fixing config and style issues #16
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Going through this now & the config might be ok. Perhaps the merge reverted a bunch of files to older style specificiations and I just need to run black again on a bunch of files. |
|
I think I've fixed the style issues. Something is confusing to me. I can look through all the file that will change with this PR to make sure it's not making other issues, but if it's not listing all files that will change, I'm not sure how to figure out which files to check. |
|
I just updated from main on my branch and it seems alright. Going to close this. |
|
Did you push your merging from main to github? I'm still seeing the same style failures in the PR. |
|
I did. Here's the style-check run: https://app.circleci.com/pipelines/github/ME-ICA/tedana/2782/workflows/cb7ba512-005e-45af-91a6-00996346fff0/jobs/23881 EDIT: Sorry, my bad! |
tsalo
added a commit
that referenced
this pull request
Apr 17, 2024
* Decision tree refactor with minimal and kundu * Fix commented-out tedana workflow * Appease the style checker * All tremble before the mighty linter * Actually fix incorrect style checker issue * Unfix another style checker error * Attempt to make Black happy, even though it does not actually say what's wrong * ran black * Added elbows to reports * fixing kundu tree and added calc_median * kundu.json added comment * kundu kappa_elbow is GTE not GT * kundu dtm matches main and minimal updated * flake8 style fixes * fixed linting * fixed report elbow warning * removed unneeded second d_table calc function * Links building decision trees to index * Adds ComponentSelector to API docs * Set language to English * Fix dead nilearn link * Add load_config and ComponentSelector to API docs * Fix mixing matrix over-save bug * Separately modularized kappa & rho elbow calcs and created liberal rho elbow (#15) * kundu tree provisionalreject to unclassified * calc_rho_elbow progress * calc_rho_elbow done * Removed calc_varex_upper_p * Removed kappa_rho_elbow tests * both decision trees running * linting fixes * Enable tedana_reclassify as console script * No errors if no xcomp but also no decide_comps (#16) * Update tedana/io.py Co-authored-by: Taylor Salo <tsalo90@gmail.com> * Appease style checker * Appease the style checker? * Force to use up to date setuptools; installation bug otherwise * Remove out of date make entry * Create functional reclassify CLI * Replace blanks with n/a * Maybe appease black * Fix typo Co-authored-by: Eneko Uruñuela <e.urunuela@bcbl.eu> * BIDSify some outputs * Appease black * Heavily revise ComponentSelector module docs * Fixing mid kappa A inconsistency (#17) * Output codes in kundu.json * fixed kappa ratio * Update tedana/selection/selection_nodes.py Co-authored-by: Joshua Teves <jbtevespro@gmail.com> * minimal tree keep kappa>2rho Co-authored-by: Joshua Teves <jbtevespro@gmail.com> * Drops 3.6 support * Remove 3.6 support from CircleCI tests * Reformat comment * Reduce line length * Update lint in Makefile * Correctly collect API submodule doc * Fix errors * Fix more sphinx * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst * Working on improving selector documentation (ME-ICA#18) * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst Co-authored-by: Joshua Teves <jbtevespro@gmail.com> * Remove manual selection * Force user to pick a tree * Fix CLI test * Revert "Force user to pick a tree" This reverts commit 4fc656f. * Revert "Fix CLI test" This reverts commit 4038336. * Make kundu default tree * Attempt to fix error * Adds input data to registry * Revert "Adds input data to registry" This reverts commit c7349bd. * Adds input registration * Appease linter * Add class template start * Add previous workflow registry into new one * Fix failure to update tags and classifications in manual * Fix missing less likely BOOLD tag * Adds more useful reporting for unused metrics * Create generated metrics * Update line terminator * Force black to run before flake8 * Updates percentile call * more doc updates * fixed meica to v2.5 in docstrings * docs building again * more updates to building decision trees * improved docs (ME-ICA#19) * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst * more doc updates * fixed meica to v2.5 in docstrings * docs building again * more updates to building decision trees Co-authored-by: Joshua Teves <jbtevespro@gmail.com> * Get rid of optional method keyword * Revert "Get rid of optional method keyword" This reverts commit e5fdec1. * Revert "Updates percentile call" This reverts commit 9d6a487. * Revert "Update line terminator" This reverts commit 8cf697c. * Autodocument ComponentSelector methods/attributes (ME-ICA#20) * Rename ComponentSelector module. * Document the ComponentSelector directly. * fixed rename of component_selector * Fixed remaining transition to component_selector (ME-ICA#21) * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst * more doc updates * fixed meica to v2.5 in docstrings * docs building again * more updates to building decision trees * fixed rename of component_selector Co-authored-by: Joshua Teves <jbtevespro@gmail.com> * more doc updates * mostly classification_output_descriptions * Fixed io API and selector API warnings * message message * key parts of docs all updated * output_file_descriptions fully updated * filled testing gaps for component_selector * Updates integration test fnames * Try a numpy fix * Try again * Remove dead code * full selector coverage (ME-ICA#23) * Add tedana_reclassify tests * Actually add test to circle workflow * Maybe actually add it * Change o to outdir * Fix noreports maybe * Fix tedort * CircleCI are you okay? * Circle if you keep this up I will switch to Actions * Revert "Circle if you keep this up I will switch to Actions" This reverts commit ad29c0d. * Maybe silence duecredit and re-trigger Circle * Try something else * Guess that wasn't legal * Switch main to _main * Add to pyproject.toml * Force it to be editable * Add references to resources package * Dispose of sanity check * Add more reclassify tests * Adaptive mask is not a bool * Add label for setup.cfg * Revert "Adaptive mask is not a bool" This reverts commit f7db360. * Add resource files * Clarify variables * Update date and weep * Fixed NoLikelyBOLDBug (ME-ICA#24) * Fixed NoLikelyBOLDBug * Updated docs for Likely BOLD * Added note for when ICA will rerun * updated message * New verbose tag for more detailed logging. * at_least_num_exist to classification_doesnt_exist * Cleaned up selector logging output * fixed debug logging * Temporarily turn on force overwrite for redo ICA * Fixed I007 divergence * calc_varex_thresh now has num_highest_var_comps * fixed linting errors * Update integration test data * Adds csv and text file reading for manual acc/rej * Add tests for CustomEncoder * Adds bibtex warning check test * Appease linter * Fix unused metrics warning * Add reclassify tests and patches to test failures * Make stylistic changes. * Remove trailing whitespace. * Spacing in io. * More minor changes. * Add custom napoleon section "Generated Files" * Replace numTrue/numFalse with n_true/n_false. * Replace ifTrue/ifFalse with if_true/if_false. * Use fill_doc. * Style fixes. * more int32 * more int32 fun * Appease linter * Fixed style issues * Add RICA to Approach section of docs * Fixed CI style check failure * DTM documentation review (ME-ICA#30) * Standardization of usage descriptions * Minor grammar edits * Minor grammar/spelling edits * Update docs/faq.rst --------- * Rename reclassify force (ME-ICA#32) * changed tedana_reclassify and force * Added default messages to CLI workflows * clean up CLI default messages * added t2smap to function from CLI * style fix * Add defaults to --help output (ME-ICA#31) * added ica_reclassify to setup.cfg * Using a more persistent cache for the testing data (ME-ICA#33) * Cleans up how testing datasets are downloaded within test_integration.py. In Main & the current JT_DTM each dataset is downloaded in a slightly different way and the five-echo data are downloaded twice. * Added `data_for_testing_info` which gives the file hash location and local directory name for each of the four files we download. All tests are updated to use this function. * The local copy of testing data will now go into the `.testing_data_cache` subdirectory * The downloaded testing data will be in separate directories from the outputs so the downloaded directories can be completely static * When `download_test_data` is called, it will first download the metadata json to see if the last updated copy on osf.io is newer than the downloaded version and will only download if osf has a newer file. Downloading the metadata will happen frequently, but it will hopefully be fast. * The logger is now used to give a warning if osf.io cannot be accessed, but it will still run using cached data * Change to TestLGR.info * Fixing high variance classification mess (ME-ICA#34) * Added dec_reclassify_high_var_comps plus * clarified diff btwn rho_kundu and _liberal thresh * Clarified docs for minimal tree * Replace versioneer with hatch (ME-ICA#35) * Update gitignore. * Delete _version.py * Adopt new packaging. * Ignore the _version.py file. * Fix CI (ME-ICA#36) * Base the cache on pyproject.toml, not setup.cfg. * Also drop use of setup.py in publishing action. * Add flake8-pyproject as a requirement. (ME-ICA#37) * Try fixing coverage. (ME-ICA#38) * Improving ica_reclassify (ME-ICA#39) * ica_reclassify docs now rendering in usage.html * moves file parsing to ica_reclassify_workflow * added error checks and tests * Ica reclassify registry fixes (ME-ICA#42) * add pandas version check >= 1.5.2 and mod behavior (ME-ICA#938) * add version check and mod behavior if pandas >= 1.5.2 to prevent error in writing csv * formatting * adding P. Molfese --------- Co-authored-by: Molfese <molfesepj@MH02217917MDI.local> * readded InputHarvester and expanduser * fixed handler base_dir path * mixing matrix file always in registry --------- Co-authored-by: Peter J. Molfese <pmolfese@gmail.com> Co-authored-by: Molfese <molfesepj@MH02217917MDI.local> * Drop Python 3.6 and 3.7 support (ME-ICA#40) * Drop Python 3.6 and 3.7 support. * line_terminator --> lineterminator * added mixm to 4echo test (ME-ICA#43) * Updating Contributor Information (ME-ICA#41) * Some contributor updates * Added doc to Marco * Added flow charts and some text (ME-ICA#44) * Added flow charts and some text * Finished flow charts and text. Co-authored-by: marco7877 <marco7877@users.noreply.github.com> --------- Co-authored-by: marco7877 <marco7877@users.noreply.github.com> * RTDfix (ME-ICA#45) * Update documentation (ME-ICA#46) * Update docs. * Update docs/building_decision_trees.rst Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com> --------- Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com> * Output docs on one page (ME-ICA#47) * Output docs on one page * added new multi-echo lectures --------- Co-authored-by: Joshua Teves <joshua.teves@nih.gov> Co-authored-by: handwerkerd <7406227+handwerkerd@users.noreply.github.com> Co-authored-by: Taylor Salo <tsalo90@gmail.com> Co-authored-by: Eneko Uruñuela <e.urunuela@bcbl.eu> Co-authored-by: handwerkerd <dan.handwerker@gmail.com> Co-authored-by: Taylor Salo <tsalo006@fiu.edu> Co-authored-by: Eneko Uruñuela <e.urunuela@icloud.com> Co-authored-by: Neha Reddy <58482773+n-reddy@users.noreply.github.com> Co-authored-by: Peter J. Molfese <pmolfese@gmail.com> Co-authored-by: Molfese <molfesepj@MH02217917MDI.local> Co-authored-by: marco7877 <marco7877@users.noreply.github.com> Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes proposed in this pull request:
.pre-commit-config.yamlandpyproject.tomlso I copied the ones from main into this branch