Update template (#19)

Author: htwangtw

.coveragerc

@@ -0,0 +1,4 @@
+[run]
+branch = True
+omit =
+    */_version.py

.github/workflows/pythonpackage.yml

@@ -1,6 +1,9 @@
 #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
@@ -10,18 +13,21 @@ env:
 on:
   push:
     branches: [ master ]
+    tags: [ '*' ]
   pull_request:
     branches: [ master ]
 
+
 jobs:
-  build:
+  devcheck:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.9]  # Check oldest and newest versions
+        pip-flags: ['', '--editable']
         pydra:
-        # - 'pydra'
-        - 'git+https://github.com/nipype/pydra.git#egg=pydra'
+        - 'pydra'
+        - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
 
     steps:
     - uses: actions/checkout@v2
@@ -38,9 +44,76 @@ jobs:
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Install task package
       run: |
-        pip install ".[dev]"
+        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]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Install task package
+      run: |
+        pip install ".[test]"
         python -c "import pydra.tasks.$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/$SUBPACKAGE
+        pytest -sv --doctest-modules pydra/tasks/$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 }}

codecov.yml

@@ -0,0 +1,14 @@
+coverage:
+  range: "50...100"
+  ignore:          # files and folders that will be removed during processing
+    - "**/tests"
+    - "**/_version.py"
+    - "setup.py"
+    - "versioneer.py"
+  status:
+    project:
+      default:
+        threshold: 1
+    patch:
+      default:
+        target: 80

pydra/tasks/fsl/_version.py

@@ -6,7 +6,7 @@
 # that just contains the computed version number.
 
 # This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
+# versioneer-0.19 (https://github.com/python-versioneer/python-versioneer)
 
 """Git implementation of _version.py."""
 
@@ -57,7 +57,7 @@ class NotThisMethod(Exception):
 
 
 def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
+    """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:
@@ -93,9 +93,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         if verbose:
             print("unable to find command, tried %s" % (commands,))
         return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
+    stdout = p.communicate()[0].strip().decode()
     if p.returncode != 0:
         if verbose:
             print("unable to run %s (error)" % dispcmd)
@@ -165,6 +163,10 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         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
@@ -300,6 +302,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     # 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
@@ -338,18 +343,18 @@ def render_pep440(pieces):
 
 
 def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+    """TAG[.post0.devDISTANCE] -- No -dirty.
 
     Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0.post0.devDISTANCE
     """
     if pieces["closest-tag"]:
         rendered = pieces["closest-tag"]
         if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
+            rendered += ".post0.dev%d" % pieces["distance"]
     else:
         # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
+        rendered = "0.post0.dev%d" % pieces["distance"]
     return rendered
 
 
@@ -385,7 +390,7 @@ def render_pep440_old(pieces):
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:

setup.cfg

@@ -5,11 +5,30 @@ subpackage = fsl
 author = Nipype Developers
 author_email = [email protected]
 description = FSL tasks for the Pydra dataflow engine
+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 :: 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 >= 0.14.1
+packages = find_namespace:
+
+[options.packages.find]
+include =
+    pydra.tasks.%(subpackage)s
+    pydra.tasks.%(subpackage)s.*
 
 [options.extras_require]
 doc =
@@ -24,14 +43,18 @@ docs =
 test =
     pytest >= 4.4.0
     pytest-cov
+    pytest-env
+    pytest-xdist
+    pytest-rerunfailures
     codecov
 tests =
     %(test)s
 dev =
     %(test)s
     nipype
-    black
     pyyaml
+    black
+    pre-commit
 all =
     %(doc)s
     %(dev)s

setup.py

@@ -8,8 +8,9 @@
 
 # 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 >= 30.3.0"]
+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 []
 
@@ -19,7 +20,4 @@
         setup_requires=SETUP_REQUIRES,
         version=versioneer.get_version(),
         cmdclass=versioneer.get_cmdclass(),
-        packages=find_namespace_packages(
-            include=(f"pydra.tasks.{SUBPACKAGE}", f"pydra.tasks.{SUBPACKAGE}.*")
-        ),
     )