✨ test Snakemake workflow with more recent Python versions #66
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added 9 commits
May 7, 2024 08:55
related to : snakemake/snakemake#2276
- check if local windows error with pandas can be reproduced in action (corr)
- add for simulated missing values - remove duplication - 🐛 do not omit last bin
if all values are higher than the default threshold, the assertion on L17 is not met. Make sure some NAs (missing values) are set.
- see if this works also with pandas 1.5.3
- for creating the latent representation, now a new DataLoader is needed.
- separate environment for PIMMS models and R based models - global environment should still work
added 5 commits
May 16, 2024 09:05
… R sesssion - only execute one job at a time in retry to see errors better
- once this passes, add ald analysis to website (for a reasonable subset of models) - maybe only showcase PIMMS models with a handful of other models
- also remove two slowest models
added 2 commits
May 22, 2024 15:42
- hide code cells for generated report - isort imports
- add some functionality required to collect source data for reporting on saved figures.
- several adaptions to slightly different design between ALD and Alzheimer data
added 3 commits
May 24, 2024 14:00
- ... and not as wildcard
- uncommon names should have a file ending specifying Snakefiles.
- execution should work, but subfolders need their own index.rst - need to adapt script for updating main index.rst See if everything runs for now.
added 3 commits
May 27, 2024 13:31
- mapping titles in sphinx (cross-referencing) otherwise does not work
- for better inspection of generated report for example
add some comments and streamline cells.
added 4 commits
May 30, 2024 11:25
- 🐛 use larger image to test tutorial on colab
added 5 commits
May 30, 2024 17:17
- rerun in codespace for inspection
- had to set model id ("model_key") as index
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test workflow against python 3.9
remove snakemake upper dependency
separate environments for R and Python in workflow
test v2 of basic Snakemake workflow, prepare switch
fix errors with mini-batches of one sample during training
added scripts using during revisions
update documentation