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updating test workflow; adding dependabot and codeQL; adding compile …
…report; removing unneeded parts of Makefile; adding pyproject file for Ruff linting/checks
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| [html] | ||
| directory = ./python-coverage | ||
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| [xml] | ||
| output = ./python-coverage/coverage.xml |
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| version: 2 | ||
| updates: | ||
| - package-ecosystem: docker | ||
| directory: "/" | ||
| schedule: | ||
| interval: monthly | ||
| time: '11:00' | ||
| open-pull-requests-limit: 10 | ||
| - package-ecosystem: pip | ||
| directory: "/" | ||
| schedule: | ||
| interval: monthly | ||
| time: '11:00' | ||
| open-pull-requests-limit: 10 | ||
| - package-ecosystem: "github-actions" | ||
| directory: ".github/workflows" | ||
| schedule: | ||
| interval: "monthly" | ||
| open-pull-requests-limit: 10 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| name: "CodeQL" | ||
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| on: | ||
| push: | ||
| branches: | ||
| - develop | ||
| - main | ||
| - master | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - reopened | ||
| - synchronize | ||
| - closed | ||
|
|
||
| jobs: | ||
| analyze: | ||
| name: Analyze | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| actions: read | ||
| contents: read | ||
| security-events: write | ||
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| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| language: [python] | ||
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| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@master | ||
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| - name: Initialize CodeQL | ||
| uses: github/codeql-action/init@main | ||
| with: | ||
| languages: ${{ matrix.language }} | ||
| queries: +security-and-quality | ||
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| - name: Autobuild | ||
| uses: github/codeql-action/autobuild@main | ||
| if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }} | ||
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| - name: Perform CodeQL Analysis | ||
| uses: github/codeql-action/analyze@main | ||
| with: | ||
| category: "/language:${{ matrix.language }}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,62 +1,51 @@ | ||
| name: KBase SDK Tests | ||
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| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| - main | ||
| - develop | ||
| push: | ||
| branches: | ||
| - master | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| - main | ||
| - develop | ||
|
|
||
| jobs: | ||
|
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| sdk_tests: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
|
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| - name: Check out GitHub repo | ||
| if: "!contains(github.event.head_commit.message, 'skip ci')" | ||
| uses: actions/checkout@v2 | ||
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| - name: Check out Actions CI files | ||
| if: "!contains(github.event.head_commit.message, 'skip ci')" | ||
| uses: actions/checkout@v2 | ||
| with: | ||
| repository: 'kbaseapps/kb_sdk_actions' | ||
| path: 'kb_sdk_actions' | ||
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||
|
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| - name: Set up test environment | ||
| if: "!contains(github.event.head_commit.message, 'skip ci')" | ||
| shell: bash | ||
| env: | ||
| KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} | ||
| run: | | ||
| # Verify kb_sdk_actions clone worked | ||
| test -f "$HOME/kb_sdk_actions/bin/kb-sdk" && echo "CI files cloned" | ||
| # Pull kb-sdk & create startup script | ||
| docker pull kbase/kb-sdk | ||
| sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/make_testdir && echo "Created test_local" | ||
| test -f "test_local/test.cfg" && echo "Confirmed config exists" | ||
| - name: Configure authentication | ||
| if: "!contains(github.event.head_commit.message, 'skip ci')" | ||
| shell: bash | ||
| env: | ||
| KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} | ||
| run: | | ||
| # Add token to config | ||
| sed -ie "s/^test_token=.*$/&$KBASE_TEST_TOKEN/g" ./test_local/test.cfg | ||
| - name: Run tests | ||
| if: "!contains(github.event.head_commit.message, 'skip ci')" | ||
| shell: bash | ||
| env: | ||
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | ||
| run: | | ||
| sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test | ||
| bash <(curl -s https://codecov.io/bash) | ||
| sdk_tests: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Check out GitHub repo | ||
| uses: actions/checkout@master | ||
|
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||
| - name: Set up test environment | ||
| shell: bash | ||
| run: | | ||
| # Cache the group for the docker file | ||
| if [ ! -e $HOME/.kbsdk.cache ] ; then | ||
| docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache | ||
| fi | ||
| # ignore the exit code | ||
| docker run -i --rm -v $HOME:$HOME -u $(id -u) -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DUSER=$USER -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 test || true | ||
| - name: Confirm config exists and add token | ||
| shell: bash | ||
| env: | ||
| KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} | ||
| run: | | ||
| test -f "test_local/test.cfg" && echo "Confirmed config exists" | ||
| # Add token to config | ||
| sed -ie "s/^test_token=.*$/&$KBASE_TEST_TOKEN/g" ./test_local/test.cfg | ||
| - name: Run tests | ||
| shell: bash | ||
| run: | | ||
| docker run -i --rm -v $HOME:$HOME -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 test --verbose | ||
| - name: Upload coverage to Codecov | ||
| uses: codecov/codecov-action@v3 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| fail_ci_if_error: true |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"functions":{"run_FastTree":{"name":"run_FastTree","comment":"Method for Tree building of either DNA or PROTEIN sequences\n**\n** input_type: MSA\n** output_type: Tree","place":null,"input":[{"type":"kb_fasttree.FastTree_Params","comment":"FastTree Input Params"}],"output":[{"type":"kb_fasttree.FastTree_Output","comment":"FastTree Output"}]}},"module_name":"kb_fasttree","sdk_version":"1.2.6","sdk_git_commit":"cedcfc2326db32bbdb09eb6d031838a93853c530","impl_file_path":"lib/kb_fasttree/kb_fasttreeImpl.py","spec_files":[{"content":"/*\n** A KBase module: kb_fasttree\n**\n** This module runs FastTree to make Trees for either DNA or PROTEIN MSAs\n** \n*/\n\nmodule kb_fasttree {\n\n /* \n ** The workspace object refs are of form:\n **\n ** objects = ws.get_objects([{'ref': params['workspace_id']+'/'+params['obj_name']}])\n **\n ** \"ref\" means the entire name combining the workspace id and the object name\n ** \"id\" is a numerical identifier of the workspace or object, and should just be used for workspace\n ** \"name\" is a string identifier of a workspace or object. This is received from Narrative.\n */\n typedef string workspace_name;\n typedef string data_obj_name;\n typedef string data_obj_ref;\n\n\n /* FastTree Input Params\n */\n typedef structure {\n workspace_name workspace_name;\n\tstring desc;\n\tdata_obj_ref input_ref;\n data_obj_name output_name;\n\tint species_tree_flag; /* boolean */\n\tdata_obj_ref intree_ref;\n\tint fastest; /* boolean */\n\tint pseudo; /* boolean */\n\tint gtr; /* boolean */\n\tint wag; /* boolean */\n\tint noml; /* boolean */\n\tint nome; /* boolean */\n int cat; /* actually is an int */\n\tint nocat; /* boolean */\n int gamma; /* boolean */\n } FastTree_Params;\n\n\n /* FastTree Output\n */\n typedef structure {\n\tdata_obj_name report_name;\n\tdata_obj_ref report_ref;\n data_obj_ref output_ref;\n } FastTree_Output;\n\t\n\n /* Method for Tree building of either DNA or PROTEIN sequences\n **\n ** input_type: MSA\n ** output_type: Tree\n */\n funcdef run_FastTree (FastTree_Params params) returns (FastTree_Output) authentication required;\n};\n","file_name":"kb_fasttree.spec","is_main":1}],"function_places":{}} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| [tool.ruff] | ||
| line-length = 100 | ||
|
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||
| extend-exclude = [ | ||
| "lib/installed_clients/*" | ||
| ] | ||
|
|
||
| # Assume Python 3.12. | ||
| target-version = "py312" | ||
|
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| [tool.ruff.lint] | ||
| select = [ | ||
| # core | ||
| "F", # Pyflakes | ||
| "E", # pycodestyle errors | ||
| "W", # pycodestyle warnings | ||
| "C90", # mccabe + | ||
| "I", # isort | ||
| "N", # pep8-naming | ||
| "D", # pydocstyle | ||
| "UP", # pyupgrade | ||
| # extensions | ||
| "YTT", # flake8-2020 | ||
| "ANN", # flake8-annotations | ||
| "ASYNC", # flake8-async | ||
| "S", # flake8-bandit | ||
| "BLE", # flake8-blind-except | ||
| "FBT", # flake8-boolean-trap | ||
| "B", # flake8-bugbear | ||
| "A", # flake8-builtins | ||
| # "COM", # flake8-commas | ||
| "CPY", # flake8-copyright | ||
| "C4", # flake8-comprehensions | ||
| "DTZ", # flake8-datetimez | ||
| "T10", # flake8-debugger | ||
| # "DJ", # flake8-django | ||
| "EM", # flake8-errmsg | ||
| "EXE", # flake8-executable | ||
| "FA", # flake8-future-annotations | ||
| "ISC", # flake8-implicit-str-concat | ||
| "ICN", # flake8-import-conventions | ||
| "G", # flake8-logging-format | ||
| "INP", # flake8-no-pep420 | ||
| "PIE", # flake8-pie | ||
| "T20", # flake8-print | ||
| "PYI", # flake8-pyi | ||
| "PT", # flake8-pytest-style | ||
| "Q", # flake8-quotes | ||
| "RSE", # flake8-raise | ||
| "RET", # flake8-return | ||
| "SLF", # flake8-self | ||
| # "SLOT", # flake8-slots | ||
| "SIM", # flake8-simplify | ||
| "TID", # flake8-tidy-imports | ||
| "TCH", # flake8-type-checking | ||
| "INT", # flake8-gettext | ||
| "ARG", # flake8-unused-arguments | ||
| "PTH", # flake8-use-pathlib | ||
| "TD", # flake8-todos | ||
| "FIX", # flake8-fixme | ||
| "ERA", # eradicate | ||
| # "PD", # pandas-vet | ||
| "PGH", # pygrep-hooks | ||
| "PL", # Pylint | ||
| "TRY", # tryceratops | ||
| "FLY", # flynt | ||
| # "NPY", # NumPy-specific rules | ||
| "AIR", # Airflow | ||
| "PERF", # Perflint | ||
| "FURB", # refurb | ||
| "LOG", # flake8-logging | ||
| "RUF", # Ruff-specific rules | ||
| ] | ||
|
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| # E203: whitespace before ‘,’, ‘;’, or ‘:’ | ||
| # E501: line length | ||
| # ISC001: conflicts with Ruff's formatter | ||
| # W503: line break after binary operator | ||
| ignore = [ | ||
| "E203", | ||
| "E501", | ||
| "ISC001", | ||
| "S101", | ||
| ] | ||
|
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| # Allow autofix for all enabled rules (when `--fix`) is provided. | ||
| fixable = ["ALL"] | ||
| unfixable = [] | ||
|
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| # Exclude a variety of commonly ignored directories. | ||
| exclude = [ | ||
| "__pypackages__", | ||
| "_build", | ||
| ".bzr", | ||
| ".direnv", | ||
| ".eggs", | ||
| ".git-rewrite", | ||
| ".git", | ||
| ".github", | ||
| ".hg", | ||
| ".mypy_cache", | ||
| ".nox", | ||
| ".pants.d", | ||
| ".pytype", | ||
| ".ruff_cache", | ||
| ".svn", | ||
| ".tox", | ||
| ".venv", | ||
| "*.pyc", | ||
| "buck-out", | ||
| "build", | ||
| "deps", | ||
| "dist", | ||
| "node_modules", | ||
| "other_schema", | ||
| "python-coverage", | ||
| "sample_data", | ||
| "venv", | ||
| ] | ||
| per-file-ignores = {} | ||
|
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| [tool.ruff.lint.pydocstyle] | ||
| convention = "google" |
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