aphp · percevalw · Oct 7, 2024 · Oct 7, 2024
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -7,25 +7,42 @@ on:
 
 env:
   BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+  # UV_INDEX_STRATEGY: "unsafe-first-match"
+  # UV_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"
+  PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"
 
 jobs:
   Documentation:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+
     - uses: actions/setup-python@v4
       with:
+        python-version: "3.9"
         cache: 'pip'
+
+    - run: echo WEEK=$(date +%V) >>$GITHUB_ENV
+      shell: bash
+
+#    - uses: hynek/setup-cached-uv@v1
+#      with:
+#        cache-suffix: -docs-${{ matrix.python-version }}-${{ env.WEEK }}
+
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install '.[dev]'
+        pip install '.[docs]'
+#        uv venv
+#        uv pip install '.[docs]'
+
     - name: Set up Git
       run: |
         git config user.name ${{ github.actor }}
         git config user.email ${{ github.actor }}@users.noreply.github.com
+
     - name: Build documentation
       run: |
         git fetch origin gh-pages
+        source .venv/bin/activate
         mike delete $BRANCH_NAME
         mike deploy --push $BRANCH_NAME
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -13,6 +13,11 @@ on:
   release:
     types: [published]
 
+env:
+  # UV_INDEX_STRATEGY: "unsafe-first-match"
+  # UV_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"
+  PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"
+
 jobs:
   build_wheels:
     name: Build wheels on ${{ matrix.os }}/${{ matrix.arch || '*' }}
@@ -70,18 +75,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
+
     - uses: actions/setup-python@v4
       with:
         python-version: "3.9"
         cache: 'pip'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install '.[dev]'
+        pip install '.[docs]'
+
     - name: Set up Git
       run: |
         git config user.name ${{ github.actor }}
         git config user.email ${{ github.actor }}@users.noreply.github.com
+
     - name: Build documentation
       run: |
         git fetch origin gh-pages

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -6,6 +6,11 @@ on:
   push:
     branches: [master]
 
+env:
+  # UV_INDEX_STRATEGY: "unsafe-first-match"
+  # UV_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"
+  PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"
+
 jobs:
   linting:
     name: Linting
@@ -16,7 +21,11 @@ jobs:
         with:
           # requites to grab the history of the PR
           fetch-depth: 0
+
       - uses: actions/setup-python@v4
+        with:
+          cache: 'pip'
+
       - uses: pre-commit/[email protected]
         with:
           extra_args: --color=always --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
@@ -46,9 +55,9 @@ jobs:
       - run: echo WEEK=$(date +%V) >>$GITHUB_ENV
         shell: bash
 
-      - uses: hynek/setup-cached-uv@v1
-        with:
-          cache-suffix: -tests-${{ matrix.python-version }}-${{ env.WEEK }}
+      # - uses: hynek/setup-cached-uv@v1
+      #   with:
+      #     cache-suffix: -tests-${{ matrix.python-version }}-${{ env.WEEK }}
 
       - name: Set up Java
         uses: actions/setup-java@v2
@@ -60,32 +69,34 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
 
       - name: Install dependencies
         run: |
-          uv venv
           pip install poetry
-          source .venv/bin/activate
-          uv pip install -e '.[dev,setup]' pytest-xdist pip
+          pip install -e '.[dev,setup]' pytest-xdist pip
+#          uv venv
+#          source .venv/bin/activate
+#          uv pip install -e '.[dev,setup]' pytest-xdist pip
 
       - name: Test with Pytest on Python ${{ matrix.python-version }}
         env:
           UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }}
         run: |
-          source .venv/bin/activate
           coverage run -m pytest --ignore tests/test_docs.py # -n auto
           # coverage combine
           # mv .coverage .coverage.${{ matrix.python-version }}
+#          source .venv/bin/activate
         if: matrix.python-version != '3.9'
 
       - name: Test with Pytest on Python ${{ matrix.python-version }}
         env:
           UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }}
         run: |
-          source .venv/bin/activate
           coverage run -m pytest # -n auto
           # coverage combine
           # mv .coverage .coverage.${{ matrix.python-version }}
+#          source .venv/bin/activate
         if: matrix.python-version == '3.9'
 
       - name: Upload coverage data
@@ -116,24 +127,26 @@ jobs:
     - uses: actions/setup-python@v4
       with:
         python-version: "3.9"
-        # cache: 'pip'
+        cache: 'pip'
 
     - run: echo WEEK=$(date +%V) >>$GITHUB_ENV
       shell: bash
 
-    - uses: hynek/setup-cached-uv@v1
-      with:
-        cache-suffix: -docs-${{ matrix.python-version }}-${{ env.WEEK }}
+    # - uses: hynek/setup-cached-uv@v1
+    #   with:
+    #     cache-suffix: -docs-${{ matrix.python-version }}-${{ env.WEEK }}
 
     - name: Install dependencies
       run: |
-        uv venv
-        uv pip install '.[dev]'
+        pip install '.[docs]'
+#        uv venv
+#        uv pip install '.[docs]'
+
 
     - name: Build documentation
       run: |
-        source .venv/bin/activate
         mkdocs build --clean
+#        source .venv/bin/activate
 
   simple-installation:
     name: Simple installation
@@ -148,15 +161,17 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
 
       - run: echo WEEK=$(date +%V) >>$GITHUB_ENV
         shell: bash
 
-      - uses: hynek/setup-cached-uv@v1
-        with:
-          cache-suffix: -simple-install-${{ matrix.python-version }}-${{ env.WEEK }}
+      # - uses: hynek/setup-cached-uv@v1
+      #   with:
+      #     cache-suffix: -simple-install-${{ matrix.python-version }}-${{ env.WEEK }}
 
       - name: Install library
         run: |
-          uv venv
-          uv pip install .
+          pip install .
+#          uv venv
+#          uv pip install .
diff --git a/Makefile b/Makefile
@@ -21,7 +21,7 @@ install : .venv
 
 documentation: .venv
 	. .venv/bin/activate
-	pip install -e '.[dev]'
+	pip install -e '.[docs]'
 	mkdocs serve
 
 test: .venv

diff --git a/contributing.md b/contributing.md
@@ -113,7 +113,7 @@ We use `MkDocs` for EDS-NLP's documentation. You can checkout the changes you ma
 
 ```console
 # Install the requirements
-$ pip install -e '.[dev]'
+$ pip install -e '.[docs]'
 ---> 100%
 color:green Installation successful
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -13,7 +13,7 @@ dependencies = [
     "pytz",
     "pysimstring>=1.2.1",
     "regex",
-    "spacy>=3.1,<4.0.0,!=3.8.0",
+    "spacy>=3.1,<3.8",
     "confit>=0.5.5",
     "tqdm",
     "umls-downloader>=0.1.1",
@@ -41,13 +41,39 @@ dev = [
     "pre-commit>=2.21.0; python_version>='3.8'",
     "pytest>=7.1.0",
     "pytest-cov>=3.0.0",
-    "polars",
 
-    # Distributed inference
+    # Data libs
     "koalas>=1.8.1; python_version<'3.8'",
     "pyspark",
+    "polars",
+
+    # Machine Learning
+    "rich-logger>=0.3.1",
+    "torch>=1.13.0",
+    "foldedtensor>=0.3.2",
+    "safetensors>=0.3.0",
+    "transformers>=4.0.0,<5.0.0",
+    "accelerate>=0.20.3,<1.0.0",
+    "mlconjug3<3.9.0",
+    "scikit-learn>=1.0.0",
 
-    # Docs
+    # Docs (same as docs group)
+    "mike~=1.1.2",
+    "mkdocs-charts-plugin==0.0.8",
+    "mkdocs-img2fig-plugin==0.9.3",
+    "mkdocs-material~=9.2.0",
+    "mkdocs-section-index==0.3.4",
+    "mkdocs~=1.5.2",
+    "mkdocstrings~=0.20",
+    "mkdocstrings-python~=1.1",
+    "mkdocs-minify-plugin",
+    "mkdocs-redirects>=1.2.1;python_version>='3.8'",
+    "pybtex~=0.24.0",
+    "pathspec>=0.11.1",  # required by vendored mkdocs-autorefs PR
+    "astunparse",
+    "griffe<0.39",
+]
+docs = [
     "mike~=1.1.2",
     "mkdocs-charts-plugin==0.0.8",
     "mkdocs-img2fig-plugin==0.9.3",
@@ -61,17 +87,13 @@ dev = [
     "pybtex~=0.24.0",
     "pathspec>=0.11.1",  # required by vendored mkdocs-autorefs PR
     "astunparse",
-    "mlconjug3<3.9.0",
     "griffe<0.39",
 
-    # Machine Learning
-    "rich-logger>=0.3.1",
     "torch>=1.13.0",
     "foldedtensor>=0.3.2",
-    "safetensors>=0.3.0",
     "transformers>=4.0.0,<5.0.0",
-    "accelerate>=0.20.3,<1.0.0",
-    "scikit-learn>=1.0.0",
+    "safetensors>=0.3.0",
+    "rich-logger>=0.3.1",
 ]
 setup = [
     "typer"
@@ -274,7 +296,7 @@ where = ["."]
 requires = [
     "setuptools",
     "cython>=0.25",
-    "spacy>=3.2,<4.0,!=3.8.0",
+    "spacy>=3.2,<3.8",
     # to update from https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
     # while setting numpy >= 1.15.0 due to spacy reqs
     "numpy==1.15.0; python_version=='3.7' and platform_machine not in 'arm64|aarch64|loongarch64' and platform_system!='AIX' and platform_python_implementation != 'PyPy'",