Try again main.yml

.github/workflows/main.yml

@@ -1,74 +1,54 @@
-# configuration derived from q2-greengenes2
+# much of this is taken from the Empress main.yml file
 name: Main CI
 
-on: [push]
+on:
+  pull_request:
+    branches:
+      - master
+      - phylo-rclr
+  push:
+    branches:
+      - master
+      - phylo-rclr
 
 jobs:
-  build-linux:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      max-parallel: 5
-      matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+  build:
+    runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        auto-update-conda: true
-        python-version: ${{ matrix.python-version }}
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install QIIME 2 ${{ matrix.os }}
-      if: matrix.os == 'macos-latest'
-      shell: bash -l {0}
-      run: |
-        wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml
-        conda env create -q -n test-env --file qiime2-latest-py38-osx-conda.yml
-    - name: Install QIIME 2 ${{ matrix.os }}
-      if: matrix.os == 'ubuntu-latest'
-      shell: bash -l {0}
-      run: |
-        wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml
-        conda env create -q -n test-env --file qiime2-latest-py38-linux-conda.yml
-    - name: Install gemelli
-      shell: bash -l {0}
-      run: |
-        source activate test-env
-        conda install -c conda-forge coveralls flake8 nose
-        pip install -e . 
-    - name: Lint with flake8
-      shell: bash -l {0}
-      run: |
-        source activate test-env
-        flake8 gemelli/*.py gemelli/tests/*.py setup.py
-    - name: Test with nose
-      shell: bash -l {0}
-      run: |
-        source activate test-env
-        nosetests -v gemelli --with-coverage --cover-package=gemelli
+      - uses: actions/checkout@v2
+        with:
+          persist-credentials: false
+          fetch-depth: 0
 
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-    - name: flake8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
-    - name: install dependencies
-      shell: bash -l {0}
-      run: |
-        python -m pip install --upgrade pip
-    - name: Check out repository code
-      uses: actions/checkout@v2
-    - name: lint
-      shell: bash -l {0}
-      run: |
-        pip install -q flake8
-        flake8 gemelli/*.py gemelli/tests/*.py setup.py
+      - name: Download Q2 file
+        run: wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: q2
+          environment-file: qiime2-latest-py36-linux-conda.yml
+
+      - name: Install conda reqs
+        shell: bash -l {0}
+        run: conda install --file ci/conda_requirements.txt -c biocore
+
+      - name: Install auxillary conda CI packages
+        shell: bash -l {0}
+        run: conda install -c conda-forge coveralls flake8 nose
+
+      - name: Install auxillary pip CI packages
+        shell: bash -l {0}
+        run: pip install iow tax2tree
+
+      - name: Install gemelli
+        shell: bash -l {0}
+        run: pip install -e .
+
+      - name: Check style
+        shell: bash -l {0}
+        run: flake8 gemelli/*.py gemelli/tests/*.py setup.py
+
+      - name: Run tests & coverage
+        shell: bash -l {0}
+        run: nosetests -v gemelli --with-coverage --cover-package=gemelli