fix and update pytests #417
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for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
ChristopherMancuso
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Oct 5, 2025
* got old tests working * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added new tests for clustering and res params * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed save name bug for windows * change min python v3.10 and latest v3.13 * tmp remove py v3.13 * tmp keep only py v 3.10 * pipeline test now sets -fl * pipeline test now sets -sr to Mouse for cli * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated assertion to be Mouse-Combined * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add back in test for py v3.11 * add back in test for py v3.12 * change requirements to greater than * tmp remove domino from pytests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add back in test for py v3.13 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
ChristopherMancuso
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Oct 8, 2025
* small changes to some comments * changed to one-sided p-val test (#413) closes #407 * refactored default params for API and CLI (#415) * added default params to API except kwargs * renamed data_dir to file_lovc in cli * flipped behavior of autodownloader and renamed it * updated some defaults and changed parameter names * removed the quite argument * updated help in pipeline control arguments * updated some of the clustering arguments in cli * updated cluster_input to take None for kwargs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added defaults for fit in CLI * updated params for small edgelist in CLI * renamed outdir to output_dir * added defaults for save_class added ALL_SAVES * changed how output_dir of None is handled * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cleaned up some config params * updated Types in config * added cluster kwargs to config * changed what file scale is saved to * changed how logreg_kwargs called --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fixed file name issue in #404 (#416) this fixed how filenames are generated when no overwriting is selected. The new way is it look for a folders or zip files with the name and then will incriminate by one if either is already existing. * fix and update pytests (#417) * got old tests working * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added new tests for clustering and res params * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed save name bug for windows * change min python v3.10 and latest v3.13 * tmp remove py v3.13 * tmp keep only py v 3.10 * pipeline test now sets -fl * pipeline test now sets -sr to Mouse for cli * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated assertion to be Mouse-Combined * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add back in test for py v3.11 * add back in test for py v3.12 * change requirements to greater than * tmp remove domino from pytests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add back in test for py v3.13 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add documentation for clustering and saving additions (#419) * changed docs packages to be >= * updated pre-commit-config.yaml based on #303 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated tests to not be duplicated in PRs * updated tests to not be duplicated in PRs take 2 * removed safe from black in pre-commit yaml * change pre-commit back to normal * changes from rolling back reorder and black * updated the main RTD figure * added new functions to geneplexus.geneplexus page * added clust_kwargs defaults to docs * updated the main RTD figure * swapped order to have input_genes worked if added in class * updates to main RTD page * updated to how to use with R * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated RTD CLI page * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * change data_dir to file_loc in download.py * added None as file_loc option in download.py * updated some doc strings in download.py * updated download code in RTD API doc * updated RTD API page * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add logreg_kward to have defaults other than None * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed fucntions starting with _ * stopped properties from showing up * added all class methods to atribute doc strings * added to example to get all major outputs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated the examples scripts * updated the examples scripts typos * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed geneplexus CLI args from README * small README changes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * bump version 2.0.4 to 3.0.0.dev0 * add ModGenePlexus to the readme * updated message about latest RTD and main --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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this will close #352