ci: Update CI to barebone python [all tests ci] (#1192)

* ci: Add installed packages listing

* ci: Add pip listing

* ci: Remove conda from PR action

* ci: Update worklows and add P2Z skip

* ci: More cleanup to workflow

* ci: Bump actions/setup-python from 4.7.0 to 4.7.1

.github/workflows/build.yaml

@@ -9,25 +9,20 @@ on:
   workflow_dispatch:
 
 env:
-  CONDA_ENV: echopype
   NUM_WORKERS: 2
 
 jobs:
   test:
     name: ${{ matrix.python-version }}-build
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }}
     continue-on-error: ${{ matrix.experimental }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]  # TODO: add back 3.11 once parsed2zarr is fixed
+        python-version: ["3.9", "3.10", "3.11"]
         runs-on: [ubuntu-latest]
         experimental: [false]
-        include:
-        - runs-on: ubuntu-latest
-          python-version: "3.11"
-          experimental: true
     services:
       # TODO: figure out how to update tag when there's a new one
       minio:
@@ -46,30 +41,20 @@ jobs:
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-      - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - name: Set up Python
+        uses: actions/setup-[email protected]
         with:
-          environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml
-          environment-name: ${{ env.CONDA_ENV }}
-          cache-environment: true
-          post-cleanup: 'all'
-      - name: Print conda environment
-        shell: bash -l {0}
-        run: |
-          micromamba info
-          micromamba list
+          python-version: ${{ matrix.python-version }}
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
       - name: Remove docker-compose python
-        if: ${{ matrix.python-version == '3.10' || matrix.python-version == '3.11' }}
-        shell: bash -l {0}
         run: sed -i "/docker-compose/d" requirements-dev.txt
       - name: Install dev tools
-        shell: bash -l {0}
-        run: |
-          micromamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt
+        run: python -m pip install -r requirements-dev.txt
       - name: Install echopype
-        shell: bash -l {0}
-        run: |
-          python -m pip install -e .[plot]
+        run: python -m pip install -e ".[plot]"
+      - name: Print installed packages
+        run: python -m pip list
       - name: Copying test data to services
         shell: bash -l {0}
         run: |

.github/workflows/pr.yaml

@@ -5,7 +5,6 @@ on:
     paths-ignore: ["**/docker.yaml", "docs"]
 
 env:
-  CONDA_ENV: echopype
   NUM_WORKERS: 2
 
 jobs:
@@ -17,16 +16,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]  # TODO: add back 3.11 once parsed2zarr is fixed
+        python-version: ["3.9", "3.10", "3.11"]
         runs-on: [ubuntu-latest]
         experimental: [false]
-        include:
-        - runs-on: ubuntu-latest
-          python-version: "3.11"
-          experimental: true
-    defaults:
-      run:
-        shell: bash -l {0}
     services:
       # TODO: figure out how to update tag when there's a new one
       minio:
@@ -42,35 +34,28 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
+      - name: Set up Python
+        uses: actions/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-      - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml
-          environment-name: ${{ env.CONDA_ENV }}
-          cache-environment: true
-          post-cleanup: 'all'
-      - name: Print conda environment
-        run: |
-          micromamba info
-          micromamba list
       - name: Remove docker-compose python
-        if: ${{ matrix.python-version == '3.10' || matrix.python-version == '3.11' }}
         run: sed -i "/docker-compose/d" requirements-dev.txt
       - name: Install dev tools
-        run: |
-          micromamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt
+        run: python -m pip install -r requirements-dev.txt
       # We only want to install this on one run, because otherwise we'll have
       # duplicate annotations.
       - name: Install error reporter
         if: ${{ matrix.python-version == '3.9' }}
-        run: |
-          python -m pip install pytest-github-actions-annotate-failures
+        run: python -m pip install pytest-github-actions-annotate-failures
       - name: Install echopype
-        run: |
-          python -m pip install -e .[plot]
+        run: python -m pip install -e ".[plot]"
+      - name: Print installed packages
+        run: python -m pip list
       - name: Copying test data to services
         run: |
           python .ci_helpers/docker/setup-services.py --deploy --data-only --http-server ${{ job.services.httpserver.id }}

echopype/tests/convert/test_parsed_to_zarr.py

@@ -15,6 +15,8 @@
 from echopype.echodata.convention import sonarnetcdf_1
 from echopype.convert.api import _check_file, SONAR_MODELS
 
+pytestmark = pytest.mark.skip(reason="Removed Parsed2Zarr")
+
 test_bucket_name = "echopype-test"
 port = 5555
 endpoint_uri = "http://127.0.0.1:%s/" % port