Merge pull request #9 from harmsm/main

massive update to topiary

.github/workflows/python-app.yml

@@ -16,119 +16,74 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.8', '3.9' ]
-    steps:
-    - name: Install Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        architecture: 'x64'
+        python-version: ['3.8', '3.9', '3.10' ]
 
-    - name: Checkout
+    steps:
+    - name: checkout
       uses: actions/checkout@v3.0.0
+
+    - name: set up miniconda
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        repository: harmsm/topiary
-        path: topiary
+        activate-environment: topiary
+        environment-file: environment.yml
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
 
-    - name: Install topiary, run flake8, run pytest
-      shell: bash
+    - name: install topiary
+      shell: bash -l {0}
       run: |
-        cd topiary
+        # platform specific packages
+        conda install -c conda-forge -c bioconda "openmpi<4.1.3" "muscle>=5.0" "raxml-ng>=1.1" "generax>=2.0" "blast>=2.2"
+        python -m pip install . -vv
 
-        $CONDA/bin/conda env create --file environment.yml
-        $CONDA/bin/conda activate topiary || true
-        export PATH=$CONDA/envs/topiary/bin:$PATH
+    - name: run flake8
+      shell: bash -l {0}
+      run: |
+        conda install flake8
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
 
-        $CONDA/bin/conda install flake8
-        $CONDA/bin/conda install pytest
-        $CONDA/bin/python -m pip install --upgrade pip
+    - name: run pytest
+      shell: bash -l {0}
+      run: |
+        conda install pytest
+        export PATH=`which conda | xargs dirname`/envs/topiary/bin/:$PATH
+        pytest
 
-        $CONDA/bin/python setup.py install
+  build-windows:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest]
+        python-version: ['3.8', '3.9', '3.10' ]
 
-        # stop the build if there are Python syntax errors or undefined names
-        $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    steps:
+    - name: checkout
+      uses: actions/checkout@v3.0.0
 
-        $CONDA/bin/pytest
+    - name: set up miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: topiary
+        environment-file: environment.yml
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
 
-        cd ..
+    - name: install topiary
+      shell: pwsh
+      run: |
+        python -m pip install . -vv
 
+    - name: run flake8
+      shell: pwsh
+      run: |
+        conda install flake8
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
 
-  # build-windows:
-  #   runs-on: windows-latest
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       os: [windows-latest]
-  #       python-version: ['3.8', '3.9' ]
-  #   steps:
-  #   - name: Install Python ${{ matrix.python-version }}
-  #     uses: actions/setup-python@v2
-  #     with:
-  #       python-version: ${{ matrix.python-version }}
-  #       architecture: 'x64'
-  #   #
-  #   # - name: Setup conda
-  #   #   uses: conda-incubator/setup-miniconda@v2
-  #   #   with:
-  #   #     auto-update-conda: true
-  #   #     python-version: ${{ matrix.python-version }}
-  #   #
-  #   # - name: Install dependencies
-  #   #   run: |
-  #   #     python -m pip install --upgrade pip
-  #
-  #   - name: Checkout
-  #     uses: actions/checkout@v3.0.0
-  #     with:
-  #       repository: harmsm/topiary
-  #       path: topiary
-  #
-  #   - name: Install the Python dependencies
-  #     shell: powershell
-  #     run: |
-  #
-  #       cd topiary
-  #
-  #       $CONDA/bin/conda env create --file environment.yml
-  #       $CONDA/bin/conda activate topiary || true
-  #       $Env:PATH += ";C:\Program Files\Scripts"
-  #       export PATH=$CONDA/envs/topiary/bin:$PATH
-  #
-  #       $CONDA/bin/conda install flake8
-  #       $CONDA/bin/conda install pytest
-  #       $CONDA/bin/python -m pip install --upgrade pip
-  #
-  #       $CONDA/bin/python setup.py install
-  #
-  #       # stop the build if there are Python syntax errors or undefined names
-  #       $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-  #       # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-  #       $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-  #
-  #       $CONDA/bin/pytest
-  #
-  #       cd ..
-  #
-  #
-  #
-  #       cd topiary
-  #       conda env update --file environment.yml --name base
-  #       python setup.py install
-  #       cd ..
-  #
-  #   - name: Lint with flake8
-  #     run: |
-  #       C:\Miniconda\condabin\conda.bat activate base
-  #       C:\Miniconda\condabin\conda.bat install flake8
-  #       # stop the build if there are Python syntax errors or undefined names
-  #       flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-  #       # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-  #       flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-  #
-  #   - name: Run the tests
-  #     run: |
-  #       C:\Miniconda\condabin\conda.bat activate base
-  #       C:\Miniconda\condabin\conda.bat install pytest
-  #       pytest
+    - name: run pytest
+      shell: pwsh
+      run: |
+        conda install pytest
+        $Env:PATH = "C:\Miniconda3\Scripts\;$Env:PATH"
+        pytest