chore(main): release 1.2.0

Author: github-actions[bot]

CHANGELOG.md

@@ -1,5 +1,129 @@
 # Changelog
 
+## [1.2.0](https://github.com/Steinbeck-Lab/coconut/compare/v1.1.0...v1.2.0) (2026-02-20)
+
+
+### Features
+
+* Add custom Spotlight search button to navbar ([301d438](https://github.com/Steinbeck-Lab/coconut/commit/301d438207749083fa155f993a2c14a0f1b00886))
+* add github worfklow for code cov, phpstan, lint and security checks ([#705](https://github.com/Steinbeck-Lab/coconut/issues/705)) ([8b64456](https://github.com/Steinbeck-Lab/coconut/commit/8b644566b303673e0f319a2b67b5eb409a35bd2b))
+* Add migration for enhanced geographic data fields ([078e19a](https://github.com/Steinbeck-Lab/coconut/commit/078e19afdd8b84ca815278cb247759ad0a115d47))
+* Add Molecules relation manager to GeoLocation view ([d9292ee](https://github.com/Steinbeck-Lab/coconut/commit/d9292eed46aa6b94f78cc18fbd467c12bfe9d127))
+* added methods to link molecules to geo_locations and citations, and citations to collections. ([c25427d](https://github.com/Steinbeck-Lab/coconut/commit/c25427d9aaf41f91bf83d4ee4af3681611f1d1bf))
+* addition of has_mapping column to collections table. ([2049a8e](https://github.com/Steinbeck-Lab/coconut/commit/2049a8ebf59d5a819e402af3257294b6187e0959))
+* assigning collection identifiers is delegated to an action. ([995df92](https://github.com/Steinbeck-Lab/coconut/commit/995df9258eb345c6d99e78c34a6a2ab814ceb89d))
+* attaching sample location to organism and ecosystem to geolocation. ([72aded6](https://github.com/Steinbeck-Lab/coconut/commit/72aded6ae62626f357469c16d1b38982641148e9))
+* command to fix old entries and create metadata json. ([fa79b90](https://github.com/Steinbeck-Lab/coconut/commit/fa79b908ef4352ad3c41a084bd46098806769d22))
+* command to import meta data into organism_molecule table. ([b51546d](https://github.com/Steinbeck-Lab/coconut/commit/b51546d206ee2cfbc0ea44484e1426ccf40ed0e0))
+* command to rebuild meta data. ([a5d9319](https://github.com/Steinbeck-Lab/coconut/commit/a5d931975770ed9f2cea20082419a68b8fec1e3f))
+* command to update source links of molecules of any collection. ([dd44217](https://github.com/Steinbeck-Lab/coconut/commit/dd44217ed8aeacf026a8208f2524aaaa468b58ee))
+* Configure Filament Spotlight Pro for both panels ([2cfbba9](https://github.com/Steinbeck-Lab/coconut/commit/2cfbba9a053b3bb067fbd1df936829f354de68e9))
+* Enhance GeoLocation with geographic data and rinvex/countries integration ([cdfa46d](https://github.com/Steinbeck-Lab/coconut/commit/cdfa46de6ae86b6ca048e55b8c13130b843f9477))
+* fk on ecosystems. ([f77deaf](https://github.com/Steinbeck-Lab/coconut/commit/f77deafe1eed71bc12d12630efe2e346b1e1dedf))
+* fk on sample_locations. ([193a716](https://github.com/Steinbeck-Lab/coconut/commit/193a716a6aec53daf83eecaa0d40d6a3e86bfa68))
+* Improve GeoLocation list page UX ([36a98e0](https://github.com/Steinbeck-Lab/coconut/commit/36a98e0b8923d060e51e1f3232f7434040695be4))
+* Install Filament Spotlight Pro package ([3388451](https://github.com/Steinbeck-Lab/coconut/commit/33884516feaaee7af55889d40e5d0b06c8c7bf09))
+* linking organism and geo_location. ([51e016f](https://github.com/Steinbeck-Lab/coconut/commit/51e016fb20381d478a02e91b30e34feb279fa20b))
+* migration to add metadata column to molecule_organism and corresponding changes. ([d7a470c](https://github.com/Steinbeck-Lab/coconut/commit/d7a470c814b91c607e063425b3e3ba49542ca801))
+* optional collection wise scoping. ([209dd23](https://github.com/Steinbeck-Lab/coconut/commit/209dd230a9bc504b1e399674b014c8a1fd89eeed))
+* reusing the collection identifier action. ([dad6c88](https://github.com/Steinbeck-Lab/coconut/commit/dad6c88e66c69ccc1ea813ef3f3b81430f860282))
+
+
+### Bug Fixes
+
+* added curation status update, error logging, creating citations by text, handling for utf8 sanitisation. ([5651123](https://github.com/Steinbeck-Lab/coconut/commit/5651123964e962b5f6fd57286c880b7a2cd2ef34))
+* added dehydration to allow saving the disabled fields. ([f1000f8](https://github.com/Steinbeck-Lab/coconut/commit/f1000f8a0ed207e021edcf7d282d82dd10de7f70))
+* allowed processing of failed entries on re-runs. ([43c8e63](https://github.com/Steinbeck-Lab/coconut/commit/43c8e63e5d8592144d59c9d444eca1b7c76b17de))
+* allowed unpkg sources in scripts and connect directives. ([1d361f6](https://github.com/Steinbeck-Lab/coconut/commit/1d361f6c69858f62c49f60ac7f87dfc7bafde534))
+* altering name column from string to text. ([643dff1](https://github.com/Steinbeck-Lab/coconut/commit/643dff17bb75a29c0fa50d81f414362e2efb3a23))
+* array key mismatch. ([aebaa4b](https://github.com/Steinbeck-Lab/coconut/commit/aebaa4ba8627e055c93816f16d0c4ffc61494cb8))
+* array out of bounds error. ([6d71344](https://github.com/Steinbeck-Lab/coconut/commit/6d713441f888625a3c2a736268883f5b91a0896f))
+* array out of bounds error. ([c985419](https://github.com/Steinbeck-Lab/coconut/commit/c98541996c5336fb02ffd358cc6bda3b2dcdfc4d))
+* brand colours reverted and expanded. ([0a4b66b](https://github.com/Steinbeck-Lab/coconut/commit/0a4b66bf284af6471f7511e8ba34f451d3c1e1eb))
+* changed the db host to pgsql. ([7ae8856](https://github.com/Steinbeck-Lab/coconut/commit/7ae885683f1cce675fdba738820660ff42200f3f))
+* changed the db to testing and added testing env. ([3d685b2](https://github.com/Steinbeck-Lab/coconut/commit/3d685b23ea4d41e910b37ff6fc9d17588b6a3e9c))
+* conditionally adding nonce and providing values in arrays. ([c470d91](https://github.com/Steinbeck-Lab/coconut/commit/c470d910ab19cd9808f873aab8b1e53abd09a1cc))
+* corrected the citation issues in the metadata of molecule_organism table ([6eff40f](https://github.com/Steinbeck-Lab/coconut/commit/6eff40f2e027406529fdd0baf231f961c24abb65))
+* corrected the citation issues in the metadata of molecule_organism table. ([1727e4e](https://github.com/Steinbeck-Lab/coconut/commit/1727e4e09163c2310dd3ba4367fa9dd265eab2ba))
+* corrected the mismatched array key. ([#702](https://github.com/Steinbeck-Lab/coconut/issues/702)) ([67c681f](https://github.com/Steinbeck-Lab/coconut/commit/67c681f800739ceecbca748a4876139cecf8c3f0))
+* corrected the relations. ([a7860fe](https://github.com/Steinbeck-Lab/coconut/commit/a7860feb6d5686603dc674ccbff7269d26d3f363))
+* display the navigation menu items only if the user is logged in. ([#707](https://github.com/Steinbeck-Lab/coconut/issues/707)) ([a1caf1e](https://github.com/Steinbeck-Lab/coconut/commit/a1caf1e021fbb23a9dfc8a9596624f2f6356ac94))
+* displaying all results except placeholders. ([84cabf0](https://github.com/Steinbeck-Lab/coconut/commit/84cabf0dfdf25737289778166e4bda6b2ee33d6c))
+* displaying all results except placeholders. ([04455f4](https://github.com/Steinbeck-Lab/coconut/commit/04455f4bc62371b40b3b56dd1ad4569d4b849e95))
+* dunglas/frankenphp:1.7.0-alpine ([8e64b38](https://github.com/Steinbeck-Lab/coconut/commit/8e64b38fb3663b7d0c304c1cdcfca1e6edc98cb4))
+* duplicate organisms are removed. ([79e6816](https://github.com/Steinbeck-Lab/coconut/commit/79e68163e0a21f1a7cd846567e1b1c34c649dba3))
+* duplicate organisms are removed. ([94ea82a](https://github.com/Steinbeck-Lab/coconut/commit/94ea82a0b069b27bbbff6fb4bb7a95848e017d41))
+* even more phpstan suggestions. ([1f34f00](https://github.com/Steinbeck-Lab/coconut/commit/1f34f00f14c1874383b371cb58ddb186c2d2c1fa))
+* filling yes for mapping flag since all the old collections have no mapping. ([d0b1862](https://github.com/Steinbeck-Lab/coconut/commit/d0b18626f98a9d8e90f871073c90daa07c933278))
+* handling array out of bounds error that prevents attaching molecules to collection. ([56b0005](https://github.com/Steinbeck-Lab/coconut/commit/56b0005f178939c49b36860de110eb1c3c2bdac6))
+* handling null values. ([ff8bee1](https://github.com/Steinbeck-Lab/coconut/commit/ff8bee10d0bc5c9f04e8e3175894f61da8ff28ca))
+* InfolistSection is not there. ([249fce7](https://github.com/Steinbeck-Lab/coconut/commit/249fce76b07df30dd41adb5da0c66709ed47c40f))
+* layout selection issue fix ([ea793f3](https://github.com/Steinbeck-Lab/coconut/commit/ea793f3c2b7aa2bf564d7d5d4895964df5d25029))
+* linking molecule to collection, converted info display to logs, and shortened the metadata json keys. ([7e81e2f](https://github.com/Steinbeck-Lab/coconut/commit/7e81e2f8bc5ab1565a5b79ab2a370553861fa535))
+* more phpstan suggested fixes. ([ca3c977](https://github.com/Steinbeck-Lab/coconut/commit/ca3c9775fb7444105f42b27b9c43e752b791a136))
+* ordering the collections by id. ([1b44783](https://github.com/Steinbeck-Lab/coconut/commit/1b44783695ebc240474b2f41c1504c25a4549207))
+* overriding the default view to add nonce ([4327e90](https://github.com/Steinbeck-Lab/coconut/commit/4327e90e2940e6ba1c45a68b66890d03a9fbd6a6))
+* overriding the default view to add nonce. ([4327e90](https://github.com/Steinbeck-Lab/coconut/commit/4327e90e2940e6ba1c45a68b66890d03a9fbd6a6))
+* overriding the default view to add nonce. ([24b628e](https://github.com/Steinbeck-Lab/coconut/commit/24b628ea5bbc300cee53b02b2f7e1e0fd9a0f34d))
+* parent molecule flags are updated. ([7cc3dbd](https://github.com/Steinbeck-Lab/coconut/commit/7cc3dbd32445892309e8cbb60d01b202766507ac))
+* phpstan error. ([a99f348](https://github.com/Steinbeck-Lab/coconut/commit/a99f34817cb65b99081dc1b6e86f2dc365ff57c5))
+* phpstan suggested fixes. ([cee6669](https://github.com/Steinbeck-Lab/coconut/commit/cee6669fac95a5d723058551b4655ceef8eb769c))
+* phpstan suggestions. ([ccb432d](https://github.com/Steinbeck-Lab/coconut/commit/ccb432dec55556723a5808588c21b7d21ea2c135))
+* phpstan suggestions. ([5599827](https://github.com/Steinbeck-Lab/coconut/commit/55998273a68e39ba976e93c51a9f713b3e1b2127))
+* preventing overriding github workflow values. ([2267697](https://github.com/Steinbeck-Lab/coconut/commit/2267697b4fb3a0fa730a9f3a4e6eb8b4e3947b59))
+* provided full image url in the infolist. ([983ac69](https://github.com/Steinbeck-Lab/coconut/commit/983ac69e6a3dd1ab1f061c9cce19c6e9b6cc8510))
+* put in place check for collection, and escaped wildcards. ([0c8fc1b](https://github.com/Steinbeck-Lab/coconut/commit/0c8fc1b73bae2d13df0137aced6485095f07222c))
+* radio button and border. ([499b83f](https://github.com/Steinbeck-Lab/coconut/commit/499b83fb1a7a727b7e9dcf27e7c211402f6b2ccc))
+* relations are made inline with new changes. ([87bf40b](https://github.com/Steinbeck-Lab/coconut/commit/87bf40b18fa70e1716b53b9859694ac79963cdc6))
+* remaining phpstan suggestions. ([7f23c4f](https://github.com/Steinbeck-Lab/coconut/commit/7f23c4f4031a655dc1e2e2a711a818e6202532e5))
+* removed debug logs. ([a8d4d52](https://github.com/Steinbeck-Lab/coconut/commit/a8d4d528618f92878bd31b67acb2c141c785e436))
+* removed modifications that should only be done after the table has been refilled. ([f5fc7de](https://github.com/Steinbeck-Lab/coconut/commit/f5fc7de20c564816e3bef9e2e24a0aab275a9d7d))
+* removed passing molecule since there are resolution errors and it is also not being used. ([a8b467c](https://github.com/Steinbeck-Lab/coconut/commit/a8b467cfaab968e628e42cc53d211c36d9d3549c))
+* removed possibility of double where clauses. ([531408a](https://github.com/Steinbeck-Lab/coconut/commit/531408ad573371e3ef6fe4d3c9fc2114cb77843e))
+* removed test statement. ([9725a2c](https://github.com/Steinbeck-Lab/coconut/commit/9725a2cc045ad44c44f245d6d1e6200b8a240f52))
+* removed testing env ([ab2fb0b](https://github.com/Steinbeck-Lab/coconut/commit/ab2fb0b843e88da0fecc552b71c657f71493593b))
+* removed the columns to correct the display of the form. ([ef13797](https://github.com/Steinbeck-Lab/coconut/commit/ef137978a85d6effe54fd6d8ebfa61910b77073f))
+* removed truncation for ecosystem names. ([91b245b](https://github.com/Steinbeck-Lab/coconut/commit/91b245bd5bed8160043f556b757d163208255e1d))
+* removed unnecessary error check. ([2512dc1](https://github.com/Steinbeck-Lab/coconut/commit/2512dc1e19f9598778e3506342f25883ea5cfe81))
+* replace dev matomo script with production version ([ba31846](https://github.com/Steinbeck-Lab/coconut/commit/ba31846dd715b08f11e206a903b97c0558cee2f4))
+* Resolve SQL ambiguous column error in GeoLocationStats ([20bfaaa](https://github.com/Steinbeck-Lab/coconut/commit/20bfaaa0cf75394785d7ef40f5d6f2b8ee35945a))
+* reverted close button to neutral colours, removed the ring classes on radio button labels. ([6e6bf1a](https://github.com/Steinbeck-Lab/coconut/commit/6e6bf1a6ae8c6d20ad441d9a2d4f2112191d682b))
+* reverting to localhost for host. ([6128a55](https://github.com/Steinbeck-Lab/coconut/commit/6128a55c8154f16f56c16d5fe9d2c91aef93ee9b))
+* running HRM using sail npm for consistency. ([a3b38ee](https://github.com/Steinbeck-Lab/coconut/commit/a3b38ee2b40729bceff49b8a5fd8a399a326eb41))
+* sanitising utf8 characters and marking status of mols with no organisms as imported. ([045a6c2](https://github.com/Steinbeck-Lab/coconut/commit/045a6c27f098fcfe1d3ad54bd28e56ca12d10f56))
+* securing the local development by allowing only local host to access the container. ([ad66b2a](https://github.com/Steinbeck-Lab/coconut/commit/ad66b2a239bde98ebcf050271d0fd28f96daed6c))
+* shifter to optional argument. ([794e068](https://github.com/Steinbeck-Lab/coconut/commit/794e0680363a791ea0261337ef9818f9a42c95fc))
+* synonyms are processed to preserve commas within each. ([dc115f5](https://github.com/Steinbeck-Lab/coconut/commit/dc115f5cfea0c6dd4bb83ab7b80c66e211d4ce11))
+* synonyms are processed to preserve commas within each. ([58ec5fb](https://github.com/Steinbeck-Lab/coconut/commit/58ec5fbb098f0feb8a0a83127023ced1970a4353))
+* tailwind css v4 stopped using js based configuration so removed it. ([32ecf44](https://github.com/Steinbeck-Lab/coconut/commit/32ecf44b0c49a897ab9a7ef6675d8cda8c435324))
+* the importer is updated to generate metadata in the new format to handle many to many relations. ([e7ac9d6](https://github.com/Steinbeck-Lab/coconut/commit/e7ac9d6ec7944afdb72f0421dfcedf4a910dcee6))
+* Update panel switch icon dark mode styling ([d73ce1d](https://github.com/Steinbeck-Lab/coconut/commit/d73ce1da332763fec77abdeca6f76119d01ca7fd))
+* update psysh to fix security audit error. ([2c6d02a](https://github.com/Steinbeck-Lab/coconut/commit/2c6d02acab59ccdbc5847200d2c720bf3ff4efac))
+* updated the impersonate path. ([36aa65b](https://github.com/Steinbeck-Lab/coconut/commit/36aa65b2c61f39b3e89821d4c4ee8b1544a5c985))
+* updates to the pipeline for importing metadata in the new format. ([d5ddb39](https://github.com/Steinbeck-Lab/coconut/commit/d5ddb398905bfa902af023541257b26ef269ca42))
+* upgrade PHP version in Dockerfile to 8.4 ([8e7ff31](https://github.com/Steinbeck-Lab/coconut/commit/8e7ff314e201e5855c2a805c3a967b581c45b6ce))
+* upgrade PHP version in Dockerfile to 8.4 ([945a280](https://github.com/Steinbeck-Lab/coconut/commit/945a280a995d3ea6cf1026f1785910691255396b))
+* using shortcut keys to save storage space. ([46f2256](https://github.com/Steinbeck-Lab/coconut/commit/46f22569543ec8b5e4dda34735d3a5f037fc14c4))
+
+
+### Miscellaneous Chores
+
+* **main:** release 1.0.0 ([a5fb309](https://github.com/Steinbeck-Lab/coconut/commit/a5fb30919d214c90ea4bd7242b2afb9fd687f794))
+* **main:** release 1.1.0 ([5c8bd03](https://github.com/Steinbeck-Lab/coconut/commit/5c8bd034a651b1d5e4d712998bbca2a4f6c229e2))
+* phpstan fix. ([887aeca](https://github.com/Steinbeck-Lab/coconut/commit/887aeca73a1c385285e2ea5104afb381c91c702c))
+* phpstan suggestion. ([b01c96f](https://github.com/Steinbeck-Lab/coconut/commit/b01c96f8a519e32ee677db0b3e45222ac1d598da))
+* pint formatting. ([be59f6f](https://github.com/Steinbeck-Lab/coconut/commit/be59f6f2ed25bdf9b55392ffe4e7c4775cd45ef1))
+* pint formatting. ([bc6f853](https://github.com/Steinbeck-Lab/coconut/commit/bc6f8538e4d40a16b6373125cba1414d7aca02d6))
+* pint updates. ([1a3b4e6](https://github.com/Steinbeck-Lab/coconut/commit/1a3b4e639e58b85902621703b330ec04b781708b))
+* pint updates. ([3ca02be](https://github.com/Steinbeck-Lab/coconut/commit/3ca02be92fec1182bd71ae7e5f5b2149ecf43584))
+* recreated both lock files using sail composer and npm. ([cfc3adc](https://github.com/Steinbeck-Lab/coconut/commit/cfc3adc208bc6fa8eb522cc9fb7bd405fd1f6fc4))
+* removed dry run code. ([6391c4b](https://github.com/Steinbeck-Lab/coconut/commit/6391c4b56f637234b65b02857ea8fd37359800f1))
+* removed since spatie model states is not being used. ([178ecfc](https://github.com/Steinbeck-Lab/coconut/commit/178ecfce0018dc0b3f312faffd77af8b82ff94b4))
+* removed the file without extension. ([622572b](https://github.com/Steinbeck-Lab/coconut/commit/622572bb117d2ca94a6141b0faefbb46ac13b5db))
+* renamed the file. ([8b6b97b](https://github.com/Steinbeck-Lab/coconut/commit/8b6b97b7f571c25f8747b0b73520fad197b4963d))
+* resolved the missed merge conflict. ([4ccf007](https://github.com/Steinbeck-Lab/coconut/commit/4ccf007266d73f16001eabb35ac02d0a5bf060b2))
+* upgrade docker to php 8.4 ([#703](https://github.com/Steinbeck-Lab/coconut/issues/703)) ([23a9281](https://github.com/Steinbeck-Lab/coconut/commit/23a9281758b1f249a09075d8c576b5fb17b3ab57))
+
 ## 1.0.0 (2025-11-27)