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
