Merge branch 'main' into joss-paper

README.md

@@ -75,3 +75,27 @@ When using pymgpipe please cite-
 
 Baldini, F., Heinken, A., Heirendt, L., Magnusdottir, S., Fleming, R. M. T., & Thiele, I. (2019). *The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.* Bioinformatics (Oxford, England), 35(13), 2332–2334. https://doi.org/10.1093/bioinformatics/bty941
 
+### Contributing
+
+We warmly welcome and appreciate contributions from everyone. There are several ways you can contribute:
+
+- Reporting Bugs: If you find a bug, please create a new issue on our GitHub page. Be sure to include as much information as possible so we can reproduce and fix the bug. The more detail you provide, the better.
+- Code Contributions: If you'd like to contribute code, great! Please fork this repository, make your changes in a separate branch, and then submit a pull request. We'll review your changes and discuss any necessary modifications or improvements before merging.
+
+Here are some general guidelines for code contributions:
+
+1. Fork the repo and create your branch from the master.
+2. If you've added code, add tests.
+3. Ensure the test suite passes.
+4. Issue that pull request!
+
+### Reporting Issues
+
+Issues should be reported using the [GitHub issue tracker](https://github.com/korem-lab/pymgpipe/issues). Please check the existing issues to avoid duplicates. When reporting an issue, please provide as much detail as possible about how to reproduce the problem, including the following information:
+
+- Operating system and version
+- Details of the problem, including any error messages and screenshots if possible
+
+Thank you for your contributions!
+
+Copyright 2023 The Trustees of Columbia University in the City of New York. See [LICENSE](https://github.com/korem-lab/pymgpipe/blob/main/LICENSE) for additional details.

setup.py

@@ -31,8 +31,7 @@
             "resources/diets/*.txt",
             "resources/models/*",
             "resources/problems/*",
-            "resources/miniTaxa/*",
-            "resources/.VERSION"
+            "resources/miniTaxa/*"
         ],
     },
     project_urls={