0.0.2

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