From 28ce0137b47b67f85e580745b216b7ff5f49dcfc Mon Sep 17 00:00:00 2001 From: VasuJ <145879890+vjaganat90@users.noreply.github.com> Date: Mon, 30 Dec 2024 21:42:56 -0500 Subject: [PATCH] fix weekly/fuzzy CI failure due to name change (#309) Co-authored-by: Vasu Jaganath --- .github/workflows/fuzzy_compile_weekly.yml | 36 +++++++++++----------- .github/workflows/lint_and_test_macos.yml | 34 ++++++++++---------- .github/workflows/run_workflows_weekly.yml | 28 ++++++++--------- 3 files changed, 49 insertions(+), 49 deletions(-) diff --git a/.github/workflows/fuzzy_compile_weekly.yml b/.github/workflows/fuzzy_compile_weekly.yml index 14bea188..8e3932e5 100644 --- a/.github/workflows/fuzzy_compile_weekly.yml +++ b/.github/workflows/fuzzy_compile_weekly.yml @@ -35,13 +35,13 @@ jobs: runs-on: [self-hosted, linux] steps: - - name: Checkout workflow-inference-compiler + - name: Checkout sophios if: always() uses: actions/checkout@v3 with: - repository: ${{ github.repository_owner }}/workflow-inference-compiler + repository: ${{ github.repository_owner }}/sophios ref: master - path: workflow-inference-compiler + path: sophios - name: Checkout biobb_adapters if: always() @@ -73,14 +73,14 @@ jobs: with: miniforge-variant: Miniforge-pypy3 miniforge-version: 24.7.1-0 - environment-file: workflow-inference-compiler/install/system_deps.yml + environment-file: sophios/install/system_deps.yml activate-environment: wic channels: conda-forge python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11 - name: Install Workflow Inference Compiler if: always() - run: cd workflow-inference-compiler/ && pip install ".[all_except_runner_src]" + run: cd sophios/ && pip install ".[all_except_runner_src]" - name: Install Molecular Modeling Workflows if: always() @@ -93,47 +93,47 @@ jobs: - name: Generate Sophios Python API Workflows (*.py -> *.wic) if: always() - run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' + run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' - name: Generate Sophios Validation Jsonschema if: always() - run: cd workflow-inference-compiler/ && sophios --generate_schemas + run: cd sophios/ && sophios --generate_schemas # Please read docs/validation.md#Property-Based-Testing # This is essentially an integration test for all of the # WIC Python API workflows as well as the WIC Python API itself. - name: Validate Sophios Python API Workflows (*.py -> *.wic) if: always() - run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' + run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' # Since a randomly chosen subschema is used every time, repeat 10X for more coverage. - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile - name: PyTest Fuzzy Compile - run: cd workflow-inference-compiler/ && pytest -k test_fuzzy_compile + run: cd sophios/ && pytest -k test_fuzzy_compile diff --git a/.github/workflows/lint_and_test_macos.yml b/.github/workflows/lint_and_test_macos.yml index a6c64ccf..87b35ae5 100644 --- a/.github/workflows/lint_and_test_macos.yml +++ b/.github/workflows/lint_and_test_macos.yml @@ -35,13 +35,13 @@ jobs: runs-on: macos-latest steps: - - name: Checkout workflow-inference-compiler + - name: Checkout sophios if: always() uses: actions/checkout@v3 with: - repository: ${{ github.repository_owner }}/workflow-inference-compiler + repository: ${{ github.repository_owner }}/sophios ref: master - path: workflow-inference-compiler + path: sophios - name: Checkout biobb_adapters if: always() @@ -73,7 +73,7 @@ jobs: with: miniforge-variant: Miniforge-pypy3 miniforge-version: 24.7.1-0 - environment-file: workflow-inference-compiler/install/system_deps.yml + environment-file: sophios/install/system_deps.yml activate-environment: wic use-mamba: true channels: conda-forge @@ -82,11 +82,11 @@ jobs: - name: ShellCheck Script Quality if: always() # "SC1017 (error): Literal carriage return. Run script through tr -d '\r' ." - run: shellcheck -e SC1017 $(find workflow-inference-compiler/ -name "*.sh" -and -not -path "./3/*") + run: shellcheck -e SC1017 $(find sophios/ -name "*.sh" -and -not -path "./3/*") - name: Install Workflow Inference Compiler if: always() - run: cd workflow-inference-compiler/ && pip install ".[all_except_runner_src]" + run: cd sophios/ && pip install ".[all_except_runner_src]" - name: Install Molecular Modeling Workflows if: always() @@ -99,39 +99,39 @@ jobs: - name: Generate Sophios Python API Workflows (*.py -> *.wic) if: always() - run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' + run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' - name: Generate Sophios Validation Jsonschema if: always() - run: cd workflow-inference-compiler/ && sophios --generate_schemas + run: cd sophios/ && sophios --generate_schemas # Please read docs/validation.md#Property-Based-Testing # This is essentially an integration test for all of the # Sophios Python API workflows as well as the Sophios Python API itself. - name: Validate Sophios Python API Workflows (*.py -> *.wic) if: always() - run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' + run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' - name: Build Documentation if: always() - run: cd workflow-inference-compiler/docs && make html + run: cd sophios/docs && make html - name: MyPy Check Type Annotations if: always() - run: cd workflow-inference-compiler/ && mypy src/ examples/ tests/ + run: cd sophios/ && mypy src/ examples/ tests/ # NOTE: Do not use `mypy .` because then mypy will check both src/ and build/ causing: - # src/workflow-inference-compiler/__init__.py: error: Duplicate module named "wic" - # (also at "./build/lib/workflow-inference-compiler/__init__.py") + # src/sophios/__init__.py: error: Duplicate module named "wic" + # (also at "./build/lib/sophios/__init__.py") - name: PyLint Check Code Quality if: always() - run: cd workflow-inference-compiler/ && pylint src/ examples/**/*.py tests/ + run: cd sophios/ && pylint src/ examples/**/*.py tests/ # NOTE: See fail-under threshold in .pylintrc - name: PEP8 Code Formatting if: always() id: autopep8 - run: cd workflow-inference-compiler/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/ + run: cd sophios/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/ - name: Fail if autopep8 made changes if: steps.autopep8.outputs.exit-code == 2 run: exit 1 @@ -140,12 +140,12 @@ jobs: - name: PyTest CWL Embedding Independence if: always() - run: cd workflow-inference-compiler/ && pytest -k test_cwl_embedding_independence # --cov --cov-config=.coveragerc_serial + run: cd sophios/ && pytest -k test_cwl_embedding_independence # --cov --cov-config=.coveragerc_serial # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout() timeout-minutes: 20 # backup timeout for windows - name: PyTest Inline Subworkflows if: always() - run: cd workflow-inference-compiler/ && pytest -k test_inline_subworkflows # --cov --cov-config=.coveragerc_serial + run: cd sophios/ && pytest -k test_inline_subworkflows # --cov --cov-config=.coveragerc_serial # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout() timeout-minutes: 20 # backup timeout for windows diff --git a/.github/workflows/run_workflows_weekly.yml b/.github/workflows/run_workflows_weekly.yml index 62d286eb..0b2de4e0 100644 --- a/.github/workflows/run_workflows_weekly.yml +++ b/.github/workflows/run_workflows_weekly.yml @@ -34,12 +34,12 @@ jobs: runs-on: [self-hosted, linux] steps: - - name: Checkout workflow-inference-compiler + - name: Checkout sophios uses: actions/checkout@v3 with: - repository: ${{ github.repository_owner }}/workflow-inference-compiler + repository: ${{ github.repository_owner }}/sophios ref: master - path: workflow-inference-compiler + path: sophios - name: Checkout biobb_adapters if: always() @@ -78,7 +78,7 @@ jobs: # Toil is currently incompatible with pypy # - name: Append pypy to conda environment files # if: runner.os != 'Windows' - # run: cd workflow-inference-compiler/install/ && echo " - pypy" >> system_deps.yml + # run: cd sophios/install/ && echo " - pypy" >> system_deps.yml - name: Setup miniforge (linux, macos) if: always() @@ -90,7 +90,7 @@ jobs: # another environment, better to avoid the problem altogether by # not using Miniforge-pypy3 miniforge-version: 24.7.1-0 - environment-file: workflow-inference-compiler/install/system_deps.yml + environment-file: sophios/install/system_deps.yml activate-environment: wic_github_actions use-mamba: true channels: conda-forge @@ -103,7 +103,7 @@ jobs: - name: Install Workflow Inference Compiler if: always() - run: cd workflow-inference-compiler/ && pip install ".[all_except_runner_src]" + run: cd sophios/ && pip install ".[all_except_runner_src]" - name: Install Molecular Modeling Workflows if: always() @@ -116,40 +116,40 @@ jobs: - name: Generate Sophios Python API Workflows (*.py -> *.wic) if: always() - run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' + run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' - name: Generate Sophios Validation Jsonschema if: always() - run: cd workflow-inference-compiler/ && sophios --generate_schemas + run: cd sophios/ && sophios --generate_schemas # Please read docs/validation.md#Property-Based-Testing # This is essentially an integration test for all of the # Sophios Python API workflows as well as the WIC Python API itself. - name: Validate Sophios Python API Workflows (*.py -> *.wic) if: always() - run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' + run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' - name: cwl-docker-extract (i.e. recursively docker pull) if: always() - run: cd workflow-inference-compiler/ && pytest -k test_cwl_docker_extract + run: cd sophios/ && pytest -k test_cwl_docker_extract # For self-hosted runners, make sure the docker cache is up-to-date. - name: PyTest Run Workflows (On Push) if: always() # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252 - run: cd workflow-inference-compiler/ && pytest -k test_run_workflows_on_push --workers 8 --cwl_runner toil-cwl-runner # --cov + run: cd sophios/ && pytest -k test_run_workflows_on_push --workers 8 --cwl_runner toil-cwl-runner # --cov - name: PyTest Run Inlined Workflows (On Push) if: always() # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252 - run: cd workflow-inference-compiler/ && pytest -k test_run_inlined_workflows_on_push --workers 8 --cwl_runner toil-cwl-runner # --cov + run: cd sophios/ && pytest -k test_run_inlined_workflows_on_push --workers 8 --cwl_runner toil-cwl-runner # --cov - name: PyTest Run Workflows (Weekly) if: always() # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252 - run: cd workflow-inference-compiler/ && pytest -k test_run_workflows_weekly --workers 8 --cwl_runner toil-cwl-runner # --cov + run: cd sophios/ && pytest -k test_run_workflows_weekly --workers 8 --cwl_runner toil-cwl-runner # --cov - name: PyTest Run Inlined Workflows (Weekly) if: always() # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252 - run: cd workflow-inference-compiler/ && pytest -k test_run_inlined_workflows_weekly --workers 8 --cwl_runner toil-cwl-runner # --cov + run: cd sophios/ && pytest -k test_run_inlined_workflows_weekly --workers 8 --cwl_runner toil-cwl-runner # --cov