diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2caeb4f6..dd402558 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -21,8 +21,6 @@ jobs: python-version: '3.7' steps: - uses: actions/checkout@v3 - with: - fetch-depth: 0 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: @@ -37,13 +35,21 @@ jobs: with: distribution: 'temurin' java-version: ${{ matrix.java-version }} - - name: Install dependencies + - name: Install dependencies (not release) + if: ${{ !startsWith(github.head_ref, 'release') && success() }} run: | python -m pip install --upgrade pip setuptools wheel pip install flake8 pytest pip install git+https://github.com/nlpie/mtap@main#egg=mtap pip install ./biomedicus_client pip install .[test] --extra-index-url https://download.pytorch.org/whl/cpu + - name: Install dependencies (release) + if: ${{ startsWith(github.head_ref, 'release') && success() }} + run: | + python -m pip install --upgrade pip setuptools wheel + pip install flake8 pytest + SETUPTOOLS_SCM_PRETEND_VERSION=${GITHUB_HEAD_REF##*/} pip install ./biomedicus_client + pip install .[test] --extra-index-url https://download.pytorch.org/whl/cpu - name: Lint with flake8 run: | pip install flake8 diff --git a/biomedicus_client/pyproject.toml b/biomedicus_client/pyproject.toml index 2cca3001..15e9c0ee 100644 --- a/biomedicus_client/pyproject.toml +++ b/biomedicus_client/pyproject.toml @@ -36,7 +36,7 @@ classifiers = [ 'Topic :: Text Processing :: Linguistic' ] dependencies = [ - "mtap>=1.0.0", + "mtap==1.1.0", "tqdm==4.65.0", "importlib_resources==5.12.0", ] @@ -61,5 +61,5 @@ include = ["biomedicus_client*"] [tool.setuptools_scm] write_to = "biomedicus_client/src/biomedicus_client/version.py" -fallback_version = "3.0.0" +fallback_version = "3.1.0" root = ".." diff --git a/docs/test_results/3.1-standard-data.yml b/docs/test_results/3.1-standard-data.yml new file mode 100644 index 00000000..5a91274f --- /dev/null +++ b/docs/test_results/3.1-standard-data.yml @@ -0,0 +1,36 @@ +Concepts: + Precision: 0.4178534254352763 + Process Method Duration: '0:00:00.054746' + Recall: 0.6810191761363636 + Remote Call Duration: '0:00:00.058147' +TnT Pos Tagger: + Accuracy: 0.9349333907344957 + Process Method Duration: '0:00:00.014837' + Remote Call Duration: '0:00:00.017379' +biomedicus-deepen: + F1: 0.9135216734957947 + Gold Standard: 2010 i2b2-VA + Per-Document Mean Process Method Duration: '0:00:00.538904' + Per-Document Mean Remote Call Duration: '0:00:00.543211' + Precision: 0.8865634156550858 + Recall: 0.9421708185053381 +biomedicus-dependencies: + Corpus: MiPACQ converted to UD from PTB test set + LAS: 0.5413549646988133 + Process Method Duration: '0:00:00.692533' + Remote Call Duration: '0:00:00.694516' + UAS: 0.6770917830854739 +biomedicus-modification: + F1: 0.7100757788380578 + Gold Standard: 2010 i2b2-VA + Per-Document Mean Process Method Duration: '0:00:00.008863' + Per-Document Mean Remote Call Duration: '0:00:00.011559' + Precision: 0.9619771863117871 + Recall: 0.5627224199288257 +biomedicus-negex: + F1: 0.8706162076481078 + Gold Standard: 2010 i2b2-VA + Per-Document Mean Process Method Duration: '0:00:00.008149' + Per-Document Mean Remote Call Duration: '0:00:00.009888' + Precision: 0.7849231868524473 + Recall: 0.9773131672597865 diff --git a/docs/test_results/3.1-umls-license-data.yml b/docs/test_results/3.1-umls-license-data.yml new file mode 100644 index 00000000..630bffbc --- /dev/null +++ b/docs/test_results/3.1-umls-license-data.yml @@ -0,0 +1,36 @@ +Concepts: + Precision: 0.4493197311250345 + Process Method Duration: '0:00:00.056146' + Recall: 0.6984197443181818 + Remote Call Duration: '0:00:00.059279' +TnT Pos Tagger: + Accuracy: 0.9349333907344957 + Process Method Duration: '0:00:00.014999' + Remote Call Duration: '0:00:00.017518' +biomedicus-deepen: + F1: 0.9135216734957947 + Gold Standard: 2010 i2b2-VA + Per-Document Mean Process Method Duration: '0:00:00.563448' + Per-Document Mean Remote Call Duration: '0:00:00.567879' + Precision: 0.8865634156550858 + Recall: 0.9421708185053381 +biomedicus-dependencies: + Corpus: MiPACQ converted to UD from PTB test set + LAS: 0.5413549646988133 + Process Method Duration: '0:00:00.657716' + Remote Call Duration: '0:00:00.659653' + UAS: 0.6770917830854739 +biomedicus-modification: + F1: 0.7100757788380578 + Gold Standard: 2010 i2b2-VA + Per-Document Mean Process Method Duration: '0:00:00.009222' + Per-Document Mean Remote Call Duration: '0:00:00.012080' + Precision: 0.9619771863117871 + Recall: 0.5627224199288257 +biomedicus-negex: + F1: 0.8706162076481078 + Gold Standard: 2010 i2b2-VA + Per-Document Mean Process Method Duration: '0:00:00.009098' + Per-Document Mean Remote Call Duration: '0:00:00.011020' + Precision: 0.7849231868524473 + Recall: 0.9773131672597865 diff --git a/java/build.gradle b/java/build.gradle index 4e7377f1..10b03553 100644 --- a/java/build.gradle +++ b/java/build.gradle @@ -73,7 +73,7 @@ dependencies { implementation group: 'org.jetbrains', name: 'annotations', version: '24.0.1' implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.6' - implementation group: 'edu.umn.nlpie', name: 'mtap', version: '[1.0.0, )' + implementation group: 'edu.umn.nlpie', name: 'mtap', version: '1.1.0' implementation group: 'args4j', name: 'args4j', version: '2.33' implementation group: 'org.rocksdb', name: 'rocksdbjni', version: '7.10.2' implementation group: 'org.apache.commons', name: 'commons-text', version: '1.10.0' diff --git a/pyproject.toml b/pyproject.toml index a1790e35..71743fb7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ classifiers = [ 'Topic :: Text Processing :: Linguistic' ] dependencies = [ - "biomedicus_client>=3.0.0", # We get mtap, tqdm, and importlib_resources transitively from the client + "biomedicus_client==3.1.0", # We get mtap, tqdm, and importlib_resources transitively from the client "numpy==1.21.6", "pyyaml==6.0", "regex==2022.10.31", @@ -68,4 +68,4 @@ include = ["biomedicus*"] [tool.setuptools_scm] write_to = "python/biomedicus/version.py" -fallback_version = "3.0.0" +fallback_version = "3.1.0"