diff --git a/.grype.yaml b/.grype.yaml deleted file mode 100644 index 7b1eaa95..00000000 --- a/.grype.yaml +++ /dev/null @@ -1,45 +0,0 @@ -exclude: - - ./requirements-dev.txt - - ./requirements-rtd.txt - - ./poetry.lock - -# initial commit; ignore vulnerabilities -ignore: - # These vulnerabilities are coming from the venv/requirements-ram.txt - - vulnerability: GHSA-xqr8-7jwr-rhp7 - package: - name: certifi - version: 2022.6.15 - type: python - - vulnerability: GHSA-v3c5-jqr6-7qm8 - package: - name: future - version: 0.18.2 - type: python - - vulnerability: GHSA-9j59-75qj-795w - package: - name: Pillow - version: 9.0.0 - type: python - - vulnerability: GHSA-8vj2-vxx3-667w - package: - name: Pillow - version: 9.0.0 - type: python - - vulnerability: GHSA-m2vv-5vj5-2hm7 - package: - name: Pillow - version: 9.0.0 - type: python - - vulnerability: GHSA-9q9m-c65c-37pq - package: - name: reportlab - version: 3.6.5 - type: python - # the setuptools vulnerability is coming from the base image in the bitbucket pipeline: - # https://github.com/docker-library/python/blob/81b6e5f0643965618d633cd6b811bf0879dee360/3.9/slim-bookworm/Dockerfile#L138 - - vulnerability: GHSA-r9hx-vwmv-q579 - package: - name: setuptools - version: 58.1.0 - type: python diff --git a/.readthedocs.yaml b/.readthedocs.yaml index b867adcc..83506d05 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,11 +9,14 @@ sphinx: # - pdf # Optionally set the version of Python and requirements required to build your docs -python: - install: - - requirements: requirements-rtd.txt +#python: +# install: +# - requirements: requirements-rtd.txt build: os: ubuntu-22.04 tools: python: "3.11" + jobs: + post_install: + - pip install .[docs] diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index de9f8aa0..3e641b36 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -21,7 +21,7 @@ definitions: - apt-get update - python -m venv venv - source venv/bin/activate - - pip install -r requirements-dev.txt + - pip install .[dev] - pip freeze artifacts: - venv/** @@ -278,7 +278,7 @@ pipelines: - apt-get update - python -m venv venv - source venv/bin/activate - - pip install -r requirements-dev.txt + - pip install .[dev] artifacts: - venv/** - step: diff --git a/docs/source/conf.py b/docs/source/conf.py index 55bb3e50..75db0212 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -83,9 +83,11 @@ # built documents. # # The short X.Y version. -version = "3.22" +from pylinac.version import __version__ # noqa + +version = ".".join(__version__.split(".")[:-1]) # chop off patch number # The full version, including alpha/beta/rc tags. -release = "3.22.0" +release = __version__ # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 4f38c6cb..8a529b37 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -54,7 +54,7 @@ Be sure to ask for help if you need it! * Clone your `forked repository to your local machine `__: ``git clone`` followed by the URL of your forked repository. Some IDEs also have a GUI for this. See also :ref:`distro_stack`. * Create a virtual environment. This is optional but highly recommended. See the `Python guide `__ to set up a new venv. -* Install the requirements and developer requirements: ``pip install -r requirements.txt -r requirements-dev.txt`` +* Install the requirements and developer requirements: ``pip install .[dev]`` * Create a new branch for your work: ``git checkout -b my_new_branch`` * Make your changes * Write tests for your changes. Most test modules in pylinac have a 1:1 correlation with the library modules and thus the diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 92dc428c..03594cfd 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -18,17 +18,7 @@ Great! To get started install via pip: .. note:: - Installing from source (``setup.py install``) is possible but not recommended as downloading the source includes numerous sizable test files. - -.. _dependencies: - -Dependencies ------------- - -Pylinac, as a scientific package, has fairly standard scientific dependencies (>= means at least that version or newer). -Installing the package via ``pip`` will install these for you: - -.. literalinclude:: ../../requirements.txt + If you plan on developing or contributing to pylinac, you'll want to set up a development environment. See :ref:`setup_dev_env`. 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{ include = "pylinac", format = 'wheel' }, -] -include = ['pylinac/files/*.png'] -exclude = ['pylinac/demo_files/**'] classifiers=[ "Intended Audience :: Developers", "Intended Audience :: Healthcare Industry", @@ -27,33 +27,62 @@ classifiers=[ "Topic :: Software Development :: Libraries" ] -[tool.poetry.dependencies] -python = "^3.8.10" -scikit-image = ">=0.17.3" -numpy = ">=0.16" -scipy = ">=1.1" -tqdm = ">=3.8" -Pillow = ">=4.0" -argue = "^0.3.1" -py-linq = "^1.3.0" -reportlab = ">=3.3" -pydicom = ">=2.0" -matplotlib = ">=2.0" -tabulate = "~0.9.0" -pydantic = ">=2.0" -eval-type-backport = {version = ">=0.2.0", python = "<=3.8"} +dependencies = [ + "scikit-image>=0.17.3", + "numpy>=0.16", + "scipy>=1.1", + "tqdm>=3.8", + "Pillow>=4.0", + "argue~=0.3.1", + "py-linq~=1.4.0", + "reportlab>=3.3", + "pydicom>=2.0", + "matplotlib>=2.0", + "tabulate~=0.9.0", + "pydantic>=2.0", + "eval-type-backport; python_version<='3.8'" +] -[tool.poetry.dev-dependencies] -pytest = {version = "^7.1.2", python = ">=3.8,<4.0"} -bump2version = "^1.0.1" -nox = "^2022.1.7" -pytest-xdist = "^2.5.0" -google-cloud-storage = {version = "^2.4.0", python = ">=3.8,<4.0"} -sphinx-autobuild = "^2021.3.14" +[project.optional-dependencies] +dev = [ + "pytest", + "pytest-xdist", + "pytest-cov", + "nox", + "furo", + "google-cloud-storage", + "sphinx", + "sphinx-autobuild", + "sphinx-copybutton", + "pre-commit", + "hatch", +] +docs = [ + "sphinx", + "sphinx-copybutton", + "furo", +] [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.hatch.build] +directory = "dist" + +[tool.hatch.version] +# https://hatch.pypa.io/latest/version/ +path = "pylinac/version.py" # hatch will automatically set the version to the value in this file. + +[tool.hatch.build.targets.wheel] +packages = ["pylinac"] +include = ['pylinac/files/*.png'] +exclude = ['pylinac/demo_files/**'] + +[tool.hatch.build.targets.sdist] +packages = ["pylinac"] +include = ['pylinac/files/*.png'] +exclude = ['pylinac/demo_files/**'] [tool.pytest.ini_options] testpaths = "tests_basic" diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index 22ff2472..00000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,15 +0,0 @@ --r requirements.txt -black -bump2version -furo -google-cloud-storage -nox -Pillow==10.* -pre-commit -pytest -pytest-cov==3.0.0 -pytest-xdist -sphinx -sphinx-autobuild -sphinx-copybutton -twine diff --git a/requirements-ram.txt b/requirements-ram.txt deleted file mode 100644 index 18085350..00000000 --- a/requirements-ram.txt +++ /dev/null @@ -1,66 +0,0 @@ -argcomplete==1.12.3 -argue==0.3.1 -atomicwrites==1.4.0 -attrs==21.4.0 -bleach==5.0.0 -bump2version==1.0.1 -certifi==2022.6.15 -charset-normalizer==2.0.12 -colorama==0.4.4 -colorlog==6.6.0 -commonmark==0.9.1 -cycler==0.11.0 -distlib==0.3.4 -docutils==0.18.1 -filelock==3.6.0 -fonttools==4.28.5 -furo -future==0.18.2 -google-cloud-storage -idna==3.3 -imageio==2.13.5 -importlib-metadata==4.11.4 -iniconfig==1.1.1 -keyring==23.6.0 -kiwisolver==1.3.2 -matplotlib==3.5.1 -networkx==2.6.3 -nox==2022.1.7 -numpy==1.22.1 -packaging==21.3 -Pillow==9.0.0 -pkginfo==1.8.3 -platformdirs==2.5.2 -pluggy==1.0.0 -py==1.11.0 -py-linq==1.3.0 -pydicom==2.2.2 -Pygments -pyparsing==3.0.6 -pytest==7.1.2 -pytest-cov==3.0.0 -pytest-xdist==2.5.0 -python-dateutil==2.8.2 -PyWavelets==1.2.0 -pywin32-ctypes==0.2.0 -readme-renderer==35.0 -reportlab==3.6.5 -requests==2.28.0 -requests-toolbelt==0.9.1 -rfc3986==2.0.0 -rich==12.4.4 -scikit-image==0.19.1 -scipy==1.7.3 -six==1.16.0 -sphinx==7.* -sphinx-autobuild -sphinx-copybutton -tabulate~=0.9.0 -tifffile==2021.11.2 -tomli==2.0.1 -tqdm==4.62.3 -twine==4.0.1 -urllib3==1.26.9 -virtualenv==20.14.1 -webencodings==0.5.1 -zipp==3.8.0 diff --git a/requirements-rtd.txt b/requirements-rtd.txt deleted file mode 100644 index 25604625..00000000 --- a/requirements-rtd.txt +++ /dev/null @@ -1,4 +0,0 @@ --r requirements.txt -furo -sphinx -sphinx-copybutton diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 6f789804..00000000 --- a/requirements.txt +++ /dev/null @@ -1,12 +0,0 @@ -argue -matplotlib >= 2.0 -numpy >= 1.16 -Pillow >= 4.0 -py-linq -pydantic >= 2.0 -pydicom >= 2.0 -reportlab >= 3.3 -scikit-image >= 0.17 -scipy >= 1.1 -tabulate~=0.9.0 -tqdm >= 3.8 diff --git a/test_bank.py b/test_bank.py deleted file mode 100644 index 5e189486..00000000 --- a/test_bank.py +++ /dev/null @@ -1,8 +0,0 @@ -"""Test the entire package; an underscore precedes this file name -so it does not include itself in the test discovery.""" -import os.path as osp - -from tests_basic import run_tests - -test_dir = osp.join(osp.dirname(__file__), "tests_bank") -run_tests(test_dir, pattern="_test*.py") diff --git a/test_basic.py b/test_basic.py deleted file mode 100644 index 1a46874c..00000000 --- a/test_basic.py +++ /dev/null @@ -1,8 +0,0 @@ -"""Test the entire package; an underscore precedes this file name -so it does not include itself in the test discovery.""" -import os.path as osp - -from tests_basic import run_tests - -test_dir = osp.join(osp.dirname(__file__), "tests_basic") -run_tests(test_dir) diff --git a/test_complete.py b/test_complete.py deleted file mode 100644 index 9236808e..00000000 --- a/test_complete.py +++ /dev/null @@ -1,8 +0,0 @@ -"""Test the entire package; an underscore precedes this file name -so it does not include itself in the test discovery.""" -import os.path as osp - -from tests_basic import run_tests - -test_dir = osp.join(osp.dirname(__file__), "tests_complete") -run_tests(test_dir, pattern="_test_all*.py")