remove reference to pypy in CI GHA and remove deadcode needed for python 3.9 and move all GHA to >=3.11 (PolusAI#338)

vjaganat90 · web-flow · commit eb8a93f3fd77 · 2025-06-13T10:43:54.000-04:00
diff --git a/.github/workflows/fuzzy_compile_weekly.yml b/.github/workflows/fuzzy_compile_weekly.yml
@@ -76,7 +76,7 @@ jobs:
           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
+          python-version: "3.11.*"
 
       - name: Install Sophios
         if: always()
@@ -97,7 +97,7 @@ jobs:
 
       - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd sophios/ && pytest -k test_compile_python_workflows 
+        run: cd sophios/ && pytest -k test_compile_python_workflows
 
       - name: Generate Sophios Validation Jsonschema
         if: always()
diff --git a/.github/workflows/lint_and_test.yml b/.github/workflows/lint_and_test.yml
@@ -124,15 +124,7 @@ jobs:
           ref: ${{ inputs.image-workflows_ref }}
           path: image-workflows
 
-      # 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 sophios/install/ && echo "  - pypy" >> system_deps.yml
-
-      # - name: Append pypy to conda environment files
-      #   if: runner.os == 'Windows'
-      #   run: cd sophios/install/ && echo "  - pypy" >> system_deps_windows.yml
-
+      # Completely moving away from pypy
       - name: Setup miniforge (linux, macos)
         if: runner.os != 'Windows'
         uses: conda-incubator/setup-miniconda@v3.0.1
@@ -142,7 +134,7 @@ jobs:
           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
+          python-version: "3.11.*"
 
       - name: Setup miniforge (windows)
         if: runner.os == 'Windows'
@@ -153,7 +145,7 @@ jobs:
           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
+          python-version: "3.11.*"
 
       - name: ShellCheck Script Quality
         if: always()
diff --git a/.github/workflows/lint_and_test_macos.yml b/.github/workflows/lint_and_test_macos.yml
@@ -77,7 +77,7 @@ jobs:
           activate-environment: wic
           use-mamba: true
           channels: conda-forge
-          python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11
+          python-version: "3.11.*"
 
       - name: ShellCheck Script Quality
         if: always()
diff --git a/.github/workflows/run_workflows.yml b/.github/workflows/run_workflows.yml
@@ -106,10 +106,7 @@ jobs:
       run: rm -rf "/home/$(whoami)/wic/" && rm -rf "/home/$(whoami)/.toil/"
       # For self-hosted runners, make sure we use new global config settings
 
-    # Using pypy increases performance / decreases cwltool runtime by about a minute.
-    - name: Append pypy to conda environment files
-      if: runner.os != 'Windows'
-      run: cd sophios/install/ && echo "  - pypy" >> system_deps.yml
+    # Completely moving away from pypy
 
     - name: Remove old mamba environment
       if: always()
@@ -131,7 +128,7 @@ jobs:
         environment-file: sophios/install/system_deps.yml
         activate-environment: wic_github_actions
         channels: conda-forge
-        python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11
+        python-version: "3.11.*"
 
     # - name: Docker pull
     #   if: always()
diff --git a/.github/workflows/run_workflows_weekly.yml b/.github/workflows/run_workflows_weekly.yml
@@ -74,27 +74,19 @@ jobs:
       if: always()
       run: rm -rf "/home/$(whoami)/miniconda3/envs/wic_github_actions/"
       # For self-hosted runners, make sure we install into a new mamba environment
-
-    # Toil is currently incompatible with pypy
-    # - name: Append pypy to conda environment files
-    #   if: runner.os != 'Windows'
-    #   run: cd sophios/install/ && echo "  - pypy" >> system_deps.yml
+      # Completely moving away from pypy
 
     - name: Setup miniforge (linux, macos)
       if: always()
       uses: conda-incubator/setup-miniconda@v3.0.1
       with:
-        miniforge-variant: Miniforge3  # NOT Miniforge-pypy3
-        # Toil is (currently) incompatible with pypy. Miniforge-pypy3
-        # installs pypy in the base environment (only). Although we are using
-        # another environment, better to avoid the problem altogether by
-        # not using Miniforge-pypy3
+        miniforge-variant: Miniforge3
         miniforge-version: 24.7.1-2
         environment-file: sophios/install/system_deps.yml
         activate-environment: wic_github_actions
         use-mamba: true
         channels: conda-forge
-        python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11
+        python-version: "3.11.*"
 
     # - name: Docker pull
     #   if: always()
diff --git a/.github/workflows/test_and_publish_pypi.yml b/.github/workflows/test_and_publish_pypi.yml
@@ -17,7 +17,7 @@ jobs:
       - name: Set up Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Remove old global config
         if: always()
diff --git a/docker/dockerBuild.sh b/docker/dockerBuild.sh
@@ -6,13 +6,8 @@
 # cwl-utils library to recursively search for the dockerPull: tags within each workflow.
 
 sudo docker build --no-cache --pull -f Dockerfile_debian -t polusai/wic_debian ..
-sudo docker build --no-cache --pull -f Dockerfile_debian_pypy -t polusai/wic_debian_pypy ..
 sudo docker build --no-cache --pull -f Dockerfile_ubuntu -t polusai/wic_ubuntu ..
-sudo docker build --no-cache --pull -f Dockerfile_ubuntu_pypy -t polusai/wic_ubuntu_pypy ..
 
 sudo docker build --no-cache --pull -f Dockerfile_fedora -t polusai/wic_fedora ..
-sudo docker build --no-cache --pull -f Dockerfile_fedora_pypy -t polusai/wic_fedora_pypy ..
 sudo docker build --no-cache --pull -f Dockerfile_redhat -t polusai/wic_redhat ..
-sudo docker build --no-cache --pull -f Dockerfile_redhat_pypy -t polusai/wic_redhat_pypy ..
 sudo docker build --no-cache --pull -f Dockerfile_amazon -t polusai/wic_amazon ..
-sudo docker build --no-cache --pull -f Dockerfile_amazon_pypy -t polusai/wic_amazon_pypy ..
diff --git a/install/pypy.yml b/install/pypy.yml
diff --git a/install/pypy_docker_deps.yml b/install/pypy_docker_deps.yml
diff --git a/install/system_deps.yml b/install/system_deps.yml
@@ -3,8 +3,7 @@ channels:
   - defaults
 
 dependencies:
-# Keep the python constraint in case we want to install pypy.
-  - "python<3.11"
+  - "python>=3.11"
 # NOTE: cwltool needs nodejs for InlineJavascriptRequirement
   - nodejs
   - graphviz
@@ -40,5 +39,5 @@ dependencies:
 # Needs binary PyQt5 dependencies.
   - kubernetes-helm
   - zstandard
-# Needed for orjson wheels
-  - orjson
+# # Needed for orjson wheels
+#   - orjson
diff --git a/install/system_deps_windows.yml b/install/system_deps_windows.yml
@@ -3,8 +3,7 @@ channels:
   - defaults
 
 dependencies:
-# Keep the python constraint in case we want to install pypy.
-  - "python<3.11"
+  - "python>=3.11"
 # NOTE: cwltool needs nodejs for InlineJavascriptRequirement
   - nodejs
   - graphviz
@@ -35,7 +34,7 @@ dependencies:
 # Similarly, toil[cwl] depends on ruamel.yaml.clib for performance.
 # Install it with conda/mamba here.
   - ruamel.yaml.clib
-# Simiarly, cryptography needs to build binary wheels
+# Similarly, cryptography needs to build binary wheels
   - cryptography
 # Needs binary PyQt5 dependencies.
   - kubernetes-helm
diff --git a/pyproject.toml b/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 dependencies = [
     # NOTE: This 'graphviz' refers to the python bindings to the underlying
     # system binary graphviz package (i.e. the `dot` executable) which we need to
diff --git a/src/sophios/ast.py b/src/sophios/ast.py
@@ -52,10 +52,7 @@ def read_ast_from_disk(homedir: str,
         # Do not display a nasty stack trace to the user; hide it in a file.
         with open(f'validation_{yaml_path.stem}.txt', mode='w', encoding='utf-8') as f:
             # https://mypy.readthedocs.io/en/stable/common_issues.html#python-version-and-system-platform-checks
-            if sys.version_info >= (3, 10):
-                traceback.print_exception(type(e), value=e, tb=None, file=f)
-            else:
-                traceback.print_exception(etype=type(e), value=e, tb=None, file=f)
+            traceback.print_exception(type(e), value=e, tb=None, file=f)
         sys.exit(1)
 
     wic = {'wic': yaml_tree.get('wic', {})}
diff --git a/src/sophios/main.py b/src/sophios/main.py
@@ -158,10 +158,7 @@ def main() -> None:
             # Do not display a nasty stack trace to the user; hide it in a file.
             with open(f'error_{yaml_stem}.txt', mode='w', encoding='utf-8') as f:
                 # https://mypy.readthedocs.io/en/stable/common_issues.html#python-version-and-system-platform-checks
-                if sys.version_info >= (3, 10):
-                    traceback.print_exception(type(e), value=e, tb=None, file=f)
-                else:
-                    traceback.print_exception(etype=type(e), value=e, tb=None, file=f)
+                traceback.print_exception(type(e), value=e, tb=None, file=f)
             sys.exit(1)
         rose_tree = compiler_info.rose
     rose_tree = plugins.cwl_prepend_dockerFile_include_path_rosetree(rose_tree)
diff --git a/src/sophios/run_local.py b/src/sophios/run_local.py
@@ -220,10 +220,7 @@ def run_local(args: argparse.Namespace, rose_tree: RoseTree, cachedir: Optional[
                 # Do not display a nasty stack trace to the user; hide it in a file.
                 with open(f'error_{yaml_stem}.txt', mode='w', encoding='utf-8') as f:
                     # https://mypy.readthedocs.io/en/stable/common_issues.html#python-version-and-system-platform-checks
-                    if sys.version_info >= (3, 10):
-                        traceback.print_exception(type(e), value=e, tb=None, file=f)
-                    else:
-                        traceback.print_exception(etype=type(e), value=e, tb=None, file=f)
+                    traceback.print_exception(type(e), value=e, tb=None, file=f)
                 if not cachedir:  # if running on CI
                     print(e)
 
@@ -279,10 +276,7 @@ def run_local(args: argparse.Namespace, rose_tree: RoseTree, cachedir: Optional[
                 print(f'See error_{yaml_stem}.txt for detailed technical information.')
                 # Do not display a nasty stack trace to the user; hide it in a file.
                 with open(f'error_{yaml_stem}.txt', mode='w', encoding='utf-8') as f:
-                    if sys.version_info >= (3, 10):
-                        traceback.print_exception(type(e), value=e, tb=None, file=f)
-                    else:
-                        traceback.print_exception(etype=type(e), value=e, tb=None, file=f)
+                    traceback.print_exception(type(e), value=e, tb=None, file=f)
                 if not cachedir:  # if running on CI
                     print(e)
 
diff --git a/tests/test_compile_python_workflows.py b/tests/test_compile_python_workflows.py
@@ -65,9 +65,6 @@ def test_compile_python_workflows() -> None:
 
         except Exception as e:
             any_import_errors = True
-            if sys.version_info >= (3, 10):
-                traceback.print_exception(type(e), value=e, tb=None)
-            else:
-                traceback.print_exception(etype=type(e), value=e, tb=None)
+            traceback.print_exception(type(e), value=e, tb=None)
     if any_import_errors:
         sys.exit(1)  # Make sure the CI fails
