Idxtools

- Re-add support for ``IDX_FILE`` and ``IDX_FORMAT`` environment variables. Close 12 (`view commit <http://github.com/emi80/idxtools/commit/870b820e21f34ff58763e415690d914b65d6c176)>`_)
- Update ``_load_index``. Load first regular dataset entries, then replicates entries to avoid missing ids. Fixes 13 (`view commit <http://github.com/emi80/idxtools/commit/369ecdeab4f7169f2ec62e345c954452f72cddab)>`_)
- Fix issue adding file to existing dataset (`view commit <http://github.com/emi80/idxtools/commit/ad5465a2ee5052a5962cb8f9bf57985f0a21ba54)>`_)
- Update command line parsing. Use ``Schema`` for validation. (`view commit <http://github.com/emi80/idxtools/commit/a507a0ef3b3e55f89014e0db1add74b0c603b370)>`_)
- Finish command line improvement and add tests. Closes 16 (`view commit <http://github.com/emi80/idxtools/commit/64a1630bc40e99b45f7753802469f78bd953ae0b)>`_)
- Implement multiple files insertion from command line and add test. Closes 15 (`view commit <http://github.com/emi80/idxtools/commit/d0b71f6e91a8bda14352d8338c46148a9c98d665)>`_)
- Update config file name and set global constants for default values (`view commit <http://github.com/emi80/idxtools/commit/53137cb76acb4c1db337d10b2cbb48bd6f8ba1d0)>`_)
- ``show`` command: Support ``attrs`` keyword for ``--tags`` option to only print attribute names (`view commit <http://github.com/emi80/idxtools/commit/a60c4ee50ed4635b9411cbf89221196356d07b6a)>`_)
- Allow deletion of files based on metadata (`view commit <http://github.com/emi80/idxtools/commit/cae1d67c11fa458a644ccf0869d9271b53e85cfd)>`_)
- Add template formatting for path (`view commit <http://github.com/emi80/idxtools/commit/ea6df9fa4356aa0ee2f44ed264424473fa225be9)>`_)
- Implement dynamic command resolution and update help messages and usages (`view commit <http://github.com/emi80/idxtools/commit/c0d5500eda5b3e3da5607c13624b3413a53ad902)>`_)
- Use type attribute as optional when importing files from metadata in tsv/csv format. Autodetect type from path extension if not given. (`view commit <http://github.com/emi80/idxtools/commit/8839d16b1bd996608b30285df7ff0d007a59176d)>`_)
- Test for non-empty path while inserting files (`view commit <http://github.com/emi80/idxtools/commit/83c843c7ea09c1da4e8b1b485a11606c1f569d33)>`_)
- Add ability to load format from YAML too (`view commit <http://github.com/emi80/idxtools/commit/870b322b5dfc7b18688f417083ff43ad76c912d0)>`_)
- Automatically add header fields to format map when importing data from tsv/csv files (`view commit <http://github.com/emi80/idxtools/commit/22902fec0fd0ea69a94f351b43ecf27ed42a85ac)>`_)
- Always flush output buffer to avoid ``sys.excepthook is missing`` error (`view commit <http://github.com/emi80/idxtools/commit/adb6030b41dbf5aa0cf13c812e3f2de174217bee)>`_)
- Rename ``add`` command file to ``update``. (`view commit <http://github.com/emi80/idxtools/commit/a9eaccbb9621a05e386f6c2dcb4ded12f26e30c4)>`_)
- Finalize implementation of ``update`` command. Keep ``add`` as command alias for backward compatibility (`view commit <http://github.com/emi80/idxtools/commit/71e4b26019f5c0f75d292cdd6376bd655471b274)>`_)
- Sort by tags order in table output or by path (`view commit <http://github.com/emi80/idxtools/commit/af05ad11c400a4be4ff6495a7ffc162b71d5bdb0)>`_)

- Fix bug: remove fileinfo from output
- Refactor Dataset get method
- Add config files support in command line tools
- Improve arguments passing and index loading in command line tools

- Improve index file lookup
- Change some APIs
- Use stdin when data is piped instead of ``IDX_FILE`` (`9 <https://github.com/emi80/idxtools/issues/9>`_)
- Implement removal of all files of a given type from a dataset (`11 <https://github.com/emi80/idxtools/issues/11>`_)

- Detect replicate id and create metadata for replicates (`3 <https://github.com/emi80/idxtools/issues/3>`_)
- Add support to remove whole dataset to the remove command (`8 <https://github.com/emi80/idxtools/issues/8>`_)

- Add option to remove command to clear metadata and modify cli to remove multiple files (`1 <https://github.com/emi80/idxtools/issues/1>`_ and `2 <https://github.com/emi80/idxtools/issues/2>`_)
- Update show command to support ids for replicates (`5 <https://github.com/emi80/idxtools/issues/5>`_)
- Use logging module (`6 <https://github.com/emi80/idxtools/issues/6>`_)
- Update signal handler for ``SIGPIPE`` (`7 <https://github.com/emi80/idxtools/issues/7>`_)

- Initial release