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Minimal Snakemake workflow#1

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Commits on Oct 7, 2024

• Add classes to read and write folders and the beginning of a possible pipeline

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Commits on Nov 5, 2024

• Update dependencies

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• Add logging and usage of pattern for glob

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• Pre-commit hook modifications

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• Fix error with logging filepath

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• WIP on filename

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• Improve log name

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• Merge branch 'dev' of github.com:neuroinformatics-unit/calcium-imaging-automation into dev

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• Be stricter on allowed sessions

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Commits on Nov 8, 2024

• Change usage of file pattern in reader

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• Change folder

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• Merge branch 'dev' of github.com:neuroinformatics-unit/calcium-imaging-automation into dev

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• Fix error related to file reading patterns

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• Add script useful to launch debugging

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• Add minimal wandb implementation

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• WIP: saving images 🐛

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Commits on Nov 11, 2024

• Fix image save bug

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• Move from wandb to mlflow

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• Store mlflow folder differently, link artifacts

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• Update manifest

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• Remove test script

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• Add first group of docstrings

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Commits on Nov 12, 2024

• WIP: nested runs, 🐛 on artifacts saving

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Commits on Nov 18, 2024

• Add dependencies

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• Refactoring

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Commits on Nov 26, 2024

• Use with real data and add integration with submitit

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• Reduce min sessions

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Commits on Nov 28, 2024

• Bye bye mlflow 👋

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Commits on Dec 3, 2024

• Add basic snakemake script (test)

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Commits on Dec 4, 2024

• Add working snakemake rule for preprocessing

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• Run datasets on the cluster ✨

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• Update debugging script

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• Move snakefile in workflow folder

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• Remove outdated scripts

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• WIP: changing script 🐛

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Commits on Dec 10, 2024

• Make via snakemake what all the other classes were doing

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• Update pyproject.toml

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Commits on Dec 11, 2024

• Generate report with datavzrd

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Commits on Jan 24, 2025

• Include all code necessary for end-to-end analysis - but it's messy

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