(chore): Add wheel build workflow (#304)

.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

src/sophios/config.json

@@ -1,7 +1,7 @@
 {
     "search_paths_cwl": {
         "global": [
-            "../workflow-inference-compiler/cwl_adapters",
+            "../sophios/cwl_adapters",
             "../image-workflows/cwl_adapters",
             "../biobb_adapters/biobb_adapters",
             "../mm-workflows/cwl_adapters"
@@ -12,7 +12,7 @@
     },
     "search_paths_wic": {
         "global": [
-            "../workflow-inference-compiler/docs/tutorials",
+            "../sophios/docs/tutorials",
             "../image-workflows/workflows",
             "../mm-workflows/examples"
         ]

src/sophios/python_cwl_adapter.py

@@ -8,7 +8,7 @@
 DRIVER_SCRIPT = '/python_cwl_driver.py'
 TYPES_SCRIPT = '/workflow_types.py'
 
-TYPES_SCRIPT_REL = '../workflow-inference-compiler/examples/scripts/workflow_types.py'
+TYPES_SCRIPT_REL = '../sophios/examples/scripts/workflow_types.py'
 
 # NOTE: VERY IMPORTANT: Since we have to programmatically import the python file in the compiler,
 # and since the act of importing it executes the entire file (i.e. including import statements),

tests/test_rest_core.py

@@ -132,7 +132,7 @@ async def receive() -> Json:
     res: Json = asyncio.run(restapi.compile_wf(req))  # call to rest api
     return res
 
-
+@pytest.mark.skip_pypi_ci
 @pytest.mark.fast
 def test_rest_core_single_node() -> None:
     """A simple single node sophios/restapi test"""
@@ -148,7 +148,7 @@ def test_rest_core_single_node() -> None:
     retval = run_cwl_local(workflow_name, 'cwltool', 'docker', False)
     assert retval == 0
 
-
+@pytest.mark.skip_pypi_ci
 def test_rest_core_single_node_bbbc() -> None:
     """A simple single node sophios/restapi test"""
     basepath = 'autogenerated'
@@ -163,7 +163,7 @@ def test_rest_core_single_node_bbbc() -> None:
     retval = run_cwl_local(workflow_name, 'cwltool', 'docker', False)
     assert retval == 0
 
-
+@pytest.mark.skip_pypi_ci
 def test_rest_core_bbbc_download_wfb() -> None:
     """A simple multi node (inline cwl) sophios/restapi test"""
     basepath = 'autogenerated'
@@ -180,6 +180,7 @@ def test_rest_core_bbbc_download_wfb() -> None:
 
 
 @pytest.mark.fast
+@pytest.mark.skip_pypi_ci
 def test_rest_core_multi_node_file() -> None:
     """A simple multi node sophios/restapi test"""
     basepath = 'autogenerated'
@@ -196,6 +197,7 @@ def test_rest_core_multi_node_file() -> None:
 
 
 @pytest.mark.fast
+@pytest.mark.skip_pypi_ci
 def test_rest_core_multi_node_inline_cwl() -> None:
     """A simple multi node (inline cwl) sophios/restapi test"""
     basepath = 'autogenerated'