v4.1.0

🚀 Enhancement

• updated nidm model to collections of entities #378 (@dbkeator)

Authors: 1

• David Keator (@dbkeator)

v4.0.0

💥 Breaking Change

• gh-actions: Bump codespell-project/actions-codespell from 1 to 2 #375 (@dependabot[bot])

🐛 Bug Fix

• Do not try to upload nonexisting junit artifacts #372 (@yarikoptic)
• Use RST links in readme #303 (@surchs @yarikoptic)
• Add 3.10 and 3.11 into testing #324 (@yarikoptic)
• codespell: action, config + fixes #321 (@yarikoptic)

⚠️ Pushed to master

• Travis is no longer used (@yarikoptic)

🏠 Internal

• Refactor printing the same text to both stdout and a file #376 (@jwodder)
• Set up auto #346 (@jwodder)
• Use versioningit #374 (@jwodder)
• Assorted minor code improvements #369 (@jwodder)
• Open all text files with UTF-8 encoding #373 (@jwodder)
• Pare down giant comment blocks that largely do what Git already does #363 (@jwodder)
• Improve string formatting syntax #364 (@jwodder)
• Don't list object as a base class #365 (@jwodder)
• Use Python 3-style super() calls #366 (@jwodder)
• Remove redundant imports #367 (@jwodder)
• Clean up Docker-related files #351 (@jwodder)
• Enable building docs locally via tox -e docs #357 (@jwodder)
• Replace uses of urllib.request with requests #359 (@jwodder)
• Delete profiler.py #362 (@jwodder)
• Add .coverage to .gitignore #354 (@jwodder)
• Shorten overly-long lines of punctuation #345 (@jwodder)
• Fix __version__ import #353 (@jwodder)
• Update workflow actions versions and keep them up to date with Dependabot #350 (@jwodder)
• Remove fallback to Python 2 import #348 (@jwodder)
• Add testing via tox #334 (@jwodder)
• Remove Python 2-specific __future__ imports #335 (@jwodder)
• Remove uses of six #336 (@jwodder)
• Prune README.md files from code directories #338 (@jwodder)
• Use a src/ layout #332 (@jwodder)
• Run linting as part of CI #333 (@jwodder)
• Run tests in CI on pushes & merges to master #331 (@jwodder)
• Use build in pythonpublish.yml #330 (@jwodder)
• Add & apply pre-commit and linting #329 (@jwodder)
• docs/build/ should not be committed #327 (@jwodder)
• Update Python packaging #326 (@jwodder)
• "Splitted" is not a word #328 (@jwodder)

📝 Documentation

• Use .readthedocs.yaml file to install pynidm in RTD environment #370 (@jwodder)
• Clean up README.rst markup #340 (@jwodder)

🧪 Tests

• Clean up Click testing #352 (@jwodder)
• Write test temp files to temp directories #343 (@jwodder)
• Measure test coverage #344 (@jwodder)
• Make pytest error on warnings #341 (@jwodder)
• Replace tmpdir fixture with tmp_path #339 (@jwodder)

🔩 Dependency Updates

• Remove practically-unused joblib #360 (@jwodder)
• Clean up install requirements #347 (@jwodder)
• Replace simplejson with stdlib json #337 (@jwodder)

Authors: 4

• @dependabot[bot]
• John T. Wodder II (@jwodder)
• Sebastian Urchs (@surchs)
• Yaroslav Halchenko (@yarikoptic)

PyNIDM tools v3.9.8 (dev)

Includes various changes to nidm_linreg.py tool and query updates.

PyNIDM tools v3.9.7 (dev)

Fixed bug with Query.py function that wasn't returning the source variable name after we changed the property to sourceVariable from source_variable to be more consistent with ReproSchemas. This resulted in tests failing and nidm_linreg.py failing. This update fixes those items.

PyNIDM tools v3.9.6 (dev)

• Fixed bug in bidsmri2nidm.py where phenotype files with identical variable names to participants.tsv file caused collision.
• Added version function so pynidm version prints version of pynidm toolkit (pynidm version)

PyNIDM tools v3.9.5 (dev)

• Updated Utils.py/read_nidm to account for missing tuple with label of isAbout concept associations after reading existing NIDM document.
• Also updated nidm2bids to save out participants.json file with annotations from NIDM source document

PyNIDM tools v3.9.4 (dev)

• Updated read_nidm function to accommodate data elements being of types nidm:DataElement, nidm:PersonalDataElement, or nidm:CommonDataElement.

• Changed query to use property path and subClassOf

PyNIDM tools v3.9.3 (dev)

Includes bug fix to read_nidm function which wasn't reading objects with rdf:type nidm:b-value or nidm:b-vector. This release fixes that issue.

PyNIDM tools v3.9.2 (dev)

Updated pynidm linear-regression tool so output file is written correctly.

PyNIDM tools v3.9.1(dev)

Fixed up some of the documentation formatting issues.