changes to TS testing CI:

* run TS tests together with Galaxy dev tests so only run once per Python version
* fail TS tests when test TS is inaccessible, don't skip

.github/workflows/test.yaml

@@ -105,6 +105,10 @@ jobs:
         run: |
           # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
           createdb -U postgres galaxy
+          # Run ToolShed tests only once per Python version
+          if [ "${{ matrix.galaxy_version }}" = 'dev' ]; then
+              export BIOBLEND_TOOLSHED_URL=https://testtoolshed.g2.bx.psu.edu/
+          fi
           # Install Galaxy
           GALAXY_DIR=galaxy-${{ matrix.galaxy_version }}
           git clone --depth=1 -b ${{ matrix.galaxy_version }} https://github.com/galaxyproject/galaxy $GALAXY_DIR
@@ -114,38 +118,3 @@ jobs:
         if: ${{ failure() }}
         run: |
           cat galaxy-${{ matrix.galaxy_version }}/*.log
-  test-toolshed:
-    if: (github.event_name != 'schedule' || github.repository_owner == 'galaxyproject') && git diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.sha }} | grep 'bioblend/toolshed'
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        galaxy_version: [dev]
-        tox_env:
-          - py39
-          - py38
-          - py37
-          - py36
-    steps:
-      - uses: actions/checkout@v2
-      - name: Cache pip dir
-        uses: actions/cache@v2
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.tox_env }}-${{ matrix.galaxy_version }}
-      - name: Calculate Python version for BioBlend from tox_env
-        id: get_bioblend_python_version
-        run: echo "::set-output name=bioblend_python_version::$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([0-9]\)\([0-9]\+\)/\1.\2/')"
-      - name: Set up Python for BioBlend
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
-      - name: Install tox
-        run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install 'tox>=1.8.0' 'virtualenv>=20.0.14'
-      - name: Run ToolShed tests
-        run: |
-          export BIOBLEND_TOOLSHED_URL=https://testtoolshed.g2.bx.psu.edu/
-          tox -e ${{ matrix.tox_env }}

bioblend/_tests/test_util.py

@@ -5,16 +5,13 @@
 import string
 import unittest
 
-import requests
-
 import bioblend
 
 NO_CLOUDMAN_MESSAGE = "CloudMan required and no CloudMan AMI configured."
 NO_GALAXY_MESSAGE = "Externally configured Galaxy required, but not found. Set BIOBLEND_GALAXY_URL and BIOBLEND_GALAXY_API_KEY to run this test."
 NO_TOOLSHED_MESSAGE = (
     "Externally configured ToolShed required, but not found. Set BIOBLEND_TOOLSHED_URL to run this test."
 )
-INACCESSIBLE_TOOLSHED_MESSAGE = "Externally configured ToolShed is not accessible."
 OLD_GALAXY_RELEASE = "Testing on Galaxy %s, but need %s to run this test."
 MISSING_TOOL_MESSAGE = "Externally configured Galaxy instance requires tool %s to run test."
 
@@ -35,10 +32,7 @@ def skip_unless_toolshed():
     """
     if "BIOBLEND_TOOLSHED_URL" not in os.environ:
         return unittest.skip(NO_TOOLSHED_MESSAGE)
-    elif requests.get(os.environ["BIOBLEND_TOOLSHED_URL"]).status_code != 200:
-        return unittest.skip(INACCESSIBLE_TOOLSHED_MESSAGE)
-    else:
-        return lambda f: f
+    return lambda f: f
 
 
 def skip_unless_galaxy(min_release=None):

run_bioblend_tests.sh

@@ -146,9 +146,6 @@ else
 fi
 export BIOBLEND_GALAXY_URL=http://localhost:${GALAXY_PORT}
 
-# Set variable for ToolShed tests
-export BIOBLEND_TOOLSHED_URL=https://testtoolshed.g2.bx.psu.edu/
-
 # Run the tests
 cd "${BIOBLEND_DIR}"
 set +e  # don't stop the script if tox fails