mcb-update-actions - Update matplotlib to latest version #22
Workflow file for this run
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| # This workflow checks that the semantic versioning (e.g. 1.1.0) of the GitHub | |
| # project is correct, and if it's "minor" or "patch", checks backwards | |
| # compatibility. | |
| # The logic of this workflow is: | |
| # - Details: EE-2699 | |
| # - Why: it helps avoiding human errors of versions in the schemas not being | |
| # changed when or how they should. | |
| # - Would block the PR if failed? Yes, as long as the PR is for a release. | |
| # - How: by executing the script check_project_version_change.py, and then, | |
| # based on its output, deploying Biovalidator with the old and new schemas | |
| # and old and new JSON examples. | |
| # | |
| # For more information, check: | |
| # https://github.com/EbiEga/ega-metadata-schema/tree/main/docs/releases | |
| name: | | |
| [REQUIRED] Check project version change | |
| on: | |
| # Executes on any commit to a PR to the "main" branch | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| check-modifications: | |
| runs-on: ubuntu-latest | |
| env: | |
| BASE_URL: "https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main" | |
| REPOSITORY_URL: "https://api.github.com/repos/EbiEga/ega-metadata-schema" | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| # This bit is needed to checkout in the branch that triggered the action | |
| # (e.g. v2.0.1) | |
| ref: ${{ github.head_ref }} | |
| - uses: actions/setup-python@v4 | |
| with: | |
| # We'll use the latest version of python from major 3 release | |
| # This bit is needed for running the following python script | |
| python-version: '3.x' | |
| - name: Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| # On subsequent runs, if the cache key matches (i.e., operating system and the hash of the requirements.txt file), | |
| # the dependencies are restored from the cache instead of being downloaded and installed again. | |
| path: ~/.cache/pip | |
| # combines the OS type and a hash of the requirements.txt file: the cache is specific to the dependencies listed | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| # If there is no cache for this key, we create it at the end of the run, even if there was an error mid-way | |
| save-always: true | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| requirements_f="./.github/scripts/requirements.txt" | |
| if [ -f "$requirements_f" ]; then pip install -r "$requirements_f" --prefer-binary --verbose; fi | |
| - name: Run version modification check | |
| id: run-version-modification-check | |
| run: | | |
| script_path="./.github/scripts/check_project_version_change.py" | |
| python3 "$script_path" --git_var_name "VERSION_CHANGE" --verbose | |
| echo "- The version change is: $VERSION_CHANGE" | |
| # The output of this previous script will determine if changes are not "major" (i.e. minor or patch), and therefore retrocompatibility | |
| # has to be tested through JSON Schema validation (combination of old and new schemas with old and new examples). | |
| # Thus, only if the output (saved at 'VERSION_CHANGE') from the script is NOT Major, the following steps will occur. | |
| - name: Check if version change is Major | |
| id: check-version | |
| # This step is just to set the logic for triggering the following steps | |
| run: | | |
| if [[ "${{ env.VERSION_CHANGE }}" != "Major" ]]; then | |
| echo "version_needs_to_be_checked=True" >> $GITHUB_ENV | |
| else | |
| echo "version_needs_to_be_checked=False" >> $GITHUB_ENV | |
| fi | |
| - name: Clone Biovalidator | |
| if: ${{ env.version_needs_to_be_checked == 'True' }} | |
| # See https://github.com/elixir-europe/biovalidator#installation | |
| run: git clone https://github.com/elixir-europe/biovalidator.git | |
| - name: Install Biovalidator | |
| if: ${{ env.version_needs_to_be_checked == 'True' }} | |
| run: | | |
| cd biovalidator | |
| npm install | |
| # We shouldn't need to audit the issues, but for now it is what it is | |
| # npm audit fix | |
| - name: Start Biovalidator server (old schemas) | |
| if: ${{ env.version_needs_to_be_checked == 'True' }} | |
| # We want to specify the OLD JSON schemas, so we DO NOT specify the schemas | |
| # at deployment level, and instead let Biovalidator fetch them from "main" | |
| run: | | |
| node biovalidator/src/biovalidator & | |
| # We stop for a few seconds to give the server some time | |
| sleep 3 | |
| - name: Validate JSON examples (old schemas, new examples) | |
| if: ${{ env.version_needs_to_be_checked == 'True' }} | |
| # Validate NEW JSON documents against the OLD (from "main") schemas | |
| run: | | |
| json_ex_dir="./examples/json_validation_tests" | |
| # The following URL points to the locally deployed server of | |
| # Biovalidator | |
| url="http://localhost:3020/validate" | |
| python3 ./.github/scripts/request_validation.py "$json_ex_dir" "$url" | |
| - name: Kill previous Biovalidator server | |
| if: ${{ env.version_needs_to_be_checked == 'True' }} | |
| # We kill the existing Biovalidator server if it exists | |
| run: | | |
| # File path | |
| file="./server.pid" | |
| # Check if the file exists | |
| if [ -f "$file" ] | |
| then | |
| # Read PID | |
| pid=$(cat "$file") | |
| # Check if the PID exists | |
| if ps -p $pid > /dev/null | |
| then | |
| echo "Killing task with PID: $pid" | |
| kill $pid | |
| else | |
| echo "No process found with PID: $pid" | |
| fi | |
| rm $file | |
| else | |
| echo "File $file does not exist" | |
| fi | |
| - name: Start Biovalidator server (New schemas) | |
| if: ${{ env.version_needs_to_be_checked == 'True' }} | |
| # We want to specify the NEW JSON schemas, so we DO specify the schemas | |
| # at deployment level | |
| run: | | |
| schemas_dir="./schemas" | |
| node biovalidator/src/biovalidator -r "$schemas_dir/*.json" & | |
| sleep 3 | |
| - name: Validate JSON examples (New schemas, old examples) | |
| if: ${{ env.version_needs_to_be_checked == 'True' }} | |
| # Validate OLD JSON documents against the NEW (from branch) schemas | |
| run: | | |
| # We fetch all old JSON examples from "main" | |
| old_json_ex_dir="./examples/old_json_validation_tests" | |
| json_ex_dir="./examples/json_validation_tests" | |
| python3 ./.github/scripts/fetch_github_documents.py --input_directory "$json_ex_dir" --destination_directory "$old_json_ex_dir" | |
| url="http://localhost:3020/validate" | |
| python3 ./.github/scripts/request_validation.py "$old_json_ex_dir" "$url" |