70 Commits (master)

Author SHA1 Message Date
Damien Goutte-Gattat 0e801b94ea Switch to Black-enforced code style. 2 months ago
Damien Goutte-Gattat fa20c968af Switch back to the original click-shell. 1 year ago
Damien Goutte-Gattat 4b3cffa39c Replace click_shell by incenp.click_shell. 1 year ago
Damien Goutte-Gattat b9723dcd10 Prepare the 0.2.0 release. 2 years ago
Damien Goutte-Gattat 671486d80c Add more documentation. 2 years ago
Damien Goutte-Gattat df47a1ed6c Allow seqtool to access user-configured databases. 2 years ago
Damien Goutte-Gattat b3d14b925f Remove the seqvault.rc configuration file. 2 years ago
Damien Goutte-Gattat 5f5f96b6ad Change option for database name in databases.ini. 2 years ago
Damien Goutte-Gattat d18fa3ea7d Change location of seqvault's configuration file. 2 years ago
Damien Goutte-Gattat 73d28dc432 Add more documentation. 2 years ago
Damien Goutte-Gattat 3fab6608c0 Improve documentation of the USA module. 2 years ago
Damien Goutte-Gattat c9e45ce936 Remove unneeded import. 2 years ago
Damien Goutte-Gattat efc07ed7ca Remove query methods from the DatabaseProvider class. 2 years ago
Damien Goutte-Gattat a82269f98c Use a dict-like interface for the DatabaseProvider. 2 years ago
Damien Goutte-Gattat 63a14f1d85 Do not use a global DatabaseProvider object. 2 years ago
Damien Goutte-Gattat 4230b44a1f Fix creation of an unprefixed database. 2 years ago
Damien Goutte-Gattat d08bde1e5a seqvault: Add support for SQLite databases. 2 years ago
Damien Goutte-Gattat b64f943c77 seqvault: Fix creation of a new database. 2 years ago
Damien Goutte-Gattat 3437bc4031 Add the expasy and entrez database sources. 2 years ago
Damien Goutte-Gattat 9e3e02afcd Support SQLite-backed BioSQL databases. 2 years ago
Damien Goutte-Gattat 30da42775b Use a single adapter for BioSQL-based databases. 2 years ago
Damien Goutte-Gattat 5cfd8b0b6f Support wildcards when querying a BioSQL database. 2 years ago
Damien Goutte-Gattat f7735db4eb Allow access to a specific subdatabase. 2 years ago
Damien Goutte-Gattat 7bf4106794 Change the DatabaseProvider interface. 2 years ago
Damien Goutte-Gattat 439255721c Rough implementation of the database access layer. 2 years ago
Damien Goutte-Gattat c1a8553eef Prepare 0.1.2 release. 2 years ago
Damien Goutte-Gattat 31b216528a Fix Click interface for the blast tool. 2 years ago
Damien Goutte-Gattat e89320c0a2 Prepare 0.1.1 release. 2 years ago
Damien Goutte-Gattat f253447794 Compile search patterns in database-based USAs. 2 years ago
Damien Goutte-Gattat ae29033b6b Only allow valid search fields. 2 years ago
Damien Goutte-Gattat d0f5ca6339 Implement per-field search in USAs. 2 years ago
Damien Goutte-Gattat c36e3f352b Match identifier against unversioned accession number. 2 years ago
Damien Goutte-Gattat b43e77c717 Use both name and id when matching a record against an identifier. 2 years ago
Damien Goutte-Gattat 660ea77f3c Support wildcard ID lookups. 2 years ago
Damien Goutte-Gattat 8a6448ad2f Support reading from program-based USAs. 2 years ago
Damien Goutte-Gattat c849b899e4 Reuse first record's details when catenating sequences. 2 years ago
Damien Goutte-Gattat a87abf8e62 Add dependencies in setup.py. 2 years ago
Damien Goutte-Gattat d26b0741c3 Fix invocation of the plasmm command. 2 years ago
Damien Goutte-Gattat c146e376f0 Autodetect format for file-based USAs. 2 years ago
Damien Goutte-Gattat 209f190b70 Add the newdb command. 2 years ago
Damien Goutte-Gattat b01e79ccdb Fix incorrect use of is_prefixed(). 2 years ago
Damien Goutte-Gattat 5d679630d2 Support edit records in unprefixed databases. 2 years ago
Damien Goutte-Gattat 3712e13548 Add support for non-modified BioSQL servers. 2 years ago
Damien Goutte-Gattat d5c5b4e4c7 Add the ipython command to seqvault. 2 years ago
Damien Goutte-Gattat 7a6c2657c4 Convert cc3d.py to Click. 2 years ago
Damien Goutte-Gattat d508e69d7f Allow missing default configuration file. 2 years ago
Damien Goutte-Gattat 71342729b9 Add some error handling. 2 years ago
Damien Goutte-Gattat ab6e617215 Rework the seqvault command. 2 years ago
Damien Goutte-Gattat 1b4084fd91 Reorganize the seq utilities. 2 years ago
Damien Goutte-Gattat 92bd0186ab Add draft version of the vault command. 2 years ago