Release 3.1.0 (#145)

nlpie · Mar 16, 2023 · c206392 · c206392
1 parent bfec0b8
commit c206392
Show file tree

Hide file tree

Showing 6 changed files with 86 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"