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Updated value classes based on JSON #1018

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merged 93 commits into from
Sep 27, 2024
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43a3b89
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jun 14, 2024
e5f3fec
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jun 14, 2024
e72b8b3
Merge branch 'master' of https://github.com/hed-standard/hed-python i…
VisLab Jun 14, 2024
6f9007a
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jun 14, 2024
12f849f
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jun 28, 2024
64a97e8
Bump spec_tests/hed-examples from `8824691` to `7117cf9`
dependabot[bot] Jul 5, 2024
e866921
Bump spec_tests/hed-specification from `5465995` to `5bc506c`
dependabot[bot] Jul 5, 2024
9cc2ba4
Merge pull request #980 from hed-standard/dependabot/submodules/devel…
VisLab Jul 6, 2024
54a5de4
Merge pull request #981 from hed-standard/dependabot/submodules/devel…
VisLab Jul 6, 2024
0fe3615
Improve .tsv loading to support children referenced before parent
IanCa Jul 11, 2024
d6ddaf4
fix typo
IanCa Jul 11, 2024
5766fcb
Merge branch 'master' of https://github.com/hed-standard/hed-python i…
VisLab Jul 14, 2024
44d3712
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jul 14, 2024
61ffbd5
Fix for unknown library hedIDs, minor updates to CI workflows(run on …
IanCa Jul 16, 2024
09722a6
Pass a tuple in word cloud, not np array
IanCa Jul 16, 2024
50b3e36
Merge pull request #983 from IanCa/develop
VisLab Jul 16, 2024
a4cfad0
Bump spec_tests/hed-examples from `7117cf9` to `bce0c7a`
dependabot[bot] Jul 17, 2024
53a4fcf
Merge pull request #984 from hed-standard/dependabot/submodules/devel…
VisLab Jul 17, 2024
d458b78
Cache and retrieve library_data.json from hed-schemas
IanCa Jul 18, 2024
38f8ab8
Merge pull request #985 from IanCa/develop
VisLab Jul 18, 2024
26857a7
Add a new add_hed_ids script. Minor documentation corrections
IanCa Jul 23, 2024
a991ef2
Bump spec_tests/hed-specification from `5bc506c` to `07812cd`
dependabot[bot] Jul 23, 2024
aa5e84e
Merge pull request #986 from IanCa/develop
VisLab Jul 23, 2024
3dff278
Merge pull request #987 from hed-standard/dependabot/submodules/devel…
VisLab Jul 23, 2024
347666f
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jul 23, 2024
6108eb7
Bump spec_tests/hed-specification from `07812cd` to `7cf62e5`
dependabot[bot] Jul 24, 2024
e6befb7
Add hedId value checking to schema validation
IanCa Jul 24, 2024
e916f74
Merge pull request #988 from hed-standard/dependabot/submodules/devel…
VisLab Jul 25, 2024
e4f4c67
Merge pull request #989 from IanCa/develop
VisLab Jul 25, 2024
7e0f66b
Don't escape double quotes in .tsv schemas
IanCa Jul 25, 2024
763e0fb
Merge pull request #990 from IanCa/develop
VisLab Jul 25, 2024
0a2056c
Fix crash in unmerged schema validation. Always cache with_standard …
IanCa Jul 25, 2024
e0d4a21
Merge pull request #991 from IanCa/develop
VisLab Jul 25, 2024
30e2453
Fix create_ontology using the wrong tag range for libraries
IanCa Jul 26, 2024
3b6d897
Merge pull request #992 from IanCa/develop
VisLab Jul 26, 2024
e9fa4ce
Bump spec_tests/hed-specification from `7cf62e5` to `19b29fe`
dependabot[bot] Jul 26, 2024
97f29bc
Fix it so it caches the local hed files when asking for all versions
IanCa Jul 26, 2024
4f62c4c
More fixes for local schema caching/testing
IanCa Jul 26, 2024
bca157d
Merge pull request #994 from IanCa/develop
IanCa Jul 26, 2024
fe9a4d3
Add optional flag to validate_schemas script to validate all 3 types …
IanCa Jul 26, 2024
26bc2f3
Merge pull request #995 from IanCa/develop
IanCa Jul 26, 2024
a8bb05d
Have the validator script save schemas merged, not unmerged, to preve…
IanCa Jul 26, 2024
5a1ff0e
Merge pull request #996 from IanCa/develop
IanCa Jul 26, 2024
2e5b708
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jul 27, 2024
448d91d
Bump spec_tests/hed-examples from `bce0c7a` to `6e265bf`
dependabot[bot] Jul 29, 2024
b8601a6
Always save schemas with newlines, never CLRF
IanCa Jul 29, 2024
9286b92
Merge pull request #993 from hed-standard/dependabot/submodules/devel…
VisLab Jul 30, 2024
6b3442f
Merge pull request #997 from hed-standard/dependabot/submodules/devel…
VisLab Jul 30, 2024
e99452f
Merge pull request #998 from IanCa/develop
VisLab Jul 30, 2024
670b3fb
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jul 30, 2024
71ea2a6
Update hed id verification to allow removal of tags without hedIDs
IanCa Jul 30, 2024
d9196f6
Merge pull request #999 from IanCa/develop
VisLab Jul 31, 2024
95335c0
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Jul 31, 2024
bc007ba
Add annotationExternal to omn generation
IanCa Jul 31, 2024
a1a54ba
Merge pull request #1000 from IanCa/develop
IanCa Jul 31, 2024
d74c321
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Aug 6, 2024
71f54ee
Bump spec_tests/hed-examples from `6e265bf` to `ba86a84`
dependabot[bot] Aug 16, 2024
5fd2cff
Merge pull request #1003 from hed-standard/dependabot/submodules/deve…
VisLab Aug 25, 2024
b05115d
Bump paambaati/codeclimate-action from 8.0.0 to 9.0.0
dependabot[bot] Aug 26, 2024
4016495
Merge pull request #1004 from hed-standard/dependabot/github_actions/…
VisLab Aug 26, 2024
2e3bfce
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Aug 26, 2024
871bae0
Updated the spec_test with additional tests
VisLab Aug 26, 2024
426a26a
Merge pull request #1007 from VisLab/develop
VisLab Aug 26, 2024
05b6e36
Bump spec_tests/hed-specification from `19b29fe` to `bae5675`
dependabot[bot] Aug 27, 2024
c40c721
Merge pull request #1008 from hed-standard/dependabot/submodules/deve…
VisLab Aug 27, 2024
e170654
Bump spec_tests/hed-specification from `bae5675` to `d3bac05`
dependabot[bot] Aug 29, 2024
8a47f63
Merge pull request #1009 from hed-standard/dependabot/submodules/deve…
VisLab Aug 29, 2024
d3599f4
Bump spec_tests/hed-specification from `d3bac05` to `abc9923`
dependabot[bot] Sep 3, 2024
c29b515
Fixed error handling when definition has no groups
VisLab Sep 13, 2024
a8fd639
Merge pull request #1011 from hed-standard/dependabot/submodules/deve…
VisLab Sep 13, 2024
c93d310
Added SCORE 2.0.0 to schema cache
VisLab Sep 13, 2024
1eb1e3f
Merge pull request #1013 from VisLab/test_branch
VisLab Sep 13, 2024
5032843
Bump spec_tests/hed-specification from `abc9923` to `f633de5`
dependabot[bot] Sep 16, 2024
a5ddb21
Fixed value tests
VisLab Sep 21, 2024
56415cb
Merge pull request #1014 from hed-standard/dependabot/submodules/deve…
VisLab Sep 21, 2024
5f05c97
Added support for alternate codes in the spec_tests
VisLab Sep 21, 2024
d777427
Merge pull request #1015 from VisLab/test_branch
VisLab Sep 22, 2024
5ba3a27
Updated project .toml to include json class_regex
VisLab Sep 22, 2024
5b99266
Merge pull request #1016 from VisLab/test_branch
VisLab Sep 22, 2024
a3b40e8
Bump spec_tests/hed-specification from `f633de5` to `62dbcb0`
dependabot[bot] Sep 23, 2024
e91bf2a
Bump spec_tests/hed-examples from `ba86a84` to `f117c4d`
dependabot[bot] Sep 26, 2024
b2c0b86
Merge pull request #1019 from hed-standard/dependabot/submodules/deve…
VisLab Sep 26, 2024
30b20ec
Merge pull request #1017 from hed-standard/dependabot/submodules/deve…
VisLab Sep 26, 2024
65366fe
Minor updates to test files
VisLab Sep 26, 2024
194b230
outputting the workspace temporarily
VisLab Sep 26, 2024
f36ecc5
Cleaned up some of the lints
VisLab Sep 26, 2024
c519f1b
Updated the actions, did test cleanup
VisLab Sep 27, 2024
6fb0497
Separated coverage action from just tests
VisLab Sep 27, 2024
56b338b
Updated the tests for remodel
VisLab Sep 27, 2024
d5475c9
Corrected continue-on-error placement
VisLab Sep 27, 2024
940f16e
Updated spec_tests path
VisLab Sep 27, 2024
c68f542
Updated gitactions
VisLab Sep 27, 2024
78c29c5
Merge pull request #1020 from VisLab/test_branch
VisLab Sep 27, 2024
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88 changes: 10 additions & 78 deletions .github/workflows/ci.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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
79 changes: 79 additions & 0 deletions .github/workflows/ci_cov.yaml
Original file line number Diff line number Diff line change
@@ -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 }}
2 changes: 1 addition & 1 deletion .github/workflows/ci_windows.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: CI
name: CI Windows

on:
push:
Expand Down
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