osl-ephys accepts bug reports (as issues), bug fixes (as pull requests) and new features (as pull requests).
If you have found a bug or problem with the code, please open an issue on github. An EXCELLENT bug report contains the following ingredients:
- Summary A concise description of the the bug.
- Versions and context Which osl-ephys/Python versions (eg osl-ephys v0.0.1 on Python 3.9) and which operating system (eg Debian 11.2, Mac OSX 10.15 or Windows 10) are you using?
- Steps to reproduce How can we reproduce the issue? - this is very important. Please use (`) to format inline code and (```) to format code blocks
- What is the expected correct behavior? What should happen instead of this current behaviour?
- Relevant logs and/or screenshots Paste any relevant logs - please use code blocks (```) to format console output, logs, and code.
- Possible fixes If you can, link to the line of code that might be responsible for the problem, any suggestions for fixes are welcome!
Small and simple bugs might not need all this info but generally a more thorough description will help find a quick solution.
If you want to contribute new code or documentation to osl-ephys - you'll need to open a 'pull request'. There are two ways to do this.
If you have developed a new features or bug fix on your own copy (fork) of OSL and would like to contribute it back to osl-ephys. Then you can create a pull request from your forked version of osl-ephys.
Please create the pull request with the base branch set to main on osl-ephys and the compare branch set to your contribution. Please include an informative title and a clear description of what changes you have made and what the expected behaviour should be. An osl-ephys developer will review the code and potentially ask for some changes before the code can be merged into osl-ephys. In some cases a pull-request may be rejected.
If you are an osl-ephys developer, or working with the osl-ephys team, you can make contributions by creating a new branch directly on the osl-ephys repository. Please create the branch relative to main and ensure that it stays up to date with subsequent changes to the main branch. Once you're ready to start sharing the branch. You can make a pull request directly from the branch on osl-ephys. If you would like to discuss and share changes but not merge them yet - please create a 'draft pull request'.
The core developer team is @matsvanes, @woolrich, @cgohil8 and @ajquinn. A few example workflows are listed below.
To install an editable version with pip:
conda create --name osl-ephys python=3
conda activate osle
git clone [email protected]:OHBA-analysis/osl-ephys.git
cd osl-ephys
pip install -e .
To run all tests:
cd osl_ephys
pytest tests
or to run a specific test, e.g. file handling:
cd osl_ephys/tests
pytest test_file_handling.py
To build the documentation:
python setup.py build_sphinx
Compiled docs can be found in doc/build/html/index.html.
To fix an isolated problem, any contributor can.
- create a fix on a branch of oslpy:main
- create a pull request with a description and links to relevant issues.
- get feedback/approval from a core developer
- make any required changes
Once changes are made and all tests pass, a core developer can complete the merge.
For urgent and obvious fixes, a core developer can do the following:
- create a fix on a branch of oslpy:main
- create a pull request with quick description of the issue
- merge it to main themselves.
Practical overview of workflows in git - I'm assuming you're roughly familiar with adding and committing before starting this.
First clone the repo into your chosen directory
git clone https://github.com/OHBA-analysis/osl-ephys.git
cd osl-ephys
Now you're ready to start making changes.
New work must be created on a 'branch' - a separate copy of the code which allows you to make changes away from the main code.
This will create, but not switch to, a new branch
git branch mynewbranch
This will switch to an existing branch
git checkout mynewbranch
This will create and switch to a new branch.
git checkout -b mynewbranch
Once you have a branch you can start making changes and adding/committing files to your local copy.
At any point, you can run this for a quick summary of your branches state
git status
This will display your local branch, whether it is up-to-date with any remote branches, any staged/unstaged changes and any untracked files all in one place.
If someone might have changed the branch whilst you've been working (or even just to be sure), you can check for any upstream changes with:
git remote update
This will check the server for changes but won't merge any changes into your local repo so it is safe to run with work in progress. If you run git status again after a remote update - you may see that the info has changed. In particular, you may now be behind the remote branch. If you are behind the remote branch you can add those changes into your repo with:
git pull
This may create a conflict if files have changed both locally and on the remote... This can be fixed locally and finalised with a 'merge commit'
If theree are no remaining conflicts, git remote update has been run and git status shows that you are ahead of the remote - you can push your local changes with:
git push origin mynewbrach
If you're working on an idea or trying out something new, then the work can stay on a branch for as long as you need it. It is recommended to keep your branch up-to-date with main where possible. You can merge the current main branch into your branch with:
git remote update
git merge origin main
This may create conflicts... these should be fixed before carrying on with other work. Once any conflicts are fixed, your local branch is now up to date with main. You can push these changes back to your remote branch with:
git push origin mynewbranch
Once you're ready to share you're changes, or would like a place to track changes and tests, you can create a pull request. You can do this on the website by nagvigating to the branch page at
https://github.com/OHBA-analysis/osl-ephys/tree/mynewbranch
There should be a grey bar below the branch name saying 'This branch is 5 commits ahead of main' or similar. If you click the "Contribute" button in the right of this box - you can create a pull request.