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…mics Remove hardcoded filepaths
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Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Only a single context can be processed at a time; if more contexts need to be processed, merge xomics should be wrapped in a for loop
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mumo-dev <samuelmumo@Samuels-MacBook-Pro.local>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
# Conflicts: # .github/workflows/continuous_integration.yml # main/COMO.ipynb # main/como/combine_distributions.py # main/como/create_context_specific_model.py # main/como/merge_xomics.py # main/como/proteomics/proteomics_preprocess.py # main/como/rnaseq_gen.py # pyproject.toml # tests/unit/test_data_types.py
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
- Enhanced docstrings for better clarity on function purposes. - Refactored metabolite creation logic to a dedicated function. - Improved variable naming and type hints for better type safety. - Streamlined reaction ID handling and logging for consistency. Signed-off-by: Josh Loecker <joshloecker@icloud.com>
… and documentation Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
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This contains a variety of fixes related to starting/using COMO on a fresh installation