added fileformats packages to template resources

tclose · tclose · commit 2934fd3edf75 · 2024-03-20T09:22:07.000+11:00
diff --git a/nipype2pydra/pkg_gen/__init__.py b/nipype2pydra/pkg_gen/__init__.py
@@ -641,9 +641,33 @@ def copy_ignore(_, names):
         gh_workflows_dir / "ci-cd.yaml",
     )
 
+    related_pkgs_dir = pkg_dir / "related-packages"
+    shutil.copytree(TEMPLATES_DIR / "related-packages", related_pkgs_dir)
+
     # Add modified README
     os.unlink(pkg_dir / "README.md")
-    shutil.copy(TEMPLATES_DIR / "README.rst", pkg_dir / "README.rst")
+    with open(TEMPLATES_DIR / "README.rst") as f:
+        readme_rst = f.read()
+    readme_rst = readme_rst.replace("=" * 31, "=" * (23 + len(pkg)))
+    with open(pkg_dir / "README.rst", "w") as f:
+        f.write(readme_rst)
+
+    fileformat_readme_path = related_pkgs_dir / "fileformats" / "README.rst"
+    with open(fileformat_readme_path) as f:
+        ff_readme_rst = f.read()
+    ff_readme_rst = ff_readme_rst.replace("=" * 29, "=" * (27 + len(pkg)))
+    with open(fileformat_readme_path, "w") as f:
+        f.write(ff_readme_rst)
+
+    fileformat_extras_readme_path = (
+        related_pkgs_dir / "fileformats-extras" / "README.rst"
+    )
+    with open(fileformat_extras_readme_path) as f:
+        ffe_readme_rst = f.read()
+    ffe_readme_rst = ffe_readme_rst.replace("=" * 36, "=" * (34 + len(pkg)))
+    with open(fileformat_extras_readme_path, "w") as f:
+        f.write(ffe_readme_rst)
+
     with open(pkg_dir / "pyproject.toml") as f:
         pyproject_toml = f.read()
     pyproject_toml = pyproject_toml.replace("README.md", "README.rst")
diff --git a/nipype2pydra/pkg_gen/resources/templates/README.rst b/nipype2pydra/pkg_gen/resources/templates/README.rst
@@ -71,14 +71,22 @@ Contributing to this package
 Developer installation
 ~~~~~~~~~~~~~~~~~~~~~~
 
+Install the `fileformats <https://arcanaframework.github.io/fileformats/>`__ packages
+corresponding to AFNI specific file formats
+
+
+.. code-block::
+
+   $ pip install -e ./related-packages/fileformats[dev]
+   $ pip install -e ./related-packages/fileformats-extras[dev]
 
 Install repo in developer mode from the source directory and install pre-commit to
 ensure consistent code-style and quality.
 
 .. code-block::
 
    $ pip install -e .[test,dev]
-$ pre-commit install
+   $ pre-commit install
 
 Next install the requirements for running the auto-conversion script and generate the
 Pydra task interfaces from their Nipype counterparts
@@ -93,7 +101,8 @@ The run the conversion script to convert Nipype interfaces to Pydra
 
    $ nipype-auto-conv/generate
 
-## Methodology
+Methodology
+~~~~~~~~~~~
 
 The development of this package is expected to have two phases
 
diff --git a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd.yaml b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd.yaml
@@ -21,12 +21,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')    
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
     - name: Install build dependencies
       run: python -m pip install --upgrade pip
     - name: Install requirements
@@ -50,7 +50,7 @@ jobs:
         - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')    
@@ -63,7 +63,7 @@ jobs:
       run: |
         sed -i '/\/pydra\/tasks\/CHANGEME\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install build dependencies
@@ -90,12 +90,12 @@ jobs:
       matrix:
         python-version: ['3.8', '3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install build dependencies
@@ -149,7 +149,7 @@ jobs:
         source $FREESURFER_HOME/SetUpFreeSurfer.sh
         echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
         export PATH=$FREESURFER_HOME/bin:$PATH
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
@@ -162,7 +162,7 @@ jobs:
       run: |
         sed -i '/\/src\/pydra\/tasks\/CHANGEME\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install build dependencies
@@ -187,12 +187,12 @@ jobs:
     needs: [devcheck, test]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
     - name: Install build tools
@@ -219,12 +219,12 @@ jobs:
     needs: [deploy-fileformats]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
     - name: Install build tools
@@ -251,7 +251,7 @@ jobs:
     needs: [deploy-fileformats-extras]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
         fetch-depth: 0
@@ -270,7 +270,7 @@ jobs:
         git commit -am"added auto-generated version to make new tag for package version"
         git tag ${TAG}post${POST}    
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
     - name: Install build tools
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/conftest.py b/nipype2pydra/pkg_gen/resources/templates/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)
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/LICENSE b/nipype2pydra/pkg_gen/resources/templates/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.
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/README.rst b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/README.rst
@@ -0,0 +1,32 @@
+FileFormats-medimage-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-medimage-CHANGEME <https://github.com/nipype/pydra-CHANGEME/>`__
+fileformats extension package, which provides additional functionality to format classes (i.e. aside
+from basic identification and validation), such as conversion tools, metadata parsers,
+sample data generators, etc...
+
+
+Quick Installation
+------------------
+
+This extension can be installed for Python 3 using *pip*::
+
+    $ pip3 install fileformats-medimage-CHANGEME-extras
+
+This will install the package, base packages, and any other dependencies required to
+implement the extra functionality.
+
+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
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME/__init__.py b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME/__init__.py
@@ -0,0 +1 @@
+from ._version import __version__
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/pyproject.toml b/nipype2pydra/pkg_gen/resources/templates/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 = "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",
+    "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']
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/LICENSE b/nipype2pydra/pkg_gen/resources/templates/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.
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/README.rst b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/README.rst
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/fileformats/medimage_CHANGEME/__init__.py b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/fileformats/medimage_CHANGEME/__init__.py
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml
