Merge pull request #35 from nipype/src-dir

Adds fileformats sub-packages and refactors pyproject and github actions

.github/workflows/pythonpackage.yaml → .github/workflows/ci-cd.yaml

@@ -4,7 +4,7 @@
 # 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
+name: CI/CD
 
 on:
   push:

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 build/
 develop-eggs/
+_version.py
 dist/
 downloads/
 eggs/

README.md

@@ -10,16 +10,18 @@ All tasks will be inserted into the `pydra.tasks.<yourtaskpackagename>` namespac
 1. Give your repo a name.
 1. Once the repo is created and cloned, search for CHANGEME (`grep -rn CHANGEME . `) and
    replace with appropriate name.
-1. One of the folders is called CHANGEME. This should also be renamed to your package
-   name.
+1. Rename the following folders to replace `CHANGEME` with the name of the package:
+   * `src/pydra/tasks/CHANGEME`
+   * `fileformats/fileformats/medimage_CHANGEME`
+   * `fileformats/fileformats/extras/medimage_CHANGEME`
 1. Under the newly renamed package (i.e. formerly CHANGEME) there is a directory named "v1",
-   `pydra/tasks/<package-name>/v1`, change this to valid Python package name starting with
+   `src/pydra/tasks/<package-name>/v1`, change this to valid Python package name starting with
    'v' to indicate the version of the tool the Pydra interfaces will be designed for,
-   e.g. FSL v6.0.2 could be `pydra/tasks/fsl/v6` or `pydra/tasks/fsl/v6_0` depending on
+   e.g. FSL v6.0.2 could be `src/pydra/tasks/fsl/v6` or `src/pydra/tasks/fsl/v6_0` depending on
    how stable the CLI of the tool is between minor versions.
-1. Edit `pydra/tasks/<package-name>/latest.py` to update references to `v1` to the
+1. Edit `src/pydra/tasks/<package-name>/latest.py` to update references to `v1` to the
    tool target version
-1. Add tasks to the `pydra/tasks/<package-name>/v<package-version>` folder.
+1. Add tasks to the `src/pydra/tasks/<package-name>/v<package-version>` folder.
 1. You may want to initialize a [Sphinx] docs directory.
 1. Review the workflow in `.github/workflows/pythonpackage.yml`. Testing editable installations
    is probably not useful unless you are reconfiguring namespace packages.
@@ -40,7 +42,7 @@ python -m build
 twine upload dist/*
 ```
 
-Note that uploading to PyPI is done via [Continuous integration](#continuous-integration)) when
+Note that uploading to PyPI is done via [Continuous integration](#continuous-integration) when
 a tag is pushed to the repository, so only the first step needs to be donne manually.
 
 Note also that we assume tags will be version numbers and not be prefixed with `v` or some other

pyproject.toml

@@ -3,15 +3,17 @@ requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]
-name = "pydra-tasks-CHANGEME"
+name = "pydra-CHANGEME"
 description = "Pydra tasks package for CHANGEME"
 readme = "README.md"
 requires-python = ">=3.8"
 dependencies = [
     "pydra >=0.22",
     "fileformats >=0.8.3",
     "fileformats-datascience >=0.1",
-    "fileformats-medimage >=0.4.1"]
+    "fileformats-medimage >=0.4.1",
+    "fileformats-medimage-CHANGEME"
+]
 license = {file = "LICENSE"}
 authors = [{name = "Nipype developers", email = "[email protected]"}]
 maintainers = [{name = "Nipype developers", email = "[email protected]"}]
@@ -51,6 +53,7 @@ test = [
     "fileformats-extras",
     "fileformats-datascience-extras",
     "fileformats-medimage-extras",
+    "fileformats-medimage-CHANGEME-extras"
 ]
 
 [tool.hatch.version]

related-packages/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)

related-packages/fileformats-extras/LICENSE

@@ -0,0 +1,13 @@
+   Copyright 2021 Nipype developers
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

related-packages/fileformats-extras/README.rst

@@ -0,0 +1,29 @@
+FileFormats-CHANGEME Extras
+======================================
+.. image:: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg
+    :target: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml
+
+
+This is a extras module for the `fileformats-CHANGEME <https://github.com/nipype/pydra-freesurfer/>`__
+fileformats extension 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-CHANGEME-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 <http://creativecommons.org/licenses/by/4.0/>`_
+
+.. 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

related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME/__init__.py

@@ -0,0 +1 @@
+from ._version import __version__

related-packages/fileformats-extras/pyproject.toml

@@ -0,0 +1,87 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "fileformats-medimage-CHANGEME-extras"
+description = "Extensions to add functionality to tool-specific *fileformats* classes"
+readme = "README.rst"
+requires-python = ">=3.8"
+dependencies = [
+    "fileformats",
+    "fileformats-medimage-CHANGEME",
+    "pydra >= 0.23.0a"
+]
+license = {file = "LICENSE"}
+authors = [
+    {name = "Thomas G. Close", email = "[email protected]"},
+]
+maintainers = [
+    {name = "Thomas G. Close", email = "[email protected]"},
+]
+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",
+]
+
+converters = [
+]
+
+[project.urls]
+repository = "https://github.com/nipype/pydra-CHANGEME"
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { root = "../.." }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "fileformats/extras/medimage_CHANGEME/_version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["fileformats"]
+
+[tool.black]
+target-version = ['py38']
+exclude = "fileformats/extras/medimage_CHANGEME/_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']

related-packages/fileformats/LICENSE

@@ -0,0 +1,13 @@
+   Copyright 2021 Nipype developers
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

related-packages/fileformats/README.rst

@@ -0,0 +1,39 @@
+How to customise this template
+==============================
+
+#. Rename the `related-packages/fileformats/CHANGEME` directory to the name of the fileformats subpackage (e.g. `medimage_fsl`)
+#. Search and replace "CHANGEME" 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/CHANGEME`
+#. Delete these instructions
+
+...
+
+FileFormats Extension - CHANGEME
+====================================
+.. image:: https://github.com/nipype/pydra-CHANGEME/actions/workflows/ci-cd.yml/badge.svg
+    :target: https://github.com/nipype/pydra-CHANGEME/actions/workflows/ci-cd.yml
+
+This is the "CHANGEME" 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-CHANGEME
+
+This will install the core package and any other dependencies
+
+License
+-------
+
+This work is licensed under a
+`Creative Commons Attribution 4.0 International License <http://creativecommons.org/licenses/by/4.0/>`_
+
+.. 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

related-packages/fileformats/fileformats/medimage_CHANGEME/__init__.py

@@ -0,0 +1 @@
+from ._version import __version__

related-packages/fileformats/pyproject.toml

@@ -0,0 +1,84 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "fileformats-medimage-CHANGEME"
+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",
+    "fileformats-medimage"
+]
+license = {file = "LICENSE"}
+authors = [
+    {name = "Thomas G. Close", email = "[email protected]"},
+]
+maintainers = [
+    {name = "Thomas G. Close", email = "[email protected]"},
+]
+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",
+    "fileformats-medimage-CHANGME-extras",
+]
+
+[project.urls]
+repository = "https://github.com/nipype/pydra-CHANGEME"
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { root = "../.." }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "fileformats/medimage_CHANGEME/_version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["fileformats"]
+
+[tool.black]
+target-version = ['py38']
+exclude = "fileformats/medimage_CHANGEME/_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']