phys2bids - 2.10.0

:tada: This release contains work from a new contributor! :tada:

Thank you, Basile (@bpinsard), for all your work!

🚀 Enhancement

• Improve performance by using numpy for trigger detection and closing matplotlib figures to avoid memleaks. #448 (@bpinsard)

🏠 Internal

• [pre-commit.ci] pre-commit autoupdate #446 (@pre-commit-ci[bot])

Authors: 2

• @pre-commit-ci[bot]
• Basile (@bpinsard)

- Python
Published by smoia almost 3 years ago

phys2bids - 2.9.0

:tada: This release contains work from a new contributor! :tada:

Thank you, Hao-Ting Wang (@htwangtw), for all your work!

🚀 Enhancement

• Add support for Spike2 files #410 (@htwangtw @smoia)

🏠 Internal

• Adopt Black and isort #327 (@tsalo @pre-commit-ci[bot] @smoia)

Authors: 4

• @pre-commit-ci[bot]
• Hao-Ting Wang (@htwangtw)
• Stefano Moia (@smoia)
• Taylor Salo (@tsalo)

- Python
Published by smoia almost 3 years ago

phys2bids - 2.8.4

:tada: This release contains work from a new contributor! :tada:

Thank you, Yaroslav Halchenko (@yarikoptic), for all your work!

🐛 Bug Fix

• Remove wrong version of exclusion strings #444 (@smoia)

⚠️ Pushed to master

• int: Add pre-commit configuration (@smoia)
• int: Fix codespell use and transfer its functionalities in setup.cfg (@smoia)
• int: Update CI environment (@smoia)
• docs: Update install requirement lines in documentation (@smoia)

📝 Documentation

• Update documentation to include GE file functionality #443 (@nw-duncan @smoia)

🏠 Internal

• Fix pre-commit configuration #445 (@smoia @pre-commit-ci[bot])
• Codespell the code, add configuration and workflow for it so no typo sneaks in #436 (@yarikoptic)

Authors: 4

• @pre-commit-ci[bot]
• Niall Duncan (@nw-duncan)
• Stefano Moia (@smoia)
• Yaroslav Halchenko (@yarikoptic)

- Python
Published by smoia almost 3 years ago

phys2bids - 2.8.3

🐛 Bug Fix

• Fix trigger index update on channel subset selection (-chsel) #433 (s.moia@bcbl.eu)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia almost 3 years ago

phys2bids - 2.8.2

🐛 Bug Fix

• Fix channel trigger variable type when the trigger is automatically detected #440 (@smoia)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia almost 3 years ago

phys2bids - 2.8.1

🐛 Bug Fix

• Fix channel selection to not remove "time channel" #439 (@smoia)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia about 3 years ago

phys2bids - 2.8.0

🚀 Enhancement

• Add GE scanner physiological file functionality #424 (@nw-duncan @smoia)

Authors: 2

• Niall Duncan (@nw-duncan)
• Stefano Moia (@smoia)

- Python
Published by smoia about 3 years ago

phys2bids - 2.7.2

🐛 Bug Fix

• fix: Update python support (@smoia)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia about 3 years ago

phys2bids - 2.7.1

⚠️ Pushed to master

• Update README.md (@smoia)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia about 3 years ago

phys2bids - 2.7.0

:tada: This release contains work from a new contributor! :tada:

Thank you, Stefano Moia (@smoia), for all your work!

🚀 Enhancement

• Fix txt reading and improve performance #432 (@smoia)

🐛 Bug Fix

• IndexError when slicing last run #415 (@sangfrois @smoia)

⚠️ Pushed to master

• Physiopylogo (@smoia)

📝 Documentation

• Fix documentation indexing #429 (@smoia)
• Fix API documentation removing deprecated interfaces and adding io. #428 (@smoia)

⚠️ Tests

• Switch CI to CircleCI, drop Windows testing #430 (@smoia)
• int: Quick linting fix [skip release] #430 (@smoia)

Authors: 2

• François Lespinasse (@sangfrois)
• Stefano Moia (@smoia)

- Python
Published by smoia about 3 years ago

phys2bids - 2.6.2

🐛 Bug Fix

• Remove breakpoint from workflow (@smoia)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia over 3 years ago

phys2bids - 2.6.1

:tada: This release contains work from a new contributor! :tada:

Thank you, Stefano Moia (@smoia), for all your work!

🐛 Bug Fix

• Rename "run" into "take" for clearer purposes and fix naming convention in multi-take overlapping #427 (@smoia)
• Fix trigger plots when trigger has different sampling than time #426 (@smoia)
• Prevent slicing from terminating program if end of last slice is above maximum timepoints. #425 (@smoia)
• Update trigger threshold guess estimation to mean of trigger channel #377 (@62442katieb)

📝 Documentation

• Update contributors list #423 (s.moia@bcbl.eu @smoia)

⚠️ Tests

• Fix testing enviroment by using apt-get install build-essential rather than apt-get install make #413 (@vinferrer)

🏠 Internal

• Add @drombas as contributor #416 (@smoia)

Authors: 4

• Katie Bottenhorn (@62442katieb)
• smoia (s.moia@bcbl.eu)
• Stefano Moia (@smoia)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia over 3 years ago

phys2bids - 2.6.0

:tada: This release contains work from a new contributor! :tada:

Thank you, Marcel Zwiers (@marcelzwiers), for all your work!

🚀 Enhancement

• Define previously unspecified Exceptions in the main workflow #406 (@marcelzwiers)

📝 Documentation

• Fix bug that would impede building the docs #399 (@eurunuela)

Authors: 2

• Eneko Uruñuela (@eurunuela)
• Marcel Zwiers (@marcelzwiers)

- Python
Published by smoia over 4 years ago

phys2bids - 2.5.0

🚀 Enhancement

• Add additional automatic detection of the trigger based on time-domain analysis #391 (@drombas)

🏠 Internal

• Upgrade to GitHub-native Dependabot #395 (@dependabot-preview[bot])

Authors: 2

• @dependabot-preview[bot]
• David Romero-Bascones (@drombas)

- Python
Published by smoia almost 5 years ago

phys2bids - 2.4.1

:tada: This release contains work from a new contributor! :tada:

Thank you, David Romero-Bascones (@drombas), for all your work!

🐛 Bug Fix

• correct chtrig check in phys2bids main workflow #390 (@drombas)

📝 Documentation

• Clarify installation instructions and tutorial #382 (@drombas)

🏠 Internal

• Provide the outcome of integration and documentation tests as downloadable artifacts from each Cirrus CI test page #384 (@vinferrer)

Authors: 2

• David Romero-Bascones (@drombas)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia almost 5 years ago

phys2bids - 2.4.0

🚀 Enhancement

• Auto-detect the trigger channel based on retrieved channel names #306 (@vinferrer @smoia)

🏠 Internal

• Testing: Use only a Windows miniconda image instead of different images for each python version #381 (@vinferrer)

Authors: 2

• Stefano Moia (@smoia)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia about 5 years ago

phys2bids - 2.3.3

:tada: This release contains work from a new contributor! :tada:

Thank you, Yaroslav Halchenko (@yarikoptic), for all your work!

🐛 Bug Fix

• Stop using powershell as windows interpreter #379 (@vinferrer)
• Update contributions and remove auto all-contribution plugin #372 (@smoia)
• Replace utils.checkinputdir() with os.path.abspath() #368 (@vinferrer)

⚠️ Tests

• Add windows CI testing #366 (@vinferrer)
• Correct BIDS validation test names #365 (@vinferrer)

🏠 Internal

• Add .mailmap to improve git shortlog -sn output #378 (@yarikoptic)
• Migrate testing to Cirrus CI #375 (@vinferrer)
• create coverage folder only in the makeenv #375 (@vinferrer)
• add the coverage folder to the shared folder #375 (@vinferrer)
• have a common folder with subfolders #375 (@vinferrer)
• add the coverage folder #375 (@vinferrer)
• add integration tests #375 (@vinferrer)
• do not pip in unittest_37 #375 (@vinferrer)
• name task properly #375 (@vinferrer)
• use as fingerprint_script #375 (@vinferrer)
• add coverage #375 (@vinferrer)
• don't use makeenv #375 (@vinferrer)
• cache name #375 (@vinferrer)
• cache enviroment folder #375 (@vinferrer)
• use full path in source #375 (@vinferrer)
• remove name option #375 (@vinferrer)
• save enviroment in working dir #375 (@vinferrer)
• add source command #375 (@vinferrer)
• create conda enviroment #375 (@vinferrer)
• add sudo comand #375 (@vinferrer)
• add python 3.7 tests #375 (@vinferrer)
• use default WD #375 (@vinferrer)
• use 3.7 from miniconda #375 (@vinferrer)
• use slim version #375 (@vinferrer)
• retry python version #375 (@vinferrer)
• change to python 3.7 container #375 (@vinferrer)
• change task name and checkout python version #375 (@vinferrer)
• check working dir #375 (@vinferrer)
• get default phys2bids install path #375 (@vinferrer)
• clone done automatically #375 (@vinferrer)
• try witout folder command #375 (@vinferrer)
• add ident #375 (@vinferrer)
• put folder in the end so it's created #375 (@vinferrer)
• set up working dir and save phys2bids folder for cache #375 (@vinferrer)
• delete some identation #375 (@vinferrer)
• rename –/tmp/src/phys2bids folder to phys2bids #375 (@vinferrer)
• eliminate env_script line #375 (@vinferrer)
• use name field #375 (@vinferrer)
• adding cirrus CI with basic enviroment #375 (@vinferrer)
• Merge branch 'master' of https://github.com/physiopy/phys2bids #375 (@vinferrer)
• delete test #375 (@vinferrer)
• add windows docker trial tests #375 (@vinferrer)

Authors: 3

• Stefano Moia (@smoia)
• Vicente Ferrer (@vinferrer)
• Yaroslav Halchenko (@yarikoptic)

- Python
Published by smoia about 5 years ago

phys2bids - 2.3.2

🐛 Bug Fix

• Add 0 before run number to multi-run trigger plot file name #369 (@vinferrer)

⚠️ Tests

• Add test to check that phys2bids output is BIDS compatible #362 (@vinferrer)
• Fix call to conda environment reference in the test configuration file #363 (@eurunuela)

Authors: 2

• Eneko Uruñuela (@eurunuela)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia about 5 years ago

phys2bids - 2.3.1

🐛 Bug Fix

• BlueprintInput deepcopies inputs at initialization #358 (@vinferrer)

Authors: 1

• Vicente Ferrer (@vinferrer)

- Python
Published by smoia about 5 years ago

phys2bids - 2.3.0

:tada: This release contains work from new contributors! :tada:

Thanks for all your work!

:heart: null@merelvdthiel

:heart: Inés Chavarría (@ineschh)

:heart: Vittorio Iacovella (@viacovella)

:heart: null@victox5

🚀 Enhancement

• Add support for MATLAB files #360 (@vinferrer)

🐛 Bug Fix

• Refactor io functions related to txt file imports. #349 (@vinferrer)
• Refactor phys2bids interfaces into single script io.py #344 (@vinferrer)
• Rename utils.writejson() to utils.write_json() to respect style conventions #346 (@merelvdthiel)
• Replace custom function utils.path_exists_or_make_it() with core function os.makedirs() #345 (@merelvdthiel)
• Rename function utils.writefile to utils.write_file to respect style conventions #343 (@ineschh)
• Remove utils.move_file() function as it is no longer used in the toolbox #342 (@viacovella)
• Updated versions required #7 (vic188m@hotmail.com @victox5)

⚠️ Pushed to master

• Update README.md (@smoia)

📝 Documentation

• Add documentation for reviewers and a checklist for PRs #315 (@smoia @RayStick)
• Add Windows installation to the documentation #329 (@vinferrer @smoia)
• Update tutorial with latest CLI options and new folder organisation (output/code/conversion) #320 (@vinferrer @RayStick)

⚠️ Tests

• Fix typo in artifact_path #331 (@tsalo)

🏠 Internal

• Add more "change type" options #347 (@smoia)

Authors: 9

• @merelvdthiel
• @victox5
• Inés Chavarría (@ineschh)
• Rachael Stickland (@RayStick)
• Stefano Moia (@smoia)
• Taylor Salo (@tsalo)
• Vicente Ferrer (@vinferrer)
• Victor (vic188m@hotmail.com)
• Vittorio Iacovella (@viacovella)

- Python
Published by smoia about 5 years ago

phys2bids - 2.2.3

🐛 Bug Fix

• Update PyYAML minimal requirements to avoid "FullLoader" attribute errors. #330 (@smoia)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia over 5 years ago

phys2bids - 2.2.2

🐛 Bug Fix

• Fix auto release workflow settings #323 (@smoia)

Authors: 1

• Stefano Moia (@smoia)

- Python
Published by smoia over 5 years ago

phys2bids - 2.2.1

🐛 Bug Fix

• Make sure we delete testing files after finishing tests #307 (@vinferrer)
• Add label colours to set auto labels #318 (@smoia)
• Reduce auto verbosity #317 (@smoia)

📝 Documentation

• Update badges in README and documentation #322 (@smoia)
• Update zenodo info #321 (@smoia)

🏠 Internal

• Setup auto release workflow #313 (@smoia)

Authors: 2

• Stefano Moia (@smoia)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia over 5 years ago

phys2bids - BIDS formatting of physiological recordings

v2.2.0 (Wed Oct 14 2020)

🚀 Enhancement

• Make trigger-based time-offset correction more generalisable (resample time before comparing it to trigger) #308 (s.moia@bcbl.eu)
• Format logger to make terminal (stdout) more human readable #312 (@vinferrer)
• Add (resampled) trigger to all output files #288 (@vinferrer)

🐛 Bug Fix

• Skip CI on all-contributors (s.moia@bcbl.eu)
• Explicitly ignore rc files and github folder (s.moia@bcbl.eu)
• Add autorc (s.moia@bcbl.eu)
• Add auto badge to documentation (s.moia@bcbl.eu)
• Add auto badge (s.moia@bcbl.eu)
• Add workflow for auto publishing (s.moia@bcbl.eu)
• Change build shield from Travis to CircleCI #297 (@eurunuela)
• Fix linting errors #294 (@eurunuela)
• Start of sampling time is now the same for all frequencies #283 (@vinferrer)
• Add travis wait command #284 (@eurunuela)
• Correct trigger channel indexing while reading AcqKnowledge files. #275 (s.moia@bcbl.eu)

⚠️ Pushed to master

• Merge branch 'int/auto' (s.moia@bcbl.eu)
• Update README.md (s.moia@bcbl.eu)
• Update ISSUETEMPLATEMEETING.md (s.moia@bcbl.eu)
• Fix message shown when skipping integration test (@eurunuela)
• Update .travis.yml (@eurunuela)
• Update setup.cfg (@eurunuela)

📝 Documentation

• Update all-contributors #310 (s.moia@bcbl.eu)
• Update documentation to reflect change from Travis CI to CircleCI #290 (@eurunuela)

⚠️ Tests

• Add tests for exceptions #291 (@eurunuela)
• Add CircleCI for automatic testing and correct integration test parameters #286 (@eurunuela)
• Switch from Travis to CircleCI for automatic testing #285 (@eurunuela)
• Add integration test for the multi run pipeline #266 (@eurunuela)

🏠 Internal

• Refactor txt.py chtrig parameter to improve code readability #305 (@vinferrer)

🖋️ Outreach

• Add link to Google Calendar #302 (@eurunuela)

Authors: 3

• Eneko Uruñuela (@eurunuela)
• Stefano Moia (@smoia)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia over 5 years ago

phys2bids - BIDS formatting of physiological recordings

v2.1.0 (Tue Jun 23 2020)

:tada: This release contains work from new contributors! :tada:

Thanks for all your work!

:heart: Taylor Salo (@tsalo)

:heart: François Lespinasse (@sangfrois)

🚀 Enhancement

• Add the possibility to split multi-run physiological recordings #206 (@sangfrois @smoia @rmarkello)
• Create folder code/conversion to store trigger and channel plots, yaml and heuristic files and the call.sh file #256 (@vinferrer @eurunuela)
• Add duecredit to handle citations #249 (@tsalo @smoia)
• Generate dataset_description.json and README.md when they do not exist and update the json file when the subject is missing #255 (@vinferrer)
• Create bids_ignore directory and redirect channels plot, trigger plot, logger output and subject log file to this directory #245 (@vinferrer @smoia)
• Generate participants.tsv if it doesn't exist or update it if subject is missing in the file #244 (@eurunuela)

🐛 Bug Fix

• Auto #236 (@smoia)
• Check branch in travisCI #235 (@smoia)

⚠️ Tests

• Change os path import and linter #260 (@smoia)
• Remove redundant integration tests #259 (@eurunuela)
• Add unit tests for participantsfile and appendlistasrow #254 (@sangfrois @eurunuela)
• Update testing to use short files. #241 (@eurunuela)

🏠 Internal

• Automate python packaging #262 (@smoia)
• Add zenodo default to improve automatic release tracking #261 (@smoia)

Authors: 9

• Eneko Uruñuela (@eurunuela)
• François Lespinasse (@sangfrois)
• Rachael Stickland (@RayStick)
• Ross Markello (@rmarkello)
• Stefano Moia (@smoia)
• Taylor Salo (@tsalo)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia over 5 years ago

phys2bids - BIDS formatting of physiological recordings v2.0.0

v2.0.0 (Mon Jun 15 2020)

:tada: This release contains work from a new contributor! :tada:

Thank you, Molly Bright (@BrightMG), for all your work!

💥 Breaking Change

• Make heuristics a simple set of "if .. elif .. else" statements and use a dictionary instead of variables. #209 (@smoia)

🚀 Enhancement

• Add BIDS-compatible automatic reformatting of units of measure #222 (@vinferrer @smoia @eurunuela)
• Add getitem and eq methods to BlueprintInput for easier slicing and comparing #213 (@smoia)
• Improve code compliance to BIDS in BlueprintOputput #189 (@smoia)

🐛 Bug Fix

• Auto #236 (@smoia)
• Check branch in travisCI #235 (@smoia)
• Print float to max 4 decimal places #212 (@RayStick)
• Enh/bids units #224 (@smoia)
• Add issue templates #220 (@smoia)

⚠️ Pushed to master

• Update ISSUETEMPLATEMEETING.md (@smoia)
• Update badges (@smoia)
• Invert Cesar & Vicente, reorganise badges (@smoia)
• Update heuristic.rst (@smoia)
• Add heuristic link (@smoia)
• Update card link (@smoia)
• Add card and mattermost channel for BrainWeb (@smoia)
• Add card for BrainWeb (@smoia)
• Updates for the BrainWeb (@smoia)

📝 Documentation

• Update reference API #231 (@rmarkello)
• Add "Why BIDS?" page to the documentation #229 (@rmarkello)
• Create LICENSE #3 (@smoia)
• Fix typos on "Best Practices for Phys Data Collection" #200 (@kristinazvolanek)
• Fix formatting on "Best Practices for Phys Data Collection" #198 (@kristinazvolanek)
• Update trigger detection tutorial #191 (@vinferrer @RayStick @smoia)
• Add section on "Best Practices for Phys Data Collection" #177 (@AyyagariA @BrightMG)
• Update viz.py docstrings and Inputs #193 (@vinferrer)
• Create README.md #4 (@smoia)

⚠️ Tests

• Fix azure pipelines non-failure bug #223 (@rmarkello)
• Add Azure Pipelines for Windows CI testing #208 (@rmarkello)

🏠 Internal

• Move bids-related functions to dedicated file #234 (@smoia)
• Remove bioread form required dependencies, ease extra modules installation #214 (@smoia @RayStick)
• Reordering of import statements in the entire phys2bids project #195 (@eurunuela)

Authors: 8

• Apoorva Ayyagari (@AyyagariA)
• Eneko Uruñuela (@eurunuela)
• Kristina Zvolanek (@kristinazvolanek)
• Molly Bright (@BrightMG)
• Rachael Stickland (@RayStick)
• Ross Markello (@rmarkello)
• Stefano Moia (@smoia)
• Vicente Ferrer (@vinferrer)

- Python
Published by smoia over 5 years ago

phys2bids - BIDS formatting of physiological recordings v1.3.0-beta

New features: - Now support AcqKnowledge files in txt format. - Features a documentation in readthedocs

- Python
Published by smoia about 6 years ago

phys2bids - BIDS formatting of physiological recordings

- Python
Published by smoia about 6 years ago

phys2bids - phys2bids: quasi-automatic BIDS formatting of physiological recordings

Now supports LabChart files through .txt files with header

- Python
Published by smoia about 6 years ago

phys2bids - phys2bids: automatic BIDS formatting of physiological recordings

- Python
Published by smoia about 6 years ago

phys2bids - v0.4.1-beta

Bug fix: changed name of main function in setup.

- Python
Published by smoia over 6 years ago

phys2bids - v0.3.0-beta

First public release of Phys2bids.

Please read the README to see what's happening there!

- Python
Published by smoia over 6 years ago