merge components of scgpt into main #813
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scGPT integration preproc module
* add script to download scgpt test resources * Update resources_test_scripts/scgpt.sh Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> * add drive folders containing data and model * chmod +x --------- Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
merge scgpt-dev into scgpt
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* add module for scgpt padding and tokenization * remove base requirement * update changelog * update component name * expand unit tests, update script with loggers and todo * fix unit tests * remove annotation script * run tests with subsampled data * use specific model input files instead of directory * remove unused binning script * update layer names and handling * Add script to download scgpt test resources (#750) * add script to download scgpt test resources * Update resources_test_scripts/scgpt.sh Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> * add drive folders containing data and model * chmod +x --------- Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> * preproc script * preproc script * tokenize and pad script * tokenize and pad script * embedding script * test resourcers and evaluation script * cross check gene set * Fix retag for viash-hub not using correct namespace separator (#745) * CI - Build: Fix second occurance of namespace separator (#746) * script to download scgpt test data * remove test resources script * pad_tokenize module * updat image * remove test resources, update inputs * use pytorch image * remove integration component * remove nvidia reqs * remove load_model option * adjust preprocessing script * add scgpt full preproc module * integration submodule * integration submodule and add normalize_total flag * add params * update scanpy version * remove branch irrelevant scripts * update output handling * update unit tests, add output compression * update key name input output * fix test * update unit tests * Update CHANGELOG.md Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> * add pars to logging --------- Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
scGPT embedding component
* base script and config added * config extended + logger set up + tests in progress * config working + script improved + tests in progress * exception handling, extended tests * extended tests + better logging * changelog entry added * test resource path in config fixed * python test setup added to config * PR comments fixed * updated to use subset data * remove batch id column logic * update authors * resources, tests and dependencies fixes * update key name input output * update key name input output * update var gene names * update config * compression param added + minor fixes --------- Co-authored-by: dorien-er <roosen.dorien@gmail.com> Co-authored-by: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
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components have already been reviewed on scGPT branch: