All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog. This project adheres to Semantic Versioning.
- Metadata fixes
- Fixed reaction SMARTS in MITE0000330 breaking deployment of
mite_web
- Update 03+04/26
- Hash-based validation of artifacts
- Update 02/26
- Separation of data and code
- Rework of validation functionality
- Rework of artifact creation/updating functionality
- Rework CI/CD logic
- Rework of pre-commit logic
- pickle-file generation (fingerprint generation in mite_web on startup instead)
- Data update 01/26
- Update pre-commit (change back)
- Data update 12/25
- Checks for MIBiG and Rhea IDs (implemented as warnings in mite_validation)
- Timeout for UniProt using requests
- Timeout for NCBI using concurrent.futures (Biopython Entrez lacks timeout, requests blocked by NCBI servers)
- Data update 11/25
- CI/CD run for new entries
- Fixed NCBI/Uniprot organism checks
- Prevent FASTA file download of retired entries
- Checks for validity of uniprot/genpept/wikidata
- Generation of molecule files for mite_web
- Added new entries
- Fixed retired uniprot IDs
- Changed installer from
hatchtouv - Updated dependencies & fixed tests to accommodate changes in Biopython's download from NCBI
- Reworked update procedure
- Data update
- Miscellaneous fixes in context of manuscript revision
- MITE dependencies (
mite_schema,mite_extras) resolve to most up-to-date version - Implemented
uvas project installer
- Implemented additional tests for metadata_mibig.json file
- Adjusted versions of
mite_extasandmite_schema
- 06-25 data update
- added cofactor info
- CI/CD: full check only on merge to main
- CI/CD: pull requests into main only check updated files
- 03/04/05-25 data update
- 02-25 data update
- Changed collaboration documents to organization-level ones
- Fixed format of CFF file
- Added entries for 01-25 data update
- Changed the license from "MIT" to "CC0" where applicable
- Added entries for 12-24 data update
- Automated fasta-file download via pre-commit
- Moved BLAST-library, .pdb-files, and enzyme visualizations to
mite_web
- Fixed error in BLAST library creation
- Completed review of all contained MITE entries
- Fixed two entries with erroneous MITE ID
- Update data: November-release
1.5 - Added "metadata_cytoscape.csv" to provide metadata for sequence similarity networks (fasta-files)
- Pinned
mite_schemaandmite_datadependencies - Replaced old IDs with ORCIDs
- Update metadata_mibig.json: changed nesting to accommodate multiple mite entries per mibig bgc
- Updated entries to adhere to MITE schema version
1.5.1
- FASTA files are now named after the MITE entry they describe
- The header of FASTA file now contains
>{MITE accession} {genpept_id/uniprotkb_id/uniparc_id}to keep track from where it originates
- Updated entries to adhere to MITE schema version
1.4 - All entries now pass automated checks of
mite_extras - Added the "Automated checks passed" reviewer ID
BBBBBBBBBBBBBBBBBBBBBBBB - Set the status of all entries to
active - Merged duplicate entries and retired them
- Reworked project structure
- Complete rework of
mite_dataCLI - Added functionality to automatically generate metadata for MITE entries
- Added functionality to download protein FASTA files and build a BLAST DB
- Added functionality to update MITE entries to the newest version of
mite_schema - Added a CI/CD pipeline to auto-check MITE entries at every commit
- Updated entries to adhere to MITE schema version
1.3
- Initial data upload
- Implementation of auxiliary scripts