Merge pull request #122 from ww-tech/prim-test

Primrose 2.0 work
ww-tech · May 22, 2023 · f4e69d0 · f4e69d0
2 parents edd6ed5 + 92245ea
commit f4e69d0
Show file tree

Hide file tree

Showing 15 changed files with 2,337 additions and 143 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,8 +20,7 @@ jobs:
           - ubuntu-latest
           - macos-latest
         python:
-          - 3.6
-          - 3.7
+          - 3.8
         pypi_build:
           - complete
           - only_plotting
@@ -30,17 +29,14 @@ jobs:
           - basic
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python }}
-          architecture: 'x64'
       - name: before_install
         run: |
           echo "PYPI_BUILD=${{ matrix.pypi_build }}" >> $GITHUB_ENV
           echo "BOTO_CONFIG=/dev/null" >> $GITHUB_ENV
+          echo "BUILD_OS=${{ matrix.os }}" >> $GITHUB_ENV
           pip install wheel
       - name: install_linux
         if: matrix.os == 'ubuntu-latest'
@@ -52,44 +48,54 @@ jobs:
           bash scripts/mac_install.sh
       - name: install R
         if: matrix.pypi_build == 'complete' || matrix.pypi_build == 'only_r'
-        uses: r-lib/actions/setup-r@v1
+        uses: r-lib/actions/setup-r@v2
         with:
-          r-version: 4.1.0
+          r-version: 4.2.0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          architecture: 'x64'
       - name: python install
         run: |
-          pip install -r requirements.txt
-
+          pip install .[test]
+          mkdir cache
           if [ $PYPI_BUILD = 'complete' ]; then
             echo "Installing postgres and plotting requirements"
-            export LDFLAGS="-L/usr/local/opt/openssl/lib"
-            export CPPFLAGS="-I/usr/local/opt/openssl/include"
-            pip install psycopg2>=2.8.3
-            pip install psycopg2_binary>=2.8.2
-            
-            export LDFLAGS="-L/usr/local/opt/graphviz/lib"
-            export CPPFLAGS="-I/usr/local/opt/graphviz/include"
-            pip install pygraphviz
+
+            if [ $BUILD_OS = 'macos-latest' ]; then
+              export LDFLAGS="-L/usr/local/opt/graphviz/lib"
+              export CPPFLAGS="-I/usr/local/opt/graphviz/include"
+            elif [ $BUILD_OS = 'ubuntu-latest' ]; then
+              export LDFLAGS="-L/usr/lib/aarch64-linux-gnu"
+              export CPPFLAGS="-I/usr/include"
+            fi
+
+            pip install .[plotting]
             unset LDFLAGS
             unset CPPFLAGS
-            pip install "rpy2>=2.9.1,<=3.2.7"
+
+            pip install .[postgres]
+            pip install .[R]
           elif [ $PYPI_BUILD = 'only_postgres' ]; then
-            export LDFLAGS="-L/usr/local/opt/openssl/lib"
-            export CPPFLAGS="-I/usr/local/opt/openssl/include"
             echo "Installing postgres requirements"
-            pip install psycopg2>=2.8.3
-            pip install psycopg2_binary>=2.8.2
-            unset LDFLAGS
-            unset CPPFLAGS
+            pip install .[postgres]
           elif [ $PYPI_BUILD = 'only_plotting' ]; then
             echo "Installing plotting requirements"
-            export LDFLAGS="-L/usr/local/opt/graphviz/lib"
-            export CPPFLAGS="-I/usr/local/opt/graphviz/include"
-            pip install pygraphviz
+
+            if [ $BUILD_OS = 'macos-latest' ]; then
+              export LDFLAGS="-L/usr/local/opt/graphviz/lib"
+              export CPPFLAGS="-I/usr/local/opt/graphviz/include"
+            elif [ $BUILD_OS = 'ubuntu-latest' ]; then
+              export LDFLAGS="-L/usr/lib/aarch64-linux-gnu"
+              export CPPFLAGS="-I/usr/include"
+            fi
+
+            pip install .[plotting]
             unset LDFLAGS
             unset CPPFLAGS
           elif [ $PYPI_BUILD = 'only_r' ]; then
             echo "Installing R requirements"
-            pip install "rpy2>=2.9.1,<=3.2.7"
+            pip install .[R]
           fi
       - name: tests
         run: |
@@ -105,26 +111,27 @@ jobs:
           else
               python -m pytest -m "not optional"
           fi
-
   build-and-publish:
     runs-on: ubuntu-latest
     needs: tests
     if: github.event_name == 'release' && github.event.action == 'created'
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.8
         architecture: 'x64'
     - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        sphinx
-        --user
+      run: |
+        python -m \
+          pip install \
+            build \
+            sphinx \
+            myst_parser \
+            sphinx-rtd-theme \
+            --user
     - name: Build a binary wheel and a source tarball
       run: >-
         python -m
@@ -135,13 +142,13 @@ jobs:
         .
     - name: publish to pypi
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.PYPI_API_TOKEN }}
     - name: build docs
-      run: bash scripts/generate_docs.sh || exit 1 
+      run: bash scripts/generate_docs.sh || exit 1
     - name: publish github pages
       uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./docs
+        publish_dir: ./docs
diff --git a/.gitignore b/.gitignore
@@ -131,4 +131,5 @@ cache/
 .vscode/
 .idea/
 
-
+# PDM specific
+.pdm.toml