tripal/tripal: Release v4.0.0-alpha3

<!-- Release notes generated using configuration in .github/release.yaml at 4.x --> What's Changed Deprecations Actually deprecate the Chado Query API in favour of Tripal DBX. by @laceysanderson in https://github.com/tripal/tripal/pull/2294 Remove deprecated functions from importers by @dsenalik in https://github.com/tripal/tripal/pull/2297 New Controller Class to replace the ChadoOrganismAutocompleteController by @vidu-wil in https://github.com/tripal/tripal/pull/2293 Bug Fixes Update Symbolic Link for base Dockerfile by @laceysanderson in https://github.com/tripal/tripal/pull/1777 GFF importer, fix loading gene sequence from FASTA section by @dsenalik in https://github.com/tripal/tripal/pull/1835 Update chado prepare sql for automated tests by @dsenalik in https://github.com/tripal/tripal/pull/1849 Catch adding Chado field to non-Chado content type by @dsenalik in https://github.com/tripal/tripal/pull/1846 Fix data leak between publish calls by @laceysanderson in https://github.com/tripal/tripal/pull/1841 Fix sequence coordinates widget when creating new feature by @dsenalik in https://github.com/tripal/tripal/pull/1874 remove duplicated yaml by @dsenalik in https://github.com/tripal/tripal/pull/1901 OBO importer - fix unsubstituted message by @dsenalik in https://github.com/tripal/tripal/pull/1905 Fix ogi CV definition by @dsenalik in https://github.com/tripal/tripal/pull/1909 Synonym field was broken on Drupal ≥ 10.2 by @dsenalik in https://github.com/tripal/tripal/pull/1918 Set default terms for field properties when chado mapping is missing. by @laceysanderson in https://github.com/tripal/tripal/pull/1940 ChadoAdditionalTypeTypeDefault can be manually added by @dsenalik in https://github.com/tripal/tripal/pull/1942 don't add to render array if no value by @dsenalik in https://github.com/tripal/tripal/pull/1949 Handle inline template and link for HTML replacements in the title by @laceysanderson in https://github.com/tripal/tripal/pull/1965 Revert one change from PR #1882 by @dsenalik in https://github.com/tripal/tripal/pull/1921 Ensure TripalFields can be added through UI and add some tests by @laceysanderson in https://github.com/tripal/tripal/pull/1968 Fix dbxref "Add another item" bug by @dsenalik in https://github.com/tripal/tripal/pull/1962 Publish update - no drupal records when no chado records by @dsenalik in https://github.com/tripal/tripal/pull/1977 Github workflow forces people to accept chado :-p by @laceysanderson in https://github.com/tripal/tripal/pull/1998 fix issue #2010 by @dsenalik in https://github.com/tripal/tripal/pull/2011 Define third-party schema in tripal entity type as well by @laceysanderson in https://github.com/tripal/tripal/pull/2026 Add character column type to string field type by @dsenalik in https://github.com/tripal/tripal/pull/2063 Ensure it's not the same field when checking for existing terms. by @laceysanderson in https://github.com/tripal/tripal/pull/2093 Ensure field has settings for view mode before adding them. by @laceysanderson in https://github.com/tripal/tripal/pull/2095 Resolves duplicated field names during discover by @dsenalik in https://github.com/tripal/tripal/pull/2096 Fix minor assay field bug by @dsenalik in https://github.com/tripal/tripal/pull/2099 Implement approach to update Drupal field tables following a chado schema update. by @laceysanderson in https://github.com/tripal/tripal/pull/2109 Ensure composer install works on all supported versions. by @laceysanderson in https://github.com/tripal/tripal/pull/2139 Fix discovery on unit type field by @dsenalik in https://github.com/tripal/tripal/pull/2178 Provide correct phpunit.xml version in 10.x docker images by @dsenalik in https://github.com/tripal/tripal/pull/2189 ChadoIdSpace/ChadoVocabulary Missing Values by @laceysanderson in https://github.com/tripal/tripal/pull/2185 Use phpunit 9.6 for any 10.x drupal version by @dsenalik in https://github.com/tripal/tripal/pull/2191 Support Field group 4.0 semversion update by @laceysanderson in https://github.com/tripal/tripal/pull/2200 Automated tests for property fields, widgets and formatters by @laceysanderson in https://github.com/tripal/tripal/pull/2133 Fix brittle test by adding check for NCBI maintenance mode by @dsenalik in https://github.com/tripal/tripal/pull/2246 Fix missing TripalEntityViewsData attribute by @dsenalik in https://github.com/tripal/tripal/pull/2264 Editing single-hop property field fixed by @dsenalik in https://github.com/tripal/tripal/pull/2271 Update Test Coverage Workflow to run on 4.x by @laceysanderson in https://github.com/tripal/tripal/pull/2277 Update OBO importer to work for EDAM by @dsenalik in https://github.com/tripal/tripal/pull/2280 Resolve missing germplasm cvterms in automated testing environment by @laceysanderson in https://github.com/tripal/tripal/pull/2288 Newick importer file is required, and options match tripal 3 by @dsenalik in https://github.com/tripal/tripal/pull/2299 Add missing optional parameter to getChadoForeignKeyDef() by @dsenalik in https://github.com/tripal/tripal/pull/2301 Fix discover bug by checking for foreign key in both directions by @dsenalik in https://github.com/tripal/tripal/pull/2305 Fixes "Organism Autocomplete adds trailing whitespace when infraspecific name is not present" by @laceysanderson in https://github.com/tripal/tripal/pull/2303 Content Pages, Fields + Display rename chado linker property field by @dsenalik in https://github.com/tripal/tripal/pull/1755 Repair the field debugger by @dsenalik in https://github.com/tripal/tripal/pull/1766 Default Layouts by @spficklin in https://github.com/tripal/tripal/pull/1792 Tripal 4 sequence coordinate field by @pdtouch in https://github.com/tripal/tripal/pull/1700 New base table third party setting + Drupal 10.2 fixes by @dsenalik in https://github.com/tripal/tripal/pull/1805 CV terms on all fields by @spficklin in https://github.com/tripal/tripal/pull/1790 Add missing terms for some chado columns, defining when necessary by @dsenalik in https://github.com/tripal/tripal/pull/1819 Fix bug in publish showing up in testing environment by @dsenalik in https://github.com/tripal/tripal/pull/1854 New Widgets for Property Fields by @laceysanderson in https://github.com/tripal/tripal/pull/1851 Fixes validation missing values bug by @dsenalik in https://github.com/tripal/tripal/pull/1855 Allow fields to link to their corresponding entity by @dsenalik in https://github.com/tripal/tripal/pull/1782 Fix dbxref field, observed after GFF3 importer by @dsenalik in https://github.com/tripal/tripal/pull/1860 Enable Wysiwyg toolbar for Tripal/Chado Text fields by @laceysanderson in https://github.com/tripal/tripal/pull/1862 Fix the sequence coordinates field by @dsenalik in https://github.com/tripal/tripal/pull/1861 Implement the fallback entity lookup by @dsenalik in https://github.com/tripal/tripal/pull/1865 URL and name field filters default to plain text by @dsenalik in https://github.com/tripal/tripal/pull/1871 Chado Contact by Role field by @laceysanderson in https://github.com/tripal/tripal/pull/1875 Checking for new fields by @spficklin in https://github.com/tripal/tripal/pull/1869 Add missing tripal icon for admin "Manage" toolbar by @dsenalik in https://github.com/tripal/tripal/pull/1887 Render HTML tags in page titles, e.g. organism scientifc name by @dsenalik in https://github.com/tripal/tripal/pull/1878 Fields move record_id_term to parent class by @dsenalik in https://github.com/tripal/tripal/pull/1889 add formatting settings to ChadoStringType field by @dsenalik in https://github.com/tripal/tripal/pull/1896 Unpublish UI by @spficklin in https://github.com/tripal/tripal/pull/1892 Tv4g1 issue1843 publishing cardinality by @spficklin in https://github.com/tripal/tripal/pull/1882 Tripal 4 yml typos by @dsenalik in https://github.com/tripal/tripal/pull/1903 Automated Field Testing: focused on the field creation forms in Drupal 10.2+ by @laceysanderson in https://github.com/tripal/tripal/pull/1842 Rename duplicated terms in tcontact.obo by @dsenalik in https://github.com/tripal/tripal/pull/1907 ChadoStorage::deleteValues() by @spficklin in https://github.com/tripal/tripal/pull/1912 Make sure the contact widget/formatter know they are compatible with both fields by @laceysanderson in https://github.com/tripal/tripal/pull/1943 Resolve discovered field name length problems by @dsenalik in https://github.com/tripal/tripal/pull/1929 Remove double-space collapse for publish by @dsenalik in https://github.com/tripal/tripal/pull/1931 Fix the "Remove" button on field widgets by @dsenalik in https://github.com/tripal/tripal/pull/1958 fix publish to store placeholders of proper type by @dsenalik in https://github.com/tripal/tripal/pull/1952 Update ChadoProperty Text widget to support filtered HTML by @laceysanderson in https://github.com/tripal/tripal/pull/1978 Provide validation for already-used field terms by @dsenalik in https://github.com/tripal/tripal/pull/1967 Update Tripal Layout to support configuring the Form Display by @laceysanderson in https://github.com/tripal/tripal/pull/1982 Add in schema for options all supported tripal_layout field group options. by @laceysanderson in https://github.com/tripal/tripal/pull/1993 Publishing in batches by @dsenalik in https://github.com/tripal/tripal/pull/1983 configurable mechanism for hiding fields when they have an "empty" value by @dsenalik in https://github.com/tripal/tripal/pull/1971 Fix url template for custom content types by @dsenalik in https://github.com/tripal/tripal/pull/2002 Add new third party settings needed by publish by @dsenalik in https://github.com/tripal/tripal/pull/1992 Fixes bug in discovery, cv should have been db for termIdSpace by @dsenalik in https://github.com/tripal/tripal/pull/2018 Publish duplicated titles, and multi-bundle chado tables by @dsenalik in https://github.com/tr

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