Updated value classes based on JSON (#1018)

* Bump spec_tests/hed-examples from `8824691` to `7117cf9` Bumps [spec_tests/hed-examples](https://github.com/hed-standard/hed-examples) from `8824691` to `7117cf9`. - [Release notes](https://github.com/hed-standard/hed-examples/releases) - [Commits](hed-standard/hed-examples@8824691...7117cf9) --- updated-dependencies: - dependency-name: spec_tests/hed-examples dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump spec_tests/hed-specification from `5465995` to `5bc506c` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `5465995` to `5bc506c`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@5465995...5bc506c) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Improve .tsv loading to support children referenced before parent * fix typo * Fix for unknown library hedIDs, minor updates to CI workflows(run on 3.11) * Pass a tuple in word cloud, not np array * Bump spec_tests/hed-examples from `7117cf9` to `bce0c7a` Bumps [spec_tests/hed-examples](https://github.com/hed-standard/hed-examples) from `7117cf9` to `bce0c7a`. - [Release notes](https://github.com/hed-standard/hed-examples/releases) - [Commits](hed-standard/hed-examples@7117cf9...bce0c7a) --- updated-dependencies: - dependency-name: spec_tests/hed-examples dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Cache and retrieve library_data.json from hed-schemas * Add a new add_hed_ids script. Minor documentation corrections * Bump spec_tests/hed-specification from `5bc506c` to `07812cd` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `5bc506c` to `07812cd`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@5bc506c...07812cd) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump spec_tests/hed-specification from `07812cd` to `7cf62e5` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `07812cd` to `7cf62e5`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@07812cd...7cf62e5) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Add hedId value checking to schema validation Fix version attribute for merged schemas Remove cache hit from scripts(I think it's not required, but we'll see...) rename tag_util -> util in the normal validator * Don't escape double quotes in .tsv schemas Slightly improve importing of load_dataframes/save_dataframes by adding to init * Fix crash in unmerged schema validation. Always cache with_standard schemas, even if merged * Fix create_ontology using the wrong tag range for libraries * Bump spec_tests/hed-specification from `7cf62e5` to `19b29fe` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `7cf62e5` to `19b29fe`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@7cf62e5...19b29fe) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Fix it so it caches the local hed files when asking for all versions * More fixes for local schema caching/testing * Add optional flag to validate_schemas script to validate all 3 types always * Have the validator script save schemas merged, not unmerged, to prevent an issue where it was saved with a with_standard schema that has since changed * Bump spec_tests/hed-examples from `bce0c7a` to `6e265bf` Bumps [spec_tests/hed-examples](https://github.com/hed-standard/hed-examples) from `bce0c7a` to `6e265bf`. - [Release notes](https://github.com/hed-standard/hed-examples/releases) - [Commits](hed-standard/hed-examples@bce0c7a...6e265bf) --- updated-dependencies: - dependency-name: spec_tests/hed-examples dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Always save schemas with newlines, never CLRF * Update hed id verification to allow removal of tags without hedIDs * Add annotationExternal to omn generation Change how schemas are sorted(so library nodes always go to the top) Move a bunch of ontology_util to df_util * Bump spec_tests/hed-examples from `6e265bf` to `ba86a84` Bumps [spec_tests/hed-examples](https://github.com/hed-standard/hed-examples) from `6e265bf` to `ba86a84`. - [Release notes](https://github.com/hed-standard/hed-examples/releases) - [Commits](hed-standard/hed-examples@6e265bf...ba86a84) --- updated-dependencies: - dependency-name: spec_tests/hed-examples dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump paambaati/codeclimate-action from 8.0.0 to 9.0.0 Bumps [paambaati/codeclimate-action](https://github.com/paambaati/codeclimate-action) from 8.0.0 to 9.0.0. - [Release notes](https://github.com/paambaati/codeclimate-action/releases) - [Changelog](https://github.com/paambaati/codeclimate-action/blob/main/CHANGELOG.md) - [Commits](paambaati/codeclimate-action@v8.0.0...v9.0.0) --- updated-dependencies: - dependency-name: paambaati/codeclimate-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Updated the spec_test with additional tests * Bump spec_tests/hed-specification from `19b29fe` to `bae5675` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `19b29fe` to `bae5675`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@19b29fe...bae5675) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump spec_tests/hed-specification from `bae5675` to `d3bac05` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `bae5675` to `d3bac05`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@bae5675...d3bac05) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump spec_tests/hed-specification from `d3bac05` to `abc9923` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `d3bac05` to `abc9923`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@d3bac05...abc9923) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Fixed error handling when definition has no groups * Added SCORE 2.0.0 to schema cache * Bump spec_tests/hed-specification from `abc9923` to `f633de5` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `abc9923` to `f633de5`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@abc9923...f633de5) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Fixed value tests * Added support for alternate codes in the spec_tests * Updated project .toml to include json class_regex * Bump spec_tests/hed-specification from `f633de5` to `62dbcb0` Bumps [spec_tests/hed-specification](https://github.com/hed-standard/hed-specification) from `f633de5` to `62dbcb0`. - [Release notes](https://github.com/hed-standard/hed-specification/releases) - [Commits](hed-standard/hed-specification@f633de5...62dbcb0) --- updated-dependencies: - dependency-name: spec_tests/hed-specification dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump spec_tests/hed-examples from `ba86a84` to `f117c4d` Bumps [spec_tests/hed-examples](https://github.com/hed-standard/hed-examples) from `ba86a84` to `f117c4d`. - [Release notes](https://github.com/hed-standard/hed-examples/releases) - [Commits](hed-standard/hed-examples@ba86a84...f117c4d) --- updated-dependencies: - dependency-name: spec_tests/hed-examples dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Minor updates to test files * outputting the workspace temporarily * Cleaned up some of the lints * Updated the actions, did test cleanup * Separated coverage action from just tests * Updated the tests for remodel * Corrected continue-on-error placement * Updated spec_tests path * Updated gitactions --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: IanCa <[email protected]> Co-authored-by: IanCa <[email protected]>
hed-standard · Sep 27, 2024 · 887f294 · 887f294
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -21,7 +21,7 @@ jobs:
             # PR to master branch
             echo 'matrix=["3.8", "3.9", "3.10", "3.11"]' >> $GITHUB_OUTPUT
           else
-            echo 'matrix=["3.9"]' >> $GITHUB_OUTPUT
+            echo 'matrix=["3.9", "3.11"]' >> $GITHUB_OUTPUT
           fi
 
   build:
@@ -48,92 +48,24 @@ jobs:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
 
+      # Install dependencies
       - name: Install dependencies
         run: |
           python -m pip install --upgrade --upgrade-strategy eager pip
-          pip install flake8
-          pip install coverage
           pip install -r requirements.txt
           pip install -r docs/requirements.txt
 
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-
-          flake8 . --count --show-source --statistics --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-
-      - name: Test with unittest
+      # Run spec tests without coverage for non Python 3.9
+      - name: Run spec_test
         env:
           HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          coverage run -m unittest
+        continue-on-error: true
+        run: |  
+           python -m unittest discover spec_tests
 
-      - name: Run spec_test coverage
+      # Run unittest without coverage
+      - name: Test with unittest
         env:
           HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: coverage run --append -m unittest spec_tests/test_errors.py
-        continue-on-error: true
-
-      - name: Archive code coverage results
-        if: ${{matrix.python-version == '3.9'}}
-        uses: actions/upload-artifact@v4
-        with:
-          name: code-coverage-report
-          path: .coverage
-
-  check-secret:
-    runs-on: ubuntu-latest
-    outputs:
-      secrets-exist: ${{ steps.check-for-secrets.outputs.defined }}
-    steps:
-      - name: Check for Secret availability
-        id: check-for-secrets
-        # perform secret check & put boolean result as an output
-        shell: bash
-        run: |
-          if [ "${{ secrets.CC_TEST_REPORTER_ID }}" != '' ]; then
-            echo "defined=true" >> $GITHUB_OUTPUT;
-          else
-            echo "defined=false" >> $GITHUB_OUTPUT;
-          fi
-
-  coverage:
-    name: Publish coverage
-    needs: [build, check-secret]
-    runs-on: ubuntu-latest
-    if: needs.check-secret.outputs.secrets-exist == 'true'
-
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-
-      - uses: actions/cache@v4
-        with:
-          path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
-
-      - name: Install dependencies
         run: |
-          python -m pip install --upgrade --upgrade-strategy eager pip
-          pip install flake8
-          pip install coverage
-          pip install -r requirements.txt
-          pip install -r docs/requirements.txt
-
-      - name: Download a single artifact
-        uses: actions/download-artifact@v4
-        with:
-          name: code-coverage-report
-
-      - name: publish-coverages
-        with:
-          coverageCommand: coverage xml
-          debug: true
-        uses: paambaati/[email protected]
-        env:
-          CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
-
+          python -m unittest discover tests
diff --git a/.github/workflows/ci_cov.yaml b/.github/workflows/ci_cov.yaml
@@ -0,0 +1,79 @@
+name: CI_COV
+
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+
+  check-secret:
+    runs-on: ubuntu-latest
+    outputs:
+      secrets-exist: ${{ steps.check-for-secrets.outputs.defined }}
+    steps:
+      - name: Check for Secret availability
+        id: check-for-secrets
+        # perform secret check & put boolean result as an output
+        shell: bash
+        run: |
+          if [ "${{ secrets.CC_TEST_REPORTER_ID }}" != '' ]; then
+            echo "defined=true" >> $GITHUB_OUTPUT;
+          else
+            echo "defined=false" >> $GITHUB_OUTPUT;
+          fi
+
+  build:
+    needs: check-secret
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [ "3.9" ]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade --upgrade-strategy eager pip
+          pip install flake8 coverage -r requirements.txt -r docs/requirements.txt
+
+      # Run flake8
+      - name: Lint with flake8
+        run: |
+          flake8 . --count --show-source --statistics --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 
+
+      # Run unittest with coverage
+      - name: Test with unittest and coverage
+        env:
+          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        continue-on-error: true
+        run: |  
+          coverage run -m unittest discover tests
+
+      # Run spec tests with coverage
+      - name: Run spec_test coverage
+        env:
+          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |  
+          coverage run --append -m unittest discover spec_tests
+          coverage xml
+          ls -la
+
+      # Upload coverage to Code Climate
+      - name: Upload coverage to Code Climate
+        if: needs.check-secret.outputs.secrets-exist == 'true'
+        uses: paambaati/[email protected]
+        env:
+          CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
diff --git a/.github/workflows/ci_windows.yaml b/.github/workflows/ci_windows.yaml
@@ -1,4 +1,4 @@
-name: CI
+name: CI Windows
 
 on:
   push: