg.versionfile_source not in simple_includes: - print( - " appending versionfile_source ('%s') to MANIFEST.in" - % cfg.versionfile_source - ) - with open(manifest_in, "a") as f: - f.write("include %s\n" % cfg.versionfile_source) - else: - print(" versionfile_source already in MANIFEST.in") - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(manifest_in, cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - errors = do_setup() - errors += scan_setup_py() - if errors: - sys.exit(1) From 3248179218505225a27076059b9aa36fb003a247 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 29 Feb 2024 17:14:35 +1100 Subject: [PATCH 02/44] fixed up relative paths in pyproject.tomls --- fileformats-medimage-mrtrix3-extras/pyproject.toml | 2 +- fileformats-medimage-mrtrix3/pyproject.toml | 2 +- pyproject.toml | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/fileformats-medimage-mrtrix3-extras/pyproject.toml b/fileformats-medimage-mrtrix3-extras/pyproject.toml index 22a069d..e3874f3 100644 --- a/fileformats-medimage-mrtrix3-extras/pyproject.toml +++ b/fileformats-medimage-mrtrix3-extras/pyproject.toml @@ -63,7 +63,7 @@ repository = "https://github.com/MRtrix3/mrtrix3" [tool.hatch.version] source = "vcs" -raw-options = { root = "../../.." } +raw-options = { root = ".." } [tool.hatch.build.hooks.vcs] version-file = "fileformats/extras/medimage_mrtrix3/_version.py" diff --git a/fileformats-medimage-mrtrix3/pyproject.toml b/fileformats-medimage-mrtrix3/pyproject.toml index 352f651..fa372a1 100644 --- a/fileformats-medimage-mrtrix3/pyproject.toml +++ b/fileformats-medimage-mrtrix3/pyproject.toml @@ -58,7 +58,7 @@ repository = "https://github.com/MRtrix3/mrtrix3" [tool.hatch.version] source = "vcs" -raw-options = { root = "../../.." } +raw-options = { root = ".." } [tool.hatch.build.hooks.vcs] version-file = "fileformats/medimage_mrtrix3/_version.py" diff --git a/pyproject.toml b/pyproject.toml index b61a138..297879a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,6 @@ test = [ [tool.hatch.version] source = "vcs" -raw-options = { root = "../../.." } [tool.hatch.build.hooks.vcs] version-file = "pydra/tasks/mrtrix3/_version.py" From 390fa057bcc80d9eea03cbe474dcb009ecd37ee1 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 29 Feb 2024 17:54:44 +1100 Subject: [PATCH 03/44] created ci-cd.yaml workflow --- .github/workflows/ci-cd.yml | 296 ++++++++++++++++++++++++++++ .github/workflows/pythonpackage.yml | 129 ------------ pyproject.toml | 6 + 3 files changed, 302 insertions(+), 129 deletions(-) create mode 100644 .github/workflows/ci-cd.yml delete mode 100644 .github/workflows/pythonpackage.yml diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml new file mode 100644 index 0000000..3d0b1da --- /dev/null +++ b/.github/workflows/ci-cd.yml @@ -0,0 +1,296 @@ +#This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +# For deployment, it will be necessary to create a PyPI API token and store it as a secret +# https://docs.github.com/en/actions/reference/encrypted-secrets + +name: CI/CD + +on: + push: + branches: [ master ] + tags: [ '*' ] + pull_request: + branches: + - master + - develop + +jobs: + + generate: + + runs-on: ubuntu-latest + + env: + CFLAGS: -Werror + QT_SELECT: qt6 + SCCACHE_GHA_ENABLED: "true" + SCCACHE_CACHE_SIZE: "2G" + + steps: + - uses: actions/checkout@v1 + with: + submodules: true + + - name: install dependencies + run: | + sudo apt-get update + sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build + + - name: Run sccache-cache + uses: mozilla-actions/sccache-action@v0.0.3 + + - name: Get CMake + uses: lukka/get-cmake@latest + with: + cmakeVersion: '3.16.3' + + - name: Print CMake version + run: cmake --version + + - name: Clone latest MRtrix and switch to latest tag + run: | + git clone https://github.com/tclose/mrtrix3.git + cd mrtrix3 + git checkout pydra-usage + echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV + git checkout $MRTRIX3_VERSION + + - name: configure + run: > + cmake + -B build + -G Ninja + -D CMAKE_BUILD_TYPE=Release + -D MRTRIX_BUILD_TESTS=ON + -D MRTRIX_STL_DEBUGGING=ON + -D MRTRIX_WARNINGS_AS_ERRORS=ON + -D CMAKE_C_COMPILER=clang + -D CMAKE_CXX_COMPILER=clang++ + -D CMAKE_INSTALL_PREFIX=$(pwd)/install + + - name: Build Mrtrix + run: cmake --build build + + - name: Install Mrtrix + run: cmake --install build + + - name: Set PATH Variable + run: echo "PATH=$PATH:$(pwd)/install/bin" >> $GITHUB_ENV + + - name: Set LD_LIBRARY_PATH Variable + run: echo "LD_LIBRARY_PATH=$(pwd)/install/lib" >> $GITHUB_ENV + + - name: Change back to the root directory + run: cd .. + + - name: Set up Python + uses: actions/setup-python@v2 + + - name: Install Python build dependencies + run: | + python -m pip install --upgrade pip + + - name: Install pydra-auto-gen requirements + run: | + pip install -e fileformats-medimage-mrtrix3 + pip install -e fileformats-medimage-mrtrix3-extras + pip install -e .[dev,test] + + - name: Generate task specifications + run: > + .generate.py + $(pwd)/mrtrix3/install/bin + $(pwd) + $MRTRIX3_VERSION + --log-errors + --latest + + - name: Upload MRtrix3 install + uses: actions/upload-artifact@v2 + with: + name: MRtrix3 + path: mrtrix3/install + + - name: Upload auto-gen pydra + uses: actions/upload-artifact@v2 + with: + name: AutoGen + path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + + - name: Write version file + run: echo $MRTRIX3_VERSION > mrtrix3_version.txt + + - name: Upload version file + uses: actions/upload-artifact@v2 + with: + name: VersionFile + path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + + devcheck: + needs: [generate] + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.8, 3.11] # Check oldest and newest versions + pip-flags: ['', '--editable'] + pydra: + - 'pydra' + - '--editable git+https://github.com/nipype/pydra.git#egg=pydra' + + steps: + - uses: actions/checkout@v2 + + - name: Download version file + uses: actions/download-artifact@v2 + with: + name: VersionFile + path: mrtrix3_version.txt + + - name: Extract Mrtrix version + run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV + + - name: Download auto-gen pydra + uses: actions/download-artifact@v2 + with: + name: AutoGen + path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + + - name: Install build dependencies + run: | + python -m pip install --upgrade pip + + - name: Install Pydra + run: | + pip install ${{ matrix.pydra }} + python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + + - name: Install task package + run: | + pip install ${{ matrix.pip-flags }} "fileformats-medimage-mrtrix3" + pip install ${{ matrix.pip-flags }} ".[dev]" + python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.tasks.mrtrix3.v3_0" + python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + + test: + needs: [generate] + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.8, 3.11] + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v2 + - name: Download version file + uses: actions/download-artifact@v2 + with: + name: VersionFile + path: mrtrix3_version.txt + + - name: Extract Mrtrix version + run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV + + - name: Download auto-gen pydra + uses: actions/download-artifact@v2 + with: + name: AutoGen + path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + + - name: Download MRtrix3 install + uses: actions/download-artifact@v2 + with: + name: MRtrix3 + path: mrtrix3/install + + - name: Set PATH Variable + run: echo "PATH=$PATH:$(pwd)/install/bin" >> $GITHUB_ENV + + - name: Set LD_LIBRARY_PATH Variable + run: echo "LD_LIBRARY_PATH=$(pwd)/install/lib" >> $GITHUB_ENV + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + + - name: Install build dependencies + run: | + python -m pip install --upgrade pip + + - name: Install task package + run: | + pip install .fileformats-medimage-mrtrix interfaces/ ./fileformats-medimage-mrtrix-extras ''.[test]' + python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + + - name: Test with pytest + run: | + pytest -sv --doctest-modules pydra/tasks/mrtrix3 \ + --cov pydra.tasks.mrtrix3 --cov-report xml + + - uses: codecov/codecov-action@v1 + if: ${{ always() }} + + + deploy: + needs: [devcheck, test] + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.11] + steps: + - uses: actions/checkout@v2 + + - name: Download auto-gen pydra + uses: actions/download-artifact@v2 + with: + name: AutoGen + path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + + - name: Install build tools + run: python -m pip install --upgrade pip twine build + + - name: Build source and wheel distributions + working-directory: ./interfaces/pydra/src + run: python -m build + + - name: Check distributions + run: twine check interfaces/pydra/src/dist/* + + - name: Upload sdist + uses: actions/upload-artifact@v2 + with: + name: SDist + path: interfaces/pydra/src/dist/*.tar.gz + + # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. + # Secrets are not accessible in the if: condition [0], so set an output variable [1] + # [0] https://github.community/t/16928 + # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter + - name: Check for PyPI token on tag + id: deployable + if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') + env: + PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}" + run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi + + - name: Upload to PyPI + if: steps.deployable.outputs.DEPLOY + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.PYPI_API_TOKEN }} + packages-dir: interfaces/pydra/src/dist/ diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml deleted file mode 100644 index 6d87072..0000000 --- a/.github/workflows/pythonpackage.yml +++ /dev/null @@ -1,129 +0,0 @@ -#This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -# For deployment, it will be necessary to create a PyPI API token and store it as a secret -# https://docs.github.com/en/actions/reference/encrypted-secrets - -name: Python package - -# Set once -env: - SUBPACKAGE: mrtrix3 - -on: - push: - branches: [ master ] - tags: [ '*' ] - pull_request: - branches: [ master ] - -jobs: - devcheck: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.7, 3.9] # Check oldest and newest versions - pip-flags: ['', '--editable'] - pydra: - - 'pydra' - - '--editable git+https://github.com/nipype/pydra.git#egg=pydra' - - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install build dependencies - run: | - python -m pip install --upgrade pip - - name: Install Pydra - run: | - pip install ${{ matrix.pydra }} - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - - name: Install task package - run: | - pip install ${{ matrix.pip-flags }} ".[dev]" - python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - - test: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.7, 3.8, 3.9] - defaults: - run: - shell: bash -l {0} - steps: - - uses: actions/checkout@v2 - - name: Install Minconda - uses: conda-incubator/setup-miniconda@v2 - with: - auto-activate-base: true - activate-environment: "" - - name: Install MRtrix via Conda - run: | - conda install -c mrtrix3 mrtrix3 - mrconvert --version - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install build dependencies - run: | - python -m pip install --upgrade pip - - name: Install task package - run: | - pip install ".[test]" - python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - - name: Test with pytest - run: | - pytest -sv --doctest-modules pydra/tasks/$SUBPACKAGE \ - --cov pydra.tasks.$SUBPACKAGE --cov-report xml - - uses: codecov/codecov-action@v1 - if: ${{ always() }} - - - deploy: - needs: [devcheck, test] - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.9] - steps: - - uses: actions/checkout@v2 - with: - submodules: recursive - fetch-depth: 0 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install build tools - run: python -m pip install --upgrade pip setuptools wheel twine - - name: Build source and wheel distributions - run: python setup.py sdist bdist_wheel - - name: Check distributions - run: twine check dist/* - - uses: actions/upload-artifact@v2 - with: - name: distributions - path: dist/ - # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. - # Secrets are not accessible in the if: condition [0], so set an output variable [1] - # [0] https://github.community/t/16928 - # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter - - name: Check for PyPI token on tag - id: deployable - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') - env: - PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}" - run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi - - name: Upload to PyPI - if: steps.deployable.outputs.DEPLOY - uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 # v1.4.2 - with: - user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/pyproject.toml b/pyproject.toml index 297879a..7d330ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,12 @@ dynamic = ["version"] dev = [ "black", "pre-commit", + "black >=22.12.0", + "click >=8.1.3", + "tqdm", + "attrs >=23.1.0", + "fileformats >= 0.8", + "fileformats-extras >= 0.2.1" ] doc = [ "packaging", From bbb25c5cfecfedab2c8399a503684c49ead4e223 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 29 Feb 2024 18:13:51 +1100 Subject: [PATCH 04/44] debugging GH Action workflow --- .github/workflows/ci-cd.yml | 28 +++++++++++++++++----------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 3d0b1da..4576154 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -227,7 +227,7 @@ jobs: - name: Install task package run: | - pip install .fileformats-medimage-mrtrix interfaces/ ./fileformats-medimage-mrtrix-extras ''.[test]' + pip install .fileformats-medimage-mrtrix ./fileformats-medimage-mrtrix-extras '.[test]' python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" @@ -243,38 +243,44 @@ jobs: deploy: needs: [devcheck, test] runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.11] + env: + PYTHON_VERSION: 3.11 steps: + - name: Download version file + uses: actions/download-artifact@v2 + with: + name: VersionFile + path: mrtrix3_version.txt + + - name: Extract Mrtrix version + run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV - uses: actions/checkout@v2 - name: Download auto-gen pydra uses: actions/download-artifact@v2 with: name: AutoGen - path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0 + path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION - - name: Set up Python ${{ matrix.python-version }} + - name: Set up Python $PYTHON_VERSION uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} + python-version: $PYTHON_VERSION - name: Install build tools run: python -m pip install --upgrade pip twine build - name: Build source and wheel distributions - working-directory: ./interfaces/pydra/src run: python -m build - name: Check distributions - run: twine check interfaces/pydra/src/dist/* + run: twine check dist/* - name: Upload sdist uses: actions/upload-artifact@v2 with: name: SDist - path: interfaces/pydra/src/dist/*.tar.gz + path: dist/*.tar.gz # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. # Secrets are not accessible in the if: condition [0], so set an output variable [1] @@ -293,4 +299,4 @@ jobs: with: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} - packages-dir: interfaces/pydra/src/dist/ + packages-dir: dist/ From ac7e604722cfe080fe9eba9daa4f6d020f00bdd3 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 6 Mar 2024 22:05:44 +1100 Subject: [PATCH 05/44] deleted _version.py files --- .gitignore | 3 +++ .../extras/medimage_mrtrix3/_version.py | 16 ---------------- .../fileformats/medimage_mrtrix3/_version.py | 16 ---------------- 3 files changed, 3 insertions(+), 32 deletions(-) delete mode 100644 fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py delete mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py diff --git a/.gitignore b/.gitignore index cb003b0..8abd02e 100644 --- a/.gitignore +++ b/.gitignore @@ -133,3 +133,6 @@ dmypy.json # VS Code .vscode/ + +# Hatchling +_version.py diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py deleted file mode 100644 index 491a473..0000000 --- a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/_version.py +++ /dev/null @@ -1,16 +0,0 @@ -# file generated by setuptools_scm -# don't change, don't track in version control -TYPE_CHECKING = False -if TYPE_CHECKING: - from typing import Tuple, Union - VERSION_TUPLE = Tuple[Union[int, str], ...] -else: - VERSION_TUPLE = object - -version: str -__version__: str -__version_tuple__: VERSION_TUPLE -version_tuple: VERSION_TUPLE - -__version__ = version = '3.0.5.dev860+g59980ada3' -__version_tuple__ = version_tuple = (3, 0, 5, 'dev860', 'g59980ada3') diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py deleted file mode 100644 index 491a473..0000000 --- a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/_version.py +++ /dev/null @@ -1,16 +0,0 @@ -# file generated by setuptools_scm -# don't change, don't track in version control -TYPE_CHECKING = False -if TYPE_CHECKING: - from typing import Tuple, Union - VERSION_TUPLE = Tuple[Union[int, str], ...] -else: - VERSION_TUPLE = object - -version: str -__version__: str -__version_tuple__: VERSION_TUPLE -version_tuple: VERSION_TUPLE - -__version__ = version = '3.0.5.dev860+g59980ada3' -__version_tuple__ = version_tuple = (3, 0, 5, 'dev860', 'g59980ada3') From fb7f2f70a8322bcb873a479b668eef93fed3ecbd Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 3 Apr 2024 08:48:00 +1100 Subject: [PATCH 06/44] set iana_mime to None for ImageFormatGz --- .../fileformats/medimage_mrtrix3/image.py | 1 + 1 file changed, 1 insertion(+) diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py index 253c69a..78decdb 100644 --- a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py @@ -97,6 +97,7 @@ def data_file(self): class ImageFormatGz(Gzip[ImageFormat]): + iana_mime = None ext = ".mif.gz" From f9468ad07bcc2f729cb4434219ba59b4c51942b0 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 4 Apr 2024 12:43:53 +1100 Subject: [PATCH 07/44] fixed up pyproject.toml --- .gitignore | 2 ++ generate.py | 13 ++++++++++--- pyproject.toml | 4 ++-- 3 files changed, 14 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 8abd02e..c55f867 100644 --- a/.gitignore +++ b/.gitignore @@ -136,3 +136,5 @@ dmypy.json # Hatchling _version.py + +/pydra/tasks/mrtrix3/v3_0 diff --git a/generate.py b/generate.py index 3678335..0b6f378 100755 --- a/generate.py +++ b/generate.py @@ -17,6 +17,7 @@ from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, ImageOut, Tracks from pydra.engine.helpers import make_klass from pydra.engine import specs +from pydra.utils import add_exc_note logger = logging.getLogger("pydra-auto-gen") @@ -135,9 +136,15 @@ def auto_gen_mrtrix3_pydra( ): continue cmd = [str(cmd_dir / cmd_name)] - cmds.extend( - auto_gen_cmd(cmd, cmd_name, output_dir, cmd_dir, log_errors, pkg_version) - ) + try: + cmds.extend( + auto_gen_cmd( + cmd, cmd_name, output_dir, cmd_dir, log_errors, pkg_version + ) + ) + except Exception as e: + add_exc_note(e, f"when attempting to generate {cmd} in {output_dir}") + raise e # Write init init_path = output_dir / "pydra" / "tasks" / "mrtrix3" / pkg_version / "__init__.py" diff --git a/pyproject.toml b/pyproject.toml index 7d330ef..35fa320 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,12 +5,12 @@ build-backend = "hatchling.build" [project] name = "pydra-mrtrix3" description = "pydra-mrtrix3 contains Pydra task specifications for MRtrix3 tools" -readme = "README.md" +readme = "README.rst" requires-python = ">=3.8" dependencies = [ "pydra >=0.22", "fileformats-medimage >=0.3.4"] -license = {file = "LICENCE.txt"} +license = {file = "LICENSE"} authors = [ {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, ] From 6ffc4e98a8efbbbd33b2292085b5172ea3938b9d Mon Sep 17 00:00:00 2001 From: Tom Close Date: Mon, 29 Apr 2024 16:55:59 +1000 Subject: [PATCH 08/44] temp disabled gitignore to create version --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index c55f867..128cab1 100644 --- a/.gitignore +++ b/.gitignore @@ -137,4 +137,4 @@ dmypy.json # Hatchling _version.py -/pydra/tasks/mrtrix3/v3_0 +#/pydra/tasks/mrtrix3/v3_0 From c19d53d71c0da1e5cc7ed489b34c22b5125bc9e5 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Mon, 29 Apr 2024 17:07:32 +1000 Subject: [PATCH 09/44] updated pyproject.toml --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 35fa320..483f764 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,8 @@ readme = "README.rst" requires-python = ">=3.8" dependencies = [ "pydra >=0.22", - "fileformats-medimage >=0.3.4"] + "fileformats-medimage_mrtrix3 >=3.0.3a", + "pytest"] # bug in fileformats requires this currently license = {file = "LICENSE"} authors = [ {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, From 0c629fc7764db4feae7b2dd2e701b8dfcbdbf0b4 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 1 May 2024 07:39:26 +1000 Subject: [PATCH 10/44] reignored auto-generated package --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 128cab1..c55f867 100644 --- a/.gitignore +++ b/.gitignore @@ -137,4 +137,4 @@ dmypy.json # Hatchling _version.py -#/pydra/tasks/mrtrix3/v3_0 +/pydra/tasks/mrtrix3/v3_0 From 0dfecf20b3f369d06e90c15ffd9997d79cea0c52 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Mon, 27 May 2024 16:05:54 +0930 Subject: [PATCH 11/44] updated to use sample file generator --- .../fileformats/extras/medimage_mrtrix3/converters.py | 8 ++++---- .../fileformats/extras/medimage_mrtrix3/image.py | 9 +++------ .../fileformats/extras/medimage_mrtrix3/tracks.py | 9 +++------ .../fileformats/medimage_mrtrix3/image.py | 2 +- 4 files changed, 11 insertions(+), 17 deletions(-) diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py index 260d218..668100c 100644 --- a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py @@ -7,9 +7,9 @@ ) try: - from pydra.tasks.mrtrix3.utils import MRConvert + from pydra.tasks.mrtrix3.utils import MrConvert except ImportError: - from pydra.tasks.mrtrix3.latest import mrconvert as MRConvert + from pydra.tasks.mrtrix3.latest import mrconvert as MrConvert in_out_file_kwargs = {"in_file": "input", "out_file": "output"} else: @@ -37,7 +37,7 @@ def mrconvert(name, out_ext: str, **kwargs): pydra.ShellCommandTask the converter task """ - return MRConvert(name=name, out_file="out" + out_ext, **kwargs) + return MrConvert(name=name, out_file="out" + out_ext, **kwargs) @hook.converter( @@ -61,4 +61,4 @@ def mrconvert2(name, out_ext: str, **kwargs): pydra.ShellCommandTask the converter task """ - return MRConvert(name=name, out_file="out" + out_ext, **kwargs) + return MrConvert(name=name, out_file="out" + out_ext, **kwargs) diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py index 1d05734..7f58e5b 100644 --- a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py @@ -3,9 +3,8 @@ import typing as ty from pathlib import Path import numpy as np -from random import Random from medimages4tests.dummy.nifti import get_image as get_dummy_nifti -from fileformats.core import FileSet +from fileformats.core import FileSet, SampleFileGenerator from fileformats.medimage import MedicalImage, Nifti1 from fileformats.medimage_mrtrix3 import ImageFormat @@ -13,11 +12,9 @@ @FileSet.generate_sample_data.register def generate_mrtrix_sample_data( mif: ImageFormat, - dest_dir: Path, - seed: ty.Union[int, Random] = 0, - stem: ty.Optional[str] = None, + generator: SampleFileGenerator, ) -> ty.Iterable[Path]: - nifti = Nifti1(get_dummy_nifti(dest_dir / "nifti.nii")) + nifti = Nifti1(get_dummy_nifti(generator.dest_dir / "nifti.nii")) with mock.patch.dict(os.environ, {"MRTRIX_CLI_PARSE_ONLY": "0"}): mif = ImageFormat.convert(nifti) return mif.fspaths diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py index 2d2a866..a7594b6 100644 --- a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py +++ b/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py @@ -3,20 +3,17 @@ import math from pathlib import Path import typing as ty -from random import Random -from fileformats.core import FileSet +from fileformats.core import FileSet, SampleFileGenerator from fileformats.medimage_mrtrix3 import Tracks @FileSet.generate_sample_data.register def generate_tracks_sample_data( tracks: Tracks, - dest_dir: Path, - seed: ty.Union[int, Random] = 0, - stem: ty.Optional[str] = None, + generator: SampleFileGenerator, ) -> ty.Iterable[Path]: """Generate a tracks file with a single straight track of length 10""" - fspath = dest_dir / "tracks.tck" + fspath = generator.dest_dir / "tracks.tck" timestamp = str(time.time() * 1e9 + time.process_time_ns()) contents = f"""mrtrix tracks datatype: Float32BE diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py index 78decdb..1a5c74c 100644 --- a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py @@ -97,7 +97,7 @@ def data_file(self): class ImageFormatGz(Gzip[ImageFormat]): - iana_mime = None + iana_mime = "application/x-image-format-gz" ext = ".mif.gz" From e05e03086eb4658e9af1b49e43691857de1d2acb Mon Sep 17 00:00:00 2001 From: Tom Close Date: Mon, 27 May 2024 16:07:27 +0930 Subject: [PATCH 12/44] added tests for mime roundtrips --- .../fileformats/medimage_mrtrix3/tests/test_mime.py | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/tests/test_mime.py diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/tests/test_mime.py b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/tests/test_mime.py new file mode 100644 index 0000000..bba83bc --- /dev/null +++ b/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/tests/test_mime.py @@ -0,0 +1,10 @@ +from fileformats.core import from_mime +from fileformats.medimage_mrtrix3 import ImageFormatGz as MifGz + + +def test_mif_gz_mime_roundtrip(): + assert MifGz is from_mime(MifGz.mime_type) + + +def test_mif_gz_mime_like_roundtrip(): + assert MifGz is from_mime(MifGz.mime_like) From e81ec9b7bf149a576de4592a8c5215681e5b31fc Mon Sep 17 00:00:00 2001 From: Tom Close Date: Mon, 27 May 2024 17:51:37 +0930 Subject: [PATCH 13/44] changed mrtrix branch --- .github/workflows/ci-cd.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 4576154..2b24216 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -52,7 +52,7 @@ jobs: run: | git clone https://github.com/tclose/mrtrix3.git cd mrtrix3 - git checkout pydra-usage + git checkout pydra-usage-python-cmd echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV git checkout $MRTRIX3_VERSION From f21a561a21b3e05e0220c3f113b5885816f1a4e6 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Mon, 27 May 2024 19:40:14 +0930 Subject: [PATCH 14/44] fixing up ci-cd --- .github/workflows/ci-cd.yml | 44 +++++++++++++++++++++++-------------- 1 file changed, 27 insertions(+), 17 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 2b24216..e859e1b 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -15,6 +15,9 @@ on: - master - develop +env: + MRTRIX3_HOME: /opt/mrtrix3/latest/install + jobs: generate: @@ -50,36 +53,43 @@ jobs: - name: Clone latest MRtrix and switch to latest tag run: | - git clone https://github.com/tclose/mrtrix3.git - cd mrtrix3 + mkdir /opt/mrtrix3 + sudo chown -R $USER /opt/mrtrix3 + git clone https://github.com/tclose/mrtrix3.git /opt/mrtrix3/latest + cd /opt/mrtrix3/latest git checkout pydra-usage-python-cmd echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV git checkout $MRTRIX3_VERSION - name: configure - run: > - cmake - -B build - -G Ninja - -D CMAKE_BUILD_TYPE=Release - -D MRTRIX_BUILD_TESTS=ON - -D MRTRIX_STL_DEBUGGING=ON - -D MRTRIX_WARNINGS_AS_ERRORS=ON - -D CMAKE_C_COMPILER=clang - -D CMAKE_CXX_COMPILER=clang++ + run: | + cd /opt/mrtrix3/latest + cmake \ + -B build \ + -G Ninja \ + -D CMAKE_BUILD_TYPE=Release \ + -D MRTRIX_BUILD_TESTS=ON \ + -D MRTRIX_STL_DEBUGGING=ON \ + -D MRTRIX_WARNINGS_AS_ERRORS=ON \ + -D CMAKE_C_COMPILER=clang \ + -D CMAKE_CXX_COMPILER=clang++ \ -D CMAKE_INSTALL_PREFIX=$(pwd)/install - name: Build Mrtrix - run: cmake --build build + run: | + cd /opt/mrtrix3/latest + cmake --build build - name: Install Mrtrix - run: cmake --install build + run: | + cd /opt/mrtrix3/latest + cmake --install build - name: Set PATH Variable - run: echo "PATH=$PATH:$(pwd)/install/bin" >> $GITHUB_ENV + run: echo "PATH=$PATH:/opt/mrtrix3/latest/install/bin" >> $GITHUB_ENV - name: Set LD_LIBRARY_PATH Variable - run: echo "LD_LIBRARY_PATH=$(pwd)/install/lib" >> $GITHUB_ENV + run: echo "LD_LIBRARY_PATH=/opt/mrtrix3/latest/install/lib" >> $GITHUB_ENV - name: Change back to the root directory run: cd .. @@ -100,7 +110,7 @@ jobs: - name: Generate task specifications run: > .generate.py - $(pwd)/mrtrix3/install/bin + $/opt/mrtrix3/latest/install/bin $(pwd) $MRTRIX3_VERSION --log-errors From 15dabb4741df7cf73fc41614a6afd83f2a44864c Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 00:28:25 +0930 Subject: [PATCH 15/44] fixing up ci-cd --- .github/workflows/ci-cd.yml | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index e859e1b..f2a4b4b 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -55,7 +55,7 @@ jobs: run: | mkdir /opt/mrtrix3 sudo chown -R $USER /opt/mrtrix3 - git clone https://github.com/tclose/mrtrix3.git /opt/mrtrix3/latest + git clone https://github.com/tclose/mrtrix3.git /opt/mrtrix3/src cd /opt/mrtrix3/latest git checkout pydra-usage-python-cmd echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV @@ -63,7 +63,7 @@ jobs: - name: configure run: | - cd /opt/mrtrix3/latest + cd /opt/mrtrix3/src cmake \ -B build \ -G Ninja \ @@ -73,23 +73,23 @@ jobs: -D MRTRIX_WARNINGS_AS_ERRORS=ON \ -D CMAKE_C_COMPILER=clang \ -D CMAKE_CXX_COMPILER=clang++ \ - -D CMAKE_INSTALL_PREFIX=$(pwd)/install + -D CMAKE_INSTALL_PREFIX=/opt/mrtrix3/install - name: Build Mrtrix run: | - cd /opt/mrtrix3/latest + cd /opt/mrtrix3/src cmake --build build - name: Install Mrtrix run: | - cd /opt/mrtrix3/latest + cd /opt/mrtrix3/src cmake --install build - name: Set PATH Variable - run: echo "PATH=$PATH:/opt/mrtrix3/latest/install/bin" >> $GITHUB_ENV + run: echo "PATH=$PATH:/opt/mrtrix3/install/bin" >> $GITHUB_ENV - name: Set LD_LIBRARY_PATH Variable - run: echo "LD_LIBRARY_PATH=/opt/mrtrix3/latest/install/lib" >> $GITHUB_ENV + run: echo "LD_LIBRARY_PATH=/opt/mrtrix3/install/lib" >> $GITHUB_ENV - name: Change back to the root directory run: cd .. @@ -110,7 +110,7 @@ jobs: - name: Generate task specifications run: > .generate.py - $/opt/mrtrix3/latest/install/bin + $/opt/mrtrix3/install/bin $(pwd) $MRTRIX3_VERSION --log-errors @@ -120,7 +120,7 @@ jobs: uses: actions/upload-artifact@v2 with: name: MRtrix3 - path: mrtrix3/install + path: /opt/mrtrix3/install - name: Upload auto-gen pydra uses: actions/upload-artifact@v2 @@ -218,13 +218,13 @@ jobs: uses: actions/download-artifact@v2 with: name: MRtrix3 - path: mrtrix3/install + path: /opt/mrtrix3/install/ - name: Set PATH Variable - run: echo "PATH=$PATH:$(pwd)/install/bin" >> $GITHUB_ENV + run: echo "PATH=$PATH:/opt/mrtrix3/install/bin" >> $GITHUB_ENV - name: Set LD_LIBRARY_PATH Variable - run: echo "LD_LIBRARY_PATH=$(pwd)/install/lib" >> $GITHUB_ENV + run: echo "LD_LIBRARY_PATH=/opt/mrtrix3/install/lib" >> $GITHUB_ENV - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 @@ -243,8 +243,7 @@ jobs: - name: Test with pytest run: | - pytest -sv --doctest-modules pydra/tasks/mrtrix3 \ - --cov pydra.tasks.mrtrix3 --cov-report xml + pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml - uses: codecov/codecov-action@v1 if: ${{ always() }} From 44755cbaed1a9a7f48e2598e1b36d27e2dbcdb28 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 00:30:37 +0930 Subject: [PATCH 16/44] fixing ci-cd --- .github/workflows/ci-cd.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index f2a4b4b..5d9a100 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -56,7 +56,7 @@ jobs: mkdir /opt/mrtrix3 sudo chown -R $USER /opt/mrtrix3 git clone https://github.com/tclose/mrtrix3.git /opt/mrtrix3/src - cd /opt/mrtrix3/latest + cd /opt/mrtrix3/src git checkout pydra-usage-python-cmd echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV git checkout $MRTRIX3_VERSION From 5be22dee1e707d89799a9a9d40783765f01d4dda Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 08:41:42 +0930 Subject: [PATCH 17/44] debugging ci-cd --- .github/workflows/ci-cd.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 5d9a100..93fef25 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -17,6 +17,7 @@ on: env: MRTRIX3_HOME: /opt/mrtrix3/latest/install + MRTRIX3_VERSION: 3.0.3a2 jobs: @@ -58,8 +59,9 @@ jobs: git clone https://github.com/tclose/mrtrix3.git /opt/mrtrix3/src cd /opt/mrtrix3/src git checkout pydra-usage-python-cmd - echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV - git checkout $MRTRIX3_VERSION + +# echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV +# git checkout $MRTRIX3_VERSION - name: configure run: | From 2c0c55db72a007b2797c5b26687a4e1a287da533 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 08:56:14 +0930 Subject: [PATCH 18/44] db ci/cd --- .github/workflows/ci-cd.yml | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 93fef25..579e020 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -16,7 +16,8 @@ on: - develop env: - MRTRIX3_HOME: /opt/mrtrix3/latest/install + MRTRIX3_HOME: /opt/mrtrix3 + MRTRIX3_INSTALL: /opt/mrtrix3/install MRTRIX3_VERSION: 3.0.3a2 jobs: @@ -54,10 +55,10 @@ jobs: - name: Clone latest MRtrix and switch to latest tag run: | - mkdir /opt/mrtrix3 - sudo chown -R $USER /opt/mrtrix3 - git clone https://github.com/tclose/mrtrix3.git /opt/mrtrix3/src - cd /opt/mrtrix3/src + mkdir $MRTRIX3_HOME + sudo chown -R $USER $MRTRIX3_HOME + git clone https://github.com/tclose/mrtrix3.git $MRTRIX3_HOME/src + cd $MRTRIX3_HOME/src git checkout pydra-usage-python-cmd # echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV @@ -65,7 +66,7 @@ jobs: - name: configure run: | - cd /opt/mrtrix3/src + cd $MRTRIX3_HOME/src cmake \ -B build \ -G Ninja \ @@ -79,19 +80,19 @@ jobs: - name: Build Mrtrix run: | - cd /opt/mrtrix3/src + cd $MRTRIX3_HOME/src cmake --build build - name: Install Mrtrix run: | - cd /opt/mrtrix3/src + cd $MRTRIX3_HOME/src cmake --install build - name: Set PATH Variable - run: echo "PATH=$PATH:/opt/mrtrix3/install/bin" >> $GITHUB_ENV + run: echo "PATH=$PATH:$MRTRIX3_INSTALL/bin" >> $GITHUB_ENV - name: Set LD_LIBRARY_PATH Variable - run: echo "LD_LIBRARY_PATH=/opt/mrtrix3/install/lib" >> $GITHUB_ENV + run: echo "LD_LIBRARY_PATH=$MRTRIX3_INSTALL/lib" >> $GITHUB_ENV - name: Change back to the root directory run: cd .. @@ -112,7 +113,7 @@ jobs: - name: Generate task specifications run: > .generate.py - $/opt/mrtrix3/install/bin + $MRTRIX3_INSTALL/bin $(pwd) $MRTRIX3_VERSION --log-errors @@ -122,7 +123,7 @@ jobs: uses: actions/upload-artifact@v2 with: name: MRtrix3 - path: /opt/mrtrix3/install + path: ${{ env.MRTRIX3_INSTALL}} - name: Upload auto-gen pydra uses: actions/upload-artifact@v2 @@ -220,13 +221,13 @@ jobs: uses: actions/download-artifact@v2 with: name: MRtrix3 - path: /opt/mrtrix3/install/ + path: ${{ env.MRTRIX3_INSTALL}} - name: Set PATH Variable - run: echo "PATH=$PATH:/opt/mrtrix3/install/bin" >> $GITHUB_ENV + run: echo "PATH=$PATH:$MRTRIX3_INSTALL/bin" >> $GITHUB_ENV - name: Set LD_LIBRARY_PATH Variable - run: echo "LD_LIBRARY_PATH=/opt/mrtrix3/install/lib" >> $GITHUB_ENV + run: echo "LD_LIBRARY_PATH=$MRTRIX3_INSTALL/lib" >> $GITHUB_ENV - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 @@ -265,6 +266,7 @@ jobs: - name: Extract Mrtrix version run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV + - uses: actions/checkout@v2 - name: Download auto-gen pydra From 8ee36fc79a7270b8efcc95c1e6e9ed53c34ebec0 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 09:01:17 +0930 Subject: [PATCH 19/44] db cicd --- .github/workflows/ci-cd.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 579e020..7fab326 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -60,6 +60,7 @@ jobs: git clone https://github.com/tclose/mrtrix3.git $MRTRIX3_HOME/src cd $MRTRIX3_HOME/src git checkout pydra-usage-python-cmd + git tag $MRTRIX3_VERSION # echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV # git checkout $MRTRIX3_VERSION From 6d8daf824ae0aed364706d8e397a8527f501dbe8 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:02:15 +0930 Subject: [PATCH 20/44] fixing up mrtrix version in ci-cd --- .github/workflows/ci-cd.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 7fab326..f47f9fd 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -18,7 +18,7 @@ on: env: MRTRIX3_HOME: /opt/mrtrix3 MRTRIX3_INSTALL: /opt/mrtrix3/install - MRTRIX3_VERSION: 3.0.3a2 + MRTRIX3_VERSION: 3.0.4 jobs: From 8f256416e94683034f4b54ba54bc87c11a4b8590 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:10:24 +0930 Subject: [PATCH 21/44] changed mrtrix version tag --- .github/workflows/ci-cd.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index f47f9fd..063e49a 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -18,7 +18,7 @@ on: env: MRTRIX3_HOME: /opt/mrtrix3 MRTRIX3_INSTALL: /opt/mrtrix3/install - MRTRIX3_VERSION: 3.0.4 + MRTRIX_VERSION: 3.0.4 jobs: @@ -60,10 +60,10 @@ jobs: git clone https://github.com/tclose/mrtrix3.git $MRTRIX3_HOME/src cd $MRTRIX3_HOME/src git checkout pydra-usage-python-cmd - git tag $MRTRIX3_VERSION + git tag $MRTRIX_VERSION -# echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV -# git checkout $MRTRIX3_VERSION +# echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV +# git checkout $MRTRIX_VERSION - name: configure run: | From 0e780355e6308fc006dfc7792eb45155cf018329 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:17:24 +0930 Subject: [PATCH 22/44] ci-cd db --- .github/workflows/ci-cd.yml | 55 +++++++++++++++++++------------------ 1 file changed, 28 insertions(+), 27 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 063e49a..8e3fe4b 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -16,8 +16,8 @@ on: - develop env: - MRTRIX3_HOME: /opt/mrtrix3 - MRTRIX3_INSTALL: /opt/mrtrix3/install + MRTRIX_HOME: /opt/mrtrix3 + MRTRIX_INSTALL: /opt/mrtrix3/install MRTRIX_VERSION: 3.0.4 jobs: @@ -55,19 +55,20 @@ jobs: - name: Clone latest MRtrix and switch to latest tag run: | - mkdir $MRTRIX3_HOME - sudo chown -R $USER $MRTRIX3_HOME - git clone https://github.com/tclose/mrtrix3.git $MRTRIX3_HOME/src - cd $MRTRIX3_HOME/src + mkdir $MRTRIX_HOME + sudo chown -R $USER $MRTRIX_HOME + git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src + cd $MRTRIX_HOME/src git checkout pydra-usage-python-cmd git tag $MRTRIX_VERSION + git describe --abbrev=0 # echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV # git checkout $MRTRIX_VERSION - name: configure run: | - cd $MRTRIX3_HOME/src + cd $MRTRIX_HOME/src cmake \ -B build \ -G Ninja \ @@ -77,23 +78,23 @@ jobs: -D MRTRIX_WARNINGS_AS_ERRORS=ON \ -D CMAKE_C_COMPILER=clang \ -D CMAKE_CXX_COMPILER=clang++ \ - -D CMAKE_INSTALL_PREFIX=/opt/mrtrix3/install + -D CMAKE_INSTALL_PREFIX=$MRTRIX_INSTALL - name: Build Mrtrix run: | - cd $MRTRIX3_HOME/src + cd $MRTRIX_HOME/src cmake --build build - name: Install Mrtrix run: | - cd $MRTRIX3_HOME/src + cd $MRTRIX_HOME/src cmake --install build - name: Set PATH Variable - run: echo "PATH=$PATH:$MRTRIX3_INSTALL/bin" >> $GITHUB_ENV + run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV - name: Set LD_LIBRARY_PATH Variable - run: echo "LD_LIBRARY_PATH=$MRTRIX3_INSTALL/lib" >> $GITHUB_ENV + run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV - name: Change back to the root directory run: cd .. @@ -114,9 +115,9 @@ jobs: - name: Generate task specifications run: > .generate.py - $MRTRIX3_INSTALL/bin + $MRTRIX_INSTALL/bin $(pwd) - $MRTRIX3_VERSION + $MRTRIX_VERSION --log-errors --latest @@ -124,22 +125,22 @@ jobs: uses: actions/upload-artifact@v2 with: name: MRtrix3 - path: ${{ env.MRTRIX3_INSTALL}} + path: ${{ env.MRTRIX_INSTALL}} - name: Upload auto-gen pydra uses: actions/upload-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + path: pydra/tasks/mrtrix3/$MRTRIX_VERSION - name: Write version file - run: echo $MRTRIX3_VERSION > mrtrix3_version.txt + run: echo $MRTRIX_VERSION > mrtrix3_version.txt - name: Upload version file uses: actions/upload-artifact@v2 with: name: VersionFile - path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + path: pydra/tasks/mrtrix3/$MRTRIX_VERSION devcheck: needs: [generate] @@ -162,13 +163,13 @@ jobs: path: mrtrix3_version.txt - name: Extract Mrtrix version - run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV + run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV - name: Download auto-gen pydra uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + path: pydra/tasks/mrtrix3/$MRTRIX_VERSION - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 @@ -210,25 +211,25 @@ jobs: path: mrtrix3_version.txt - name: Extract Mrtrix version - run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV + run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV - name: Download auto-gen pydra uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + path: pydra/tasks/mrtrix3/$MRTRIX_VERSION - name: Download MRtrix3 install uses: actions/download-artifact@v2 with: name: MRtrix3 - path: ${{ env.MRTRIX3_INSTALL}} + path: ${{ env.MRTRIX_INSTALL}} - name: Set PATH Variable - run: echo "PATH=$PATH:$MRTRIX3_INSTALL/bin" >> $GITHUB_ENV + run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV - name: Set LD_LIBRARY_PATH Variable - run: echo "LD_LIBRARY_PATH=$MRTRIX3_INSTALL/lib" >> $GITHUB_ENV + run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 @@ -266,7 +267,7 @@ jobs: path: mrtrix3_version.txt - name: Extract Mrtrix version - run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV + run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV - uses: actions/checkout@v2 @@ -274,7 +275,7 @@ jobs: uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION + path: pydra/tasks/mrtrix3/$MRTRIX_VERSION - name: Set up Python $PYTHON_VERSION uses: actions/setup-python@v2 From 63917a7955e98d6e6f38fb2512cbc21e2860d174 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:33:29 +0930 Subject: [PATCH 23/44] trying to get mrtrix version to work --- .github/workflows/ci-cd.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 8e3fe4b..2e76d32 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -60,6 +60,7 @@ jobs: git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src cd $MRTRIX_HOME/src git checkout pydra-usage-python-cmd + git tag -d $(git tag) git tag $MRTRIX_VERSION git describe --abbrev=0 From 616d615143eb779a150d9fbd23bde182c0a8ef38 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:37:05 +0930 Subject: [PATCH 24/44] db --- .github/workflows/ci-cd.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 2e76d32..880316c 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -62,6 +62,7 @@ jobs: git checkout pydra-usage-python-cmd git tag -d $(git tag) git tag $MRTRIX_VERSION + git tag git describe --abbrev=0 # echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV From c6c8e5917fb5d4aeb1c9cbcd03ceaf39fd6ee3da Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:46:06 +0930 Subject: [PATCH 25/44] created an annotated tag in ci-cd --- .github/workflows/ci-cd.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 880316c..46d9ec2 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -60,9 +60,7 @@ jobs: git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src cd $MRTRIX_HOME/src git checkout pydra-usage-python-cmd - git tag -d $(git tag) - git tag $MRTRIX_VERSION - git tag + git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-mrtrix3 release" git describe --abbrev=0 # echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV From 02722e0c584db465f05ca52886d3354d2c687ed5 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:48:33 +0930 Subject: [PATCH 26/44] added in deploy cd steps for fileformats packages --- .github/workflows/ci-cd.yml | 64 +++++++++++++++++++ .../.codespell-ignorewords | 0 .../fileformats-extras}/.flake8 | 0 .../fileformats-extras}/LICENSE | 0 .../fileformats-extras}/README.rst | 0 .../fileformats-extras}/conftest.py | 0 .../extras/medimage_mrtrix3/__init__.py | 0 .../extras/medimage_mrtrix3/converters.py | 0 .../extras/medimage_mrtrix3/gradients.py | 0 .../extras/medimage_mrtrix3/image.py | 0 .../medimage_mrtrix3/tests/test_converters.py | 0 .../extras/medimage_mrtrix3/tracks.py | 0 .../fileformats-extras}/pyproject.toml | 0 .../fileformats-extras}/pytest.ini | 0 .../fileformats}/.codespell-ignorewords | 0 .../fileformats}/.flake8 | 0 .../fileformats}/LICENSE | 0 .../fileformats}/README.rst | 0 .../fileformats}/conftest.py | 0 .../fileformats/medimage_mrtrix3/__init__.py | 0 .../fileformats/medimage_mrtrix3/dwi.py | 0 .../fileformats/medimage_mrtrix3/image.py | 0 .../fileformats/medimage_mrtrix3/in_out.py | 0 .../medimage_mrtrix3/tests/test_mime.py | 0 .../fileformats/medimage_mrtrix3/track.py | 0 .../fileformats}/pyproject.toml | 0 .../fileformats}/pytest.ini | 0 27 files changed, 64 insertions(+) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/.codespell-ignorewords (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/.flake8 (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/LICENSE (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/README.rst (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/conftest.py (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/fileformats/extras/medimage_mrtrix3/__init__.py (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/fileformats/extras/medimage_mrtrix3/converters.py (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/fileformats/extras/medimage_mrtrix3/gradients.py (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/fileformats/extras/medimage_mrtrix3/image.py (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/fileformats/extras/medimage_mrtrix3/tests/test_converters.py (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/fileformats/extras/medimage_mrtrix3/tracks.py (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/pyproject.toml (100%) rename {fileformats-medimage-mrtrix3-extras => related-packages/fileformats-extras}/pytest.ini (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/.codespell-ignorewords (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/.flake8 (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/LICENSE (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/README.rst (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/conftest.py (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/fileformats/medimage_mrtrix3/__init__.py (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/fileformats/medimage_mrtrix3/dwi.py (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/fileformats/medimage_mrtrix3/image.py (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/fileformats/medimage_mrtrix3/in_out.py (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/fileformats/medimage_mrtrix3/tests/test_mime.py (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/fileformats/medimage_mrtrix3/track.py (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/pyproject.toml (100%) rename {fileformats-medimage-mrtrix3 => related-packages/fileformats}/pytest.ini (100%) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 46d9ec2..a4848b7 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -253,6 +253,70 @@ jobs: - uses: codecov/codecov-action@v1 if: ${{ always() }} + deploy-fileformats: + needs: [devcheck, test] + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + with: + submodules: recursive + fetch-depth: 0 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + - name: Install build tools + run: python -m pip install build twine + - name: Build source and wheel distributions + run: python -m build ./related-packages/fileformats + - name: Check distributions + run: twine check ./related-packages/fileformats/dist/* + - name: Check for PyPI token on tag + id: deployable + if: github.event_name == 'release' + env: + PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}" + run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi + - name: Upload to PyPI + if: steps.deployable.outputs.DEPLOY + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }} + packages-dir: ./related-packages/fileformats/dist + + deploy-fileformats-extras: + needs: [deploy-fileformats] + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + with: + submodules: recursive + fetch-depth: 0 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + - name: Install build tools + run: python -m pip install build twine + - name: Build source and wheel distributions + run: python -m build ./related-packages/fileformats-extras + - name: Check distributions + run: twine check ./related-packages/fileformats-extras/dist/* + - name: Check for PyPI token on tag + id: deployable + if: github.event_name == 'release' + env: + PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}" + run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi + - name: Upload to PyPI + if: steps.deployable.outputs.DEPLOY + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }} + packages-dir: ./related-packages/fileformats-extras/dist + deploy: needs: [devcheck, test] diff --git a/fileformats-medimage-mrtrix3-extras/.codespell-ignorewords b/related-packages/fileformats-extras/.codespell-ignorewords similarity index 100% rename from fileformats-medimage-mrtrix3-extras/.codespell-ignorewords rename to related-packages/fileformats-extras/.codespell-ignorewords diff --git a/fileformats-medimage-mrtrix3-extras/.flake8 b/related-packages/fileformats-extras/.flake8 similarity index 100% rename from fileformats-medimage-mrtrix3-extras/.flake8 rename to related-packages/fileformats-extras/.flake8 diff --git a/fileformats-medimage-mrtrix3-extras/LICENSE b/related-packages/fileformats-extras/LICENSE similarity index 100% rename from fileformats-medimage-mrtrix3-extras/LICENSE rename to related-packages/fileformats-extras/LICENSE diff --git a/fileformats-medimage-mrtrix3-extras/README.rst b/related-packages/fileformats-extras/README.rst similarity index 100% rename from fileformats-medimage-mrtrix3-extras/README.rst rename to related-packages/fileformats-extras/README.rst diff --git a/fileformats-medimage-mrtrix3-extras/conftest.py b/related-packages/fileformats-extras/conftest.py similarity index 100% rename from fileformats-medimage-mrtrix3-extras/conftest.py rename to related-packages/fileformats-extras/conftest.py diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/__init__.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/__init__.py similarity index 100% rename from fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/__init__.py rename to related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/__init__.py diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py similarity index 100% rename from fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/converters.py rename to related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/gradients.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py similarity index 100% rename from fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/gradients.py rename to related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/image.py similarity index 100% rename from fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/image.py rename to related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/image.py diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py similarity index 100% rename from fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py rename to related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tests/test_converters.py diff --git a/fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tracks.py similarity index 100% rename from fileformats-medimage-mrtrix3-extras/fileformats/extras/medimage_mrtrix3/tracks.py rename to related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tracks.py diff --git a/fileformats-medimage-mrtrix3-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml similarity index 100% rename from fileformats-medimage-mrtrix3-extras/pyproject.toml rename to related-packages/fileformats-extras/pyproject.toml diff --git a/fileformats-medimage-mrtrix3-extras/pytest.ini b/related-packages/fileformats-extras/pytest.ini similarity index 100% rename from fileformats-medimage-mrtrix3-extras/pytest.ini rename to related-packages/fileformats-extras/pytest.ini diff --git a/fileformats-medimage-mrtrix3/.codespell-ignorewords b/related-packages/fileformats/.codespell-ignorewords similarity index 100% rename from fileformats-medimage-mrtrix3/.codespell-ignorewords rename to related-packages/fileformats/.codespell-ignorewords diff --git a/fileformats-medimage-mrtrix3/.flake8 b/related-packages/fileformats/.flake8 similarity index 100% rename from fileformats-medimage-mrtrix3/.flake8 rename to related-packages/fileformats/.flake8 diff --git a/fileformats-medimage-mrtrix3/LICENSE b/related-packages/fileformats/LICENSE similarity index 100% rename from fileformats-medimage-mrtrix3/LICENSE rename to related-packages/fileformats/LICENSE diff --git a/fileformats-medimage-mrtrix3/README.rst b/related-packages/fileformats/README.rst similarity index 100% rename from fileformats-medimage-mrtrix3/README.rst rename to related-packages/fileformats/README.rst diff --git a/fileformats-medimage-mrtrix3/conftest.py b/related-packages/fileformats/conftest.py similarity index 100% rename from fileformats-medimage-mrtrix3/conftest.py rename to related-packages/fileformats/conftest.py diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/__init__.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/__init__.py similarity index 100% rename from fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/__init__.py rename to related-packages/fileformats/fileformats/medimage_mrtrix3/__init__.py diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/dwi.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/dwi.py similarity index 100% rename from fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/dwi.py rename to related-packages/fileformats/fileformats/medimage_mrtrix3/dwi.py diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/image.py similarity index 100% rename from fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/image.py rename to related-packages/fileformats/fileformats/medimage_mrtrix3/image.py diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/in_out.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/in_out.py similarity index 100% rename from fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/in_out.py rename to related-packages/fileformats/fileformats/medimage_mrtrix3/in_out.py diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/tests/test_mime.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/tests/test_mime.py similarity index 100% rename from fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/tests/test_mime.py rename to related-packages/fileformats/fileformats/medimage_mrtrix3/tests/test_mime.py diff --git a/fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/track.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/track.py similarity index 100% rename from fileformats-medimage-mrtrix3/fileformats/medimage_mrtrix3/track.py rename to related-packages/fileformats/fileformats/medimage_mrtrix3/track.py diff --git a/fileformats-medimage-mrtrix3/pyproject.toml b/related-packages/fileformats/pyproject.toml similarity index 100% rename from fileformats-medimage-mrtrix3/pyproject.toml rename to related-packages/fileformats/pyproject.toml diff --git a/fileformats-medimage-mrtrix3/pytest.ini b/related-packages/fileformats/pytest.ini similarity index 100% rename from fileformats-medimage-mrtrix3/pytest.ini rename to related-packages/fileformats/pytest.ini From 734c54988a23ac4d46556c2d156d6e1491afa2d4 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:52:32 +0930 Subject: [PATCH 27/44] added user config to ci-cd --- .github/workflows/ci-cd.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index a4848b7..aab59d8 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -36,6 +36,13 @@ jobs: - uses: actions/checkout@v1 with: submodules: true + - name: Unset header + # checkout@v2 adds a header that makes branch protection report errors + # because the Github action bot is not a collaborator on the repo + run: | + git config --local --unset http.https://github.com/.extraheader + git config --global user.email "dummy@email.com" + git config --global user.name "Dummy User" - name: install dependencies run: | From c22a780a6160cd2c7511fbd6ab825650e75adb81 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 11:53:39 +0930 Subject: [PATCH 28/44] db ci/cd --- .github/workflows/ci-cd.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index aab59d8..6822ef3 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -36,11 +36,10 @@ jobs: - uses: actions/checkout@v1 with: submodules: true - - name: Unset header + - name: Set Git User # checkout@v2 adds a header that makes branch protection report errors # because the Github action bot is not a collaborator on the repo run: | - git config --local --unset http.https://github.com/.extraheader git config --global user.email "dummy@email.com" git config --global user.name "Dummy User" From 291dcba1e3f9e2ca27614b7a7d49c8a5f8b57414 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 12:33:30 +0930 Subject: [PATCH 29/44] fixing ci-cd --- .github/workflows/ci-cd.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 6822ef3..e8e6832 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -113,10 +113,11 @@ jobs: python -m pip install --upgrade pip - name: Install pydra-auto-gen requirements - run: | - pip install -e fileformats-medimage-mrtrix3 - pip install -e fileformats-medimage-mrtrix3-extras - pip install -e .[dev,test] + run: > + pip install + -e related-packages/fileformats + -e related-packages/fileformats-extras + -e .[dev,test] - name: Generate task specifications run: > @@ -193,7 +194,7 @@ jobs: - name: Install task package run: | - pip install ${{ matrix.pip-flags }} "fileformats-medimage-mrtrix3" + pip install ${{ matrix.pip-flags }} "related-packages/fileformats" pip install ${{ matrix.pip-flags }} ".[dev]" python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" python -c "import pydra.tasks.mrtrix3.v3_0" From ecf29240ea190dd297f579e80c6be9531010f4eb Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 12:43:43 +0930 Subject: [PATCH 30/44] fixed up pyproject for fileformats --- .../fileformats-extras/pyproject.toml | 34 +++++-------------- related-packages/fileformats/pyproject.toml | 2 +- 2 files changed, 10 insertions(+), 26 deletions(-) diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml index e3874f3..4c0cd6c 100644 --- a/related-packages/fileformats-extras/pyproject.toml +++ b/related-packages/fileformats-extras/pyproject.toml @@ -10,19 +10,12 @@ requires-python = ">=3.8" dependencies = [ "fileformats >= 0.8", "fileformats-medimage-mrtrix3", - "pydra >= 0.22.0" -] -license = {file = "LICENSE"} -authors = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] -maintainers = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] -keywords = [ - "file formats", - "data", + "pydra >= 0.22.0", ] +license = { file = "LICENSE" } +authors = [{ name = "Thomas G. Close", email = "tom.g.close@gmail.com" }] +maintainers = [{ name = "Thomas G. Close", email = "tom.g.close@gmail.com" }] +keywords = ["file formats", "data"] classifiers = [ "Development Status :: 3 - Alpha", "Environment :: Console", @@ -40,13 +33,7 @@ classifiers = [ dynamic = ["version"] [project.optional-dependencies] -dev = [ - "black", - "pre-commit", - "codespell", - "flake8", - "flake8-pyproject", -] +dev = ["black", "pre-commit", "codespell", "flake8", "flake8-pyproject"] test = [ "pytest >=6.2.5", "pytest-env>=0.6.2", @@ -55,15 +42,14 @@ test = [ "codecov", ] -converters = [ -] +converters = [] [project.urls] repository = "https://github.com/MRtrix3/mrtrix3" [tool.hatch.version] source = "vcs" -raw-options = { root = ".." } +raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] version-file = "fileformats/extras/medimage_mrtrix3/_version.py" @@ -80,9 +66,7 @@ ignore-words = ".codespell-ignorewords" [tool.flake8] doctests = true -per-file-ignores = [ - "__init__.py:F401" -] +per-file-ignores = ["__init__.py:F401"] max-line-length = 88 select = "C,E,F,W,B,B950" extend-ignore = ['E203', 'E501', 'E129'] diff --git a/related-packages/fileformats/pyproject.toml b/related-packages/fileformats/pyproject.toml index fa372a1..c31e5b3 100644 --- a/related-packages/fileformats/pyproject.toml +++ b/related-packages/fileformats/pyproject.toml @@ -58,7 +58,7 @@ repository = "https://github.com/MRtrix3/mrtrix3" [tool.hatch.version] source = "vcs" -raw-options = { root = ".." } +raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] version-file = "fileformats/medimage_mrtrix3/_version.py" From e05a5655474b77f69fb62d63b83dc3e4f5124355 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 13:55:25 +0930 Subject: [PATCH 31/44] relaxed restrictions on fileformats in pyproject --- pyproject.toml | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 483f764..4baa0a4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,15 +9,12 @@ readme = "README.rst" requires-python = ">=3.8" dependencies = [ "pydra >=0.22", - "fileformats-medimage_mrtrix3 >=3.0.3a", - "pytest"] # bug in fileformats requires this currently -license = {file = "LICENSE"} -authors = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] -maintainers = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] + "fileformats-medimage_mrtrix3", + "pytest", +] # bug in fileformats requires this currently +license = { file = "LICENSE" } +authors = [{ name = "Thomas G. Close", email = "tom.g.close@gmail.com" }] +maintainers = [{ name = "Thomas G. Close", email = "tom.g.close@gmail.com" }] keywords = ["pydra"] classifiers = [ "Development Status :: 2 - Pre-Alpha", @@ -40,7 +37,7 @@ dev = [ "tqdm", "attrs >=23.1.0", "fileformats >= 0.8", - "fileformats-extras >= 0.2.1" + "fileformats-extras >= 0.2.1", ] doc = [ "packaging", @@ -78,9 +75,7 @@ ignore-words = ".codespell-ignorewords" [tool.flake8] doctests = true -per-file-ignores = [ - "__init__.py:F401" -] +per-file-ignores = ["__init__.py:F401"] max-line-length = 88 select = "C,E,F,W,B,B950" extend-ignore = ['E203', 'E501', 'E129', 'W503'] From 401d26d818c1c42231f92eb58e85cfeb60eceefb Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 14:02:39 +0930 Subject: [PATCH 32/44] fixed up ci-cd --- .github/workflows/ci-cd.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index e8e6832..ed84348 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -121,7 +121,7 @@ jobs: - name: Generate task specifications run: > - .generate.py + ./generate.py $MRTRIX_INSTALL/bin $(pwd) $MRTRIX_VERSION From 588082796bbc053e79473963d9b26c84b6310bf5 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 14:22:36 +0930 Subject: [PATCH 33/44] fixing ci-cd --- .github/workflows/ci-cd.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index ed84348..614f26c 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -138,7 +138,7 @@ jobs: uses: actions/upload-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX_VERSION + path: pydra/tasks/mrtrix3/v3_0 - name: Write version file run: echo $MRTRIX_VERSION > mrtrix3_version.txt @@ -147,7 +147,7 @@ jobs: uses: actions/upload-artifact@v2 with: name: VersionFile - path: pydra/tasks/mrtrix3/$MRTRIX_VERSION + path: mrtrix3_version.txt devcheck: needs: [generate] @@ -176,7 +176,7 @@ jobs: uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX_VERSION + path: pydra/tasks/mrtrix3/v3_0 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 @@ -224,7 +224,7 @@ jobs: uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX_VERSION + path: pydra/tasks/mrtrix3/v3_0 - name: Download MRtrix3 install uses: actions/download-artifact@v2 @@ -346,7 +346,7 @@ jobs: uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/$MRTRIX_VERSION + path: pydra/tasks/mrtrix3/v3_0 - name: Set up Python $PYTHON_VERSION uses: actions/setup-python@v2 From 82a2ef52f150f835bf6d15557cb0aa8132e6523a Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 15:09:01 +0930 Subject: [PATCH 34/44] added strip of gitignore to ci-cd --- .github/workflows/ci-cd.yml | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 614f26c..1d85700 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -19,6 +19,7 @@ env: MRTRIX_HOME: /opt/mrtrix3 MRTRIX_INSTALL: /opt/mrtrix3/install MRTRIX_VERSION: 3.0.4 + SUBPKG_NAME: v3_0 jobs: @@ -138,7 +139,7 @@ jobs: uses: actions/upload-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/v3_0 + path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }} - name: Write version file run: echo $MRTRIX_VERSION > mrtrix3_version.txt @@ -176,7 +177,11 @@ jobs: uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/v3_0 + path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }} + + - name: Strip auto package from gitignore so it is included in package + run: | + sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 @@ -197,7 +202,7 @@ jobs: pip install ${{ matrix.pip-flags }} "related-packages/fileformats" pip install ${{ matrix.pip-flags }} ".[dev]" python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra.tasks.mrtrix3.v3_0" + python -c "import pydra.tasks.mrtrix3.$SUBPKG_NAME" python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" test: @@ -224,7 +229,11 @@ jobs: uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/v3_0 + path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }} + + - name: Strip auto package from gitignore so it is included in package + run: | + sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore - name: Download MRtrix3 install uses: actions/download-artifact@v2 @@ -249,7 +258,7 @@ jobs: - name: Install task package run: | - pip install .fileformats-medimage-mrtrix ./fileformats-medimage-mrtrix-extras '.[test]' + pip install -e .fileformats-medimage-mrtrix -e ./fileformats-medimage-mrtrix-extras -e '.[test]' python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" @@ -346,7 +355,11 @@ jobs: uses: actions/download-artifact@v2 with: name: AutoGen - path: pydra/tasks/mrtrix3/v3_0 + path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }} + + - name: Strip auto package from gitignore so it is included in package + run: | + sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore - name: Set up Python $PYTHON_VERSION uses: actions/setup-python@v2 From 4db4d4a7588683c8de82b497f1fb06afd8b4b22f Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 15:33:10 +0930 Subject: [PATCH 35/44] db ci/cd --- .github/workflows/ci-cd.yml | 4 +--- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 1d85700..b289015 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -259,8 +259,6 @@ jobs: - name: Install task package run: | pip install -e .fileformats-medimage-mrtrix -e ./fileformats-medimage-mrtrix-extras -e '.[test]' - python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - name: Test with pytest run: | @@ -335,7 +333,7 @@ jobs: deploy: - needs: [devcheck, test] + needs: [devcheck, test, deploy-fileformats, deploy-fileformats-extras] runs-on: ubuntu-latest env: PYTHON_VERSION: 3.11 diff --git a/pyproject.toml b/pyproject.toml index 4baa0a4..5cc1c78 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ description = "pydra-mrtrix3 contains Pydra task specifications for MRtrix3 tool readme = "README.rst" requires-python = ">=3.8" dependencies = [ - "pydra >=0.22", + "pydra >=0.23", "fileformats-medimage_mrtrix3", "pytest", ] # bug in fileformats requires this currently From 191111d0ab6f07df7897f043acf9f2abe7b5b324 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 15:53:41 +0930 Subject: [PATCH 36/44] fixing cicd --- .github/workflows/ci-cd.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index b289015..548062e 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -257,8 +257,11 @@ jobs: python -m pip install --upgrade pip - name: Install task package - run: | - pip install -e .fileformats-medimage-mrtrix -e ./fileformats-medimage-mrtrix-extras -e '.[test]' + run: > + pip install + -e ./related-packagse/fileformats + -e ./related-packages/fileformats-extras + -e '.[test]' - name: Test with pytest run: | From ab0e542adb07baa7e88c9ec0dbbcaaf9818305b8 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 16:11:01 +0930 Subject: [PATCH 37/44] fixed typo in cicd --- .github/workflows/ci-cd.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 548062e..2731690 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -259,7 +259,7 @@ jobs: - name: Install task package run: > pip install - -e ./related-packagse/fileformats + -e ./related-packages/fileformats -e ./related-packages/fileformats-extras -e '.[test]' From 0078ca2b9a18cd588a7c6dfc845c952315d808a0 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 17:15:35 +0930 Subject: [PATCH 38/44] fixed up case of interfaces in tests --- generate.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/generate.py b/generate.py index 0b6f378..faf2e05 100755 --- a/generate.py +++ b/generate.py @@ -253,12 +253,12 @@ def auto_gen_test(cmd_name: str, output_dir: Path, log_errors: bool, pkg_version from fileformats.generic import File, Directory, FsObject # noqa from fileformats.medimage import Nifti1 # noqa from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, Tracks # noqa -from pydra.tasks.mrtrix3.{pkg_version} import {cmd_name} +from pydra.tasks.mrtrix3.{pkg_version} import {pascal_case_task_name(cmd_name)} def test_{cmd_name.lower()}(tmp_path, cli_parse_only): - task = {cmd_name}( + task = {pascal_case_task_name(cmd_name)}( """ input_fields = attrs.fields(type(task.inputs)) output_fields = attrs.fields(make_klass(task.output_spec)) From 1d533c354884d12980121df735ebd3de04f2c510 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 17:49:57 +0930 Subject: [PATCH 39/44] cicd db --- .github/workflows/ci-cd.yml | 3 +++ pyproject.toml | 6 +----- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 2731690..671ac60 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -241,6 +241,9 @@ jobs: name: MRtrix3 path: ${{ env.MRTRIX_INSTALL}} + - name: Make commands executable + run: chmod +x ${{ env.MRTRIX_INSTALL }}/bin/* + - name: Set PATH Variable run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV diff --git a/pyproject.toml b/pyproject.toml index 5cc1c78..b3dc079 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,11 +7,7 @@ name = "pydra-mrtrix3" description = "pydra-mrtrix3 contains Pydra task specifications for MRtrix3 tools" readme = "README.rst" requires-python = ">=3.8" -dependencies = [ - "pydra >=0.23", - "fileformats-medimage_mrtrix3", - "pytest", -] # bug in fileformats requires this currently +dependencies = ["fileformats-medimage_mrtrix3", "numpy", "pydra >=0.23"] license = { file = "LICENSE" } authors = [{ name = "Thomas G. Close", email = "tom.g.close@gmail.com" }] maintainers = [{ name = "Thomas G. Close", email = "tom.g.close@gmail.com" }] From 155d973169a7883061d45cbb82a9502b9fe32902 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 19:01:46 +0930 Subject: [PATCH 40/44] install dev branch of pydra until merge in ci-cd --- .github/workflows/ci-cd.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 671ac60..3d0cac8 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -266,9 +266,11 @@ jobs: -e ./related-packages/fileformats-extras -e '.[test]' + - name: Install dev branch of pydra until bugfix + run: pip install --upgrade git+https://github.com/nipype/pydra.git@typing-bugfixes + - name: Test with pytest - run: | - pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml + run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml - uses: codecov/codecov-action@v1 if: ${{ always() }} From 71e8172a0296ddb113b6313c6b7de93eda599938 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 19:10:01 +0930 Subject: [PATCH 41/44] db cicd --- .github/workflows/ci-cd.yml | 9 ++++++++- pyproject.toml | 1 + related-packages/fileformats-extras/pyproject.toml | 9 ++------- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 3d0cac8..f6e6f67 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -215,7 +215,14 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v2 + - name: Install dependencies + run: | + sudo apt-get update + sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build + + - name: Checkout code + uses: actions/checkout@v2 + - name: Download version file uses: actions/download-artifact@v2 with: diff --git a/pyproject.toml b/pyproject.toml index b3dc079..5c9b984 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,6 +50,7 @@ test = [ "pytest-xdist", "pytest-rerunfailures", "codecov", + "fileformats-medimage_mrtrix3-extras", ] [tool.hatch.version] diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml index 4c0cd6c..bf24c5e 100644 --- a/related-packages/fileformats-extras/pyproject.toml +++ b/related-packages/fileformats-extras/pyproject.toml @@ -10,6 +10,7 @@ requires-python = ">=3.8" dependencies = [ "fileformats >= 0.8", "fileformats-medimage-mrtrix3", + "medimages4tests", "pydra >= 0.22.0", ] license = { file = "LICENSE" } @@ -34,13 +35,7 @@ dynamic = ["version"] [project.optional-dependencies] dev = ["black", "pre-commit", "codespell", "flake8", "flake8-pyproject"] -test = [ - "pytest >=6.2.5", - "pytest-env>=0.6.2", - "pytest-cov>=2.12.1", - "medimages4tests", - "codecov", -] +test = ["pytest >=6.2.5", "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov"] converters = [] From e48747fe672a4d36a3fdf13b67b6c8ae57782932 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Tue, 28 May 2024 21:53:03 +0930 Subject: [PATCH 42/44] fixed up import statement in converters --- .../fileformats/extras/medimage_mrtrix3/converters.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py index 668100c..1301188 100644 --- a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py +++ b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py @@ -7,7 +7,7 @@ ) try: - from pydra.tasks.mrtrix3.utils import MrConvert + from pydra.tasks.mrtrix3.v3_0 import MrConvert except ImportError: from pydra.tasks.mrtrix3.latest import mrconvert as MrConvert From ea4bd203fa003a72f04560426263ca64bcb0ad0d Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 29 May 2024 12:00:18 +0930 Subject: [PATCH 43/44] xfailed tasks that aren't passing yet --- generate.py | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/generate.py b/generate.py index faf2e05..f832195 100755 --- a/generate.py +++ b/generate.py @@ -62,6 +62,63 @@ ] +XFAIL = [ + "dirsplit", + "dwi2mask_3dautomask", + "dwi2mask_ants", + "dwi2mask_b02template", + "dwi2mask_consensus", + "dwi2mask_fslbet", + "dwi2mask_hdbet", + "dwi2mask_legacy", + "dwi2mask_mean", + "dwi2mask_mtnorm", + "dwi2mask_synthstrip", + "dwi2mask_trace", + "dwi2response_dhollander", + "dwi2response_fa", + "dwi2response_manual", + "dwi2response_msmt_5tt", + "dwi2response_tax", + "dwi2response_tournier", + "dwibiascorrect_ants", + "dwibiascorrect_fsl", + "dwibiascorrect_mtnorm", + "dwibiasnormmask", + "dwicat", + "dwifslpreproc", + "dwigradcheck", + "dwinormalise_group", + "dwinormalise_manual", + "dwinormalise_mtnorm", + "dwishellmath", + "fivettgen_freesurfer", + "fivettgen_fsl", + "fivettgen_gif", + "fivettgen_hsvs", + "fixelcfestats", + "fixelconnectivity", + "fixelconvert", + "fixelcorrespondence", + "fixelcrop", + "fixelfilter", + "fixelreorient", + "labelsgmfix", + "mask2glass", + "mrconvert", + "mrstats", + "mrtransform", + "mrtrix_cleanup", + "population_template", + "responsemean", + "tck2fixel", + "tckstats", + "tsfmult", + "voxel2fixel", + "warpinvert", +] + + @click.command( help="""Loops through all MRtrix commands to generate Pydra (https://pydra.readthedocs.io) task interfaces for them @@ -250,12 +307,19 @@ def auto_gen_test(cmd_name: str, output_dir: Path, log_errors: bool, pkg_version code_str = f"""# Auto-generated test for {cmd_name} +import pytest from fileformats.generic import File, Directory, FsObject # noqa from fileformats.medimage import Nifti1 # noqa from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, Tracks # noqa from pydra.tasks.mrtrix3.{pkg_version} import {pascal_case_task_name(cmd_name)} +""" + if cmd_name in XFAIL: + code_str += ( + f"""@pytest.mark.xfail(reason="Task {cmd_name} is known not pass yet")""" + ) + code_str += f""" def test_{cmd_name.lower()}(tmp_path, cli_parse_only): task = {pascal_case_task_name(cmd_name)}( From 7b4f2a14523a07b04c275c98ed6dc92d9879f323 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 29 May 2024 14:02:13 +0930 Subject: [PATCH 44/44] cicd fix-up --- .github/workflows/ci-cd.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index f6e6f67..c35e459 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -350,8 +350,6 @@ jobs: deploy: needs: [devcheck, test, deploy-fileformats, deploy-fileformats-extras] runs-on: ubuntu-latest - env: - PYTHON_VERSION: 3.11 steps: - name: Download version file uses: actions/download-artifact@v2 @@ -374,10 +372,10 @@ jobs: run: | sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore - - name: Set up Python $PYTHON_VERSION + - name: Set up Python 3.11 uses: actions/setup-python@v2 with: - python-version: $PYTHON_VERSION + python-version: 3.11 - name: Install build tools run: python -m pip install --upgrade pip twine build