Move basic Python configuration to the root of the repo. (#80)

After way too much trying to figure stuff out I realized: why not just
put the `pyproject.toml` right at the root of the repo? This eliminates
all the `#subdirectory=...` when doing `pip install`s and also makes
`setuptools-scm` work right again. As a bonus, lots of tools now work
without any additional configuration and we can just run them as-is.

This moves the bare minimum files needed to the repo root:

- `pyproject.toml`
- `MANIFEST.in`

and updates everything else to make that work right.

.github/workflows/python-somacore.yaml

@@ -21,17 +21,12 @@ jobs:
           cache: pip
           cache-dependency-path: python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
       - uses: psf/black@stable
-        with:
-          src: "./python-spec"
       - uses: isort/isort-action@v1
-        with:
-          sort-paths: "./python-spec"
       - name: Install typing packages
         run: |
           pip install -r python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
       - name: Run mypy
-        working-directory: ./python-spec
-        run: mypy ./src
+        run: mypy ./python-spec/src
 
   run-tests:
     runs-on: ubuntu-latest
@@ -41,6 +36,10 @@ jobs:
         python-version: ["3.7", "3.8", "3.9", "3.10"]
     steps:
       - uses: actions/checkout@v3
+        with:
+          # setuptools-scm needs a deep clone so it can look through history
+          # to find a relevant tag.
+          fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
@@ -50,7 +49,7 @@ jobs:
         run: |
           pip install --upgrade pip wheel pytest pytest-cov setuptools
           pip install -r python-spec/requirements-py${{ matrix.python-version }}.txt
-          pip install ./python-spec
+          pip install .
       - name: Run tests
         working-directory: ./python-spec
         run: |
@@ -75,10 +74,9 @@ jobs:
       - name: Set up environment
         run: |
           pip install --upgrade build pip wheel setuptools setuptools-scm
-          ./python-spec/write-version-file
-          python -m build python-spec
+          python -m build .
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}
-          packages_dir: python-spec/dist
+          packages_dir: dist

.gitignore

@@ -1,2 +1,7 @@
 temp/
 tmp/
+**/__pycache__
+**/*.egg-info
+build/
+dist/
+python-spec/src/somacore/_version.py

.pre-commit-config.yaml

@@ -8,15 +8,11 @@ repos:
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
-
-  # Because the built-in pre-commit hooks don't natively support projects
-  # not at the root of their directory, we have to roll our own hooks.
-  - repo: local
+  - repo: https://github.com/psf/black
+    rev: '22.12.0'
     hooks:
-      - id: format-check
-        name: Format check
-        language: python
-        files: ^python-spec/
-        types_or: [python, pyi]
-        entry: ./.pre-commit/format-check.sh
-        additional_dependencies: [black, isort]
+      - id: black
+  - repo: https://github.com/PyCQA/isort
+    rev: '5.11.4'
+    hooks:
+      - id: isort

MANIFEST.in

@@ -0,0 +1,9 @@
+# Python package manifest. We have to do this manually because otherwise
+# setuptools-scm will try to include literally everything in the repo
+# and we only want to include the Python-specific stuff in our build.
+
+global-exclude *
+include pyproject.toml
+include MANIFEST.in
+recursive-include python-spec/README.md
+recursive-include python-spec/src *.py py.typed

python-spec/pyproject.toml → pyproject.toml

@@ -1,12 +1,15 @@
+# Build and release configuration for the Python version of core SOMA.
+# This lives at the root directory to save us lots of headaches with versioning.
+
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["setuptools", "setuptools-scm", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "somacore"
 description = "Python-language API specification and base utilities for implementation of the SOMA system."
 dynamic = ["version"]
-readme = "./README.md"
+readme = "./python-spec/README.md"
 dependencies = [
   "anndata",
   "attrs>=22.1",
@@ -22,14 +25,20 @@ classifiers = ["License :: OSI Approved :: MIT License"]
 dev = ["black", "isort", "setuptools-scm"]
 
 [tool.setuptools]
-packages.find.where = ["src"]
+packages.find.where = ["python-spec/src"]
 package-data.somacore = ["py.typed"]
-dynamic.version.attr = "somacore._version.version"
+
+[tool.setuptools_scm]
+write_to = "python-spec/src/somacore/_version.py"
+# Keep Python executable package versioning separate from the spec and R impl
+# by requiring `python-` at the start of the tag (e.g. `python-v1.2.3`).
+tag_regex = '^python-(?P<version>[vV]?\d+(?:\.\d+){0,2}[^\+]*)(?:\+.*)?$'
 
 [tool.isort]
 profile = "black"
 line_length = 88
 force_single_line = true
+known_first_party = ["somacore"]
 single_line_exclusions = ["typing", "typing_extensions"]
 
 [[tool.mypy.overrides]]

python-spec/src/somacore/__init__.py

@@ -4,15 +4,21 @@
 unified namespace.
 """
 
-from somacore import _version
 from somacore import base
 from somacore import data
 from somacore import ephemeral
 from somacore import options
 from somacore.query import axis
 
-__version__ = _version.version
-__version_tuple__ = _version.version_tuple
+try:
+    # This trips up mypy since it's a generated file:
+    from somacore import _version  # type: ignore[attr-defined]
+
+    __version__ = _version.version
+    __version_tuple__ = _version.version_tuple
+except ImportError:
+    __version__ = "0.0.0.dev+invalid"
+    __version_tuple__ = (0, 0, 0, "dev", "invalid")
 
 SOMAObject = base.SOMAObject
 Collection = base.Collection

python-spec/update-requirements-txt

@@ -14,12 +14,12 @@ LINTVER=3.7
 for PYVER in 3.7 3.8 3.9 3.10; do
   CONDIR="$TEMPDIR/py-$PYVER"
   conda create -y -p "$CONDIR" "python=$PYVER"
-  conda run -p "$CONDIR" pip install .
+  conda run -p "$CONDIR" pip install ..
   conda run -p "$CONDIR" pip freeze --exclude somacore >"requirements-py$PYVER.txt"
 done
 
 CONDIR="$TEMPDIR/py-$LINTVER-lint"
 conda create -y -p "$CONDIR" "python=$LINTVER"
-conda run -p "$CONDIR" pip install . mypy
+conda run -p "$CONDIR" pip install .. mypy
 conda run -p "$CONDIR" mypy --install-types --non-interactive ./src
 conda run -p "$CONDIR" pip freeze --exclude somacore >"requirements-py$LINTVER-lint.txt"