Publish package (#237)

* update docker builds * Change package name to sophios * rename directory * Refactor tests * adding config.json back * update test * update gitattributes * Update workflows * Disable test - temporary * Update manifest file * try minimal setup.py * roll back __init__.py * update workflow * add tests back * update docs * Fix some pep8 issues * reset index.js
PolusAI · May 30, 2024 · ad81195 · ad81195
1 parent 25fb6f7
commit ad81195
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diff --git a/.gitattributes b/.gitattributes
@@ -1 +1 @@
-src/wic/_version.py export-subst
+src/sophios/_version.py export-subst
diff --git a/.github/workflows/fuzzy_compile_weekly.yml b/.github/workflows/fuzzy_compile_weekly.yml
@@ -91,20 +91,20 @@ jobs:
         # (Many of the packages conflict with pypy.)
         run: cd mm-workflows/ && pip install ".[test]" && mm-workflows --generate_schemas
 
-      - name: Generate WIC Python API Workflows (*.py -> *.wic)
+      - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd workflow-inference-compiler/ && python -c 'import wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+        run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
-      - name: Generate WIC Validation Jsonschema
+      - name: Generate Sophios Validation Jsonschema
         if: always()
-        run: cd workflow-inference-compiler/ && wic --generate_schemas
+        run: cd workflow-inference-compiler/ && 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 WIC Python API Workflows (*.py -> *.wic)
+      - name: Validate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd workflow-inference-compiler/ && python -c 'import wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+        run: cd workflow-inference-compiler/ && 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.
 

diff --git a/.github/workflows/lint_and_test.yml b/.github/workflows/lint_and_test.yml
@@ -173,20 +173,20 @@ jobs:
         # (Many of the packages conflict with pypy.)
         run: cd mm-workflows/ && pip install ".[test]" && mm-workflows --generate_schemas
 
-      - name: Generate WIC Python API Workflows (*.py -> *.wic)
+      - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd workflow-inference-compiler/ && python -c 'import wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+        run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
-      - name: Generate WIC Validation Jsonschema
+      - name: Generate Sophios Validation Jsonschema
         if: always()
-        run: cd workflow-inference-compiler/ && wic --generate_schemas
+        run: cd workflow-inference-compiler/ && 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 WIC Python API Workflows (*.py -> *.wic)
+        # 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 wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+        run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
       - name: Build Documentation
         if: always()

diff --git a/.github/workflows/lint_and_test_macos.yml b/.github/workflows/lint_and_test_macos.yml
@@ -97,20 +97,20 @@ jobs:
         # (Many of the packages conflict with pypy.)
         run: cd mm-workflows/ && pip install ".[test]" && mm-workflows --generate_schemas
 
-      - name: Generate WIC Python API Workflows (*.py -> *.wic)
+      - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd workflow-inference-compiler/ && python -c 'import wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+        run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
-      - name: Generate WIC Validation Jsonschema
+      - name: Generate Sophios Validation Jsonschema
         if: always()
-        run: cd workflow-inference-compiler/ && wic --generate_schemas
+        run: cd workflow-inference-compiler/ && 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 WIC Python API Workflows (*.py -> *.wic)
+        # 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 wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+        run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
       - name: Build Documentation
         if: always()

diff --git a/.github/workflows/run_workflows.yml b/.github/workflows/run_workflows.yml
@@ -151,20 +151,20 @@ jobs:
       # (Many of the packages conflict with pypy.)
       run: cd mm-workflows/ && pip install ".[test]" && mm-workflows --generate_schemas
 
-    - name: Generate WIC Python API Workflows (*.py -> *.wic)
+    - name: Generate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd workflow-inference-compiler/ && python -c 'import wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+      run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
-    - name: Generate WIC Validation Jsonschema
+    - name: Generate Sophios Validation Jsonschema
       if: always()
-      run: cd workflow-inference-compiler/ && wic --generate_schemas
+      run: cd workflow-inference-compiler/ && 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 WIC Python API Workflows (*.py -> *.wic)
+    - name: Validate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd workflow-inference-compiler/ && python -c 'import wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+      run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
     - name: cwl-docker-extract (i.e. recursively docker pull)
       if: always()

diff --git a/.github/workflows/run_workflows_weekly.yml b/.github/workflows/run_workflows_weekly.yml
@@ -114,20 +114,20 @@ jobs:
       # (Many of the packages conflict with pypy.)
       run: cd mm-workflows/ && pip install ".[test]" && mm-workflows --generate_schemas
 
-    - name: Generate WIC Python API Workflows (*.py -> *.wic)
+    - name: Generate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd workflow-inference-compiler/ && python -c 'import wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+      run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
-    - name: Generate WIC Validation Jsonschema
+    - name: Generate Sophios Validation Jsonschema
       if: always()
-      run: cd workflow-inference-compiler/ && wic --generate_schemas
+      run: cd workflow-inference-compiler/ && 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 WIC Python API Workflows (*.py -> *.wic)
+      # 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 wic; import wic.plugins; wic.plugins.blindly_execute_python_workflows()'
+      run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
     - name: cwl-docker-extract (i.e. recursively docker pull)
       if: always()

diff --git a/.github/workflows/test_and_publish_pypi.yml b/.github/workflows/test_and_publish_pypi.yml
@@ -19,15 +19,15 @@ jobs:
         with:
           python-version: 3.9
 
-      - name: Install wic 🔧
+      - 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 wic
+      - name: Build sophios
         run: |
           python -m pip install twine build
 
@@ -36,5 +36,6 @@ jobs:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
         run: |
-          python -m build
+          python -m build --wheel
+          python -m build --sdist
           twine upload dist/*
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,2 +1,2 @@
 include versioneer.py
-include src/wic/_version.py
+include src/sophios/_version.py
diff --git a/docs/dev/api.rst b/docs/dev/api.rst
@@ -1,66 +1,66 @@
 Developer API
 ====================================
 
-wic.ast
+sophios.ast
 ------------------------------------
-.. automodule:: wic.ast
+.. automodule:: sophios.ast
 
-wic.cli
+sophios.cli
 ------------------------------------
-.. automodule:: wic.cli
+.. automodule:: sophios.cli
 
-wic.compiler
+sophios.compiler
 ------------------------------------
-.. automodule:: wic.compiler
+.. automodule:: sophios.compiler
 
-wic.cwl_subinterpreter
+sophios.cwl_subinterpreter
 ------------------------------------
-.. automodule:: wic.cwl_subinterpreter
+.. automodule:: sophios.cwl_subinterpreter
 
-wic.inference
+sophios.inference
 ------------------------------------
-.. automodule:: wic.inference
+.. automodule:: sophios.inference
 
-wic.inlineing
+sophios.inlineing
 ------------------------------------
-.. automodule:: wic.inlineing
+.. automodule:: sophios.inlineing
 
-wic.input_output
+sophios.input_output
 ------------------------------------
-.. automodule:: wic.input_output
+.. automodule:: sophios.input_output
 
-wic.main
+sophios.main
 ------------------------------------
-.. automodule:: wic.main
+.. automodule:: sophios.main
 
-wic.plugins
+sophios.plugins
 ------------------------------------
-.. automodule:: wic.plugins
+.. automodule:: sophios.plugins
 
-wic.python_cwl_adapter
+sophios.python_cwl_adapter
 ------------------------------------
-.. automodule:: wic.python_cwl_adapter
+.. automodule:: sophios.python_cwl_adapter
 
-wic.run_local
+sophios.run_local
 ------------------------------------
-.. automodule:: wic.run_local
+.. automodule:: sophios.run_local
 
-wic.schemas.wic_schema
+sophios.schemas.wic_schema
 ------------------------------------
-.. automodule:: wic.schemas.wic_schema
+.. automodule:: sophios.schemas.wic_schema
 
-wic.utils
+sophios.utils
 ------------------------------------
-.. automodule:: wic.utils
+.. automodule:: sophios.utils
 
-wic.utils_cwl
+sophios.utils_cwl
 ------------------------------------
-.. automodule:: wic.utils_cwl
+.. automodule:: sophios.utils_cwl
 
-wic.utils_graphs
+sophios.utils_graphs
 ------------------------------------
-.. automodule:: wic.utils_graphs
+.. automodule:: sophios.utils_graphs
 
-wic.wic_types
+sophios.wic_types
 ------------------------------------
-.. automodule:: wic.wic_types
+.. automodule:: sophios.wic_types
diff --git a/examples/scripts/scatter_pyapi.py b/examples/scripts/scatter_pyapi.py
@@ -1,4 +1,4 @@
-from wic.api.pythonapi import Step, Workflow
+from sophios.api.pythonapi import Step, Workflow
 
 
 def small_workflow() -> Workflow:

diff --git a/ipycytoscape.ipynb b/ipycytoscape.ipynb
@@ -18,13 +18,13 @@
     "from pathlib import Path\n",
     "\n",
     "import wic\n",
-    "import wic.cli\n",
-    "import wic.plugins\n",
+    "import sophios.cli\n",
+    "import sophios.plugins\n",
     "\n",
-    "args = wic.cli.get_args()\n",
+    "args = sophios.cli.get_args()\n",
     "\n",
-    "tools_cwl = wic.plugins.get_tools_cwl(args.homedir)\n",
-    "yml_paths = wic.plugins.get_yml_paths(args.homedir)"
+    "tools_cwl = sophios.plugins.get_tools_cwl(args.homedir)\n",
+    "yml_paths = sophios.plugins.get_yml_paths(args.homedir)"
    ]
   },
   {
@@ -37,17 +37,17 @@
     "import networkx as nx\n",
     "import yaml\n",
     "\n",
-    "import wic.ast, wic.utils, wic.utils_graphs\n",
-    "from wic.schemas import wic_schema\n",
-    "from wic.utils_yaml import wic_loader\n",
-    "from wic.wic_types import Yaml, YamlTree, GraphReps, NodeData, GraphData, StepId\n",
+    "import sophios.ast, sophios.utils, sophios.utils_graphs\n",
+    "from sophios.schemas import wic_schema\n",
+    "from sophios.utils_yaml import wic_loader\n",
+    "from sophios.wic_types import Yaml, YamlTree, GraphReps, NodeData, GraphData, StepId\n",
     "\n",
     "yml_path_str = 'tutorial'\n",
     "yml_namespace = 'global'\n",
     "yml_path = yml_paths[yml_namespace][yml_path_str]\n",
     "\n",
     "# Generate schemas for validation and vscode IntelliSense code completion\n",
-    "yaml_stems = wic.utils.flatten([list(p) for p in yml_paths.values()])\n",
+    "yaml_stems = sophios.utils.flatten([list(p) for p in yml_paths.values()])\n",
     "validator = wic_schema.get_validator(tools_cwl, yaml_stems, write_to_disk=True)\n",
     "\n",
     "# Load the high-level yaml workflow file.\n",
@@ -58,20 +58,20 @@
     "plugin_ns = wic_tag['wic'].get('namespace', 'global')\n",
     "step_id = StepId(yml_path_str, plugin_ns)\n",
     "y_t = YamlTree(step_id, root_yaml_tree)\n",
-    "yaml_tree_raw = wic.ast.read_ast_from_disk(args.homedir, y_t, yml_paths, tools_cwl, validator)\n",
+    "yaml_tree_raw = sophios.ast.read_ast_from_disk(args.homedir, y_t, yml_paths, tools_cwl, validator)\n",
     "with open(f'autogenerated/{Path(yml_path).stem}_tree_raw.wic', mode='w', encoding='utf-8') as f:\n",
     "    f.write(yaml.dump(yaml_tree_raw.yml))\n",
-    "yaml_tree = wic.ast.merge_yml_trees(yaml_tree_raw, {}, tools_cwl)\n",
+    "yaml_tree = sophios.ast.merge_yml_trees(yaml_tree_raw, {}, tools_cwl)\n",
     "with open(f'autogenerated/{Path(yml_path).stem}_tree_merged.wic', mode='w', encoding='utf-8') as f:\n",
     "    f.write(yaml.dump(yaml_tree.yml))\n",
     "root_yml_dir_abs = Path(yml_path).parent.absolute()\n",
-    "yaml_tree = wic.ast.python_script_generate_cwl(yaml_tree, root_yml_dir_abs, tools_cwl)\n",
+    "yaml_tree = sophios.ast.python_script_generate_cwl(yaml_tree, root_yml_dir_abs, tools_cwl)\n",
     "with open(f'autogenerated/{Path(yml_path).stem}_tree_python_script.wic', mode='w', encoding='utf-8') as f:\n",
     "    f.write(yaml.dump(yaml_tree.yml))\n",
     "\n",
     "\n",
-    "yaml_forest = wic.ast.tree_to_forest(yaml_tree, tools_cwl)\n",
-    "yaml_forest_lst =  wic.utils.flatten_forest(yaml_forest)\n",
+    "yaml_forest = sophios.ast.tree_to_forest(yaml_tree, tools_cwl)\n",
+    "yaml_forest_lst =  sophios.utils.flatten_forest(yaml_forest)\n",
     "yaml_subtrees_lst = [subforest.yaml_tree for subforest in yaml_forest_lst]\n",
     "yaml_subtrees = {t.step_id.stem:t.yml for t in yaml_subtrees_lst}\n",
     "#print(yaml_subtrees.keys())\n",
@@ -82,7 +82,7 @@
     "graph_nx = nx.DiGraph()\n",
     "graphdata = GraphData(yml_path)\n",
     "graph = GraphReps(graph_gv, graph_nx, graphdata)\n",
-    "compiler_info = wic.compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, tools_cwl, True, relative_run_path=True, testing=False)\n",
+    "compiler_info = sophios.compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, tools_cwl, True, relative_run_path=True, testing=False)\n",
     "rose_tree = compiler_info.rose\n",
     "sub_node_data: NodeData = rose_tree.data\n",
     "yaml_stem = sub_node_data.name"
@@ -95,10 +95,10 @@
    "outputs": [],
    "source": [
     "gd = sub_node_data.graph.graphdata\n",
-    "gd_flat = wic.utils_graphs.flatten_graphdata(gd)\n",
+    "gd_flat = sophios.utils_graphs.flatten_graphdata(gd)\n",
     "#print(len(gd_flat.nodes))\n",
     "#print(len(gd_flat.edges))\n",
-    "json_cyto = wic.utils_graphs.graphdata_to_cytoscape(gd_flat)\n",
+    "json_cyto = sophios.utils_graphs.graphdata_to_cytoscape(gd_flat)\n",
     "#import json\n",
     "#json.dumps(json_cyto)"
    ]
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		src/wic/_version.py export-subst
		src/sophios/_version.py export-subst