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CHANGELOG
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0.1.3 (June 18, 2021)
=====================
More bug fixes for (identified thanks to @richardajdear and @Silflame!) as well
as some minor QOL updates for getting sample-level information from workflows.
* [REF] Handle atlases w/decimal vox sizes (#197), @rmarkello
* [REF] Re-orient img in `leftify_atlas()` (#193), @rmarkello
* [FIX] Fixes logger error w/reports (#192), @rmarkello
* [FIX] Error with donor-specific atlases and tolerance=0 (#191), @rmarkello
* [REF] Fix coordinates of get_samples_in_mask (#189), @rmarkello
0.1.1 (March 29, 2021)
======================
Small bug fix when `probe_selection='average'` and minor QOL update to
`check_atlas()`.
* [ENH] Add geometry/space option to check_atlas (#186), @rmarkello
* [FIX] Fixes 'average' probe selection bug (#185), @rmarkello
0.1 (March 25, 2021)
====================
First minor release! :tada: This update brings some major changes to the
codebase, including a massive internal refactoring to allow handling of surface
parcellations, new methods for interpolating missing data, and more!
**Important**: as this is our first official minor release, note that the
changes in this release are *not backwards compatible* with previous versions.
* [ENH] Adds interareal similarity thresholding (#184), @rmarkello
* [REF] Allow negative tolerance for surfaces (#183), @rmarkello
* [REF] Updates reports for `missing` param (#182), @rmarkello
* [DOC] Updates master refs to main (#181), @rmarkello
* [ENH] Adds interpolation options for missing data (#180), @rmarkello
* [REF] Updates mouse data cache location (#179), @rmarkello
* [FIX] Bugfix for lr_mirror parameter (#178), @rmarkello
* [ENH] Adds reporting of processing methods (#177), @rmarkello
* [FIX] Nan hemisphere designation (#176), @rmarkello
* [FIX] Addresses bug when `tolerance=0` (#175), @rmarkello
* [TEST] Add py3.8 to azure tests (#174), @rmarkello
* [REF] Constrains centroid matching by atlas_info (#173), @rmarkello
* [REF] Updates CLI to match main workflow (#172), @rmarkello
* [REF] Modifies `lr_mirror` to accept single hemisphere mirroring (#171), @rmarkello
* [ENH] Add `norm_structures` parameter (#170), @rmarkello
* [ENH] Adds ability to handle surface parcellations (#169), @rmarkello
* [TEST] Parametrize `test_resid_dist` (#164), @4lovi4
0.0.8 (January 29, 2021)
========================
Largely internal codebase changes, but an important bug fix for compatibility
with newer versions of ``pandas``.
Huge thanks to @4lovi4 for all their contributions!
* [FIX] Read_csv error when using pandas >= 1.2.0 (#167), @rmarkello
* [TEST] Change Azure VM image to fix SSL (#165), @rmarkello
* Adds Python 3.8 testing support to CircleCI (#163), @4lovi4
* issue #73 unquote url (#162), @4lovi4
* issue #80 doc string fix (#161), @4lovi4
* issue #139 readme fix (#160), @4lovi4
0.0.7 (October 15, 2020)
========================
Only two changes—but relatively impactful ones—including the addition of a new
workflow-style function (``abagen.get_samples_in_mask()``) to get preprocessed
tissue samples without aggregating in specific brain regions and the ability to
provide parcellations in donor-native space (rather than MNI space).
Documentation has been updated to reflect all new features!
* [ENH] Adds handling for donor-specific atlases (#156), @rmarkello
* [ENH] Allows users to get microarray samples in mask (#155), @rmarkello
0.0.6 (August 17, 2020)
=======================
Minor bug fixes, including:
* [FIX] Allow None input to CLI norm opts (#153), @rmarkello
* [MNT] Pin minimum pandas version to 0.25 (#151), @rmarkello
* [DOC] Adds Fulcher norm ref (#149), @rmarkello
* [FIX] Always remap annotation dataframe cols (#147), @rmarkello
* [FIX] Allow 'common' for donor_probes method (#146), @rmarkello
0.0.5 (March 24, 2020)
======================
This release includes quite a bit of new functionality, including:
- Several new gene/sample normalization methods,
- A fetcher / new loader functions for RNAseq data (``abagen.fetch_rnaseq()``),
- The ability to use RNAseq data for selecting probes (``probe_selection='rnaseq``), and
- A new ``donor_probes`` parameter for ``abagen.get_expression_data()`` to control how probe selection is performed
Check out the documentation for more details!
* [ENH] Adds new mechanisms for probe selection (#145), @rmarkello
* [ENH,REF] Adds RNAseq probe selection method (#144), @rmarkello
* [TEST] Fix Azure maybe? (#143), @rmarkello
* [ENH] Adds FreeSurfer data fetcher (#142), @rmarkello
* [ENH] Adds fetchers / loaders for RNAseq data (#140), @rmarkello
* [TEST] Adds Windows testing with Azure (#141), @rmarkello
* [FIX,ENH] Error in get_expression_data, gene stability calculation (#136), @rmarkello
* [ENH,REF] New norms, utils, renamed modules (#135), @rmarkello
0.0.4 (February 26, 2020)
=========================
A release with a small bugfixes (#134) and a small fix-fix (#133)!
* [FIX] Coerce atlas dataobj to arr before indexing (#134), @rmarkello
* [REF] Drop probes with invalid/missing Entrez ID (#133), @rmarkello
0.0.3 (November 26, 2019)
=========================
A new release with some added features but primarily a good bit of re-arranging
in the primary ``abagen.get_expression_data()`` workflow. Notable changes
include:
- New parameters ``region_agg``, ``agg_metric``, ``sample_norm``, and
``gene_norm`` (the latter of which supplants ``donor_norm``), controlling how
microarray samples are normalized and aggregated across donors;
- Large reductions in memory usage (#130), such that the primary workflow
should only use ~2GB of RAM at its peak; and,
- Migration to CircleCI for all testing purposes!
Special thanks to @rhannema, @Ellen8780, @gifuni, and @VinceBaz for their
contributions.
* [REF] Adds option to suppress norm warnings (#132), @rmarkello
* [ENH,REF] Adds new `region_agg` parameter (#131), @rmarkello
* [REF] Massive reduction in memory usage (#130), @rmarkello
* [FIX] Solves pandas bug with max_variance method (#128), @gifuni
* [STY] Fixes trailing whitespace (#129), @rmarkello
* [FIX] Fixes strange TypeError for pc_loading (#1), @rmarkello
* [REF] Ensures integer DataFrame when `return_count=True` (#127), @rhannema
* [ENH] Add fetcher for donor info (#126), @Ellen8780
* [REF,ENH] Modifies and adds normalization procedures (#119), @rmarkello
* [TEST] Updating CircleCI build (#122), @rmarkello
* [TEST] TravisCI --> CircleCI (#121), @rmarkello
* [REF] Removes `.get_data()` nibabel calls (#120), @rmarkello
* [FIX] Specify `engine='python'` in pandas queries (#117), @VinceBaz
0.0.2 (September 19, 2019)
==========================
This release comes with a **lot** of new changes, including:
- Several new arguments for ``abagen.get_expression_data()``, including new
probe selection methods, donor normalization techniques, and hemispheric
mirroring of tissue samples;
- A command-line version of the primary workflow accessible via the ``abagen``
command;
- Improved data handling, using $HOME/abagen-data as the default storage
location for data from the AHBA;
- New functionality for fetching raw AHBA donor MRI scans;
- Zenodo integration to make it easy to cite ``abagen``; and,
- Massive documentation overhauls, with a dramatically updated user guide and
API reference!
Special thanks to Golia Shafiei (@gshafiei), Ying-Qiu Zheng (@yingqiuz), James
Frierson (@JamesFrierson1), and Arda Kosar (@abkosar) for their contributions.
* [MNT] Finishes Zenodo integration (#109), @rmarkello
* [MNT] Adds framework for Zenodo integration (#108), @rmarkello
* [REF] Fixes one-donor bug in get_expression_data() (#107), @rmarkello
* [REF] Identifies hippocampus as subcortex in Allen ontology (#106), @rmarkello
* [DOC] Updates documentation + contributing (#105), @rmarkello
* [REF] Mirroring before probe filtering (#101), @rmarkello
* [FIX] Installation not correctly bundling package data (#102), @rmarkello
* [MNT] Docs / package structure updates in prep for 0.2.0 (#95), @rmarkello
* [REF] abagen.io functions don't copy dataframes by default (#94), @rmarkello
* [FIX] Fixes broken include directive in API reference (#91), @rmarkello
* [ENH] Adds parameter for normalizing donor microarray expression values (#90), @rmarkello
* [ENH] Adds option to mirror samples across L/R hemispheres (#87), @rmarkello
* [ENH] Adds CLI for `abagen.get_expression_data` functionality (#82), @rmarkello
* [ENH] Adds ability to fetch raw AHBA MRIs (#85), @rmarkello
* [ENH] Adds ability to query gene groups (#83), @rmarkello
* [MNT,REF] Updates install, versioning, dependencies (#84), @rmarkello
* [REF] Adds brainstem to abagen.process ontology (#81), @rmarkello
* [DOC] Updates API documentation (#76), @rmarkello
* [REF,ENH] Adds new abagen.probes module (#67), @rmarkello
* [REF] Changes data directory locator for abagen data (#66), @rmarkello
* [FIX] Fixes doctest in abagen.mouse (#65), @rmarkello
* [REF] Removes .get_values() references (#64), @rmarkello
* [DOC] Adds logging to workflow functions (#61), @rmarkello
* Fixed abagen.mouse column ordering (#62), @abkosar
* [DOC] Update refs and http (#60), @rmarkello
* [REF] Use cached alleninf coordinates only (#59), @rmarkello
* [FIX] Removes RuntimeWarning in example code (#58), @rmarkello
* Updated README to include Allen Institute citations and disclaimers (#57), @JamesFrierson1
* [FIX] Catches AttributeError w/pandas fastparquet (#41), @rmarkello
* [REF] Updates get_expression_data() (#38), @rmarkello
* [TEST] Fixes tests (#34), @rmarkello
* Add mouse features (#32), @yingqiuz
* [TEST] Fix pytest version and update travis (#33), @rmarkello
* [TEST] Update travis testing (#31), @rmarkello
* [FIX] More fixes for atlas numbering (#30), @rmarkello
* [FIX] Allow non-sequential atlas numbering (#29), @rmarkello
* [ENH] Adds input check for remove_distance() (#28), @rmarkello
* [ENH] Allow label exclusion in `remove_distance()` (#27), @rmarkello
* [REF] Changes `remove_distance()` inputs (#26), @rmarkello
* [ENH] Add function for aggregating donors (#25), @rmarkello
* [ENH] Adds reannotated probe information (#24), @rmarkello
* [ENH] Adds `abagen.correct` for postprocessing (#20), @rmarkello
* [TEST] Removes pytest capturing (#23), @rmarkello
* [TEST] Calculates coverage only for extras (#22), @rmarkello
* [DOC] Updates doc-strings for primary functions (#19), @rmarkello
* [TEST] Add early test to reduce timeouts (#21), @rmarkello
* [FIX] Adds updated MNI coordinates file as backup (#17), @rmarkello
* [DOC] Updates default tolerance (#16), @gshafiei
0.0.1 (September 7, 2018)
==========================
Initial release of ``abagen``, a toolbox for working with the `Allen Brain Atlas
<http://human.brain-map.org/>`_ human genetics data.
* [DOC] Updates various documentation (#15), @rmarkello
* [DOC] Adds LICENSE reference for alleninf (#14), @rmarkello
* [DOC] Updates README links and example usage (#13), @rmarkello
* [TEST] Updates tests of `abagen.get_expression_data()` (#12), @rmarkello
* [DOC] Adds Sphinx documentation (#11), @rmarkello
* [FIX] Resolves dataframe formatting issue (#10), @rmarkello
* [ENH] Adds DK atlas fetcher and updates README.md (#8), @rmarkello
* [REF] Cleaning up unused code (#7), @rmarkello
* [ENH] MAJOR refactoring of IO and processing (#4), @rmarkello
* [TEST] Adds .travis.yml and initial tests (#3), @rmarkello
* [STY] Stylistic updates to abagen.datasets (#2), @rmarkello