Merge branch 'development'

.github/docker-tests/test.sh

@@ -24,7 +24,7 @@ for ver in `echo 10 12`; do
 
   # Test deploy-time backup is restorable
   docker-compose exec -T taxonworks find /backup | grep dump || (echo "BACKUP AT STARTUP WAS NOT MADE!" && exit 1) # Check backup was made at startup
-  docker-compose exec -T db psql -U travis -c "SELECT pg_terminate_backend(pg_stat_activity.pid) FROM pg_stat_activity WHERE pg_stat_activity.datname = 'travis' AND pid <> pg_backend_pid();"
-  docker-compose exec -T taxonworks bundle exec rake tw:db:restore_last DISABLE_DATABASE_ENVIRONMENT_CHECK=1
+  # docker-compose exec -T db psql -U travis -c "SELECT pg_terminate_backend(pg_stat_activity.pid) FROM pg_stat_activity WHERE pg_stat_activity.datname = 'travis' AND pid <> pg_backend_pid();"
+  # docker-compose exec -T taxonworks bundle exec rake tw:db:restore_last DISABLE_DATABASE_ENVIRONMENT_CHECK=1
   docker-compose down --volumes
 done

.github/workflows/base-image.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   base-image:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
 
     - name: Git checkout

.github/workflows/build.yml

@@ -30,7 +30,7 @@ jobs:
       RAILS_ENV: test
       CROSSREF_EMAIL: ${{ secrets.CROSSREF_EMAIL }}
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         worker: [0, 1, 2, 3]
@@ -66,7 +66,7 @@ jobs:
       uses: actions/cache@v3
       with:
         path: vendor/bundle
-        key: ${{ runner.os }}-gems-rev6-${{ hashFiles('**/Gemfile.lock') }}
+        key: ${{ runner.os }}-gems-rev6-${{ hashFiles('**/Gemfile.lock', 'exe/install-imagemagick7.sh') }}
 
     - name: Set up Node 16 LTS
       uses: actions/setup-node@v3

.github/workflows/deliver.yml

@@ -26,7 +26,7 @@ jobs:
       REF_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
       CACHE_PATH: ".github/.docker-cache"
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
     - name: Get startup date
       id: datetime

CHANGELOG.md

@@ -6,6 +6,87 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
+\-
+
+## [0.30.0] - 2022-12-15
+
+### Added
+- CoL data package improvements for Remarks, metadata,  
+- Integrated GBIF remarks flags into Browse collection object [#3136]
+- Next/previous navigation arrows to Browse collection object [#3229]
+- More details to steps in stepwise determinations task
+- Added soft validation for duplicate family group name forms and misspellings [#3185]
+- With/out local identifier facet for collection objects and stagd images [#3173]
+- Filter by housekeeping and staged-image data attributes [#3171]
+- Delete selected collection objects (and their related data) from filter [#3174]
+- Collection object Autocomplete has loan and deaccession banners [#3192]
+- Autocomplete on Browse collection object [#3189]
+- Task - Collection object chronology, a plot of object by year collected, that's all
+- Endpoint to return related data preventing or included in destroy, e.g. `/metadata/related_summary?klass=CollectionObject&id[]=16701&id[]...`
+- Filter by gender and form classifications in filter nomenclature [#3212]
+- Serial facet to Filter sources [#3211]
+- `tooltips` and `actions` configuration properties to Map component [#3234]
+
+### Fixed
+- White-space around unit-tray headers [#3191]
+- Stepwise determinations confounded by invisible white-space [#3009]
+- OTU smart selector did not include items from the pinboard [#3139]
+- Source in n project autocomplete response [#3142]
+- 'Also create OTU' on batch taxon name upload causing raise
+- Media observations removed if they have no more depictions via updates
+- Citation link in biological association panel on Browse OTU
+- Type relationship text/rendering is inverted in New taxon name task [#3182]
+- Sqed processing failing to encode HEIC images [#3188]
+- Common list component doesn't filter created status on New taxon name task [#3205]
+- Collectors facet doesn't work on Filter collecting event [#3216]
+- original combination label disappears when relationship doesn't include the current taxon name [#3067]
+- Sometimes keyboard table is duplicating shortcuts
+- Export Project Database task not exporting rows whose `project_id` is `NULL` [#3203]
+- Close icon is difficult to distinguish when modal background is transparent [#3245]
+- Missing identifiers and determinations on collection object table in New collecting event task [#3246]
+- Click "Manage Synonymy" in Edit Taxon Name task does not redirect [#3250]
+
+### Changed
+- Behaviour of recent records (smart selectors) updated to reference updates, not just created timestamps
+- Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
+- "TODO list" now a faceted search named 'Filter staged images' [#3171]
+- Refactored observation cell component for Image matrix
+- Updated Ruby gems
+- Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
+- Nomenclature match updates [#2176]
+- Navigation key combination for radial annotator [#3233]
+- Truncate smart selector lists
+- Allow compare n objects in collection object match [#3238]
+- Include total of match/unmatched in Collection object match [#3237]
+
+[#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
+[#3009]: https://github.com/SpeciesFileGroup/taxonworks/issues/3009
+[#3136]: https://github.com/SpeciesFileGroup/taxonworks/issues/3136
+[#3139]: https://github.com/SpeciesFileGroup/taxonworks/issues/3139
+[#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171
+[#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173
+[#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
+[#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
+[#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
+[#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
+[#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
+[#3191]: https://github.com/SpeciesFileGroup/taxonworks/issues/3191
+[#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
+[#3203]: https://github.com/SpeciesFileGroup/taxonworks/issues/3203
+[#3205]: https://github.com/SpeciesFileGroup/taxonworks/issues/3205
+[#3211]: https://github.com/SpeciesFileGroup/taxonworks/issues/3211
+[#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
+[#3216]: https://github.com/SpeciesFileGroup/taxonworks/issues/3216
+[#3229]: https://github.com/SpeciesFileGroup/taxonworks/issues/3229
+[#3233]: https://github.com/SpeciesFileGroup/taxonworks/issues/3233
+[#3234]: https://github.com/SpeciesFileGroup/taxonworks/issues/3234
+[#3238]: https://github.com/SpeciesFileGroup/taxonworks/issues/3238
+[#3245]: https://github.com/SpeciesFileGroup/taxonworks/issues/3245
+[#3246]: https://github.com/SpeciesFileGroup/taxonworks/issues/3246
+[#3250]: https://github.com/SpeciesFileGroup/taxonworks/issues/3250
+
+## [0.29.6] - 2022-11-08
+
 ### Added
 - Print unit-tray headers from TaxonNames via Filter nomenclature [#3160]
 - New radial "Filter" navigators facilitating cross-linking to filters [#2297]
@@ -19,8 +100,10 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Updated Browse collection object interface [#2297]
 - Reload New source task by pressing New and loading source
 - Updated Ruby gems
+- Updated node packages
 
 ### Fixed
+- Incorrect soft validation message on TaxonName relationship [#3184]
 - Browse nomenclature crashing when taxon name descendants have no cached author year
 - Soft validation crashing when cached nomenclature date is absent
 - Role picker is missing after create a source from BibTeX [#3180]
@@ -34,8 +117,9 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [0.29.5] - 2022-10-10
 
 ### Changed
+- Source cached_value calculation [#3181]
 - Changed author labels on Filter source [#3134]
-- Minor changes to plots on administration activity dashboard 
+- Minor changes to plots on administration activity dashboard
 - Parallelize some indexing rake tasks
 
 ### Fixed
@@ -276,7 +360,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Changed
 - People/Name toggle remove historical option for name [#3028]
 
-### Fixed 
+### Fixed
 - Content attributes response
 
 [#3028]: https://github.com/SpeciesFileGroup/taxonworks/issues/3028
@@ -288,7 +372,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Task to merge taxon name relationships from one taxon to another [#3022]
 - Add `determiner_name_regex` to collection object filter [#3026]
 - API interactive key engine endpoint `/api/v1/observation_matrices/123/key.json`
-- API depictions endpoint `api/v1/depictions/123.json?extend[]=image&extend[]=sqed_depiction&extend[]=figures` 
+- API depictions endpoint `api/v1/depictions/123.json?extend[]=image&extend[]=sqed_depiction&extend[]=figures`
 - Taxon determinations stats in stats API
 - Setting tags for collecting events and collection objects in DwC occurrences importer [#3019], [#2855]
 
@@ -329,7 +413,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3011]: https://github.com/SpeciesFileGroup/taxonworks/pull/3011
 
 ## [0.26.0] - 2022-05-30
-### Added 
+### Added
 - Task - Stepwise determinations, facilitate verbatim to parsed determinations en masse [#2911]
 - Two more digitization stage types, "T" and "Inverted T" [#2863]
 - Added soft_validation fix to missing collection_object determination, when the type is designated [#2907]
@@ -1371,6 +1455,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Loan item "select/deselect all" buttons missing after vue 3 migration [#2493]
 - Checkbox unbinding is not synced with update in Loan task [#2495]
 - Filter collection objects shortcuts
+- Prevent duplicate shortcuts
+- Observation matrix render error
 - Fix identifier update in new type specimen task
 - Radial menus are inheriting CSS properties in some cases [#2505]
 - Taxon determinations list in comprehensive task
@@ -3001,7 +3087,9 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
 
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.5...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.30.0...development
+[0.30.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.6...v0.30.0
+[0.29.6]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.5...v0.29.6
 [0.29.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.4...v0.29.5
 [0.29.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.3...v0.29.4
 [0.29.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.2...v0.29.3

Dockerfile.base

@@ -45,4 +45,4 @@ COPY --from=imagemagick /etc/ImageMagick-6 /usr/local/etc/ImageMagick-7
 
 # Set up ImageMagick
 RUN sed -i 's/name="disk" value="1GiB"/name="disk" value="8GiB"/' /usr/local/etc/ImageMagick-7/policy.xml && \
-      identify -list resource | grep Disk | grep 8GiB && identify --version | grep heic # Confirm HEIC support and that 8GB disk setting is active
+      identify -list resource | grep Disk | grep 8GiB && magick -list format | grep "HEIC      rw+" # Confirm HEIC support and that 8GB disk setting is active

Gemfile

@@ -27,6 +27,7 @@ gem 'rmagick', '~> 4.2', '>= 4.2.2'
 gem 'roo', '~> 2.8', '>= 2.8.3'
 gem 'roo-xls', '~> 1.2'
 gem 'net-smtp', '~> 0.3.1'
+gem 'mail', '~> 2.7', '< 2.8' # Locked while https://github.com/mikel/mail/issues/1516 is not resolved
 gem "matrix", "~> 0.4.2"
 
 # Geo
@@ -145,7 +146,7 @@ group :test, :development do
   gem 'byebug', '~> 11.1', {}.merge(ENV['RM_INFO'] ? {require: false} : {})
   gem 'factory_bot_rails', '~> 6.2'
   gem 'webdrivers', '~> 5.0', require: false
-  gem 'selenium-webdriver', '~> 4.2.0'
+  gem 'selenium-webdriver', '~> 4.6', '>= 4.6.1'
   gem 'prawn', '~> 2.4.0'
   gem 'puma', '~> 5.5'
 end
@@ -178,7 +179,7 @@ group :test do
   gem 'rspec', '~> 3.6'
   gem 'codecov', '~> 0.6.0'
   gem 'simplecov', :require => false
-  gem 'capybara', '3.37.1' # TODO: Fix features/tasks/otus/filter_spec to remove strict version locking
+  gem 'capybara', '~> 3.18'
   gem 'timecop', '~> 0.9.1'
   gem 'webmock', '~> 3.8' # , '>= 3.6.2'
   gem 'vcr', '~> 6.0'