MAINT: Migrate to PEP517/518 packaging

.circleci/config.yml

@@ -74,8 +74,7 @@ jobs:
       - run:
           name: Initiate versioning
           command: |
-            python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                                  setuptools_scm_git_archive pip twine docutils
+            python3 -m pip install -U build hatch hatchling pip twine docutils
 
             pip install /tmp/src/eddymotion[all]
 

.github/workflows/contrib.yml

@@ -11,15 +11,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-      - name: Install flake8
-        run: python -m pip install flake8
-      - name: Check EddyMotion
-        run: python -m flake8 src
+          python-version: 3
+      - name: Lint EddyMotion
+        run: pipx run flake8-pyproject

.github/workflows/docs-build-pr.yml

@@ -7,11 +7,11 @@ on:
 
 jobs:
   build:
-    if: "(github.repository_owner != 'nipreps') && !contains(github.event.head_commit.message, '[skip ci]')"
+    if: "!contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -39,10 +39,11 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --no-cache-dir "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
+        pip install -U build hatch pip
         pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1
 
     - name: Build docs
       run: |
-          python -m setuptools_scm  # Generate _version.py file
+          python -m hatch build --hooks-only
           make -C docs/ SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html

.github/workflows/docs-build-update.yml

@@ -42,12 +42,13 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --no-cache-dir "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
+        pip install -U build hatch pip
         pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1
 
     - name: Build docs
       run: |
-          python -m setuptools_scm  # Generate _version.py file
+          python -m hatch build --hooks-only
           make -C docs/ SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html
 
     - name: Push created tag to gh-pages

.github/workflows/pythonpackage.yml

@@ -16,19 +16,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        pip: ["pip==21.2", "pip~=22.0"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     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@v4
+      with:
+        submodules: recursive
+        fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v1
+    - uses: actions/cache@v4
       with:
         path: $HOME/.cache/pip
         key: pip-cache-v1
@@ -39,20 +38,18 @@ jobs:
       run: |
         python -m venv /tmp/buildenv
         source /tmp/buildenv/bin/activate
-        python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                              setuptools_scm_git_archive pip twine docutils
+        pip install -U build hatch pip twine
 
         python -m build -s -w
         python -m twine check dist/eddymotion-*
 
         mv dist /tmp/package
-        rm -rf eddymotion.egg-info/
 
         # Interpolate version
         if [[ "$GITHUB_REF" == refs/tags/* ]]; then
           TAG=${GITHUB_REF##*/}
         fi
-        THISVERSION=$( python -m setuptools_scm )
+        THISVERSION=$( python -m hatch version | tail -n1 | xargs )
         THISVERSION=${TAG:-$THISVERSION}
         echo "Expected VERSION: \"${THISVERSION}\""
         echo "THISVERSION=${THISVERSION}" >> $GITHUB_ENV
@@ -61,7 +58,7 @@ jobs:
       run: |
         python -m venv /tmp/pip
         source /tmp/pip/bin/activate
-        python -m pip install -U "setuptools >= 45" "setuptools_scm >= 6.2" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install .
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -72,7 +69,7 @@ jobs:
       run: |
         python -m venv /tmp/install_sdist
         source /tmp/install_sdist/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install /tmp/package/eddymotion*.tar.gz
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -83,7 +80,7 @@ jobs:
       run: |
         python -m venv /tmp/install_wheel
         source /tmp/install_wheel/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install /tmp/package/eddymotion*.whl
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "INSTALLED: \"${INSTALLED_VERSION}\""

.maint/update_requirements.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+from copy import copy
+from pathlib import Path
+from packaging.requirements import Requirement, SpecifierSet
+
+try:
+    from tomllib import loads  # Python +3.11
+except ImportError:
+    from pip._vendor.tomli import loads
+
+repo_root = Path(__file__).parent.parent
+pyproject = repo_root / "pyproject.toml"
+reqs = repo_root / "requirements.txt"
+min_reqs = repo_root / "min-requirements.txt"
+
+requirements = [
+    Requirement(req)
+    for req in loads(pyproject.read_text())["project"]["dependencies"]
+]
+
+script_name = Path(__file__).relative_to(repo_root)
+
+
+def to_min(req):
+    if req.specifier:
+        req = copy(req)
+        try:
+            min_spec = [
+                spec
+                for spec in req.specifier
+                if spec.operator in (">=", "~=")
+            ][0]
+        except IndexError:
+            return req
+        min_spec._spec = ("==",) + min_spec._spec[1:]
+        req.specifier = SpecifierSet(str(min_spec))
+    return req
+
+
+lines = [f"# Auto-generated by {script_name}", ""]
+
+# Write requirements
+lines[1:-1] = [str(req) for req in requirements]
+reqs.write_text("\n".join(lines))
+
+# Write minimum requirements
+lines[1:-1] = [str(to_min(req)) for req in requirements]
+min_reqs.write_text("\n".join(lines))

min-requirements.txt

@@ -0,0 +1,10 @@
+# Auto-generated by .maint/update_requirements.py
+dipy==1.3.0
+joblib
+nipype==1.5.1
+nitransforms==21.0.0
+nireports
+numpy==1.17.3
+nest-asyncio==1.5.1
+scikit-image==0.14.2
+scipy==1.8.0