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Recent Releases of biospecdb

biospecdb - v1.1.3

What's Changed

  • Group dependabot PRs by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/335
  • Bump the all-minor-and-patch-dependency-updates group with 8 updates by @dependabot in https://github.com/RISPaDD/biospecdb/pull/336
  • Bump boto3 from 1.34.95 to 1.34.96 in the all-minor-and-patch-dependency-updates group by @dependabot in https://github.com/RISPaDD/biospecdb/pull/338
  • Add some research project details to the README by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/339
  • Add user documentation by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/337
  • AWS apprunner: install deps from docs.txt not dev.txt by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/340
  • Build docs within pipenv by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/341
  • debug by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/342
  • Use make -C docs by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/343
  • Build package for docs by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/344
  • Hard code version since apprunner removes .git from repo by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/345
  • Hard code version since apprunner removes .git from repo (take 2) by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/346
  • Don't install deps when building package in apprunner when building docs by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/347
  • Fix docs/source/conf by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/348
  • Protect media files by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/349
  • Build package for correct version reporting by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/350
  • S3 storage: don't clobber and make more secure by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/351
  • Fix s3 storages by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/352
  • Fix apprunner docs by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/353
  • Build docs in apprunner build, not post-build stage by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/354
  • Remove apprunner debug code by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/355

Full Changelog: https://github.com/RISPaDD/biospecdb/compare/v1.1.2...v1.1.3

- Python
Published by jamienoss about 2 years ago

biospecdb - v1.1.2

What's Changed

  • Drop SQL views before migrating by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/331
  • Fail early in model.full_clean so field validators bubble up by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/333

Full Changelog: https://github.com/RISPaDD/biospecdb/compare/v1.1.1...v1.1.2

- Python
Published by jamienoss about 2 years ago

biospecdb - v1.1.1

What's Changed

  • Give more space for Sample Tagging::sample_processing help text by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/324
  • Bump gunicorn from 21.2.0 to 22.0.0 in /requirements by @dependabot in https://github.com/RISPaDD/biospecdb/pull/326
  • 322 Fix broken inline observations by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/327
  • Print Observable.description & field.helptext from getcolumn_names management cmd by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/328
  • 321 Change units of thawing time to minutes & freezing time to days by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/323
  • Fix RelatedObjectDoesNotExist error when Model.clean() access related fields by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/329
  • Add --includeinstrumentfields to getcolumnnames management cmd by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/330
  • Bump pytest-cov from 4.1.0 to 5.0.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/314

Full Changelog: https://github.com/RISPaDD/biospecdb/compare/v1.1.0...v1.1.1

- Python
Published by jamienoss about 2 years ago

biospecdb - v1.1.0

What's Changed

  • Bulk upload on patientcid not patientid by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/317
  • Bump ruff from 0.1.7 to 0.3.5 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/316
  • Bump setuptools from 69.0.3 to 69.2.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/315
  • Bump build from 1.1.1 to 1.2.1 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/313

Full Changelog: https://github.com/RISPaDD/biospecdb/compare/v1.0.1...v1.1.0

- Python
Published by jamienoss about 2 years ago

biospecdb - v1.0.1

What's Changed

  • Revert #282 zenodo doi update by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/294
  • 292 Add extended sql explorer perms by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/293
  • Missing migration from #292 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/296
  • Remove ploty dash dir by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/298
  • Fix migrations from #293 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/299
  • Correct DOI in citation.cff to point to latest by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/301
  • 300 Protect User.center relation by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/304
  • 302 Don't load Django fixture data on AWS deployment by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/305
  • 295 Fix center deletion by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/297
  • Use AWS secrets for DJANGOLOGLEVEL so it can be configured from AWS… by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/306
  • Remove assert len(settings.DATABASES) == 2 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/307
  • Fix password reset email by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/308
  • Dedupe from_email from #308 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/309
  • Add EMAIL_TIMEOUT settings to debug #285 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/310
  • Use env vars and aws secrets for all email settings by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/311

Full Changelog: https://github.com/RISPaDD/biospecdb/compare/v1.0.0...v1.0.1

- Python
Published by jamienoss over 2 years ago

biospecdb - v1.0.0

What's Changed

  • Correct path for media file removal by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/157
  • Use storage.delete() instead of os.remove() by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/158
  • Close file before attempting to remove from fs (required for windows) by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/156
  • Bump pytest from 7.4.0 to 7.4.3 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/163
  • Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/160
  • Bump xlsxwriter from 3.1.2 to 3.1.9 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/162
  • Bump django from 4.2.5 to 4.2.7 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/161
  • Bump pytest-django from 4.5.2 to 4.6.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/159
  • Clean before saving in uploader.loaddata.savedatato_db by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/166
  • Deactivate data input form by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/168
  • Model BioSample.sample_type by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/169
  • Model spectralData.spectra_measurement by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/170
  • Store spectral data file on file as json and in memory as dataclass by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/167
  • Don't use login shell for test action by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/171
  • Replace symptom -> observation & disease -> observable by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/173
  • Migration for #177 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/175
  • Add models.Observable.category by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/174
  • Refactor admin classes adding mixins by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/176
  • Cast None as None in uploader.base_models.Types.cast by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/178
  • Add nested inline forms to data admin by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/179
  • Filter only existing bool pie chart data by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/184
  • Check against null self.data.name rather than self.data by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/181
  • Restrict access to home to staff users (all pages now require login) by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/180
  • Run annotator for new annotation on save and not clean by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/182
  • Bump pandas from 2.1.0 to 2.1.3 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/195
  • Bump ruff from 0.0.288 to 0.1.7 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/197
  • Bump plotly from 5.17.0 to 5.18.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/194
  • Bump setuptools from 68.2.2 to 69.0.2 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/192
  • Restrict access to SQL explorer to superusers only by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/187
  • Bump setuptools-scm[toml] from 8.0.3 to 8.0.4 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/191
  • Default User.is_staff=True by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/189
  • Relate instrument and center by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/185
  • Admin tweaks by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/183
  • Explicitly set login URL and fix anonymous missing User.is_sqluser attr by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/198
  • Bulk upload: find existing patient against CID AND center, not just CID by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/190
  • Remove data inpout form by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/199
  • Don't chart "empty" data by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/201
  • Refactor model bulk upload parsing by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/202
  • Expand instrument and measurement fields by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/200
  • Add data catalog app by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/196
  • Individual persistent docker volumes for media files by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/204
  • Bump pytest-django from 4.6.0 to 4.7.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/206
  • Bump httpx from 0.25.0 to 0.26.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/208
  • Bump tox from 4.11.3 to 4.11.4 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/205
  • Bump bandit from 1.7.5 to 1.7.6 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/209
  • List observables by category in inline forms plus other admin tweaks by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/203
  • Bump sphinx-rtd-theme from 1.3.0 to 2.0.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/207
  • Gunicorn, nginx, and (semi) prd deployment by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/210
  • SSL support by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/211
  • Remove Visit.previous_visit by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/212
  • 152 Don't remove sqlite3 files but only db/sqlite3 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/214
  • Revert "Remove Visit.previous_visit" by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/215
  • Improvements to Visit.previous_visit by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/216
  • Add Visit.daysobserved and re-handle Observation.daysobserved & Observation.severity by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/217
  • Delete media files upon deletion from db by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/218
  • Update missing catalog migration by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/222
  • Make Visit.patientage -> Observable(category=PATIENTINFO, name='patient_age') by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/223
  • Use GitHub actions cache for pip deps by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/221
  • Use DB-side count rather than len(queryset) by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/224
  • Add favicon by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/227
  • Fix previousvisit formfieldfor_foreignkey regression from #216 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/226
  • Bump pytest-django from 4.7.0 to 4.8.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/232
  • Turn codecov back on for dependabot PRs by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/234
  • Bump setuptools from 69.0.2 to 69.0.3 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/233
  • Bump bandit from 1.7.6 to 1.7.7 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/230
  • Bump pandas from 2.1.3 to 2.2.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/231
  • Add prune_files management command to delete orphaned files by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/220
  • Expand BioSample model fields by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/235
  • Only auto-populate Observation.observable for inline forms by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/236
  • Remove old model commented-out code by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/237
  • Collapsable inline observations by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/240
  • Add DB model diagram to README by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/241
  • Gender observable by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/239
  • Fix formfieldforforeignkey inheritance call order clobbering by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/228
  • Explicit SQL table names by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/243
  • Exclude user, catalog, & uploader_center from sql explorer schema by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/244
  • Bump tox from 4.11.4 to 4.12.1 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/229
  • Return 301 (permanent), not 307 (temporary) redirect http resp by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/247
  • Add health checks by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/246
  • Fix bulk upload patient center bug & non-form-field validation errors by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/245
  • Bump django from 4.2.7 to 4.2.10 in /requirements by @dependabot in https://github.com/RISPaDD/biospecdb/pull/238
  • Add get_column_names.py management command by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/242
  • Don't run Model.clean() when field errors already exist by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/250
  • Double down on SQL explorer access perm settings by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/251
  • Remove tech support link to ssec by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/252
  • Add basic info for url path usage by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/254
  • Semantic changes to Observable.center and form auto inlining by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/225
  • Docker healthchecks by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/248
  • Add password recovery by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/253
  • Session expirations settings to auto-expire by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/261
  • Separate out deps into more req files by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/263
  • Bump plotly from 5.18.0 to 5.19.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/256
  • Bump django from 4.2.10 -> 4.2.11 by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/264
  • Bump django-sql-explorer[charts] from 3.2.1 to 4.0.2 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/260
  • Use Django storage API for all file access by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/265
  • Use django-crontab to run prune_files as a cronjob by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/266
  • Bump httpx from 0.26.0 to 0.27.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/258
  • Bump pytest from 7.4.3 to 8.1.1 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/267
  • Nuke unused sphinx-issues dep by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/269
  • Nuke SSEC center and replace usage with spadda by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/270
  • Trigger sql-explorer to rebuild schema info by invalidating cached schema entries by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/268
  • AWS AppRunner setup w/postgres RDS by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/255
  • Exclude from sql-explorer schema health_check & whitenoise app tables by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/272
  • Dedupe domain_name setting by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/273
  • run prune_files on deployment by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/274
  • Add version view by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/262
  • Update repo urls by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/280
  • Update codecov badge by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/281
  • Update zenodo badge by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/282
  • Update AWS secret ARNs for apprunner by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/283
  • Hook up AWS workmail account via SES and SMTP gateway by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/284
  • Auto gen sql view columns from model fields by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/271
  • Bump bandit from 1.7.7 to 1.7.8 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/275
  • Bump pandas from 2.2.0 to 2.2.1 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/276
  • Bump xlsxwriter from 3.1.9 to 3.2.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/279
  • Bump build from 1.0.3 to 1.1.1 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/278
  • Bump sphinx-automodapi from 0.16.0 to 0.17.0 by @dependabot in https://github.com/RISPaDD/biospecdb/pull/277
  • Remove explicit urls from Home.html & change app title by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/288
  • Add utility funcs & scripts to retrieve AWS secrets, parsed from apprunner.yaml by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/290
  • 289 Correct static path in Home.html by @jamienoss in https://github.com/RISPaDD/biospecdb/pull/291

Full Changelog: https://github.com/RISPaDD/biospecdb/compare/v0.1.2...v1.0.0

- Python
Published by jamienoss over 2 years ago

biospecdb - v0.1.2

What's Changed

  • Update DOI with version that points to latest by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/155

Full Changelog: https://github.com/ssec-jhu/biospecdb/compare/v0.1.1...v0.1.2

- Python
Published by jamienoss over 2 years ago

biospecdb - v0.1.1

What's Changed

  • Update zenodo doi by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/154

Full Changelog: https://github.com/ssec-jhu/biospecdb/compare/v0.1.0...v0.1.1

- Python
Published by jamienoss over 2 years ago

biospecdb - v0.1.0

What's Changed

  • Updates from base template by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/10
  • Replace refs to flake8 -> ruff by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/11
  • Turn off uploads to codecov.io until repo is public by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/12
  • Simple plotly dash example by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/9
  • Bump ruff from 0.0.263 to 0.0.270 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/14
  • Django setup by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/8
  • Bump tox from 4.5.1 to 4.6.0 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/16
  • Bump httpx from 0.24.0 to 0.24.1 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/6
  • Bump pytest-cov from 4.0.0 to 4.1.0 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/17
  • Bump sphinx-rtd-theme from 1.2.0 to 1.2.2 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/18
  • Change dependabot sched from weekly -> monthly by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/19
  • Bump ruff from 0.0.270 to 0.0.272 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/20
  • Bump nbsphinx from 0.9.1 to 0.9.2 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/21
  • Bump django from 4.2.1 to 4.2.2 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/22
  • File upload - beta version by @vkluzner in https://github.com/ssec-jhu/biospecdb/pull/23
  • Improved model by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/24
  • Bump tox from 4.6.0 to 4.6.3 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/34
  • Bump ruff from 0.0.272 to 0.0.275 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/33
  • Bump pytest from 7.3.1 to 7.4.0 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/32
  • Bump django from 4.2.2 to 4.2.3 in /requirements by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/35
  • Remove QC fields from data model by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/36
  • Bulk upload to models by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/29
  • Use SQL explorer for raw SQL querying dashboard by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/41
  • Fix schema exclusions by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/50
  • Fix silly typo when calling super by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/51
  • Nuke some fields from the model by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/53
  • 42 Validate Symptom disease value can be cast to expected disease value type by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/54
  • 52 Make Disease.name and Disease.alias unique by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/55
  • Bump django from 4.2.3 to 4.2.4 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/58
  • Add mockdata pytest fixture that loads our mocked django fixture data testdata.json by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/49
  • Fix days symptomatic bug in loaddata by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/62
  • Bump tox from 4.6.3 to 4.6.4 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/59
  • Bump uvicorn[standard] from 0.22.0 to 0.23.2 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/57
  • Bump ruff from 0.0.275 to 0.0.286 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/67
  • Add db views by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/56
  • Adding some basic framework for QC validation plugins. by @amitschang in https://github.com/ssec-jhu/biospecdb/pull/25
  • Refactor getfileinfo to biospecdb.utils by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/68
  • Django data migration for #56 by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/70
  • Bump nbsphinx from 0.9.2 to 0.9.3 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/74
  • Add updatesqlviews management command by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/79
  • Implement QC validators and annotators by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/69
  • Improve admin forms by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/80
  • Give app verbose name by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/87
  • Test updatesqlviews management command by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/88
  • Allow QCAnnotator.value_type to be editable from admin page by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/89
  • Bump pandas from 2.0.3 to 2.1.0 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/76
  • Bump build from 0.10.0 to 1.0.3 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/90
  • Bump ruff from 0.0.286 to 0.0.288 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/92
  • Bump tox from 4.6.4 to 4.11.3 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/91
  • Data Input Form by @vkluzner in https://github.com/ssec-jhu/biospecdb/pull/64
  • Redirect root url to home by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/94
  • Editable patient ID by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/96
  • Add plots to sql-explorer results pages by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/85
  • Zip spectraldata files with data downloads from sql-explorer by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/78
  • Form validation must also include full model validations and not just model field validations. by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/95
  • Use forms.NullBooleanField instead of forms.BooleanField by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/99
  • Index as UUID and validate bulk upload indexes match by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/102
  • Dynamic instrument addition by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/103
  • Annotate in save and not clean by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/107
  • Add 'Unspecified' gender by @vkluzner in https://github.com/ssec-jhu/biospecdb/pull/105
  • Run CI testing using tox by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/111
  • Update README with custom management commands and deployment settings by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/112
  • Register custom pytest markers by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/110
  • Add datedmodel base by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/84
  • List qcannotation updated time by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/113
  • Save bulk uploaded data in save and not clean by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/108
  • Use ModelChoicesField for instrument in form by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/106
  • Add io mod by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/114
  • Restrict data upload to 'staff' status by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/118
  • Add specific data (only) admin site by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/119
  • Add basic user permission groups by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/120
  • Add custom user app by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/121
  • Fix versioning and codecov by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/125
  • Create mulitple databases by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/124
  • Update codecov badge for README by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/126
  • Increase coverage of biosepcdb.util * uploader.charts by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/127
  • Disable codecov upload for dependabot PRs by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/133
  • Bump django from 4.2.4 to 4.2.5 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/132
  • Bump httpx from 0.24.1 to 0.25.0 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/131
  • Bump sphinx-automodapi from 0.15.0 to 0.16.0 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/130
  • git rm biospecdb/apps/uploader/fixtures/user_groups.json by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/134
  • Bump plotly from 5.16.1 to 5.17.0 by @dependabot in https://github.com/ssec-jhu/biospecdb/pull/129
  • Disable codecov inline PR annotations by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/135
  • Auto populate data input form by @vkluzner in https://github.com/ssec-jhu/biospecdb/pull/122
  • Add center model by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/116
  • Add dev DB rebuild scripts by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/136
  • Fix indent from #116 by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/140
  • Correct spectraldata filename by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/139
  • Nuke all uploaded files from scripts/dev/rebuild_db.sh by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/142
  • Rename UploadedFile verbose name -> 'Bulk Data Upload' by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/143
  • Update CI badges by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/145
  • Install requirements/docs.txt from .readthedocs.yml by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/144
  • Update doc build by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/146
  • Update README docs badge by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/147
  • Post review changes to #138 by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/148
  • Add previous visit finding functionality by @vkluzner in https://github.com/ssec-jhu/biospecdb/pull/138
  • Update .gitignore by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/149
  • Update docker build by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/150
  • Use dynamic package versioning when building docs by @jamienoss in https://github.com/ssec-jhu/biospecdb/pull/153

New Contributors

  • @dependabot made their first contribution in https://github.com/ssec-jhu/biospecdb/pull/14
  • @vkluzner made their first contribution in https://github.com/ssec-jhu/biospecdb/pull/23
  • @amitschang made their first contribution in https://github.com/ssec-jhu/biospecdb/pull/25

Full Changelog: https://github.com/ssec-jhu/biospecdb/commits/v0.1.0

- Python
Published by jamienoss over 2 years ago