Upgrade to psycopg 3 #2666
Workflow file for this run
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| # Copyright 2020 Open Reaction Database Project Authors | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| name: Tests | |
| on: [ pull_request, push ] | |
| jobs: | |
| test_ord_schema: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-14] | |
| python-version: [3.10, 3.11, 3.12] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| PGDATA: $GITHUB_WORKSPACE/rdkit-postgres | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| - name: Setup PostgreSQL | |
| shell: bash -l {0} | |
| run: | | |
| # NOTE(skearnes): conda is only used for postgres (not python). | |
| # NOTE(skearnes): rdkit-postgresql may not be available for ARM. | |
| conda install -c rdkit rdkit-postgresql || conda install -c conda-forge postgresql | |
| initdb | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install ord_schema | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install wheel | |
| python -m pip install .[tests] | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| coverage erase | |
| pytest -vv --cov=ord_schema --durations=0 --durations-min=1 | |
| coverage xml | |
| - uses: codecov/codecov-action@v1 | |
| test_notebooks: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-14] | |
| python-version: [3.10, 3.11, 3.12] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install ord_schema | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install wheel | |
| python -m pip install .[examples,tests] | |
| - name: Test notebooks | |
| run: | | |
| treon | |
| test_proto_wrappers: | |
| strategy: | |
| matrix: | |
| python-version: [3.10, 3.11, 3.12] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install protoc | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install wheel | |
| mkdir protoc | |
| cd protoc | |
| wget https://github.com/protocolbuffers/protobuf/releases/download/v22.3/protoc-22.3-linux-x86_64.zip | |
| unzip protoc-22.3-linux-x86_64.zip | |
| wget https://github.com/protocolbuffers/protobuf-javascript/releases/download/v3.21.2/protobuf-javascript-3.21.2-linux-x86_64.zip | |
| unzip protobuf-javascript-3.21.2-linux-x86_64.zip | |
| PATH=$GITHUB_WORKSPACE/protoc/bin:$PATH protoc --version | |
| - name: Run protoc | |
| run: | | |
| PATH=$GITHUB_WORKSPACE/protoc/bin:$PATH ./compile_proto_wrappers.sh | |
| ./format.sh # Add license headers. | |
| - name: Check for drift | |
| run: | | |
| # Ignore the copyright line in the diff so the year can change. | |
| [[ -z $(git diff -I "^(#| \*) Copyright") ]] || { echo "proto wrappers do not match:\n$(git diff)"; exit 1; } | |
| test_js: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v3 | |
| with: | |
| node-version: '16.x' | |
| - name: Test NPM package | |
| run: | | |
| cd js/ord-schema | |
| npm install-test | |
| test_publish: | |
| strategy: | |
| matrix: | |
| python-version: [3.10, 3.11, 3.12] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/setup-node@v3 | |
| with: | |
| node-version: '16.x' | |
| registry-url: 'https://registry.npmjs.org' | |
| - name: Test bump patch version | |
| run: | | |
| git config user.name github-actions | |
| git config user.email [email protected] | |
| python -m pip install bump2version | |
| bump2version patch --verbose | |
| - name: Test python | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade build twine wheel | |
| python -m build | |
| - name: Test javascript | |
| run: | | |
| cd js/ord-schema | |
| npm install | |
| npm run build | |
| npm publish --dry-run |