tag:github.com,2008:https://github.com/incf-nidash/PyNIDM/releases 2025-04-18T23:13:52Z tag:github.com,2008:Repository/90911621/v4.2.2 2025-04-24T15:47:51Z <h2>What's Changed</h2> <ul> <li><a href="/incf-nidash/PyNIDM/blob/v4.2.2/deps">gh-actions</a>: Bump codecov/codecov-action from 3 to 4 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2118764518" data-permission-text="Title is private" data-url="https://github.com/incf-nidash/PyNIDM/issues/395" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/395/hovercard" href="https://github.com/incf-nidash/PyNIDM/pull/395">#395</a></li> <li>Make PyNIDM codespell-clean again by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/yarikoptic/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/yarikoptic">@yarikoptic</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2980271172" data-permission-text="Title is private" data-url="https://github.com/incf-nidash/PyNIDM/issues/412" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/412/hovercard" href="https://github.com/incf-nidash/PyNIDM/pull/412">#412</a></li> <li>updating for supporting derivatives with csv2nidm by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/dbkeator/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dbkeator">@dbkeator</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2986752213" data-permission-text="Title is private" data-url="https://github.com/incf-nidash/PyNIDM/issues/413" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/413/hovercard" href="https://github.com/incf-nidash/PyNIDM/pull/413">#413</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/incf-nidash/PyNIDM/compare/v4.2.1...v4.2.2"><tt>v4.2.1...v4.2.2</tt></a></p> djarecka tag:github.com,2008:Repository/90911621/v4.2.1 2025-03-14T15:58:21Z <h2>What's Changed</h2> <ul> <li>new version of release and publish workflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/djarecka/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/djarecka">@djarecka</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2920543418" data-permission-text="Title is private" data-url="https://github.com/incf-nidash/PyNIDM/issues/411" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/411/hovercard" href="https://github.com/incf-nidash/PyNIDM/pull/411">#411</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/incf-nidash/PyNIDM/compare/v4.2.0...v4.2.1"><tt>v4.2.0...v4.2.1</tt></a></p> djarecka tag:github.com,2008:Repository/90911621/v4.2.0 2025-03-04T01:24:14Z <p>Updates to read_nidm to support nidm files created from structural segmentations only. Fixed some tests that were failing because some metadata moved from nidm:Project activity to a prov:Entity collection as they were more appropriate for inclusion in entity objects.</p> dbkeator tag:github.com,2008:Repository/90911621/v4.1.1 2024-12-10T00:58:13Z <p>Added pyontutils to setup.cfg so it gets installed for connecting to InterLex information resource remotely.</p> dbkeator tag:github.com,2008:Repository/90911621/v4.1.0 2023-07-22T19:09:54Z <h4>🚀 Enhancement</h4> <ul> <li>updated nidm model to collections of entities <a href="https://github.com/incf-nidash/PyNIDM/pull/378" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/378/hovercard">#378</a> (<a href="https://github.com/dbkeator">@dbkeator</a>)</li> </ul> <h4>Authors: 1</h4> <ul> <li>David Keator (<a href="https://github.com/dbkeator">@dbkeator</a>)</li> </ul> github-actions[bot] tag:github.com,2008:Repository/90911621/v4.0.0 2023-05-30T18:23:57Z <h4>💥 Breaking Change</h4> <ul> <li><a href="/incf-nidash/PyNIDM/blob/v4.0.0/deps">gh-actions</a>: Bump codespell-project/actions-codespell from 1 to 2 <a href="https://github.com/incf-nidash/PyNIDM/pull/375" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/375/hovercard">#375</a> (<a href="https://github.com/dependabot%5Bbot%5D">@dependabot[bot]</a>)</li> </ul> <h4>🐛 Bug Fix</h4> <ul> <li>Do not try to upload nonexisting junit artifacts <a href="https://github.com/incf-nidash/PyNIDM/pull/372" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/372/hovercard">#372</a> (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li> <li>Use RST links in readme <a href="https://github.com/incf-nidash/PyNIDM/pull/303" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/303/hovercard">#303</a> (<a href="https://github.com/surchs">@surchs</a> <a href="https://github.com/yarikoptic">@yarikoptic</a>)</li> <li>Add 3.10 and 3.11 into testing <a href="https://github.com/incf-nidash/PyNIDM/pull/324" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/324/hovercard">#324</a> (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li> <li>codespell: action, config + fixes <a href="https://github.com/incf-nidash/PyNIDM/pull/321" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/321/hovercard">#321</a> (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li> </ul> <h4><g-emoji class="g-emoji" alias="warning">⚠️</g-emoji> Pushed to <code>master</code></h4> <ul> <li>Travis is no longer used (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li> </ul> <h4>🏠 Internal</h4> <ul> <li>Refactor printing the same text to both stdout and a file <a href="https://github.com/incf-nidash/PyNIDM/pull/376" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/376/hovercard">#376</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Set up auto <a href="https://github.com/incf-nidash/PyNIDM/pull/346" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/346/hovercard">#346</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Use versioningit <a href="https://github.com/incf-nidash/PyNIDM/pull/374" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/374/hovercard">#374</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Assorted minor code improvements <a href="https://github.com/incf-nidash/PyNIDM/pull/369" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/369/hovercard">#369</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Open all text files with UTF-8 encoding <a href="https://github.com/incf-nidash/PyNIDM/pull/373" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/373/hovercard">#373</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Pare down giant comment blocks that largely do what Git already does <a href="https://github.com/incf-nidash/PyNIDM/pull/363" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/363/hovercard">#363</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Improve string formatting syntax <a href="https://github.com/incf-nidash/PyNIDM/pull/364" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/364/hovercard">#364</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Don't list <code>object</code> as a base class <a href="https://github.com/incf-nidash/PyNIDM/pull/365" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/365/hovercard">#365</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Use Python 3-style <code>super()</code> calls <a href="https://github.com/incf-nidash/PyNIDM/pull/366" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/366/hovercard">#366</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Remove redundant imports <a href="https://github.com/incf-nidash/PyNIDM/pull/367" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/367/hovercard">#367</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Clean up Docker-related files <a href="https://github.com/incf-nidash/PyNIDM/pull/351" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/351/hovercard">#351</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Enable building docs locally via <code>tox -e docs</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/357" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/357/hovercard">#357</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Replace uses of <code>urllib.request</code> with <code>requests</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/359" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/359/hovercard">#359</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Delete <code>profiler.py</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/362" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/362/hovercard">#362</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Add <code>.coverage</code> to <code>.gitignore</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/354" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/354/hovercard">#354</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Shorten overly-long lines of punctuation <a href="https://github.com/incf-nidash/PyNIDM/pull/345" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/345/hovercard">#345</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Fix <code>__version__</code> import <a href="https://github.com/incf-nidash/PyNIDM/pull/353" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/353/hovercard">#353</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Update workflow actions versions and keep them up to date with Dependabot <a href="https://github.com/incf-nidash/PyNIDM/pull/350" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/350/hovercard">#350</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Remove fallback to Python 2 import <a href="https://github.com/incf-nidash/PyNIDM/pull/348" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/348/hovercard">#348</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Add testing via tox <a href="https://github.com/incf-nidash/PyNIDM/pull/334" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/334/hovercard">#334</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Remove Python 2-specific <code>__future__</code> imports <a href="https://github.com/incf-nidash/PyNIDM/pull/335" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/335/hovercard">#335</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Remove uses of <code>six</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/336" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/336/hovercard">#336</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Prune <code>README.md</code> files from code directories <a href="https://github.com/incf-nidash/PyNIDM/pull/338" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/338/hovercard">#338</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Use a <code>src/</code> layout <a href="https://github.com/incf-nidash/PyNIDM/pull/332" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/332/hovercard">#332</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Run linting as part of CI <a href="https://github.com/incf-nidash/PyNIDM/pull/333" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/333/hovercard">#333</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Run tests in CI on pushes &amp; merges to master <a href="https://github.com/incf-nidash/PyNIDM/pull/331" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/331/hovercard">#331</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Use <code>build</code> in <code>pythonpublish.yml</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/330" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/330/hovercard">#330</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Add &amp; apply pre-commit and linting <a href="https://github.com/incf-nidash/PyNIDM/pull/329" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/329/hovercard">#329</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li><code>docs/build/</code> should not be committed <a href="https://github.com/incf-nidash/PyNIDM/pull/327" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/327/hovercard">#327</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Update Python packaging <a href="https://github.com/incf-nidash/PyNIDM/pull/326" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/326/hovercard">#326</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>"Splitted" is not a word <a href="https://github.com/incf-nidash/PyNIDM/pull/328" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/328/hovercard">#328</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> </ul> <h4>📝 Documentation</h4> <ul> <li>Use <code>.readthedocs.yaml</code> file to install pynidm in RTD environment <a href="https://github.com/incf-nidash/PyNIDM/pull/370" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/370/hovercard">#370</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Clean up <code>README.rst</code> markup <a href="https://github.com/incf-nidash/PyNIDM/pull/340" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/340/hovercard">#340</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> </ul> <h4>🧪 Tests</h4> <ul> <li>Clean up Click testing <a href="https://github.com/incf-nidash/PyNIDM/pull/352" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/352/hovercard">#352</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Write test temp files to temp directories <a href="https://github.com/incf-nidash/PyNIDM/pull/343" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/343/hovercard">#343</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Measure test coverage <a href="https://github.com/incf-nidash/PyNIDM/pull/344" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/344/hovercard">#344</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Make pytest error on warnings <a href="https://github.com/incf-nidash/PyNIDM/pull/341" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/341/hovercard">#341</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Replace <code>tmpdir</code> fixture with <code>tmp_path</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/339" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/339/hovercard">#339</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> </ul> <h4>🔩 Dependency Updates</h4> <ul> <li>Remove practically-unused <code>joblib</code> <a href="https://github.com/incf-nidash/PyNIDM/pull/360" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/360/hovercard">#360</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Clean up install requirements <a href="https://github.com/incf-nidash/PyNIDM/pull/347" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/347/hovercard">#347</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Replace simplejson with stdlib json <a href="https://github.com/incf-nidash/PyNIDM/pull/337" data-hovercard-type="pull_request" data-hovercard-url="/incf-nidash/PyNIDM/pull/337/hovercard">#337</a> (<a href="https://github.com/jwodder">@jwodder</a>)</li> </ul> <h4>Authors: 4</h4> <ul> <li><a href="https://github.com/dependabot%5Bbot%5D">@dependabot[bot]</a></li> <li>John T. Wodder II (<a href="https://github.com/jwodder">@jwodder</a>)</li> <li>Sebastian Urchs (<a href="https://github.com/surchs">@surchs</a>)</li> <li>Yaroslav Halchenko (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li> </ul> github-actions[bot] tag:github.com,2008:Repository/90911621/v3.9.8 2022-10-06T14:59:58Z <p>Includes various changes to nidm_linreg.py tool and query updates.</p> dbkeator tag:github.com,2008:Repository/90911621/v3.9.7 2022-07-27T01:04:13Z <p>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.</p> dbkeator tag:github.com,2008:Repository/90911621/v3.9.6 2022-02-16T19:02:45Z <ul> <li>Fixed bug in bidsmri2nidm.py where phenotype files with identical variable names to participants.tsv file caused collision.</li> <li>Added version function so pynidm version prints version of pynidm toolkit (pynidm version)</li> </ul> dbkeator tag:github.com,2008:Repository/90911621/v3.9.5 2021-12-07T23:13:03Z <ul> <li>Updated Utils.py/read_nidm to account for missing tuple with label of isAbout concept associations after reading existing NIDM document.</li> <li>Also updated nidm2bids to save out participants.json file with annotations from NIDM source document</li> </ul> dbkeator