rochefort-lab/fissa issues and pull requests

#292 - CI: Fix running doc bulid test with ghpages action

Pull Request - State: closed - Opened by scottclowe 20 days ago - 1 comment

#291 - Add cap to numpy and shapely version support, fix tests, upgrade precommit

Pull Request - State: closed - Opened by scottclowe 20 days ago - 2 comments

#290 - Bump black from 21.12b0 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 2 comments
Labels: dependencies

#289 - IndexError: list index out of range

Issue - State: open - Opened by aurallaura 11 months ago - 2 comments

#288 - ROIs segmented using ImageJ cannot be converted

Issue - State: open - Opened by just-meng 12 months ago - 16 comments

#287 - Sklearn compatibility

Pull Request - State: open - Opened by darikoneil over 1 year ago - 2 comments

#286 - Raw signals do not match suite2p raw signals for the same rois

Issue - State: open - Opened by just-meng about 2 years ago - 1 comment

#285 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago - 1 comment

#284 - REL: Add updates from release of Version 1.0.0

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment

#283 - REL: Release version 1.0.0

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 2 comments
Labels: vX.0.0 New Major Release

#282 - DOC: Add a step in release notes to map hard documentation links

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: doc

#281 - DOC: Remove elastic search from on readthedocs

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: doc

#280 - API: Rename run_fissa argument export_to_matlab -> export_to_matfile

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 2 comments

#279 - JNB: Improve basic notebooks

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 2 comments
Labels: doc

#278 - DOC: Change HTML notebook links to point to docs page

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: doc

#277 - DOC+BUG: Prevent nbconvert error missing jinja2.utils.escape

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: bug, doc

#276 - `IndexError: list index out of range` while doing experiment.separate()

Issue - State: open - Opened by GergelyTuri over 2 years ago - 3 comments

#275 - MNT: Don't tell people to use legacy mode on experiment.to_matfile

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: maint

#274 - MNT: Prevent deprecation warning about alpha removal in sklearn v1.2

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: maint

#273 - DOC: Incorporate notebooks into Sphinx docs using nbsphinx

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 2 comments
Labels: doc

#272 - MNT: Change Shapely polygons to use geoms attribute

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: maint

#271 - MNT: sklearn deprecation of alpha parameter to NMF

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: maint

#270 - DOC: Fix URL pointing to function-based notebook

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: doc

#269 - DOC: Update copyright year, 2022

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment
Labels: doc

#268 - DOC: Change functional to function-based

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 2 comments
Labels: doc

#267 - JNB: Fix typo in notebook

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 2 comments
Labels: doc

#266 - REL: Fix dependency rot of pytest-flake8 for Python 2.7

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 1 comment

#265 - Matlab output & nRegions

Issue - State: open - Opened by MikiBii over 2 years ago - 1 comment

#264 - CI: Test on Python 3.10

Pull Request - State: closed - Opened by scottclowe over 2 years ago - 2 comments
Labels: ci

#263 - CI: Remove broken pdf documentation action

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: ci

#262 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 3 years ago - 2 comments

#261 - JNB+DEV: Updates to nbqa for notebook pre-commit

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: ci

#260 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 3 years ago - 1 comment

#259 - JNB:DOC:RF: update Binder environment and move Suite2p example to different Binder

Pull Request - State: closed - Opened by swkeemink about 3 years ago - 7 comments

#258 - DEV: Bump black 21.6b0 -> 21.7b0

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 3 years ago - 1 comment

#257 - JNB:BUG: updated Suite2p notebook for Suite2p API changes

Pull Request - State: closed - Opened by swkeemink about 3 years ago - 1 comment

#256 - MNT: Decorate DataHandlerAbstract as an abstract class

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: maint

#255 - TST: Improvements to core tests

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: test

#254 - ENH: Automatically wipe output properties when parameter attributes change

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 4 comments
Labels: enhancement

#253 - DOC: Improve docstrings

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: doc

#252 - MNT: Rename loop variables

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: maint

#251 - RF: Make loop more pythonic

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: maint

#250 - REL: Add pyproject.toml

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment

#249 - API: Add to_matfile which saves all the FISSA parameters and outputs

Pull Request - State: closed - Opened by scottclowe about 3 years ago
Labels: enhancement

#248 - JNB: Improvements to notebooks

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment

#247 - MNT: Suppress warnings (again)

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: maint

#246 - API: Rename output preparation.npz -> prepared.npz

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment

#245 - ENH: Compare analysis params when loading from cache

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: enhancement

#244 - BUG: De-synchronisation in shape

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: bug

#243 - MNT: Suppress warnings

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: maint

#242 - API: Change outputs from extract func

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment

#241 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 3 years ago - 1 comment

#240 - ENH: New verbosity=2: argument description and progress bars

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: enhancement

#239 - JNB: Add verbosity control example to notebooks

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: enhancement

#238 - ENH: Verbosity improvements

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 2 comments
Labels: enhancement

#237 - API:ENH: Adding raw traces as an output for the functional interface

Pull Request - State: closed - Opened by swkeemink about 3 years ago - 2 comments

#236 - DOC: Improve docstrings

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: doc

#235 - TST: Test neuropil.separate verbosity

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: test

#234 - DEV: Update pre-commit stack and fix executable files

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment

#233 - DOC: Don't need to specify version added for params in unreleased function

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: doc

#232 - DOC: Add default values to docstrings

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: doc

#231 - API: Add maxiter, tol, maxtries, verbosity to str and repr

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment

#230 - API: Rename maxiter and maxtries to max_iter and max_tries

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 2 comments
Labels: vX.Y.0 New Minor Release

#229 - CI: Timeout tests that run too long

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: ci, test

#228 - JNB: Remove holoviews

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 2 comments

#227 - ENH: use joblib instead of multiprocessing

Pull Request - State: closed - Opened by swkeemink about 3 years ago - 5 comments

#226 - TST: Remove unnecessary caching during tests

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: test

#225 - Verbosity fixes

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 2 comments

#224 - API: Expose three separation parameters to fissa UI

Pull Request - State: closed - Opened by swkeemink about 3 years ago - 4 comments

#223 - ENH: Save analysis params to prep/sep npz cache

Pull Request - State: closed - Opened by scottclowe about 3 years ago - 1 comment
Labels: enhancement, test

#222 - TST: Explicitly test with cores set to None

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: test

#221 - TST: Don't run separate when only testing prep steps

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: test

#220 - JNB:BUG:ENH: Fix Suite2p example, and update Binder environment for Python 3.9

Pull Request - State: closed - Opened by swkeemink over 3 years ago - 8 comments

#219 - API: Rename module ROI -> polygons

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: vX.Y.0 New Minor Release

#218 - DOC: Don't mention Py 3 requirement in _parse_roi_file_py3

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: doc

#217 - DEV: Fix flake8 issues and add pre-commit

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: maint

#216 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 2 comments

#215 - STY: Change code style to black

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: maint

#214 - DOC: Fix docstrings

Pull Request - State: closed - Opened by scottclowe over 3 years ago
Labels: doc

#213 - MNT: Fix deprecated np.float

Pull Request - State: closed - Opened by scottclowe over 3 years ago
Labels: maint

#212 - MNT: Init arrays with np.empty, dtype=object instead lists of None

Pull Request - State: closed - Opened by scottclowe over 3 years ago
Labels: maint

#211 - TST:MNT: Ignore ConvergenceWarning when intentionally not converging

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: test, maint

#210 - DOC+BUG: Missing : separator on readthedocs

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: bug, doc

#209 - ENH: Add repr and str methods

Pull Request - State: closed - Opened by scottclowe over 3 years ago
Labels: enhancement

#208 - MNT: Move self.clear to top of init

Pull Request - State: closed - Opened by scottclowe over 3 years ago
Labels: maint

#207 - DOC: Add note about deltaf_result baseline

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: doc

#206 - MNT: Raise an error when both lowmemory mode and manual datahandler are set

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: maint

#205 - JNB: Don't overwrite output_folder from datetime-based folder

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment

#204 - DOC: Improve core docstrings

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: doc

#203 - RF: Change pool functions to take keyword arguments

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: maint

#202 - TST: Extend core tests

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: test

#200 - ENH: Add verbosity argument

Pull Request - State: closed - Opened by swkeemink over 3 years ago - 3 comments

#198 - API: Change the shape of deltaf_raw to have the same number of dimensions as other outputs

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: vX.Y.0 New Minor Release

#188 - RF: Refactor neuropil.separate

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: maint

#187 - RF: Migrate duplicated rois2masks code to function in roitools

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 1 comment
Labels: maint

#181 - JNB:BUG: Updated Suite2P example workflow for new Suite2p API and multiprocessing bug

Pull Request - State: closed - Opened by swkeemink over 3 years ago - 12 comments

#170 - Update the tif reading testing and implementation

Pull Request - State: closed - Opened by swkeemink over 3 years ago - 8 comments

#169 - ENH+API: Add functional interface

Pull Request - State: closed - Opened by scottclowe over 3 years ago - 12 comments
Labels: enhancement, vX.0.0 New Major Release

#156 - API: Datahandler now functions as a class

Pull Request - State: closed - Opened by swkeemink over 3 years ago - 7 comments
Labels: vX.Y.0 New Minor Release

#155 - Too much printed feedback

Issue - State: closed - Opened by swkeemink over 3 years ago - 6 comments

GitHub / rochefort-lab/fissa issues and pull requests