MEmilio simulations PyPI package

.github/workflows/build_wheels.yml

@@ -0,0 +1,58 @@
+name: Build wheels 
+
+on: [pull_request, release]
+
+jobs:
+
+  build_wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest] # windows-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: pypa/cibuildwheel@v2.16
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist: 
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    # if: github.event_name == 'release' && github.event.action == 'published'
+    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        # To test uploads to TestPyPI, uncomment the following:
+        with:
+          skip-existing: true
+          # password: ${{ secrets.PYPI_TEST_TOKEN }}
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/epidata_main.yml

@@ -1,158 +1,158 @@
-name: Epidata-CI
+# name: Epidata-CI
 
-on: 
-  schedule:
-    - cron: "40 1 * * *"
-  push:
-    branches:
-      - 'main'
-    tags:
-      - version-*
-    paths:
-      - '**/memilio-epidata/**'
-      - '.github/**'
-  pull_request:
-    types: [opened, reopened, synchronize, ready_for_review]
-    paths:
-      - '**/memilio-epidata/**'
-      - '.github/**'
-  workflow_dispatch:
+# on: 
+#   schedule:
+#     - cron: "40 1 * * *"
+#   push:
+#     branches:
+#       - 'main'
+#     tags:
+#       - version-*
+#     paths:
+#       - '**/memilio-epidata/**'
+#       - '.github/**'
+#   pull_request:
+#     types: [opened, reopened, synchronize, ready_for_review]
+#     paths:
+#       - '**/memilio-epidata/**'
+#       - '.github/**'
+#   workflow_dispatch:
 
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: 3.12
-    - uses: pre-commit/action@v3.0.1
+# jobs:
+#   pre-commit:
+#     runs-on: ubuntu-latest
+#     steps:
+#     - uses: actions/checkout@v4
+#     - uses: actions/setup-python@v5
+#       with:
+#         python-version: 3.12
+#     - uses: pre-commit/action@v3.0.1
 
-  build-py-epidata:
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: epidata
+#   build-py-epidata:
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: epidata
 
-  build-py-plot:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: plot
+#   build-py-plot:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: plot
 
-  test-py-epidata:
-    needs: build-py-epidata
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with: 
-          version: ${{ matrix.version }}
-          package: epidata
-          coverage: ON
+#   test-py-epidata:
+#     needs: build-py-epidata
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with: 
+#           version: ${{ matrix.version }}
+#           package: epidata
+#           coverage: ON
 
-  test-py-plot:
-    if: github.event.pull_request.draft == false
-    needs: [build-py-plot, build-py-epidata]
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with: 
-          version: ${{ matrix.version }}
-          package: plot
-          coverage: ON 
+#   test-py-plot:
+#     if: github.event.pull_request.draft == false
+#     needs: [build-py-plot, build-py-epidata]
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with: 
+#           version: ${{ matrix.version }}
+#           package: plot
+#           coverage: ON 
 
-  merge-artifacts:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        packages: [epidata, plot]
-    needs: [test-py-plot, test-py-epidata]
-    steps:
-      - name: merge epidata reports
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-py-coverage-reports-${{ matrix.packages }}
-          pattern: test-py-coverage-reports-${{ matrix.packages }}-*
+#   merge-artifacts:
+#     runs-on: ubuntu-latest
+#     strategy:
+#       matrix:
+#         packages: [epidata, plot]
+#     needs: [test-py-plot, test-py-epidata]
+#     steps:
+#       - name: merge epidata reports
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-py-coverage-reports-${{ matrix.packages }}
+#           pattern: test-py-coverage-reports-${{ matrix.packages }}-*
 
-  test-pylint-epidata:
-    needs: build-py-epidata
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-pylint
-        with:
-          package: epidata
+#   test-pylint-epidata:
+#     needs: build-py-epidata
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-pylint
+#         with:
+#           package: epidata
 
-  test-pylint-plot:
-    needs: build-py-plot
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-pylint
-        with:
-          package: plot
+#   test-pylint-plot:
+#     needs: build-py-plot
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-pylint
+#         with:
+#           package: plot
 
-  download-data:
-    needs: build-py-epidata
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - uses: actions/checkout@v4
-      - name: Install dependencies
-        run: |
-          sudo apt-get -qq update
-          sudo apt-get -qq -y install python3-pip gnupg
-          python -m pip install --upgrade pip
-      - name: Download Python Wheels
-        uses: actions/download-artifact@v4
-        with:
-          name: python-wheels-epidata
-          path: pycode/wheelhouse
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - name: Install Python Wheels
-        run: |
-          for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
-          for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
-      - name: Download Data
-        run: |
-          mkdir -p data_dl
-          getcasedata -o data_dl --no-progress-indicators
-          getpopuldata -o data_dl --no-progress-indicators
-          getjhdata -o data_dl --no-progress-indicators
-          getdividata -o data_dl --no-progress-indicators
-          getcommutermobility -o data_dl --no-progress-indicators
-          getvaccinationdata -o data_dl --no-progress-indicators
-          gethospitalizationdata -o data_dl --no-progress-indicators
-      - name: Upload Data
-        uses: actions/upload-artifact@v4
-        with:
-          name: data
-          path: |
-            data_dl/*.json
-            data_dl/Germany/*.json
-            data_dl/Spain/*.json
-            data_dl/France/*.json
-            data_dl/Italy*.json
-            data_dl/SouthKorea/*.json
-            data_dl/US/*.json
-            data_dl/China/*.json
-          retention-days: 1
+#   download-data:
+#     needs: build-py-epidata
+#     runs-on: ubuntu-latest
+#     continue-on-error: true
+#     steps:
+#       - uses: actions/checkout@v4
+#       - name: Install dependencies
+#         run: |
+#           sudo apt-get -qq update
+#           sudo apt-get -qq -y install python3-pip gnupg
+#           python -m pip install --upgrade pip
+#       - name: Download Python Wheels
+#         uses: actions/download-artifact@v4
+#         with:
+#           name: python-wheels-epidata
+#           path: pycode/wheelhouse
+#       - name: Set up Python 3.12
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: 3.12
+#       - name: Install Python Wheels
+#         run: |
+#           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
+#           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
+#       - name: Download Data
+#         run: |
+#           mkdir -p data_dl
+#           getcasedata -o data_dl --no-progress-indicators
+#           getpopuldata -o data_dl --no-progress-indicators
+#           getjhdata -o data_dl --no-progress-indicators
+#           getdividata -o data_dl --no-progress-indicators
+#           getcommutermobility -o data_dl --no-progress-indicators
+#           getvaccinationdata -o data_dl --no-progress-indicators
+#           gethospitalizationdata -o data_dl --no-progress-indicators
+#       - name: Upload Data
+#         uses: actions/upload-artifact@v4
+#         with:
+#           name: data
+#           path: |
+#             data_dl/*.json
+#             data_dl/Germany/*.json
+#             data_dl/Spain/*.json
+#             data_dl/France/*.json
+#             data_dl/Italy*.json
+#             data_dl/SouthKorea/*.json
+#             data_dl/US/*.json
+#             data_dl/China/*.json
+#           retention-days: 1