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Merge pull request #554 from populationgenomics/dev
Metamist release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -7,6 +7,10 @@ on: | |
| - main | ||
| - dev | ||
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| permissions: | ||
| id-token: write | ||
| contents: read | ||
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| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
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@@ -21,23 +25,28 @@ jobs: | |
| run: | ||
| shell: bash -eo pipefail -l {0} | ||
| steps: | ||
| - uses: actions/checkout@main | ||
| - uses: actions/checkout@v3 | ||
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||
| - name: "gcloud setup" | ||
| uses: google-github-actions/setup-gcloud@v0 | ||
| - id: "google-cloud-auth" | ||
| name: "Authenticate to Google Cloud" | ||
| uses: "google-github-actions/auth@v1" | ||
| with: | ||
| project_id: sample-metadata | ||
| service_account_key: ${{ secrets.GCP_SERVER_DEPLOY_KEY }} | ||
| workload_identity_provider: "projects/774248915715/locations/global/workloadIdentityPools/gh-deploy-pool/providers/gh-provider" | ||
| service_account: "[email protected]" | ||
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| - id: "google-cloud-sdk-setup" | ||
| name: "Set up Cloud SDK" | ||
| uses: google-github-actions/setup-gcloud@v1 | ||
|
|
||
| - name: "gcloud docker auth" | ||
| run: | | ||
| gcloud auth configure-docker australia-southeast1-docker.pkg.dev | ||
| - uses: actions/setup-python@v2 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.10" | ||
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| - uses: actions/setup-java@v2 | ||
| - uses: actions/setup-java@v3 | ||
| with: | ||
| distribution: "temurin" # See 'Supported distributions' for available options | ||
| java-version: "17" | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,92 +1,98 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.4.0 | ||
| hooks: | ||
| - id: check-yaml | ||
| exclude: '\.*conda/.*' | ||
| - id: end-of-file-fixer | ||
| - id: trailing-whitespace | ||
| exclude: '\.txt$|\.tsv$' | ||
| - id: check-case-conflict | ||
| - id: check-merge-conflict | ||
| - id: detect-private-key | ||
| - id: debug-statements | ||
| - id: check-added-large-files | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.4.0 | ||
| hooks: | ||
| - id: check-yaml | ||
| exclude: '\.*conda/.*' | ||
| - id: end-of-file-fixer | ||
| - id: trailing-whitespace | ||
| exclude: '\.txt$|\.tsv$' | ||
| - id: check-case-conflict | ||
| - id: check-merge-conflict | ||
| - id: detect-private-key | ||
| - id: debug-statements | ||
| - id: check-added-large-files | ||
|
|
||
| - repo: https://github.com/igorshubovych/markdownlint-cli | ||
| rev: v0.33.0 | ||
| hooks: | ||
| - id: markdownlint | ||
| args: ["--config", ".markdownlint.json"] | ||
| - repo: https://github.com/igorshubovych/markdownlint-cli | ||
| rev: v0.33.0 | ||
| hooks: | ||
| - id: markdownlint | ||
| args: ["--config", ".markdownlint.json"] | ||
|
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||
| - repo: https://github.com/ambv/black | ||
| rev: 23.3.0 | ||
| hooks: | ||
| - id: black | ||
| args: [.] | ||
| pass_filenames: false | ||
| always_run: true | ||
| exclude: ^metamist/ | ||
| - repo: https://github.com/ambv/black | ||
| rev: 23.3.0 | ||
| hooks: | ||
| - id: black | ||
| args: [.] | ||
| pass_filenames: false | ||
| always_run: true | ||
| exclude: ^metamist/ | ||
|
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||
| - repo: https://github.com/PyCQA/flake8 | ||
| rev: "6.0.0" | ||
| hooks: | ||
| - id: flake8 | ||
| additional_dependencies: [flake8-bugbear, flake8-quotes] | ||
| - repo: https://github.com/PyCQA/flake8 | ||
| rev: "6.0.0" | ||
| hooks: | ||
| - id: flake8 | ||
| additional_dependencies: [flake8-bugbear, flake8-quotes] | ||
|
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||
| # Using system installation of pylint to support checking python module imports | ||
| - repo: local | ||
| hooks: | ||
| - id: pylint | ||
| name: pylint | ||
| entry: pylint | ||
| language: system | ||
| types: [python] | ||
| # Using system installation of pylint to support checking python module imports | ||
| - repo: local | ||
| hooks: | ||
| - id: pylint | ||
| name: pylint | ||
| entry: pylint | ||
| language: system | ||
| types: [python] | ||
|
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| # mypy | ||
| - repo: https://github.com/pre-commit/mirrors-mypy | ||
| rev: v0.961 | ||
| hooks: | ||
| - id: mypy | ||
| args: | ||
| [ | ||
| --pretty, | ||
| --show-error-codes, | ||
| --no-strict-optional, | ||
| --ignore-missing-imports, | ||
| --install-types, | ||
| --non-interactive, | ||
| ] | ||
| additional_dependencies: | ||
| - strawberry-graphql[fastapi]==0.138.1 | ||
| # mypy | ||
| - repo: https://github.com/pre-commit/mirrors-mypy | ||
| rev: v1.5.1 | ||
| hooks: | ||
| - id: mypy | ||
| args: | ||
| [ | ||
| --pretty, | ||
| --show-error-codes, | ||
| --no-strict-optional, | ||
| --ignore-missing-imports, | ||
| --install-types, | ||
| --non-interactive, | ||
| --show-error-context, | ||
| --check-untyped-defs, | ||
| --explicit-package-bases, | ||
| --disable-error-code, | ||
| operator, | ||
| ] | ||
| additional_dependencies: | ||
| - strawberry-graphql[fastapi]==0.206.0 | ||
| - types-PyMySQL==1.1.0.1 | ||
|
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||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: "v3.0.0-alpha.4" | ||
| hooks: | ||
| - id: prettier | ||
| # I'm not exactly sure why it changes behaviour, but | ||
| # calling `cd web`, then calling `ls src/**/*.tsx` | ||
| # returns different results to `cd web && ls src/**/*.tsx` | ||
| # so just include both patterns here | ||
| entry: bash -c 'cd web && prettier --write --ignore-unknown --check src/*.{ts,tsx,css} src/**/*.{ts,tsx,css}' | ||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: "v3.0.0-alpha.4" | ||
| hooks: | ||
| - id: prettier | ||
| # I'm not exactly sure why it changes behaviour, but | ||
| # calling `cd web`, then calling `ls src/**/*.tsx` | ||
| # returns different results to `cd web && ls src/**/*.tsx` | ||
| # so just include both patterns here | ||
| entry: bash -c 'cd web && prettier --write --ignore-unknown --check src/*.{ts,tsx,css} src/**/*.{ts,tsx,css}' | ||
|
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||
| - repo: https://github.com/pre-commit/mirrors-eslint | ||
| rev: "v8.33.0" | ||
| hooks: | ||
| - id: eslint | ||
| entry: bash -c 'cd web && eslint' | ||
| files: \.[jt]sx?$ | ||
| types: [file] | ||
| additional_dependencies: | ||
| - eslint@^7.32.0 | ||
| - eslint-config-airbnb@^19.0.4 | ||
| - eslint-config-airbnb-base@^15.0.0 | ||
| - eslint-config-airbnb-typescript@^17.0.0 | ||
| - eslint-config-prettier@^8.6.0 | ||
| - eslint-plugin-import@^2.26.0 | ||
| - eslint-plugin-jsx-a11y@^6.6.1 | ||
| - eslint-plugin-prettier@^4.2.1 | ||
| - eslint-plugin-react@^7.31.11 | ||
| - eslint-plugin-react-hooks@^4.6.0 | ||
| - "@typescript-eslint/eslint-plugin@^5.48.0" | ||
| - "@typescript-eslint/parser@^5.48.0" | ||
| - repo: https://github.com/pre-commit/mirrors-eslint | ||
| rev: "v8.33.0" | ||
| hooks: | ||
| - id: eslint | ||
| entry: bash -c 'cd web && eslint' | ||
| files: \.[jt]sx?$ | ||
| types: [file] | ||
| additional_dependencies: | ||
| - eslint@^7.32.0 | ||
| - eslint-config-airbnb@^19.0.4 | ||
| - eslint-config-airbnb-base@^15.0.0 | ||
| - eslint-config-airbnb-typescript@^17.0.0 | ||
| - eslint-config-prettier@^8.6.0 | ||
| - eslint-plugin-import@^2.26.0 | ||
| - eslint-plugin-jsx-a11y@^6.6.1 | ||
| - eslint-plugin-prettier@^4.2.1 | ||
| - eslint-plugin-react@^7.31.11 | ||
| - eslint-plugin-react-hooks@^4.6.0 | ||
| - "@typescript-eslint/eslint-plugin@^5.48.0" | ||
| - "@typescript-eslint/parser@^5.48.0" |
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