finish up initial draft for testing

.github/workflows/lib-community-ci.yaml

@@ -11,10 +11,9 @@
 #     with:
 #       distro: amplicon
 #       release-epoch: 2024.10
-#       additional-pkg-deps:
 #       github-org-name: qiime2
 #       github-repo-name: q2-vizard
-# TODO: note that default is 'main'; users can leave blank if this is their ref
+# TODO: note that default is main branch; can leave blank unless special target
 #       github-env-ref: dev
 #       env-file-name: 2024.5-vizard-environment.yml
 
@@ -31,13 +30,6 @@ on:
         type: number
         required: true
 
-      # TODO: figure out how to pass multiple external deps in correct syntax
-      additional-pkg-deps:
-        description: "Additional package dependencies"
-        type: string
-        required: false
-        default: ''
-
       github-org:
         description: "Organization or username on Github"
         type: string
@@ -52,7 +44,7 @@ on:
         description: "Target branch/ref name on Github for environment file"
         type: string
         required: false
-        default: 'main'
+        default: ''
 
       env-file-name:
         description: "Name of environment file to test with"
@@ -67,91 +59,31 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     env:
-      github_repo: ${{ inputs.github-repo }}
-      github_org: ${{ inputs.github-org }}
-      github_env_ref: ${{ inputs.github-env-ref }}
-      env_file_name: ${{ inputs.env-file-name }}
-      plugin_path: ./repo
+      name: ${{ inputs.github-repo }}
+      filepath: https://raw.githubusercontent.com/${{ inputs.github-org }}/${{ inputs.github-repo }}/${{ inputs.github-env-ref }}/environment-files/${{ inputs.env-file-name }}
 
-    steps:
       - uses: actions/checkout@v3
+
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          path: ${{ env.plugin_path }}
-          fetch-depth: 0
+          miniconda-version: 'latest'
+          python-version: 3.9
+          environment-file: ${{ env.filepath }}
+          activate-environment: ${{ env.name }}
 
-      - name: 'Install and activate test environment'
+      - name: 'install pytest, run qiime info & run tests'
+        shell: bash -el {0}
         run: |
-          conda env create
-          -n ${{ env.github_repo }}
-          -f https://raw.githubusercontent.com/{{ github-org }}/{{ github-repo }}/{{ github-env-ref }}/environment-files/{{ env-file-name }}
-          conda activate ${{ env.github_repo }}
+          conda install pytest
+          qiime info
+          pytest
+
+      # - name: 'Install and activate test environment'
+      #   run: |
+      #     conda env create
+      #     -n ${{ env.github_repo }}
+      #     -f https://raw.githubusercontent.com/{{ github-org }}/{{ github-repo }}/{{ github-env-ref }}/environment-files/{{ env-file-name }}
+      #     conda activate ${{ env.github_repo }}
 
       # TODO: run tests using makefile
       - name: 'Run tests for ${{ env.github_repo }}'
-
-
-# USING AS A REFERENCE, DONT ERASE ME YET
-
-# jobs:
-#   build-and-test:
-#     name: '${{ github.event.repository.name }} (${{ matrix.os }})'
-#     needs: setup
-#     strategy:
-#       fail-fast: false
-#       matrix:
-#         os: [ubuntu-latest, macos-12]
-#     runs-on: ${{ matrix.os }}
-#     env:
-#       plugin_path: ./repo
-#       built_channel_path: ./built-channel
-#       epoch: ${{ needs.setup.outputs.active-epoch }}
-#       seed_env_path: ${{ needs.setup.outputs.active-epoch }}/${{ inputs.distro }}/staged/seed-environment-conda.yml
-#       env_prefix: ./test-env
-#     steps:
-#       - uses: actions/checkout@v3
-#         with:
-#           path: ${{ env.plugin_path }}
-#           fetch-depth: 0
-
-#       - name: 'Set up test environment'
-#         run: |
-#           conda create -y -p ${{ env.env_prefix }}
-#           mkdir -p ${{ env.env_prefix }}/etc
-#           cat <<EOF > '${{ env.env_prefix }}/etc/activate.sh'
-#             . "$CONDA/etc/profile.d/conda.sh"
-#             conda activate '${{ env.env_prefix }}'
-#           EOF
-#           chmod +x '${{ env.env_prefix }}/etc/activate.sh'
-
-#       - name: 'set up yaml for test env'
-#         shell: bash
-#         run: |
-#           source ${{ env.env_prefix }}/etc/activate.sh
-#           conda activate '${{ env.env_prefix }}'
-#           pip install pyyaml
-
-#       - uses: qiime2/action-library-packaging/test-package@beta
-#         name: 'Test ${{ github.event.repository.name }}'
-#         with:
-#           conda-activate: source ${{ env.env_prefix }}/etc/activate.sh
-#           package-path: ${{ env.built_channel_path }}/${{ steps.build-package.outputs.conda-subdir }}/${{ steps.build-package.outputs.package-filename }}
-#           channels: ${{ steps.make-cbc.outputs.channels }}
-
-#   lint:
-#     runs-on: ubuntu-latest
-#     steps:
-#     - name: checkout source
-#       uses: actions/checkout@v3
-
-#     - name: set up python 3.9
-#       uses: actions/setup-python@v4
-#       with:
-#         python-version: 3.9
-
-#     - name: install dependencies
-#       run: |
-#         python -m pip install --upgrade pip
-#         pip install -q flake8
-
-#     - name: run flake8
-#       run: flake8