v1.1.3

What's Changed

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

Full Changelog: v1.1.2...v1.1.3

v1.1.2

What's Changed

• Drop SQL views before migrating by @jamienoss in #331
• Fail early in model.full_clean so field validators bubble up by @jamienoss in #333

Full Changelog: v1.1.1...v1.1.2

v1.1.1

What's Changed

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

Full Changelog: v1.1.0...v1.1.1

v1.1.0

What's Changed

• Bulk upload on patient_cid not patient_id by @jamienoss in #317
• Bump ruff from 0.1.7 to 0.3.5 by @dependabot in #316
• Bump setuptools from 69.0.3 to 69.2.0 by @dependabot in #315
• Bump build from 1.1.1 to 1.2.1 by @dependabot in #313

Full Changelog: v1.0.1...v1.1.0

v1.0.1

What's Changed

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

Full Changelog: v1.0.0...v1.0.1

v1.0.0

What's Changed

• Correct path for media file removal by @jamienoss in #157
• Use storage.delete() instead of os.remove() by @jamienoss in #158
• Close file before attempting to remove from fs (required for windows) by @jamienoss in #156
• Bump pytest from 7.4.0 to 7.4.3 by @dependabot in #163
• Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 by @dependabot in #160
• Bump xlsxwriter from 3.1.2 to 3.1.9 by @dependabot in #162
• Bump django from 4.2.5 to 4.2.7 by @dependabot in #161
• Bump pytest-django from 4.5.2 to 4.6.0 by @dependabot in #159
• Clean before saving in uploader.loaddata.save_data_to_db by @jamienoss in #166
• Deactivate data input form by @jamienoss in #168
• Model BioSample.sample_type by @jamienoss in #169
• Model spectralData.spectra_measurement by @jamienoss in #170
• Store spectral data file on file as json and in memory as dataclass by @jamienoss in #167
• Don't use login shell for test action by @jamienoss in #171
• Replace symptom -> observation & disease -> observable by @jamienoss in #173
• Migration for #177 by @jamienoss in #175
• Add models.Observable.category by @jamienoss in #174
• Refactor admin classes adding mixins by @jamienoss in #176
• Cast None as None in uploader.base_models.Types.cast by @jamienoss in #178
• Add nested inline forms to data admin by @jamienoss in #179
• Filter only existing bool pie chart data by @jamienoss in #184
• Check against null self.data.name rather than self.data by @jamienoss in #181
• Restrict access to home to staff users (all pages now require login) by @jamienoss in #180
• Run annotator for new annotation on save and not clean by @jamienoss in #182
• Bump pandas from 2.1.0 to 2.1.3 by @dependabot in #195
• Bump ruff from 0.0.288 to 0.1.7 by @dependabot in #197
• Bump plotly from 5.17.0 to 5.18.0 by @dependabot in #194
• Bump setuptools from 68.2.2 to 69.0.2 by @dependabot in #192
• Restrict access to SQL explorer to superusers only by @jamienoss in #187
• Bump setuptools-scm[toml] from 8.0.3 to 8.0.4 by @dependabot in #191
• Default User.is_staff=True by @jamienoss in #189
• Relate instrument and center by @jamienoss in #185
• Admin tweaks by @jamienoss in #183
• Explicitly set login URL and fix anonymous missing User.is_sqluser attr by @jamienoss in #198
• Bulk upload: find existing patient against CID AND center, not just CID by @jamienoss in #190
• Remove data inpout form by @jamienoss in #199
• Don't chart "empty" data by @jamienoss in #201
• Refactor model bulk upload parsing by @jamienoss in #202
• Expand instrument and measurement fields by @jamienoss in #200
• Add data catalog app by @jamienoss in #196
• Individual persistent docker volumes for media files by @jamienoss in #204
• Bump pytest-django from 4.6.0 to 4.7.0 by @dependabot in #206
• Bump httpx from 0.25.0 to 0.26.0 by @dependabot in #208
• Bump tox from 4.11.3 to 4.11.4 by @dependabot in #205
• Bump bandit from 1.7.5 to 1.7.6 by @dependabot in #209
• List observables by category in inline forms plus other admin tweaks by @jamienoss in #203
• Bump sphinx-rtd-theme from 1.3.0 to 2.0.0 by @dependabot in #207
• Gunicorn, nginx, and (semi) prd deployment by @jamienoss in #210
• SSL support by @jamienoss in #211
• Remove Visit.previous_visit by @jamienoss in #212
• 152 Don't remove *sqlite3 files but only db/*sqlite3 by @jamienoss in #214
• Revert "Remove Visit.previous_visit" by @jamienoss in #215
• Improvements to Visit.previous_visit by @jamienoss in #216
• Add Visit.days_observed and re-handle Observation.days_observed & Observation.severity by @jamienoss in #217
• Delete media files upon deletion from db by @jamienoss in #218
• Update missing catalog migration by @jamienoss in #222
• Make Visit.patient_age -> Observable(category=PATIENT_INFO, name='patient_age') by @jamienoss in #223
• Use GitHub actions cache for pip deps by @jamienoss in #221
• Use DB-side count rather than len(queryset) by @jamienoss in #224
• Add favicon by @jamienoss in #227
• Fix previous_visit formfield_for_foreignkey regression from #216 by @jamienoss in #226
• Bump pytest-django from 4.7.0 to 4.8.0 by @dependabot in #232
• Turn codecov back on for dependabot PRs by @jamienoss in #234
• Bump setuptools from 69.0.2 to 69.0.3 by @dependabot in #233
• Bump bandit from 1.7.6 to 1.7.7 by @dependabot in #230
• Bump pandas from 2.1.3 to 2.2.0 by @dependabot in #231
• Add prune_files management command to delete orphaned files by @jamienoss in #220
• Expand BioSample model fields by @jamienoss in #235
• Only auto-populate Observation.observable for inline forms by @jamienoss in #236
• Remove old model commented-out code by @jamienoss in #237
• Collapsable inline observations by @jamienoss in #240
• Add DB model diagram to README by @jamienoss in #241
• Gender observable by @jamienoss in #239
• Fix formfield_for_foreignkey inheritance call order clobbering by @jamienoss in #228
• Explicit SQL table names by @jamienoss in #243
• Exclude user, catalog, & uploader_center from sql explorer schema by @jamienoss in #244
• Bump tox from 4.11.4 to 4.12.1 by @dependabot in #229
• Return 301 (permanent), not 307 (temporary) redirect http resp by @jamienoss in #247
• Add health checks by @jamienoss in #246
• Fix bulk upload patient center bug & non-form-field validation errors by @jamienoss in #245
• Bump django from 4.2.7 to 4.2.10 in /requirements by @dependabot in #238
• Add get_column_names.py management command by @jamienoss in #242
• Don't run Model.clean() when field errors already exist by @jamienoss in #250
• Double down on SQL explorer access perm settings by @jamienoss in #251
• Remove tech support link to ssec by @jamienoss in #252
• Add basic info for url path usage by @jamienoss in #254
• Semantic changes to Observable.center and form auto inlining by @jamienoss in #225
• Docker healthchecks by @jamienoss in #248
• Add password recovery by @jamienoss in #253
• Session expirations settings to auto-expire by @jamienoss in #261
• Separate out deps into more req files by @jamienoss in #263
• Bump plotly from 5.18.0 to 5.19.0 by @dependabot in #256
• Bump django from 4.2.10 -> 4.2.11 by @jamienoss in https://github.co...

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: ssec-jhu/biospecdb@v0.1.1...v0.1.2

v0.1.1

What's Changed

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

Full Changelog: ssec-jhu/biospecdb@v0.1.0...v0.1.1

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 mock_data pytest fixture that loads our mocked django fixture data test_data.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 get_file_info 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 update_sql_views 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 update_sql_views 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...