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CLEX CMS Utility Library


To add to the repository, first create your own fork on Github at, then download new forked repository (either to Raijin or your own computer)

Create and activate a new conda environment so you can work on the library without affecting your other environments, then install the library in development mode using pip:

# # On Raijin/VDI only:
# module use /g/data3/hh5/public/modules
# module load conda

# This creates an environment named 'coecms'
conda env create -f conda/dev-environment.yml

conda activate coecms

# '-e' installs in editable mode
pip install -e .

You can then run the tests to confirm everything is working correctly using:


Making Changes

Changes need to be done in a new branch as a pull request:

git checkout -b my-branch

# Make changes...

git push --set-upstream origin my-branch

Then make a pull request at

Please make sure code changes include tests and documentation

Changes must be reviewed by someone in the CMS team before they are committed to master

Adding Dependencies

To add a dependency, you need to edit two files:

  • conda/meta.yaml: This has the conda package names of dependencies. They might not be the same as the actual Python library names. This is used by conda build to create the conda package. Add dependencies to the requirements: run: list.
  • This has the Python name of dependencies. This is used if you pip install the package locally for testing. Add dependencies to the install_requires list.

Creating new versions

To create a new version of the library, use the Github interface at

Versions should be named like v1.2.3, using semantic versioning.

The Python and Conda packages will automatically set their version based on the tag that Github creates (you may need to git fetch the tag first)

To upload a new version to conda, check out the tag (e.g. git checkout v1.2.3) then run:

conda build --user coecms --python=3.7 ./conda

setting the python version as desired (you will need to be a member of the coecms group on to do this)