Ursgal - Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis
In general, contribution to Ursgal is very welcome! Feel free to fork and/or clone Ursgal. If you want to improve code or contribute new nodes/tools/algorithms please read these guidelines first. If something is unclear please contact one of the authors for help or let us know via e.g. an issue.
We are happy to include your name to the list of contributors in the README. Drop a line to one of the developers if you want to get included (and of course you actually contributed something)
First of all, please be concise and as descriptive (explicit is better than implicit :) ) as possible. It is always helpful to point out, which parts of Ursgal were changed/fixed (e.g. documentation or example scripts etc. ). In the same time, please avoid unneccesarily long messages.
The central idea of Ursgal are the unified parameters. The central parameter is tranlated, so that every engine can use it. This means, if you implement a new engine, you have to go through the (more or less) tedious process to check, if parameter X of the new engine Y is already listed in uparams.py. We require to be very thorough in this process. Having the same parameter multiple times must be avoided! There may be difficult cases, to decide if the parameter is actually the same, but by using the translation system in Ursgal, some adjusments can be made. Please refer to the documentation for further instructions and considerations on the parameters.
Code standards and conventions¶
Since this a collaborative project, you will encounter different coding styles. Despite the fact that we know that diversity is beautiful, we need to keep some common line on how to code (This list may be further extended). We generally use PEP8 style (https://www.python.org/dev/peps/pep-0008/) with the exception of E203 (whitespaces before : in order to align values in dicts). Additionally this list will give you some things to think about:
Re-think naming of variables at least twiceRe-check deleting of own debug code before sending Pull requestsRe-check own files created by nosetests and add it into ‘.gitignore’ before sending Pull requests
Test your code! Seriously, test you code! If you add new functionality or nodes at the same time provide (a) test function(s). We have already a set of tests and different files, which can be used for the test. Avoid adding new test files if possible to keep the repo small.
We use Sphinx to automatically build and format the documentation. Please keep this style in your docstrings
Other rules and cosiderations¶
None so far.
Please use the pull request to push your code to the master repository. It will be automatically tested by Travis and AppVeyor if the module is still working in unix and Windows environments. Pull requests will be discussed by the main dev team and merged into Ursgal.
If you have an issue or problem, please first search all open issues and pull request to avoid duplication of efforts. If you have a fix for the problem you may directly open a pull requets. On the other hand, if you plan to or are already working on implementing new stuff, you may also open an issue and (pre-) announce your contribution. Please tag then the issue with ‘enhancement’. In general the core team of Ursgal will also take care of crucial bugs in the main code. Since Ursgal is open source, we cannot maintain every detail and assure its compatibility and functionality (please be reminded here to test your code, seriously, test your code)
Be reminded, that in an academic world, citations are the only credit that one can hope for ;) Therefore, please make sure to properly cite every tool that you use or implement. And of course, if you use Ursagl, do not forget to cite us
Kremer, L. P. M., Leufken, J., Oyunchimeg, P., Schulze, S. and Fufezan, C. (2015): Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis , Journal of Proteome research, 15, 788-. DOI:10.1021/acs.jproteome.5b00860