Merge pull request #19 from nipype/auto-gen

Auto generated interfaces from MRtrix3 source code

.gitignore

@@ -133,3 +133,8 @@ dmypy.json
 
 # VS Code
 .vscode/
+
+# Hatchling
+_version.py
+
+/pydra/tasks/mrtrix3/v3_0

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/*

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

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