CI: Package bids-examples and bids-error-examples into Python distrib…

…utions on schema-* tags (#1252)

Co-authored-by: Christopher J. Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>

.github/workflows/schemacode_ci.yml

@@ -4,52 +4,81 @@ on:
   push:
     branches:
       - "master"
-    paths:
-      - "tools/schemacode/**"
-      - "src/schema/**"
+    tags:
+      - "schema-*"
   pull_request:
     branches:
       - "*"
-    paths:
-      - "tools/schemacode/**"
-      - "src/schema/**"
 
-jobs:
+defaults:
+  run:
+    shell: bash
 
-  run_tests:
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: "Install build dependencies"
+        run: pip install --upgrade build twine
+      - name: "Install test dependencies on tag"
+        run: pip install --upgrade pytest pyyaml pandas tabulate
+        if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
+      - name: "Build archive on tag"
+        run: pytest tools/schemacode/bidsschematools -k make_archive
+        env:
+          BIDSSCHEMATOOLS_RELEASE: 1
+        if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
+      - name: "Build source distribution and wheel"
+        run: python -m build tools/schemacode
+      - name: "Check distribution metadata"
+        run: twine check tools/schemacode/dist/*
+      - uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: tools/schemacode/dist/
 
+  test:
     runs-on: ${{ matrix.os }}
+    needs: [build]
     strategy:
-        fail-fast: false
-        matrix:
-            os: ["ubuntu-latest"]
-            python-version: ["3.7", "3.8", "3.9", "3.10"]
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
-    defaults:
-      run:
-        shell: bash
     steps:
       - uses: actions/checkout@v3
 
       - name: "Set up Python"
         uses: actions/setup-python@v4
         with:
-            python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python-version }}
 
       - name: "Display Python version"
-        shell: bash {0}
         run: python -c "import sys; print(sys.version)"
 
-      - name: "Install the schemacode package"
-        shell: bash {0}
+      - name: "Fetch packages"
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+      - name: "Install package"
         run: |
-          python -m pip install --progress-bar off --upgrade pip
-          python -m pip install ./tools/schemacode[all]
+          pip install $( ls dist/*.whl )[all]
 
       - name: "Run tests"
-        shell: bash {0}
         run: |
-          python -m pytest --pyargs bidsschematools -m "not validate_schema" --cov-append --cov-report=xml --cov=bidsschematools
+          python -m pytest -vs --pyargs bidsschematools -m "not validate_schema" \
+              --cov-append --cov-report=xml --cov=bidsschematools
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v3
@@ -58,6 +87,34 @@ jobs:
           path: coverage.xml
         if: success()
 
+  publish:
+    runs-on: ${{ matrix.os }}
+    name: Publish Python Package
+    needs: [test]
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
+    steps:
+      - name: "Fetch packages"
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+      - name: "Test PyPI upload"
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+          skip_existing: true
+      - name: "Upload to PyPI (on tags)"
+        if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
   flake8-lint:
     runs-on: ubuntu-latest
     name: Lint schemacode
@@ -71,56 +128,53 @@ jobs:
           python-version: "3.7"
 
       - name: Install the schemacode package
-        shell: bash {0}
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
           python -m pip install -e ./tools/schemacode[all]
 
       - name: Run flake8
         working-directory: ./tools/schemacode/
-        shell: bash {0}
         run: |
           flake8 .
 
   validate_schema:
     runs-on: ubuntu-latest
     name: Validate schema
     steps:
-    - uses: actions/checkout@v3
+      - uses: actions/checkout@v3
 
-    - name: Set Up Python environment
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.9"
+      - name: Set Up Python environment
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
 
-    - name: Install the schemacode package
-      shell: bash {0}
-      run: |
-        python -m pip install --progress-bar off --upgrade pip setuptools wheel
-        python -m pip install -e ./tools/schemacode[all]
+      - name: Install the schemacode package
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install -e ./tools/schemacode[all]
 
-    - name: Run schema validation tests
-      run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools
+      - name: Run schema validation tests
+        run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools
 
-    - name: Upload artifacts
-      uses: actions/upload-artifact@v3
-      with:
-        name: schema_validation
-        path: coverage.xml
-      if: success()
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: schema_validation
+          path: coverage.xml
+        if: success()
 
   upload_to_codecov:
     runs-on: "ubuntu-latest"
     name: Upload coverage
-    needs: [run_tests,validate_schema]
+    needs: [test, validate_schema]
     steps:
-    - name: Checkout
-      uses: actions/checkout@v2
+      - name: Checkout
+        uses: actions/checkout@v2
 
-    - name: Download artifacts
-      uses: actions/download-artifact@v3
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
 
-    - name: Upload to CodeCov
-      uses: codecov/codecov-action@v3
-      with:
-        fail_ci_if_error: true
+      - name: Upload to CodeCov
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true

scripts/test_tag

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+# Execute this script from anywhere in the repository to push to a new unique testing tag.
+# This is a script which automates creation and pushing of unique tags for github actions.
+# It is particularly useful when debugging the upload hooks for pypi.
+# The workflow for that is to edit `.github/workflows/schemacode_ci.yml` and add a secondary branch name to the `on` section right after master.
+# This will allow you to keep pushing to the branch as if it were master and unix-time tagged archives being uploaded to test.pypi.
+
+EPOCH="$(date +%s)"
+
+GIT_DIR=$( git rev-parse --git-dir )
+REPO_ROOT=$( ls -d ${GIT_DIR%.git} )
+
+VERSION_FILE="$REPO_ROOT/src/schema/SCHEMA_VERSION"
+
+REAL_VERSION=$(cat "${VERSION_FILE}")
+DUMMY_VERSION="0.0.${EPOCH}-dev"
+
+echo "${DUMMY_VERSION}" > "${VERSION_FILE}"
+git commit -a -m "Test release $DUMMY_VERSION"
+git tag -a "schema-$DUMMY_VERSION" -m "Test release $DUMMY_VERSION"
+
+echo "${REAL_VERSION}" > "${VERSION_FILE}"

tools/schemacode/bidsschematools/tests/conftest.py

@@ -1,11 +1,13 @@
 import logging
-import os
 import tempfile
 from subprocess import run
 
-import pytest
+try:
+    from importlib.resources import as_file, files
+except ImportError:  # PY<3.9
+    from importlib_resources import as_file, files
 
-from bidsschematools import schema, utils
+import pytest
 
 lgr = logging.getLogger()
 
@@ -35,22 +37,21 @@ def get_gitrepo_fixture(url, whitelist):
     @pytest.fixture(scope="session")
     def fixture():
         archive_name = url.rsplit("/", 1)[-1]
-        testdata_archive = os.path.join(os.getcwd(), "testdata", archive_name)
-        if os.path.isdir(testdata_archive):
+        testdata_dir = files("bidsschematools.tests.data") / archive_name
+        if testdata_dir.is_dir():
             lgr.info(
-                "Found static testdata archive under `%s`. "
-                "Not downloading latest data from version control.",
-                testdata_archive,
+                f"Found static testdata archive under `{testdata_dir}`. "
+                "Not downloading latest data from version control."
             )
-            yield testdata_archive
+            with as_file(testdata_dir) as path:
+                yield path
         else:
             lgr.info(
                 "No static testdata available under `%s`. "
                 "Attempting to fetch live data from version control.",
-                testdata_archive,
+                testdata_dir,
             )
             with tempfile.TemporaryDirectory() as path:
-                assert os.path.exists(path)
                 lgr.debug("Cloning %r into %r", url, path)
                 runout = run(
                     [
@@ -79,14 +80,18 @@ def fixture():
 @pytest.fixture(scope="session")
 def schema_dir():
     """Path to the schema housed in the bids-specification repo."""
+    from bidsschematools import utils
+
     bids_schema = utils.get_schema_path()
     return bids_schema
 
 
 @pytest.fixture(scope="session")
-def schema_obj(schema_dir):
+def schema_obj():
     """Schema object."""
-    return schema.load_schema(schema_dir)
+    from bidsschematools import schema
+
+    return schema.load_schema()
 
 
 bids_examples = get_gitrepo_fixture(

tools/schemacode/bidsschematools/tests/test_make_testdata.py

@@ -1,9 +1,12 @@
 import os
-import tarfile
+import shutil
 
-import pytest
+try:
+    from importlib.resources import files
+except ImportError:  # PY<3.9
+    from importlib_resources import files
 
-from .. import __version__
+import pytest
 
 
 def require_env(var):
@@ -30,9 +33,15 @@ def test_make_archive(bids_examples, bids_error_examples):
     * Archives will be generated under `/tmp/bidsschematools-testdata-SCHEMA_VERSION.tar.gz`
     """
 
-    archive_name = f"bidsschematools-testdata-{__version__}"
-    archive_path = f"/tmp/{archive_name}.tar.gz"
+    testdata_dir = files("bidsschematools.tests.data")
+    ignore_git = shutil.ignore_patterns(".git*")
+    shutil.copytree(bids_examples, testdata_dir / "bids-examples", ignore=ignore_git)
+    shutil.copytree(bids_error_examples, testdata_dir / "bids-error-examples", ignore=ignore_git)
+
+    # Keeping this for now, it would be really nice to have a separate archive someday.
+    # archive_name = f"bidsschematools-testdata-{__version__}"
+    # archive_path = f"/tmp/{archive_name}.tar.gz"
 
-    with tarfile.open(archive_path, "w:gz") as tar:
-        tar.add(bids_examples, arcname=f"{archive_name}/bids-examples")
-        tar.add(bids_error_examples, arcname=f"{archive_name}/bids-error-examples")
+    # with tarfile.open(archive_path, "w:gz") as tar:
+    #     tar.add(bids_examples, arcname=f"{archive_name}/bids-examples")
+    #     tar.add(bids_error_examples, arcname=f"{archive_name}/bids-error-examples")

tools/schemacode/setup.cfg

@@ -52,7 +52,7 @@ bidsschematools =
     data/schema/BIDS_VERSION
     data/schema/SCHEMA_VERSION
     data/schema/**/*.yaml
-    tests/data/*
+    tests/data/**/*
 
 [options.entry_points]
 console_scripts =