Merge pull request #239 from sameeul/update_docs

Minor documentation update

.github/workflows/test_and_publish_pypi.yml

@@ -30,12 +30,19 @@ jobs:
       - 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
 
       - name: Publish to PyPi
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
         run: |
-          python -m build --wheel
-          python -m build --sdist
           twine upload dist/*

README.md

@@ -6,34 +6,23 @@ Scientific computing can be difficult in practice due to various complex softwar
 
 ## Documentation
 The documentation is available on [readthedocs](https://workflow-inference-compiler.readthedocs.io/en/latest/).
-## Example Workflows
-The following repositories contain example workflows:
-
-[Molecular Modeling Workflows](https://github.com/PolusAI/mm-workflows)
-
-[Image Workflows](https://github.com/PolusAI/image-workflows)
-
-Like CWL, the compiler is general purpose and is not limited to any specific domain.
-You do not need to install these to use wic. They are completely optional.
-
-(But obviously if you're just getting started and you don't have any workflows of your own, you probably want to install at least one of them.)
 ## Quick Start
 See the [installation guide](docs/installguide.md) for more details, but:
 
 For pip users:
 
-`pip install wic` # Please read the next sentence
+`pip install sophios`
 
-Unlike conda, **pip cannot install the binary system dependencies needed to actually run most workflows!**
+In order to execute the CWL workflows that are generated by `sophios`, the `cwltool` and all of its underlying dependencies need to be present in the system. Unfortunately
+`pip` has no capability to resolve and install these dependencies. PLease refer to the `cwltool` [installation guide](https://cwltool.readthedocs.io/en/latest/#install) to prepare the system to run CWL workflows.
 
-If you want to actually run workflows, you (or your sysadmin) will have to manually install and configure additional software!
 
 For conda users / developers:
 
 See the [installation guide for developers](docs/dev/installguide.md)
 
 ```
-wic --yaml ../workflow-inference-compiler/docs/tutorials/helloworld.wic --graphviz --run_local --quiet
+sophios --yaml ../workflow-inference-compiler/docs/tutorials/helloworld.wic --graphviz --run_local --quiet
 ```
 
 The Workflow Inference Compiler is a [Domain Specific Language](https://en.wikipedia.org/wiki/Domain-specific_language) (DSL) based on the [Common Workflow Language](https://www.commonwl.org). CWL is fantastic, but explicitly constructing the Directed Acyclic Graph (DAG) associated with a non-trivial workflow is not so simple. Instead of writing raw CWL, you can write your workflows in a much simpler yml DSL. For technical reasons edge inference is far from unique, so ***`users should always check that edge inference actually produces the intended DAG`***.

docs/dev/installguide.md

@@ -92,7 +92,7 @@ You should now have the `wic` executable available in your terminal.
 To test your installation, you can run the example in README.md:
 
 ```
-wic --yaml ../workflow-inference-compiler/docs/tutorials/helloworld.wic --run_local --quiet
+sophios --yaml ../workflow-inference-compiler/docs/tutorials/helloworld.wic --run_local --quiet
 ```
 
 You can also run the automated test suite. Note that the tests are based on the workflows; if you have more workflows, the tests will take longer.

docs/installguide.md

@@ -2,11 +2,10 @@
 
 For pip users:
 
-`pip install wic` # Please read the next sentence
+`pip install sophios`
 
-Unlike conda, **pip cannot install the binary system dependencies needed to actually run most workflows!**
-
-If you want to actually run workflows, you (or your sysadmin) will have to manually install and configure additional software!
+In order to execute the CWL workflows that are generated by `sophios`, the `cwltool` and all of its underlying dependencies need to be present in the system. Unfortunately
+`pip` has no capability to resolve and install these dependencies. PLease refer to the `cwltool` [installation guide](https://cwltool.readthedocs.io/en/latest/#install) to prepare the system to run CWL workflows.
 
 For conda users / developers:
 

pyproject.toml

@@ -1,8 +1,6 @@
 # Based on https://packaging.python.org/en/latest/tutorials/packaging-projects/
 [build-system]
 requires = ["setuptools>=42", "wheel", "versioneer[toml]==0.29", "tomli"]
-# NOTE: Use upper bound of <68 for setuptools due to 2to3 error.
-# See https://stackoverflow.com/questions/72414481/error-in-anyjson-setup-command-use-2to3-is-invalid
 
 build-backend = "setuptools.build_meta"