machado 0.5.0

https://pypi.org/project/machado/

Release Notes

Improvements

• data loading: refactoring -> now the system allows features to have the same id within different organisms
• data loading: creates a function to retrieve cvterm by name or synonym
• general: adds new sample files for some commands
• general: adds new tests

Fixes

• ontologies: the term 'contained in' from sequence ontology is now obsolete in favor of 'located in'

machado 0.4.0

https://pypi.org/project/machado/

Release Notes

Improvements

• API: retrieves API examples from the settings.py file
• feature page: includes a single fixed submit button
• feature page: loads expression data from the API and renders in a dynamic table
• JBrowse: adds SNV tracks and addition description to features
• search index: allows to find features based on overlapping features uniquename
• search index: adds feature name and dbxrefs to the index
• data loading: defines the valid_types in the settings file
• data loading: refactoring -> creates a class to handle feature attributes
• data loading: update regex to handle uncommon dbxrefs like Gene3D:G3DSA:3.30.920.10
• data loading: updates to handle multiple feature annotation attributes
• data loading: adds the option DOI to the load_feature_annotation command
• general: updates retrieve_feature_id to identify soterm-accession
• general: distinguish infraspecific name throughout the code
• general: performance improvements

Fixes

• API: fixes drf-yasg securityDefinition

What's Changed

• retrieves API examples from the settings.py file by @azneto in #290
• fixes drf-yasg securityDefinition by @azneto in #291
• species name in italics by @azneto in #293
• upgrades to django 3.1.7 and updates the docs by @azneto in #295
• includes a single fixed submit button in replacement for several appl… by @azneto in #296
• includes a single fixed submit button in replacement for several appl… by @azneto in #297
• defines the valid_types in the settings file and by @azneto in #298
• adds accession to jbrowse tracks and includes feature.name, feature.uniquename, and overlapping_features.uniquename to the text search by @azneto in #299
• Bump django from 3.1.7 to 3.1.8 by @dependabot in #302
• feature.js publication corrections by @mmudado in #304
• search_indexes: performance tweak and error handling by @azneto in #305
• creates a class feature_attribute and configures it to handle QTLDB.gff files. by @azneto in #307
• assay.py implemented get_or_create for assay_prop by @mmudado in #306
• exclude feature annotation of overlapping features of the same type by @azneto in #308
• handles the DOI attribute by @azneto in #309
• fix obj.name == None by @azneto in #310
• modify search to run partial searches rather than starts_with searches by @azneto in #311
• updates retrieve_feature_id to ignore case by @azneto in #313
• adds dbxrefs to the elasticsearch index by @azneto in #314
• updates index to ignore case and the prefix of dbxrefs by @azneto in #315
• updates searches to Raw by @azneto in #316
• feature page: loads expression data from the API and renders in a dynamic table by @azneto in #317
• Indexing improvement by @njbooher in #318
• updates to handle CNV by @azneto in #319
• Call init properly by @njbooher in #320
• updates the Django version and changes the operator to ~= in order to allow compatible versions by @azneto in #322
• Infraspecific name by @njbooher in #323
• minor fixes to display empty rather than None by @azneto in #324
• Handle weird xrefs during loading by @njbooher in #327
• Upgrade django to 3.2 by @njbooher in #329
• configures API endpoints to cache results, updates dependencies versions, and updates travis for ubuntu focal by @azneto in #332
• Bump django from 3.2.10 to 3.2.12 by @dependabot in #334
• Allows to add DOI to feature_properties and make DOI searcheable by elasticsearch by @azneto in #336
• minor changes to improve sonarcloud score by @azneto in #337
• minor changes to improve sonarcloud score by @azneto in #338
• Bump django from 3.2.12 to 3.2.13 by @dependabot in #339
• updates django and includes django-haystack to the dependencies by @azneto in #340
• updates docs to use elasticsearch 7 by @azneto in #341
• Update to django 3.2.14 by @njbooher in #342
• new tests for travis CI by @azneto in #343
• Speed up JBrowse RefSeqs endpoint by @njbooher in #346

New Contributors

• @njbooher made their first contribution in #318

Full Changelog: v0.3.0...0.4.0

machado v0.3.0

https://pypi.org/project/machado/

Release Notes

New features

• API: the API was updated to run OpenAPI rather than coreAPI
• API: the API documentation was created using Swagger
• API: new endpoints to retrieve feature information
• feature.html: most cards are now getting the information from the API
• settings.py: the new variable MACHADO_JBROWSE_TRACKS allows to set the jbrowse tracks

Improvements

• feature.html: dbxrefs were included
• feature.html: links to NCBI proteins were included
• export TSV: organism info was included
• tests: flake8 was included to perform static code analysis
• tests: ubuntu focal and python 3.8 were included

Fixes

• load_gff: fixes store_relationship call
• load _gff: handles SignalP results from InterproScan analyses
• load_coexpression_clusters: fixes function to use retrieve_feature_id
• load_orthomcl: fixes function to use retrieve_feature_id
• search_result.html: formats species using italic

machado v0.2.1

https://pypi.org/project/machado/

Release Notes:

• Optimization of the search results page by avoiding hitting the database

• Implementation the organism column, column sorting functionality, and changing the number of records functionality in the search results page

• Implementation of APIs for sequences, orthologs, and publications

• Optimization of the feature page by loading some cards dinamicaly from APIs

• Optimization of the load_gff command by loading relationships using multithreads

• Dependencies upgraded to newer versions

machado v0.2.0

https://pypi.org/project/machado/

Release Notes:

• Optimization of the search results page by avoiding hitting the database

• Implementation the organism column, column sorting functionality, and changing the number of records functionality in the search results page

• Implementation of APIs for sequences, orthologs, and publications

• Optimization of the feature page by loading some cards dinamicaly from APIs

• Optimization of the load_gff command by loading relationships using multithreads

• Dependencies upgraded to newer versions

machado 0.1.1

https://pypi.org/project/machado/

machado 0.1.0

https://pypi.org/project/machado/