Merge pull request #106 from templateflow/rel/23.0.0

effigies · web-flow · commit 1c81342f2830 · 2023-02-02T15:45:12.000-05:00
REL: 23.0.0
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -26,7 +26,7 @@ jobs:
             pip install -U pip
             pip install -r /tmp/src/templateflow/requirements.txt
             pip install "datalad ~= 0.11.8"
-            pip install "setuptools>=45" "setuptools_scm >= 6.2" twine codecov
+            pip install "setuptools>=45" "setuptools_scm >= 6.2" nipreps-versions build twine codecov
 
       - run:
           name: Install git and git-annex
@@ -120,7 +120,7 @@ jobs:
           command: |
             source /tmp/venv/bin/activate
             cd /tmp/src/templateflow
-            python setup.py sdist
+            python -m build
             twine check dist/*
 
   build_docs:
@@ -150,8 +150,8 @@ jobs:
             if ! [ -x "$(command -v conda)" ]; then
               curl -sSLO https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh 
               bash Miniconda3-py39_4.11.0-Linux-x86_64.sh -b -p $HOME/.conda
-              $HOME/.conda/bin/conda env update -f docs/environment.yml --prune
             fi
+            $HOME/.conda/bin/conda env update -f docs/environment.yml --prune
 
       - save_cache:
           key: env-v7-{{ .Branch }}
@@ -194,8 +194,8 @@ jobs:
           name: Deploy to PyPi
           command: |
             source /tmp/venv/bin/activate
-            pip install "setuptools>=45" "setuptools_scm >= 6.2" wheel twine
-            python setup.py sdist bdist_wheel
+            pip install build twine
+            python -m build
             twine check dist/*
             twine upload dist/*
 
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
@@ -10,193 +10,123 @@ on:
   pull_request:
     branches: [ master ]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
 jobs:
   build:
-    if: "!startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.get_version.outputs.version }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-v1
+          restore-keys: |
+            pip-cache-
+      - run: pip install --upgrade build twine
+      - name: Build sdist and wheel
+        run: python -m build
+      - run: twine check dist/*
+      - uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist/
+      - name: Interpolate version in confined environment
+        id: get_version
+        run: |
+          python -m venv /tmp/buildenv
+          source /tmp/buildenv/bin/activate
+          python -m pip install --upgrade setuptools setuptools_scm nipreps-versions
+          if [[ "$GITHUB_REF" == refs/tags/* ]]; then
+            TAG=${GITHUB_REF##*/}
+          fi
+          THISVERSION=$( python -m setuptools_scm )
+          THISVERSION=${TAG:-$THISVERSION}
+          echo "Expected VERSION: \"${THISVERSION}\""
+          echo "version=${THISVERSION}" >> $GITHUB_OUTPUT
+
+  test-install:
+    runs-on: ubuntu-latest
+    needs: build
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
-        pip: ["pip==21.2", "pip~=22.0"]
-
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        mode: ['wheel']
+        include:
+          - {python-version: '3.9', mode: 'repo'}
+          - {python-version: '3.9', mode: 'sdist'}
+          - {python-version: '3.9', mode: 'editable'}
+
+    env:
+      TEMPLATEFLOW_HOME: /tmp/home
+      THISVERSION: ${{ needs.build.outputs.version }}
     steps:
-    - uses: actions/checkout@v2
-    - name: Fetch all tags (for setuptools_scm to work)
-      run: |
-        /usr/bin/git -c protocol.version=2 fetch --tags --prune --unshallow origin
+    - uses: actions/checkout@v3
+      if: matrix.mode == 'repo'  || matrix.mode == 'editable'
+      with:
+        fetch-depth: 0
+    - uses: actions/download-artifact@v3
+      if: matrix.mode == 'sdist'  || matrix.mode == 'wheel'
+      with:
+        name: dist
+        path: /tmp/package/
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v1
+    - uses: actions/cache@v3
       with:
-        path: $HOME/.cache/pip
+        path: ~/.cache/pip
         key: pip-cache-v1
         restore-keys: |
           pip-cache-
-
-    - name: Build in confined environment and interpolate version
-      run: |
-        python -m venv /tmp/buildenv
-        source /tmp/buildenv/bin/activate
-        python -m pip install -U "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                              setuptools_scm_git_archive pip twine docutils
-        python setup.py sdist bdist_wheel
-        python -m twine check dist/templateflow*
-
-        mv dist /tmp/package
-        rm -rf templateflow.egg-info/
-
-        # Interpolate version
-        if [[ "$GITHUB_REF" == refs/tags/* ]]; then
-          TAG=${GITHUB_REF##*/}
-        fi
-        THISVERSION=$( python setup.py --version )
-        THISVERSION=${TAG:-$THISVERSION}
-        echo "Expected VERSION: \"${THISVERSION}\""
-        echo "THISVERSION=${THISVERSION}" >> $GITHUB_ENV
-
-    - name: Install in confined environment [pip]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/pip
+    - name: Upgrade pip
+      run: pip install --upgrade pip wheel
+    - name: Set install command
       run: |
-        python -m venv /tmp/pip
-        source /tmp/pip/bin/activate
-        python -m pip install -U "setuptools >= 45" "setuptools_scm >= 6.2" "${{ matrix.pip }}"
-        python -m pip install .
-        INSTALLED_VERSION=$(python -c 'import templateflow as tf; print(tf.__version__, end="")')
-        echo "VERSION: \"${THISVERSION}\""
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
-    - name: Install in confined environment [sdist]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/sdist
+        case ${{ matrix.mode }} in
+          repo)
+            echo "TARGET=." >> $GITHUB_ENV
+            ;;
+          editable)
+            echo "TARGET=-e ." >> $GITHUB_ENV
+            ;;
+          sdist)
+            echo "TARGET=$( ls /tmp/package/templateflow*.tar.gz )" >> $GITHUB_ENV
+            ;;
+          wheel)
+            echo "TARGET=$( ls /tmp/package/templateflow*.whl )" >> $GITHUB_ENV
+            ;;
+        esac
+    - name: Install and check version
       run: |
-        python -m venv /tmp/install_sdist
-        source /tmp/install_sdist/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
-        python -m pip install /tmp/package/templateflow*.tar.gz
+        pip install $TARGET
         INSTALLED_VERSION=$(python -c 'import templateflow as tf; print(tf.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
         test "${INSTALLED_VERSION}" = "${THISVERSION}"
 
-    - name: Re-install in confined environment [sdist]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/sdist
-      run: |
-        source /tmp/install_sdist/bin/activate
-        python -m pip install /tmp/package/templateflow*.tar.gz --force-reinstall
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.sdist-install.txt
-    - name: Re-install in confined environment [sdist - missing template]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/sdist
-      run: |
-        rm -rf ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
-        source /tmp/install_sdist/bin/activate
-        python -m pip install /tmp/package/templateflow*.tar.gz --force-reinstall
-        python -c "import templateflow; templateflow.update(overwrite=False)"
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.sdist-install-2.txt
-        diff /tmp/.sdist-install.txt /tmp/.sdist-install-2.txt
-        exit $?
-
-    - name: Install in confined environment [wheel]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/wheel
-      run: |
-        python -m venv /tmp/install_wheel
-        source /tmp/install_wheel/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
-        python -m pip install /tmp/package/templateflow*.whl
-        INSTALLED_VERSION=$(python -c 'import templateflow as tf; print(tf.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
-    - name: Re-install in confined environment [wheel]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/wheel
-      run: |
-        source /tmp/install_wheel/bin/activate
-        python -m pip install /tmp/package/templateflow*.whl --force-reinstall
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.wheel-install.txt
-    - name: Re-install in confined environment [wheel - missing template]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/wheel
-      run: |
-        rm -rf ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
-        source /tmp/install_wheel/bin/activate
-        python -m pip install /tmp/package/templateflow*.whl --force-reinstall
-        # Wheels do not run post-install hooks:
-        test ! -d ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
-        python -c "import templateflow; templateflow.update(overwrite=False)"
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.wheel-install-2.txt
-        diff /tmp/.wheel-install.txt /tmp/.wheel-install-2.txt
-        exit $?
-
-    - name: Install in confined environment [setup.py - install]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/setup_install
-      run: |
-        python -m venv /tmp/setup_install
-        source /tmp/setup_install/bin/activate
-        python -m pip install -U "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                              setuptools_scm_git_archive "${{ matrix.pip }}"
-        python -m pip install "numpy==1.20" Cython "pandas==1.3" "scipy==1.7"
-        python setup.py install
-        INSTALLED_VERSION=$(python -c 'import templateflow as tf; print(tf.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
-    - name: Re-install in confined environment [setup.py - install]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/setup_install
-      run: |
-        source /tmp/setup_install/bin/activate
-        python setup.py install
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.setup-install.txt
-    - name: Re-install in confined environment [setup.py - install - missing template]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/setup_install
-      run: |
-        rm -rf ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
-        source /tmp/setup_install/bin/activate
-        python setup.py install
-        python -c "import templateflow; templateflow.update(overwrite=False)"
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.setup-install-2.txt
-        diff /tmp/.setup-install.txt /tmp/.setup-install-2.txt
-        exit $?
-
-    - name: Install in confined environment [setup.py - develop]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/setup_develop
+    - name: Re-install
       run: |
-        python -m venv /tmp/setup_develop
-        source /tmp/setup_develop/bin/activate
-        python -m pip install -U "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                              setuptools_scm_git_archive "${{ matrix.pip }}"
-        python -m pip install "numpy==1.20" Cython "pandas==1.3" "scipy==1.7"
-        python setup.py develop
-        INSTALLED_VERSION=$(python -c 'import templateflow as tf; print(tf.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
-    - name: Re-install in confined environment [setup.py - develop]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/setup_develop
-      run: |
-        source /tmp/setup_develop/bin/activate
-        python setup.py develop
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.setup-develop.txt
-
-    - name: Re-install in confined environment [setup.py - develop - missing template]
-      env:
-        TEMPLATEFLOW_HOME: /tmp/home/setup_develop
+        pip install $TARGET --force-reinstall
+        find ${TEMPLATEFLOW_HOME} >> /tmp/.install.txt
+    - name: Re-install [missing template]
       run: |
         rm -rf ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
-        source /tmp/setup_develop/bin/activate
-        python setup.py develop
+        pip install $TARGET --force-reinstall
         python -c "import templateflow; templateflow.update(overwrite=False)"
-        find ${TEMPLATEFLOW_HOME} >> /tmp/.setup-develop-2.txt
-        diff /tmp/.setup-develop.txt /tmp/.setup-develop-2.txt
+        find ${TEMPLATEFLOW_HOME} >> /tmp/.install-2.txt
+        diff /tmp/.install.txt /tmp/.install-2.txt
         exit $?
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,15 @@
+23.0.0 (February 2, 2023)
+=========================
+Minor release including additional API features and an updated skeleton.
+
+* FIX: Preempt ``BIDSLayout`` from indexing dot-folders (#99)
+* ENH: Make sure existing ``layout.get_*`` are not bubbled in (#102)
+* ENH: Allow access to PyBIDS' magic ``get_*`` (#101)
+* ENH: Add an ``api.ls()`` function to list (without getting) files (#97)
+* MAINT: Discontinue legacy docker runners of CircleCI (#104)
+* MAINT: Rotate CircleCI secrets and setup up org-level context (#103)
+* MAINT: Fix docs build environment in CircleCI (#96)
+
 0.8.1 (May 7, 2022)
 ===================
 Patch release updating the S3 skeleton to include the fixed version of ``tpl-MouseIn``.
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -152,8 +152,6 @@ dependencies:
   - requests=2.27.1=pyhd8ed1ab_0
   - scipy=1.8.0=py39hee8e79c_1
   - setuptools=62.1.0=py39hf3d152e_0
-  - setuptools-scm=6.4.2=pyhd8ed1ab_0
-  - setuptools_scm=6.4.2=hd8ed1ab_0
   - six=1.16.0=pyh6c4a22f_0
   - snowballstemmer=2.2.0=pyhd8ed1ab_0
   - soupsieve=2.3.1=pyhd8ed1ab_0
@@ -202,6 +200,8 @@ dependencies:
     - docopt==0.6.2
     - formulaic==0.3.4
     - nibabel==3.2.2
+    - nipreps-versions==1.0.3
     - pandas==1.4.2
     - pybids==0.15.2
+    - setuptools_scm==7.1.0
     - sqlalchemy==1.3.24
diff --git a/pyproject.toml b/pyproject.toml
@@ -2,7 +2,7 @@
 requires = [
     "setuptools >= 45",
     "setuptools_scm >= 6.2",
-    "wheel"
+    "nipreps-versions",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -13,3 +13,4 @@ write_to_template = """\
 __version__ = "{version}"
 """
 fallback_version = "0.0"
+version_scheme = "nipreps-calver"
diff --git a/update_changes.sh b/update_changes.sh
