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 #264
• Bump django-sql-explorer[charts] from 3.2.1 to 4.0.2 by @dependabot in #260
• Use Django storage API for all file access by @jamienoss in #265
• Use django-crontab to run prune_files as a cronjob by @jamienoss in #266
• Bump httpx from 0.26.0 to 0.27.0 by @dependabot in #258
• Bump pytest from 7.4.3 to 8.1.1 by @dependabot in #267
• Nuke unused sphinx-issues dep by @jamienoss in #269
• Nuke SSEC center and replace usage with spadda by @jamienoss in #270
• Trigger sql-explorer to rebuild schema info by invalidating cached schema entries by @jamienoss in #268
• AWS AppRunner setup w/postgres RDS by @jamienoss in #255
• Exclude from sql-explorer schema health_check & whitenoise app tables by @jamienoss in #272
• Dedupe domain_name setting by @jamienoss in #273
• run prune_files on deployment by @jamienoss in #274
• Add version view by @jamienoss in #262
• Update repo urls by @jamienoss in #280
• Update codecov badge by @jamienoss in #281
• Update zenodo badge by @jamienoss in #282
• Update AWS secret ARNs for apprunner by @jamienoss in #283
• Hook up AWS workmail account via SES and SMTP gateway by @jamienoss in #284
• Auto gen sql view columns from model fields by @jamienoss in #271
• Bump bandit from 1.7.7 to 1.7.8 by @dependabot in #275
• Bump pandas from 2.2.0 to 2.2.1 by @dependabot in #276
• Bump xlsxwriter from 3.1.9 to 3.2.0 by @dependabot in #279
• Bump build from 1.0.3 to 1.1.1 by @dependabot in #278
• Bump sphinx-automodapi from 0.16.0 to 0.17.0 by @dependabot in #277
• Remove explicit urls from Home.html & change app title by @jamienoss in #288
• Add utility funcs & scripts to retrieve AWS secrets, parsed from apprunner.yaml by @jamienoss in #290
• 289 Correct static path in Home.html by @jamienoss in #291

Full Changelog: v0.1.2...v1.0.0