fix weekly/fuzzy CI failure due to name change (#309)

Co-authored-by: Vasu Jaganath <vasu.jaganath@axleinfo.com>
PolusAI · Dec 31, 2024 · 28ce013 · 28ce013
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Showing 3 changed files with 49 additions and 49 deletions.
diff --git 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
@@ -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
@@ -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