Merge pull request galaxyproject#13358 from mvdbeek/codecoverage

Report code coverage (for pytest test suites)
jmchilton · Feb 18, 2022 · fa3ae1d · fa3ae1d
2 parents f13faf8 + 4dca001
commit fa3ae1d
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Showing 11 changed files with 51 additions and 24 deletions.
diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
@@ -56,8 +56,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
       - name: Run tests
-        run: ./run_tests.sh --skip_flakey_fails -api
+        run: ./run_tests.sh --coverage --skip_flakey_fails -api
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: api
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/api_paste.yaml b/.github/workflows/api_paste.yaml
@@ -57,8 +57,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api-paste
       - name: Run tests
-        run: ./run_tests.sh --skip_flakey_fails -api
+        run: ./run_tests.sh --coverage --skip_flakey_fails -api
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: api-paste
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
@@ -56,8 +56,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Run tests
-        run: ./run_tests.sh --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
+        run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: cwl-conformance
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework.yaml
@@ -54,8 +54,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
       - name: Run tests
-        run: ./run_tests.sh --framework
+        run: ./run_tests.sh --coverage --framework
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: framework
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
@@ -81,8 +81,12 @@ jobs:
       - name: Run tests
         run: |
           . .ci/minikube-test-setup/start_services.sh
-          ./run_tests.sh -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
+          ./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: integration
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/integration_selenium.yaml b/.github/workflows/integration_selenium.yaml
@@ -60,8 +60,12 @@ jobs:
           yarn-lock-file: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@master
       - name: Run tests
-        run: ./run_tests.sh -integration test/integration_selenium
+        run: ./run_tests.sh --coverage -integration test/integration_selenium
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: integration-selenium
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml
@@ -61,8 +61,12 @@ jobs:
           yarn-lock-file: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@master
       - name: Run tests
-        run: ./run_tests.sh -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: selenium
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/selenium_beta.yaml b/.github/workflows/selenium_beta.yaml
@@ -62,8 +62,12 @@ jobs:
           yarn-lock-file: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@master
       - name: Run tests
-        run: ./run_tests.sh -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: selenium-beta-history
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
@@ -44,11 +44,13 @@ jobs:
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-unit
       - name: Install ffmpeg
         run: sudo apt-get update && sudo apt-get -y install ffmpeg
-      - name: Install tox
-        run: pip install tox
       - name: Run tests
-        run: tox -e unit
+        run: ./run_tests.sh --coverage -u
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: py-unit
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:

diff --git a/run_tests.sh b/run_tests.sh
@@ -644,7 +644,7 @@ fi
 export GALAXY_TEST_TOOL_CONF
 if [ "$test_script" = 'pytest' ]; then
     if [ "$coverage_arg" = '--with-coverage' ]; then
-        coverage_arg="--cov-report term --cov=lib"
+        coverage_arg="--cov-report xml --cov-report term --cov=lib"
     fi
     if [ -n "$marker" ]; then
         marker_args=(-m "$marker")

diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
@@ -140,30 +140,23 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
             if command -v virtualenv >/dev/null; then
                 virtualenv -p "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
             else
-                vvers=16.7.9
-                vurl="https://files.pythonhosted.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
-                vsha=0d62c70883c0342d59c11d0ddac0d954d0431321a41ab20851facf2b222598f3
+                min_python_version=3.7
+                vurl="https://bootstrap.pypa.io/virtualenv/${min_python_version}/virtualenv.pyz"
                 vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
                 vsrc="$vtmp/$(basename $vurl)"
-                # SSL certificates are not checked to prevent problems with messed
-                # up client cert environments. We verify the download using a known
-                # good sha256 sum instead.
                 echo "Fetching $vurl"
                 if command -v curl >/dev/null; then
-                    curl --insecure -L -o "$vsrc" "$vurl"
+                    curl -L -o "$vsrc" "$vurl"
                 elif command -v wget >/dev/null; then
-                    wget --no-check-certificate -O "$vsrc" "$vurl"
+                    wget -O "$vsrc" "$vurl"
                 else
                     "$GALAXY_PYTHON" -c "try:
     from urllib import urlretrieve
 except:
     from urllib.request import urlretrieve
 urlretrieve('$vurl', '$vsrc')"
                 fi
-                echo "Verifying $vsrc checksum is $vsha"
-                "$GALAXY_PYTHON" -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
-                tar zxf "$vsrc" -C "$vtmp"
-                "$GALAXY_PYTHON" "$vtmp/virtualenv-$vvers/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
+                "$GALAXY_PYTHON" "$vsrc" "$GALAXY_VIRTUAL_ENV"
                 rm -rf "$vtmp"
             fi
         fi