Merge pull request #313 from sameeul/v022

PolusAI · Jan 10, 2025 · 8c9be32 · 8c9be32
2 parents 7c1708d + f288370
commit 8c9be32
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diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
@@ -0,0 +1,39 @@
+name: Build and Test Wheel
+
+on:
+  pull_request: 
+  workflow_dispatch:
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install sophios 🔧
+        run: |
+          pip install .[test]
+      - name: Test with pytest
+        run: |
+          python -m pytest -k test_cwl_docker_extract
+          python -m pytest -m "not skip_pypi_ci" -vv
+
+      - name: Build sophios
+        run: |
+          python -m pip install twine build
+          python -m build --wheel
+          python -m build --sdist
+
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v3
+        with:
+            name: sophios-wheels
+            path: dist/*
+            retention-days: 1
diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
@@ -23,8 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         # NOTE: Use a matrix (instead of dockerBuild.sh) for parallelism
-        dockerfile: [amazon, debian, fedora, redhat,
-                     amazon_pypy, debian_pypy, fedora_pypy, redhat_pypy]
+        dockerfile: [amazon, debian, fedora, redhat]
     runs-on: [ubuntu-latest]
 
     steps:

diff --git a/.github/workflows/docker_build_plugins.yml b/.github/workflows/docker_build_plugins.yml
@@ -6,6 +6,7 @@ on:
   schedule:
   # Run it every Tuesday at midnight.
     - cron: '0 0 * * 2'
+  workflow_dispatch:
 
 permissions:
   actions: read

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
-          ref: master
-          path: workflow-inference-compiler
+          repository: ${{ github.repository_owner }}/sophios
+          ref: ${{ inputs.wic_ref }}
+          path: sophios
 
       - name: Checkout biobb_adapters
         if: always()
@@ -56,31 +56,31 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: ${{ github.repository_owner }}/mm-workflows
-          ref: main
+          ref: ${{ inputs.mm-workflows_ref }}
           path: mm-workflows
 
       - name: Checkout image-workflows
         if: always()
         uses: actions/checkout@v3
         with:
           repository: ${{ github.repository_owner }}/image-workflows
-          ref: main
+          ref: ${{ inputs.image-workflows_ref }}
           path: image-workflows
 
       - name: Setup miniforge (linux, macos)
         if: runner.os != 'Windows'
         uses: conda-incubator/setup-miniconda@v3.0.1
         with:
-          miniforge-variant: Miniforge-pypy3
-          miniforge-version: 24.7.1-0
-          environment-file: workflow-inference-compiler/install/system_deps.yml
+          miniforge-variant: Miniforge3
+          miniforge-version: 24.7.1-2
+          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.yml b/.github/workflows/lint_and_test.yml
@@ -90,13 +90,13 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - name: Checkout workflow-inference-compiler
+      - name: Checkout sophios
         if: always()
         uses: actions/checkout@v3
         with:
-          repository: ${{ inputs.wic_owner }}/workflow-inference-compiler
+          repository: ${{ inputs.wic_owner }}/sophios
           ref: ${{ inputs.wic_ref }}
-          path: workflow-inference-compiler
+          path: sophios
 
       - name: Checkout biobb_adapters
         if: always()
@@ -127,19 +127,19 @@ jobs:
       # NOTE: pypy actually decreases performance for lint_and_test.yml (by a factor of ~2)
       # - 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: Append pypy to conda environment files
       #   if: runner.os == 'Windows'
-      #   run: cd workflow-inference-compiler/install/ && echo "  - pypy" >> system_deps_windows.yml
+      #   run: cd sophios/install/ && echo "  - pypy" >> system_deps_windows.yml
 
       - name: Setup miniforge (linux, macos)
         if: runner.os != 'Windows'
         uses: conda-incubator/setup-miniconda@v3.0.1
         with:
-          miniforge-variant: Miniforge-pypy3
-          miniforge-version: 24.7.1-0
-          environment-file: workflow-inference-compiler/install/system_deps.yml
+          miniforge-variant: Miniforge3
+          miniforge-version: 24.7.1-2
+          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
@@ -148,21 +148,21 @@ jobs:
         if: runner.os == 'Windows'
         uses: conda-incubator/setup-miniconda@v3.0.1
         with:
-          miniforge-variant: Miniforge-pypy3
-          miniforge-version: 24.7.1-0
-          environment-file: workflow-inference-compiler/install/system_deps_windows.yml
+          miniforge-variant: Miniforge3
+          miniforge-version: 24.7.1-2
+          environment-file: sophios/install/system_deps_windows.yml
           activate-environment: wic
           channels: conda-forge
           python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11
 
       - 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()
@@ -175,39 +175,39 @@ 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
@@ -216,13 +216,13 @@ 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
 
@@ -231,7 +231,7 @@ jobs:
         # Avoid Windows and macOS due to 2X and 10X minute multipliers.
         # https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#minute-multipliers
         # Also, cannot run on Windows (natively) yet
-        run: cd workflow-inference-compiler/ && pytest -k test_scattering_scaling
+        run: cd sophios/ && pytest -k test_scattering_scaling
 
       # NOTE: The steps below are for repository_dispatch only. For all other steps, please insert above
       # this comment.
@@ -269,7 +269,7 @@ jobs:
         # https://github.com/actions/runner/issues/834#issuecomment-907096707
         # Use inputs.sender_repo to reply the original sender.
         if: always()
-        uses: ./workflow-inference-compiler/.github/my_actions/reply_sender/ # Must start with ./
+        uses: ./sophios/.github/my_actions/reply_sender/ # Must start with ./
         with:
           github_repository: ${{ github.repository }}
           event_type: ${{ inputs.event_type }}