Abagen

======================
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

=========================
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

=========================
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

==========================
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

==========================
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