sync

.devcontainer/devcontainer.json

@@ -0,0 +1,4 @@
+{
+	"image": "condaforge/miniforge3",
+	"postCreateCommand": "apt-get update && apt-get install -y build-essential && pip install -U -r dev-requirements.txt"
+}

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/pip_install_unitest.yml

@@ -1,60 +1,67 @@
 name: pip_install_unitest
 on:
-  workflow_dispatch
+  workflow_dispatch:
+    inputs:
+      install_prerelease:
+        description: 'Check this to install the prerelease version of medspacy if available and the version is newer than formal release.'  
+        type: boolean   
+        required: false
+        default: false
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
-  cancel-in-progress: true
 
 jobs:
-  build_wheels:
-    name: Build wheel for ${{ matrix.python-version }}-${{ matrix.buildplat[1] }}
-    if: >-
-      github.event_name == 'schedule' ||
-      github.event_name == 'workflow_dispatch' ||
-      (github.event_name == 'pull_request' &&
-      contains(github.event.pull_request.labels.*.name, 'Build System'))
-    runs-on: ${{ matrix.buildplat[0] }}
+
+  test:  
+    # TODO: Do we care if this only runs on allowed branches since we check push/pull_request above?
+    # if: github.ref == 'refs/heads/master' OR github.ref == 'refs/heads/develop'
     strategy:
-      # Ensure that a wheel builder finishes even if another fails
-      fail-fast: false
       matrix:
-        # Github Actions doesn't support pairing matrix values together, let's improvise
-        # https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
-        buildplat:
-          - [ ubuntu-20.04, ubuntu-20.04 ]
-          - [ macos-10.15, macosx_10 ]
-          - [ macos-11, macosx_11 ]
-          - [ macos-12, macosx_12 ]
-          - [ windows-2019, windows-2019 ]
-          - [ windows-2022, windows-2022 ]
-        #        spacy doesn't compile win32
-        #        python: ["cp36"] # Note: Wheels not needed for PyPy
-        python-version: [ "3.6", "3.7", "3.8", "3.9","3.10.x","3.11.0-rc.2"] # Note: Wheels not needed for PyPy
-        # python-version: [ "3.7"]
-    timeout-minutes: 45
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.9, "3.10.x", "3.11.x","3.12"]
+        # revised from https://github.com/actions/cache/blob/main/examples.md#python---pip
+    runs-on: ${{ matrix.os }}
+
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: set up python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install cython
-          pip install PyRuSH==1.0.8 pytest
-
-      - name: nose tests
-        run: |                            
-          # ls /opt/hostedtoolcache/Python/3*/x64/lib/python*/site-packages/conf
-          python -c "import shutil;shutil.rmtree('PyRuSH')"
-          python -c "import shutil;shutil.rmtree('conf')"
-          ls
-          python --version
-          pytest
+    - uses: actions/checkout@v4
+    - name: Git clone repo and remove source code
+      run: |
+        pwd
+        ls
+
+    - name: Set up pip
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}   
+        cache: 'pip'   
+        cache-dependency-path: |
+          'requirements/dev-requirements.txt'
+    - run: |
+        python --version
+        pip install --upgrade pip
+
+
+    - name: Install prereleased PyRuSH
+      if: ${{ github.event.inputs.install_prerelease == 'true' }} 
+      run: |
+        # use this to avoid install prereleases of dependencies packages        
+        pip install --pre PyRuSH
+        pip install -r dev-requirements.txt
+
+    - name: Install formal released medspacy
+      if: ${{ github.event.inputs.install_prerelease == 'false' }}  
+      run: |
+        pip install -I PyRuSH
+
+
+    - name: tests
+      run: |                            
+        # ls /opt/hostedtoolcache/Python/3*/x64/lib/python*/site-packages/conf
+        pip install pytest
+        python -c "import shutil;shutil.rmtree('PyRuSH')"
+        # python -c "import shutil;shutil.rmtree('conf')"
+        ls
+        python --version
+        pytest
 
 
 

.github/workflows/pip_old_install_unitest.yml

@@ -0,0 +1,68 @@
+name: pip_old_install_unitest
+on:
+  workflow_dispatch:
+    inputs:
+      install_prerelease:
+        description: 'Check this to install the prerelease version of medspacy if available and the version is newer than formal release.'  
+        type: boolean   
+        required: false
+        default: false
+
+
+jobs:
+
+  test:  
+    # TODO: Do we care if this only runs on allowed branches since we check push/pull_request above?
+    # if: github.ref == 'refs/heads/master' OR github.ref == 'refs/heads/develop'
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-12, windows-latest]
+        # python-version: [3.8]
+        python-version: [3.6,3.7]
+        # revised from https://github.com/actions/cache/blob/main/examples.md#python---pip
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Git clone repo and remove source code
+      run: |
+        pwd
+        ls
+
+    - name: Set up pip
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}   
+        cache: 'pip'   
+        cache-dependency-path: |
+          'requirements/requirements.txt'
+    - run: |
+        python --version
+        pip install --upgrade pip
+
+
+    - name: Install prereleased PyRuSH
+      if: ${{ github.event.inputs.install_prerelease == 'true' }} 
+      run: |
+        # use this to avoid install prereleases of dependencies packages
+        pip install -r requirements.txt
+        pip install --pre PyRuSH
+
+    - name: Install formal released medspacy
+      if: ${{ github.event.inputs.install_prerelease == 'false' }}  
+      run: |
+        pip install PyRuSH
+
+
+    - name: tests
+      run: |                            
+        # ls /opt/hostedtoolcache/Python/3*/x64/lib/python*/site-packages/conf
+        pip install pytest
+        python -c "import shutil;shutil.rmtree('PyRuSH')"
+        python -c "import shutil;shutil.rmtree('conf')"
+        ls
+        python --version
+        pytest
+
+
+

.github/workflows/run_pytests.yml

@@ -22,23 +22,22 @@ jobs:
         # Github Actions doesn't support pairing matrix values together, let's improvise
         # https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
         buildplat:
-          - [ ubuntu-20.04, ubuntu-20.04 ]
-          - [ macos-10.15, macosx_10 ]
-          - [ macos-11, macosx_11 ]
-          - [ macos-12, macosx_12 ]
-          - [ windows-2019, windows-2019 ]
-          - [ windows-2022, windows-2022 ]
+          - [ ubuntu-latest, ubuntu-latest ]
+          - [ macos-latest, macosx_latest ]
+          - [ windows-latest, windows-latest ]
         #        spacy doesn't compile win32
         #        python: ["cp36"] # Note: Wheels not needed for PyPy
-        python-version: [ "3.6", "3.7", "3.8", "3.9","3.10.x","3.11"] # Note: Wheels not needed for PyPy
+        python-version: [ "3.9","3.10.x","3.11.x", "3.12"] # Note: Wheels not needed for PyPy
     timeout-minutes: 45
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: set up python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python-version }}   
+          cache: 'pip'   
+          cache-dependency-path: 'dev-requirements.txt'
 
       - name: Install dependencies
         run: |
@@ -48,14 +47,15 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r dev-requirements.txt
-          pip install -U spacy==3.4.1
+          pip install -U setuptools
 
       - name:  pytests
         run: |
           python --version
+          python -c "import numpy;print(numpy.__version__)"
+          python setup.py build_ext --inplace
           pip install ./
           pytest tests
 
 
 
-

.github/workflows/wheelbuilder.yml → .github/workflows/wheelbuilder3.6.yml

@@ -1,4 +1,4 @@
-name: Wheel Builder
+name: Build_Pub<3.9
 on:
   workflow_dispatch
 
@@ -18,29 +18,30 @@ jobs:
     timeout-minutes: 50
     strategy:
       # Ensure that a wheel builder finishes even if another fails
-      fail-fast: false
+      fail-fast: true
       matrix:
         # Github Actions doesn't support pairing matrix values together, let's improvise
         # https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
         buildplat:
         - [ubuntu-20.04, manylinux_x86_64]
         - [ubuntu-20.04, musllinux_x86_64]
-        - [macos-10.15, macosx_*]
-        - [windows-2019, win_amd64]
+        - [macos-12, macosx_*]
+        - [windows-2022, win_amd64]
         # - [windows-2019, win32]
 #        spacy doesn't compile win32
 #        python: ["cp37"] # Note: Wheels not needed for PyPy
-        python: ["cp36", "cp37", "cp38", "cp39", "cp310","cp311"] # Note: Wheels not needed for PyPy
+#   cp37 not working with manylinux_x86_64 somehow
+        python: ["cp36", "cp38"] # Note: Wheels not needed for PyPy
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.11.1
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           # TODO: Build Cython with the compile-all flag?
           # Unfortunately, there is no way to modify cibuildwheel's build command
@@ -50,59 +51,35 @@ jobs:
           CIBW_BEFORE_BUILD: pip install -r requirements.txt
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
           CIBW_ENVIRONMENT: CFLAGS='-O3 -g0 -mtune=generic -pipe -fPIC' LDFLAGS='-fPIC'
-          CIBW_BEFORE_TEST: pip install pytest
+          CIBW_BEFORE_TEST: pip install -r dev-requirements.txt
           CIBW_TEST_COMMAND: pytest {package}/tests
 
       - name: check build
         run: |
           ls -l wheelhouse
 
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.python }}-${{ startsWith(matrix.buildplat[1], 'macosx') && 'macosx' || matrix.buildplat[1] }}
           path: ./wheelhouse/*.whl
 
 
 
-  build_sdist:
-    name: Build sdist
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout quicksectx
-        uses: actions/checkout@v3
-      # Used to push the built wheels
-      - uses: actions/setup-python@v3
-        with:
-          # Build sdist on lowest supported Python
-          python-version: '3.6'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-
-      - name: Build sdist
-        run: |
-          python setup.py sdist
-      - uses: actions/upload-artifact@v3
-        with:
-          name: sdist
-          path: ./dist/*.tar.gz
-
   upload_pypi:
-    needs: [build_wheels, build_sdist]
+    needs: [build_wheels]
     runs-on: ubuntu-latest
     # upload to PyPI on every tag starting with 'v'
 #    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     # alternatively, to publish when a GitHub Release is created, use the following rule:
     # if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
       - name: Install dependencies
         run: |
           pip install twine
 
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           path: dist