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* More docstring edits * Mock out imports directly * Apply suggestions from code review Co-Authored-By: Sergey Venev <sergpolly@gmail.com> * Restore numpy to docs requirements * Fix trans bad pixel counting * fixed typo, added scalar extraction from array * Update cooltools/expected.py Co-Authored-By: Nezar Abdennur <nabdennur@gmail.com> * Set default zoom order to 1 Somehow default zoom order was set to 3 instead of a much better default of 1! Goes against the docstring too. * Change to new bioframe function names (#149) * updated bioframe.slice_bedframe to bioframe.bedslice in line 337 * updated bioframe.bisect_bedframe to bioframe.bedbisect in line 356 * Update license * Bump to dev version * Revert changes to bioframe functions * Pin dependency of cooltools 0.3 to bioframe 0.0 * Release v0.3.2 Co-authored-by: Nezar Abdennur <nabdennur@gmail.com> Co-authored-by: Ilya Flyamer <flyamer@gmail.com> Co-authored-by: Maksim Imakaev <mimakaev@gmail.com> Co-authored-by: Sameer Abraham <sameer.abraham0@gmail.com>
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…170) * added initial dot-calling notebook * updated notebook * updated the dots notebook * updated notebook again * before vacation notebook updates * dot-calling notebook cleanup * Remove deprecated functions * added logbin_expected * split logbin_expected into two functions * improved logbins; added persistent logbins * updated docs for logbin_expected; black * added black * expected: rename regions->supports * common.py: add assign_regions_to_bins * expected.py: bugfix; rename diag->dist * Allow regions in expected CLI (#146) * Make saddle strength work with NaNs * Allow regions in CLI for expected * Fix region_names without regions * merge latest from master to develop (#155) * More docstring edits * Mock out imports directly * Apply suggestions from code review Co-Authored-By: Sergey Venev <sergpolly@gmail.com> * Restore numpy to docs requirements * Fix trans bad pixel counting * fixed typo, added scalar extraction from array * Update cooltools/expected.py Co-Authored-By: Nezar Abdennur <nabdennur@gmail.com> * Set default zoom order to 1 Somehow default zoom order was set to 3 instead of a much better default of 1! Goes against the docstring too. * Change to new bioframe function names (#149) * updated bioframe.slice_bedframe to bioframe.bedslice in line 337 * updated bioframe.bisect_bedframe to bioframe.bedbisect in line 356 * Update license * Bump to dev version * Revert changes to bioframe functions * Pin dependency of cooltools 0.3 to bioframe 0.0 * Release v0.3.2 Co-authored-by: Nezar Abdennur <nabdennur@gmail.com> Co-authored-by: Ilya Flyamer <flyamer@gmail.com> Co-authored-by: Maksim Imakaev <mimakaev@gmail.com> Co-authored-by: Sameer Abraham <sameer.abraham0@gmail.com> * Bump again to 0.4.0-dev * Start using CliRunner for testing cli commands * Develop (#156) * Bump again to 0.4.0-dev * Start using CliRunner for testing cli commands * fixed saddle code to accept bedslice * refactored diagsum * implement bad_bins in make_diag_tables * deprecate/remove cis_/trans_expected * implement bad_bins in count_bad_pixels_per_block * fix bad_bins docstrings in diag and block-sums * changes in saddle and expected to accept new expected format * fix silly changes brought from master * now actually fixed * minimize diffs for Max, resolve new bioframe * saddles tentatively working * renamed normalize_regions * bad_bins masking for diagsum_symm * mask var name fix * added compose masking and transforms to diagsum_asymm and blocksum * column names fix in new _diagsum_asymm * more var names fixing in _diagsum_asymm * attempt to unify block/diagsum API * quick fixes, add contact-type docstrings * typo fix bad_bins_dict * change transforms default to empty dict * fixed some bugs so more tests pass * blocksum and diagsum with arbitraty regions * minor fix in diagsum_asymm * minor fix in diagsum_asymm * cis eig rewritten; added mp.Pool.map to it * allow symmetric diagsum to handle overlapping regions * fix diagsum regions casting to ndarray * docstrings regarding regions2 touchedup in expected * initial tests for newer expected * minor test expected fixes, names and typos * fixing requirements conflict: conda vs pip, travis please work * remove pytables fron conda-env in favor of tables in pip-reqs * drop conda-environment-yaml, update travis-config * travis fix: source activate instead of conda activate * typo fix * Update .travis.yml * temporarily use bioframe-develop, make travis go * Restore bioframe>=0.1.0 requirement * typo in bioframe requirement * Update formatting * Update formatting * Install bioframe from github develop branch * Fix eigdecomp and saddle to work with new bioframe * Formatting Co-authored-by: Sergey Venev <sergpolly@gmail.com> Co-authored-by: Nezar <nabdennur@gmail.com> Co-authored-by: Anton Goloborodko <goloborodko.anton@gmail.com> Co-authored-by: Ilya Flyamer <flyamer@gmail.com> Co-authored-by: Sameer Abraham <sameer.abraham0@gmail.com> Co-authored-by: sergpolly <sergpolly@pop-os.localdomain>
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eigdecomp.cooler_cis_eig was throwing errors because of the new names of the bioframe functions bedslice and bedbisect in the latest version. In the current master branch, cool_cis_eig tries to call slice_bedframe and bisect_bedframe and hence throws errors.
I've changed the names of the functions being called and resolved the errors.