Recent Releases of redbiom
redbiom - Performance and bug fix release
PR https://github.com/biocore/redbiom/pull/122 in particular included quite a few issues, as well as performance boost for fetch, a new API method for fetching a Qiita study, clean up of warnings, removal of Py3.6 from build testing (the environments won't create) and addition of Python 3.10 into the matrix.
Specific other items addressed in https://github.com/biocore/redbiom/pull/122 include:
- Allow for resolution of ambiguities while retaining the artifact ID https://github.com/biocore/redbiom/issues/119
- A particular sample always crashes for me https://github.com/biocore/redbiom/issues/117
- It would be nice to have an easy option to pull a specific qiita study https://github.com/biocore/redbiom/issues/116
- redbiom summarize taxonomy should handle no hits gracefully https://github.com/biocore/redbiom/issues/43
- redbiom search metadata NUMBER should fail gracefully https://github.com/biocore/redbiom/issues/44
- Fixing instructions in readme https://github.com/biocore/redbiom/issues/46
- If context creation fails, error gracefully https://github.com/biocore/redbiom/issues/52
- search for phrases https://github.com/biocore/redbiom/issues/50
- Where queries should support "in" correctly when the left hand is a string https://github.com/biocore/redbiom/issues/41
What's Changed
- API/PERF: allow avoiding fetch of taxonomy by @wasade in https://github.com/biocore/redbiom/pull/114
- add msgpack by @wasade in https://github.com/biocore/redbiom/pull/115
- ping! by @antgonza in https://github.com/biocore/redbiom/pull/118
Full Changelog: https://github.com/biocore/redbiom/compare/0.3.8...0.3.9
- Python
Published by wasade about 3 years ago
redbiom - Speed improvement on load
Important bulk load operation to reduce load/refresh times.
- Python
Published by wasade over 4 years ago
redbiom - Important bug fix
PR #113 carries an important fix where samples with a .raw suffix were not being loaded.
- Python
Published by wasade over 4 years ago
redbiom - Bug fixes, py39 support and more
As the title says :)
- Python
Published by wasade over 4 years ago
redbiom - Resolve ambiguities at fetch and select specific metadata columns
This micro-release includes additions that allow for the resolution of ambiguities at data and metadata retrieval through two different means. The first is to retain the sample with the most sequence data, the second is to merge ambiguous samples together.
This release also includes a bug fix where periods were not being escaped, and in some extreme examples getting interpreted by webdis as denoting an altered return type over the default of JSON.
Finally, we now also allow for the retrieval of specific metadata columns!
- Python
Published by wasade over 6 years ago
redbiom - Bug fix to allow indexing "/" characters
This is primarily a bug fix release to allow indexing of "/" characters at cache generation. Strings containing these characters were previously omitted as they are reserved in the case of a URL. These values are now formally encoded using urllib.
This release also includes support for optionally hashing features on fetch -- thanks @antgonza!
- Python
Published by wasade over 6 years ago
redbiom - Minor release for allowing timestamps
A minor release to allow storing timestamps in the cache to reflect points of update.
- Python
Published by wasade over 6 years ago
redbiom - Deployment and installation improvements
Modifications to improve how redbiom is installed from pypi and conda, thanks @BenKaehler!
- Python
Published by wasade almost 7 years ago
redbiom - Tag information and taxonomy representation updates
Updates to the taxonomy representation, and the ability to pull out tag specific information (e.g., preparation detail).
- Python
Published by wasade about 7 years ago
redbiom - List based backend for sample data
This release changes the database backend to use a list-based structure instead of the sorted set structure. We're bumping the minor version because this modifies how the data representation.
- Python
Published by wasade about 8 years ago
redbiom - Qiita's September 27th, 2017 Release
This tag marks the version of RedBiom deployed in the main Qiita server or September 27th, 2017
- Python
Published by josenavas over 8 years ago
redbiom - Alpha release
We're excited to announce the first release of redbiom with default support to query the public facing studies housed in Qiita, which is in excess of 100,000 samples!
As of this release, it is possible to:
- find samples by metadata searches (including restriction clauses like
where ph < 7) - find metadata categories of interest
- find features by taxonomy
- fetch sample data
- fetch sample metadata
- summarize samples over a metadata category
...and more. The project is still rough around the edges. Much of the functionality exposed right now are "building blocks" where users need to pipe together commands. We're excited to see how the uses cases evolve, and as they become more clear we will build in explicit commands for desired sets of operations -- an example is redbiom summarize table.
We're denoting this release as alpha because we're still exploring the data model, adding in new types of queries, improving clarity on results, and because this tool has not seen wide use yet.
- Python
Published by wasade over 8 years ago