develop

This chapter has info for developers.

Installation for development

The best practice is to create conda environment dedicated for the development.

conda create -y -n <dev_env> -c conda-forge python=3.10 mayavi pyqt scikit-image xrayutilities
conda activate <dev_env>
Clone the latest cohere repository from GitHub. This will include the cohere-ui directory with all of the cohere-ui content, such users scripts and example.
git clone https://github.com/advancedPhotonSource/cohere --recurse-submodules
After the package is installed checkout the Dev environment and create your branch. Then install the cohere into the environment:
cd cohere
git checkout Dev
git checkout -b <dev_branch>
pip install -e .
Go to cohere-ui directory and checkout the Dev branch and create your own branch, then run setup.py. The setup.py script modifies paths from relative to absolute in the provided example configuration.
cd cohere-ui
git checkout Dev
git checkout -b <dev_branch>
python setup.py
If planning to use GPUs, install the packages/libraries that you wish to use.
conda install -y cupy=12.2.0 -c conda-forge # if using cupy library
pip install torch # if using torch

Adding new trigger

The design allows to add a new feature in a standardized way. Typical feature is defined by a trigger and supporting parameters. The following modifications/additions need to be done to add a new feature:

  • In cohere_core/controller/phasing.py, Rec constructor, insert a new function name ending with ‘_operation’ to the self.iter_functions list in the correct order.

  • Implement the new trigger function in cohere_core/controller/phasing.py, Rec class.

  • In cohere_core/controller/phasing.py add code to set any new defaults when creating Rec object.

  • In utilities/config_verifier.py add code to verify added parameters.

Adding new sub-trigger

If the new feature will be used in a context of sub-triggers, in addition to the above steps, the following modifications/additions need to be done:

  • In cohere_core/controller/op_flow.py add entry in the sub_triggers dictionary, where key is the arbitrary assigned mnemonics, and value is the trigger name.

  • In cohere_core/controller/phasing.py, Rec.init function, create_feat_objects sub-function, add the new feature object, created the same way as shrink_wrap_obj, and other features.

  • In cohere_core/controller/phasing.py, Rec class add the trigger function. The code inside should call the trigger on the feature object with *args.

  • in cohere_core/controller/features.py add new feature class.

    The constructor factory function create should have a new lines to construct the new object.
    The feature class should be subclass of Feature and
    should have implemented create_obj function that creates sub-object(s) and
    should have defined the sub-object(s) class(es). The embedded class contains the apply_trigger function that has the trigger code. Some features can be configured to different types and therefore multiple classes can be defined.

    The easiest way to implement the feature is to copy one already implemented and modify.

Adding new algorithm

The algorithm sequence defines functions executed during modulus projection and during modulus. Adding new algorithm requires the following steps:

  • In cohere_core/controller/op_flow.py add entry in the algs dictionary, where key is the mnemonic used in algorithm_sequence, and value is the tuple defining functions, ex: ‘ER’: (‘to_reciprocal_space’, ‘modulus’, ‘to_direct_space’, ‘er’)

  • In cohere_core/controller/phasing.py, Rec constructor, insert a new function name to the self.iter_functions list in the correct order.

  • In cohere_core/controller/phasing.py, Rec class add the new algorithm function(s).

Pypi Build

For a new build change version in and setup.py files to the new version and run pypi build:

pip install .
python setup.py check
python setup.py sdist
python setup.py bdist_wheel --universal
Upload to the test server and test
pip install twine
twine upload --repository testpypi dist/*
Test in a new environment
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ cohere_core --user
Test Linux, Windows, and Mac
upload build to pypi cloud
twine upload dist/*