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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| # Why is this file here in OAK? -> https://github.com/linkml/schema-automator/pull/104#issuecomment-1307388416 | ||
| # This file may be removed after funowl is fixed to work with platform-specific line endings. | ||
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| # https://docs.github.com/en/get-started/getting-started-with-git/configuring-git-to-handle-line-endings | ||
| # Declare files that will always have LF line endings on checkout. | ||
| *.ofn text eol=lf |
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@@ -17,9 +17,9 @@ jobs: | |
| matrix: | ||
| python-version: [ '3.9', '3.10' ] | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| uses: actions/setup-python@v4.3.0 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Install dependencies | ||
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@@ -29,10 +29,16 @@ jobs: | |
| run: tox -e flake8 | ||
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| test: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: [ '3.9', '3.10' ] | ||
| os: [ ubuntu-latest, windows-latest ] | ||
| python-version: [ "3.9", "3.10" ] | ||
| exclude: | ||
| - os: windows-latest | ||
| python-version: "3.9" | ||
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| runs-on: ${{ matrix.os }} | ||
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| steps: | ||
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@@ -43,21 +49,24 @@ jobs: | |
| uses: actions/checkout@v3 | ||
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| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v3 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| #---------------------------------------------- | ||
| # install & configure poetry | ||
| #---------------------------------------------- | ||
| - name: Install Poetry | ||
| uses: snok/[email protected] | ||
| with: | ||
| virtualenvs-create: true | ||
| virtualenvs-in-project: true | ||
| run: | | ||
| pip install --upgrade pip | ||
| pip install poetry | ||
| # uses: snok/[email protected] | ||
| # with: | ||
| # virtualenvs-create: true | ||
| # virtualenvs-in-project: true | ||
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| #---------------------------------------------- | ||
| # load cached venv if cache exists | ||
| # load cached venv if cache exists | ||
| #---------------------------------------------- | ||
| # - name: Load cached venv | ||
| # id: cached-poetry-dependencies | ||
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@@ -67,17 +76,24 @@ jobs: | |
| # key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }} | ||
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| #---------------------------------------------- | ||
| # install dependencies if cache does not exist | ||
| # install dependencies if cache does not exist | ||
| #---------------------------------------------- | ||
| - name: Install dependencies | ||
| # if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' | ||
| run: poetry install --no-interaction --no-root | ||
| run: | | ||
| poetry add setuptools@latest | ||
| poetry install --no-interaction --no-root | ||
| #---------------------------------------------- | ||
| # install your root project, if required | ||
| #---------------------------------------------- | ||
| # install your root project, if required | ||
| #---------------------------------------------- | ||
| - name: Install library | ||
| run: poetry install --no-interaction --extras gilda | ||
| run: poetry install --no-interaction --extras "gilda" | ||
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| - name: Get Gilda resources | ||
| run: | | ||
| poetry run python -c "import nltk; nltk.download('punkt'); nltk.download('stopwords')" | ||
| poetry run python -m adeft.download | ||
| #---------------------------------------------- | ||
| # run test suite + coverage report | ||
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@@ -89,16 +105,17 @@ jobs: | |
| poetry run coverage combine | ||
| poetry run coverage xml | ||
| poetry run coverage report -m | ||
| shell: bash | ||
| env: | ||
| BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }} | ||
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| #---------------------------------------------- | ||
| # upload coverage results | ||
| #---------------------------------------------- | ||
| - name: Upload coverage report | ||
| uses: codecov/codecov-action@v1.0.5 | ||
| uses: codecov/codecov-action@v3.1.1 | ||
| with: | ||
| name: codecov-results-${{ matrix.python-version }} | ||
| name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }} | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| fail_ci_if_error: true | ||
| fail_ci_if_error: false | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,24 +1,32 @@ | ||
| .idea | ||
| .vscode | ||
| __pycache__ | ||
| .idea/ | ||
| .tox/ | ||
| __pycache__/ | ||
| .ipynb_checkpoints/ | ||
| docs/_build/ | ||
| docs/src/ | ||
| docs/datamodels/*/*.md | ||
| tests/output/ | ||
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| dist/ | ||
| db/ | ||
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| .DS_Store | ||
| .template.db | ||
| .vscode | ||
| .venv | ||
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| docs/_build/ | ||
| docs/src/ | ||
| docs/datamodels/*/*.md | ||
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| notebooks/output/*json | ||
| notebooks/output/*tsv | ||
| notebooks/input/* | ||
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| notebooks/*/output/*json | ||
| notebooks/*/output/*tsv | ||
| notebooks/api-key.txt | ||
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| .template.db | ||
| .venv | ||
| .tox/ | ||
| .coverage.* | ||
| .coverage | ||
| coverage.* | ||
| tests/input/fhirjson_conf.json | ||
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| oak_hp.profile | ||
| oak_semsimian_hp.profile | ||
| notebooks/demo.tsv |
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@@ -3,23 +3,32 @@ RUN = poetry run | |
| test: | ||
| $(RUN) python -m unittest tests/test_*py tests/*/test_*py | ||
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| # not yet deployed | ||
| doctest: | ||
| find src docs -type f \( -name "*.rst" -o -name "*.md" -o -name "*.py" \) -print0 | xargs -0 $(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE | ||
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| %-doctest: % | ||
| $(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE $< | ||
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| ## Compiled | ||
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| MODELS = ontology_metadata obograph validation_datamodel summary_statistics_datamodel lexical_index mapping_rules_datamodel text_annotator oxo taxon_constraints similarity search_datamodel cross_ontology_diff association | ||
| MODELS = ontology_metadata obograph validation_datamodel summary_statistics_datamodel lexical_index mapping_rules_datamodel text_annotator oxo taxon_constraints similarity search_datamodel cross_ontology_diff association class_enrichment value_set_configuration fhir mapping_cluster_datamodel cx item_list input_specification | ||
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| pyclasses: $(patsubst %, src/oaklib/datamodels/%.py, $(MODELS)) | ||
| jsonschema: $(patsubst %, src/oaklib/datamodels/%.schema.json, $(MODELS)) | ||
| owl: $(patsubst %, src/oaklib/datamodels/%.owl.ttl, $(MODELS)) | ||
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| src/oaklib/datamodels/%.py: src/oaklib/datamodels/%.yaml | ||
| # $(RUN) gen-pydantic $< > [email protected] && mv [email protected] $@ | ||
| $(RUN) gen-python $< > [email protected] && mv [email protected] $@ | ||
| $(RUN) tox -e lint | ||
| src/oaklib/datamodels/%.schema.json: src/oaklib/datamodels/%.yaml | ||
| $(RUN) gen-json-schema $< > $@.tmp && mv $@.tmp $@ | ||
| src/oaklib/datamodels/%.owl.ttl: src/oaklib/datamodels/%.yaml | ||
| $(RUN) gen-owl --no-metaclasses --no-type-objects $< > $@.tmp && mv $@.tmp $@ | ||
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| RUN_GENDOC = $(RUN) gen-doc --dialect myst | ||
| gendoc: gendoc-om gendoc-og gendoc-ss gendoc-val gendoc-mr gendoc-li gendoc-ann gendoc-search gendoc-xodiff gendoc-sim gendoc-assoc | ||
| gendoc: gendoc-om gendoc-og gendoc-ss gendoc-val gendoc-mr gendoc-li gendoc-ann gendoc-search gendoc-xodiff gendoc-sim gendoc-assoc gendoc-tc gendoc-itemlist gendoc-ce | ||
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| gendoc-om: src/oaklib/datamodels/ontology_metadata.yaml | ||
| $(RUN_GENDOC) $< -d docs/datamodels/ontology-metadata/ | ||
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@@ -43,6 +52,12 @@ gendoc-xodiff: src/oaklib/datamodels/cross_ontology_diff.yaml | |
| $(RUN_GENDOC) $< -d docs/datamodels/cross-ontology-diff | ||
| gendoc-assoc: src/oaklib/datamodels/association.yaml | ||
| $(RUN_GENDOC) $< -d docs/datamodels/association | ||
| gendoc-tc: src/oaklib/datamodels/taxon_constraints.yaml | ||
| $(RUN_GENDOC) $< -d docs/datamodels/taxon-constraints | ||
| gendoc-itemlist: src/oaklib/datamodels/item_list.yaml | ||
| $(RUN_GENDOC) $< -d docs/datamodels/item-list | ||
| gendoc-ce: src/oaklib/datamodels/class_enrichment.yaml | ||
| $(RUN_GENDOC) $< -d docs/datamodels/class-enrichment | ||
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| nb: | ||
| $(RUN) jupyter notebook | ||
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@@ -70,3 +85,34 @@ tests/input/%.db: tests/input/%.owl | |
| # this can be used outside the poetry environment | ||
| bin/runoak: | ||
| echo `poetry run which runoak` '"$$@"' > $@ && chmod +x $@ | ||
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| # Benchmarking for Semsimian | ||
| RUNOAK := $(shell which runoak) | ||
| SEMSIMIAN_HP_PROFILE = "oak_semsimian_hp.profile" | ||
| NON_SEMSIMIAN_HP_PROFILE = "oak_hp.profile" | ||
| SEMSIMIAN_PHENIO_PROFILE = "oak_semsimian_phenio.profile" | ||
| NON_SEMSIMIAN_PHENIO_PROFILE = "oak_phenio.profile" | ||
| HP_TERMS = "HPO_terms.txt" | ||
| MP_TERMS = "MP_terms.txt" | ||
| PROFILER_SCRIPT= "src/oaklib/implementations/semsimian/profiler.py" | ||
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| run_benchmark: benchmarks profiles | ||
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| benchmarks: | ||
| time python -m cProfile -o $(SEMSIMIAN_HP_PROFILE) -s tottime $(RUNOAK) -i semsimian:sqlite:obo:hp similarity -p i,p HP:0002205 @ HP:0000166 HP:0012461 HP:0002167 HP:0012390 HP:0002840 HP:0002840 HP:0012432 > /dev/null | ||
| time python -m cProfile -o $(NON_SEMSIMIAN_HP_PROFILE) -s tottime $(RUNOAK) -i sqlite:obo:hp similarity -p i,p HP:0002205 @ HP:0000166 HP:0012461 HP:0002167 HP:0012390 HP:0002840 HP:0002840 HP:0012432 > /dev/null | ||
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| profiles: | ||
| python $(PROFILER_SCRIPT) $(SEMSIMIAN_HP_PROFILE) | ||
| python $(PROFILER_SCRIPT) $(NON_SEMSIMIAN_HP_PROFILE) | ||
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| phenio-benchmarks: | ||
| $(RUNOAK) -i sqlite:obo:hp descendants -p i HP:0000118 > $(HP_TERMS) | ||
| $(RUNOAK) -i sqlite:obo:mp descendants -p i MP:0000001 > $(MP_TERMS) | ||
| time python -m cProfile -o $(SEMSIMIAN_PHENIO_PROFILE) -s tottime $(RUNOAK) -i semsimian:sqlite:obo:phenio similarity -p i --set1-file $(HP_TERMS) --set2-file $(MP_TERMS) -O csv -o HP_vs_MP_semsimian.tsv | ||
| time python -m cProfile -o $(NON_SEMSIMIAN_PHENIO_PROFILE) -s tottime $(RUNOAK) -i sqlite:obo:phenio similarity -p i --set1-file $(HP_TERMS) --set2-file $(MP_TERMS) -O csv -o HP_vs_MP_semsimian.tsv | ||
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| phenio-profiles: | ||
| python $(PROFILER_SCRIPT) $(SEMSIMIAN_PHENIO_PROFILE) | ||
| python $(PROFILER_SCRIPT) $(NON_SEMSIMIAN_PHENIO_PROFILE) | ||
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