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Branch: master
Commits on Jan 30, 2019
  1. Added check for missing header to schema validation in python API.

    javh committed Jan 30, 2019
Commits on Oct 15, 2018
  1. Update IgBLAST version for AIRR v1.2 schema support in docs.

    javh committed Oct 15, 2018
Commits on Oct 5, 2018
  1. Python library bug fix - v1.2.1 (#160)

    javh committed Oct 5, 2018
    * Fixed a bug with start coordinate conversion leading to empty values in python library writer class.
    * Updated python library NEWS.
Commits on Sep 13, 2018
  1. Schema terminology updates. (#153)

    javh committed Sep 13, 2018
    Schema description updates with consistent use of "gene" and "segment".
Commits on Aug 28, 2018
  1. Minor correction ot DataRep example docs.

    javh committed Aug 28, 2018
Commits on Aug 17, 2018
  1. Update Rearrangement support table in docs to v1.2 schema.

    javh committed Aug 17, 2018
  2. Switched `toy_data.tsv` start positions to 1-based.

    javh committed Aug 17, 2018
  3. Another typo...

    javh committed Aug 17, 2018
  4. Long travis build.

    javh committed Aug 17, 2018
  5. Typo.

    javh committed Aug 17, 2018
  6. Rearrangement doc polish.

    javh committed Aug 17, 2018
  7. Poke Travis.

    javh committed Aug 17, 2018
Commits on Aug 16, 2018
  1. Minor changes to docs toc tree.

    javh committed Aug 16, 2018
  2. Rearrangement updates for v1.2 (#149)

    javh committed Aug 16, 2018
    Various updates for v1.2
    
    * Swap to 1-based coordinates and fill optional columns with explicit optional label in docs.
    * Set default coordinate scheme to "1" in R package.
    * Python package Windows fix
    * Removal of automatic handle closure upon end of RearrangementReader iteration.
    * Added `Encoding` field to R package DESCRIPTION file.
    * Rewrite python validation and update tests
    * Added doc text about custom columns in the Rearrangement TSV.
    * Corrected some doc terminology and adding a table of software supporting the Rearrangement spec.
    * Sync terminology between manuscript and docs.
    * Fixed terminology in R package and updated news.
    * Added `base` argument to the Rearrangement reader/writer in the python library to control conversion of 0-based and 1-based coordinates.
    * Added dataset definition to docs.
    * Moved validate methods in python library to schema objects. Some performance tweaks.
    * Swapped python `airr.interface` functions to accept file paths instead of handles and changed `airr.interface.validate_rearrangement` to process only a single file.
    * Modified bad_data2.tsv to have of one each kind of bad value and no missing fields. Added bad_data3.tsv with missing fields and bad values.
    * Fixed R travis build
    * Add germline_alignment data to R rearrangement example file.
    * Simplified R example TSV sequence_id values.
    * Bumped R package version and rebuilt R docs.
    * Fixed formatting of downloadable tables for Rearrangement and Alignment field definitions.
    * Updated package NEWS.
Commits on May 2, 2018
  1. Fix R package validate example.

    javh committed May 2, 2018
  2. Things that CRAN wants. (#135)

    javh committed May 2, 2018
Commits on May 1, 2018
  1. Fix R package DESCRIPTION per CRAN request. Fixed license in R and Py…

    javh committed May 1, 2018
    …thon package.
  2. Minor.

    javh committed May 1, 2018
  3. Python package doc and keyword fixes.

    javh committed May 1, 2018
  4. DataRep usage example and doc cleanup (#130)

    javh committed May 1, 2018
    1. Added DataRep usage example to docs under a top level "Examples & Workflows" section.
    2. Restructured doc folders for future-proofing.
    3. Bumped package dates, versions and updated news.
    4. R package doc cleanup.
    5. Python package doc cleanup.
    6. Added python 2.7 to python package test matrix.
Commits on Apr 25, 2018
  1. Removed prov and numpy dependencies from python package. (#127)

    javh committed Apr 25, 2018
Commits on Apr 24, 2018
  1. Actually fixed missing R vignette and changed gitignore list for vign…

    javh committed Apr 24, 2018
    …ette files.
  2. Fixing missing R usage vignette.

    javh committed Apr 24, 2018
  3. Added R package documentation to main docs site (#125)

    javh committed Apr 24, 2018
Commits on Apr 21, 2018
  1. Minor R docs cleanup.

    javh committed Apr 21, 2018
Commits on Apr 20, 2018
  1. R vignette typos.

    javh committed Apr 20, 2018
  2. Minor R vignette fix.

    javh committed Apr 20, 2018
  3. Rename definitions.yaml to airr-schema.yaml per #66. (#124)

    javh committed Apr 20, 2018
    * Rename definitions.yaml to airr-schema.yaml per #66.
    * Updated docs to denoted Alignment spec as experimental, removed metadata information, and some xrefs.
  4. Integration of pandas template code (#118)

    javh committed Apr 20, 2018
    * Integrate pandas read/write code for potential future work.
    * Added pandas validation code as TODO comment in airr.io.
    * Add numpy to mock imports for ReadTheDocs.
    * Attempts to insulate against future changes
    * Swapped schema in `io.RearrangementReader` and `io.RearrangementWriter` to an instance variable so we can just inherit for multiple readers/writers if we keep this structure in the future.
    * Renamed interface.py functions to `*_rearrangement` to denote they are specific to the Rearrangement spec.
    * Changed import behavior in `__init__.py`.
    * Rename `airr.write` to `airr.dump`.
    * Update python README and integrate with docs better.
Commits on Apr 19, 2018
  1. Demote all headers by one step in R vignette for doc integration purp…

    javh committed Apr 19, 2018
    …oses.
Commits on Apr 18, 2018
  1. Fixed a bug in the `from_bool` method.

    javh committed Apr 18, 2018
  2. Minor import cleanup in setup.py.

    javh committed Apr 18, 2018
  3. Remove pip from setup imports.

    javh committed Apr 18, 2018
  4. pip>=10 install fix.

    javh committed Apr 18, 2018
  5. Delete vestigial data objects and data generation scripts from R pack…

    javh committed Apr 18, 2018
    …age.