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chore(main): release 1.0.0 #247

Merged
merged 1 commit into from
Sep 12, 2024
Merged

chore(main): release 1.0.0 #247

merged 1 commit into from
Sep 12, 2024

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Kohulan
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@Kohulan Kohulan commented Sep 12, 2024 •
edited by CS76
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🤖 I have created a release beep boop

1.0.0 (2024-09-12)

Features

  • a command to refresh widgets of dashboard, collections and geolocations (not those of molecules and organism) (2e97965)
  • a new command for updating the number of molecules each organism has. (16994e7)
  • a new script is now available to update the auto increment columns (13378b3)
  • add assign identifiers command (174e96e)
  • added bioschema to molecule pages (3ccfdb2)
  • added button for publishing the collection. (98d3ba4)
  • added chembl name importer (8fa1c88)
  • added command to generate api docs (75e2121)
  • added copy to clipboard button (884fe74)
  • added default sort and tags for report resource (9c3e22b)
  • added docs and other command updates (2380fbf)
  • added functionality to display the status of the collection (e14219b)
  • added new columns to sample location tables (00f7e68)
  • added NPAtlas import script, annotations score species scoring updates, docker file updates to install bcmath (28c4ceb)
  • added organism and citation search (368fd97)
  • added relationship managers for report resource as well as one for audits. (d2278a6)
  • added search to landing page (757c5e1)
  • added SEO (34a62d9)
  • added structure editor (ca53f30)
  • added view report functionality to allow user to view the report after receiving mail confirmation. (82f4a9a)
  • added vitepress docs (b7fddc8)
  • advanced filters are now available on molecules (69252cd)
  • advanced filters are now available on organism table (6d69142)
  • all the models are now auditable (7d84f6f)
  • allow activation and deactivation of molecules (f704256)
  • assign identifiers to collections (ee60475)
  • bug fixes and other updates (6772b7c)
  • bulk activate and deactivate of molecules is now available (497727e)
  • ChEBI names importer is now available (6ecf269)
  • collections in the search page can also now show display images (c7658ed)
  • compound time line is now available (b844ba8)
  • Create bug_report.yml (5de141f)
  • Create natural_products_submission.yml (8f1b74f)
  • created a separate widget for molecules in the dashboard (18e57cb)
  • created a view for collection and added widgets (c4d7282)
  • created dashboard widgets for all resources (709e21c)
  • created geolocation and organism resources (294a25c)
  • created geolocation and organism resources and their relation managers for molecule resource (c51050c)
  • created molecule relation manger for collection resource, added functionality for processing molecules in entries table, and added forget the collection molecules count at the end of import (6130df4)
  • created relationship managers for geolocation and organism (0cb7652)
  • created view page for geolocation and added widgets (be02cd8)
  • created view page for molecule and added widgets (a5bc781)
  • created view page for organism and added widgets (7562377)
  • db schema is updated and now linked to info.coconut account (ae86e9f)
  • display images can be uploaded to collections (2894396)
  • displays the counts of resources by the side (641ea96)
  • displays tool tips for the report fields (041b1bd)
  • displays various counts in the collection table and added two widgets in collection stats (698184c)
  • doi fetching in citation (wip) (8f43650)
  • enable local docker composer prod deployement (edb928b)
  • enabled cache and various bug fixes (97f9acb)
  • enabled REGAPP SSO (fb97420)
  • enabled SEO meta tags, organisms search page and other small updates (caf2acb)
  • enabled structure editor - paste from clipboard (58aeeab)
  • extend Bioschemas metadata (11ce7ca)
  • generated policies for geolocation and organism (35d1d1d)
  • history of the compound is now available in the compound details page (bc26426)
  • home page collection cards will now display images (1e6aac1)
  • implemented advanced tables and various other minor updates (3afe3f7)
  • implemented citations, collections, organisms rest controllers and corresponding resources (4b9e8ae)
  • implemented REST API service and swagger documentation, migrated from l5-swagger to lomkit (bf20706)
  • implemented social login, ui updates and bug fixes (428a201)
  • improved the user friendliness of the command using prompts (d405d60)
  • iri and rank fields are now available in the forms for organism (8ef926a)
  • IRI is now displayed below rank and is clickable (a1ff54d)
  • landing page updates (036eb3d)
  • molecule relation manager for sample locations is now available (9b0c1fe)
  • molecule_reporting_template.yml (668284e)
  • molecules of an organism can now be moved to another organism including to a specific part of this organism (df5cd10)
  • moved the updated docs into the coconut repository (af21601)
  • new columns are made available and filters are tuned (6260958)
  • new command to copy names from entries and add them to synonyms for all the molecules (4f1988a)
  • new docs (2b2e433)
  • new interactive command to reassign molecules to a selected organism from the list of duplicates based on slug (7adb664)
  • new pages added (4ecf171)
  • new registrations can now provide additional data like orcid, username, affiliation, etc (31555c0)
  • new slug column is added to organisms table (2d268c3)
  • now users can add collections, molecules or citations while creating the report itself (022a4c3)
  • now users can skip a group of records and proceed to the next (af543ec)
  • now users can suggest changes to the properties of molecules, citations, collections and organisms (313b736)
  • now users have to provide a reason for deactivating molecules (07248d4)
  • now users receive new mail after reporting (5f93e7c)
  • part of previous commit (5fdc58d)
  • pdf download is now available for user views (c2642e9)
  • prod build (925c2ec)
  • reporting of molecules can now be done from molecules table and restructure of the table for better user experience (9614fb0)
  • resolved issues with open-api documentation, resources updates and basic api testing done (9cfcb4e)
  • sample location relation manager for organism is now available (8d2b947)
  • sample location resource is now available but not in navigation (104ad85)
  • sample_locations table is now available in place of organism_parts and a few more columns are also made available to store collections data (c8e80fe)
  • scheduled a refresh of cache for dashboard widgets (d825bc3)
  • search updates and other minor changes (4203ab2)
  • shows active and inactive molecules in separate views with advanced filters enabled (a98ac14)
  • shows the related organisms in the relations in edit mode (8ebfb66)
  • similar named organisms are displayed on the edit page of organisms with an option to edit them (36622d4)
  • the new fileds in registrations are also now available in profile updation (2e1fe7f)
  • unified search options across pages, default search caching, mobile screen bug fixes (de6e6f5)
  • updated logo (96715fc)
  • updated pagination logic and added loading screen while fetching results. fixes #220 (7fabdd4)
  • user views can now be exported in various spread sheet formats (710f0c4)
  • ux/ui updates, text changes and commands added (3b84e5d)
  • various updates and bug fixes (9b3cac4)
  • various ux/ui updates and other minor changes (822760b)

Bug Fixes

  • 3d rendering login updates, various other small updates (ed75cf0)
  • a new column for counting molecules is now added to organisms table (50b1221)
  • abbreviation correction (92e7e85)
  • abbreviation correction for coconut (efe3d38)
  • abbreviation of coconut is fixed (1e58f8e)
  • accessibility issues resolved and also enabled source maps (b9fad04)
  • add chembiosys about.blade.php (cc04cf9)
  • add more button when synonyms are available and above certain count (3e1197c)
  • add zenodo logo README.md (a2b7c3c)
  • added a csv column to reports table to avoid preloading in the form (191c605)
  • added a new migration for new columns of user and filling name with first and last names (1fcf7eb)
  • added cache policy for images and also updated links in application logo (87295ca)
  • added cache to welcome page (ceaa44b)
  • added checks for the creation of report (28d01b3)
  • added composer private repo install capabilities (00d4c22)
  • added css from vendor folders (a894fad)
  • added gzip compression (faf9c9c)
  • added img alt text (96cd466)
  • added IRI link to the organisms table (ff6df46)
  • added local env variable to allow proper redirection (cee868e)
  • added matomo scripts to layout pages (2f051ad)
  • added missing bcmath extension to php docker container (5a83108)
  • added missing libraries (20d6b23)
  • added preview link to structure image (055e66b)
  • added remove duplicates command (4bda2f8)
  • added support for old coconut urls (f7d8eed)
  • added transparent favicon (163e683)
  • added variety of checks to hide and/or edit fields in accordance with the operation on report resource form (2ac35ca)
  • added view more button to compound details page and other minor improvements (18eddbe)
  • adding full path (dd8a692)
  • adjusted collection width on home page (d96e5a7)
  • all the values caches are set to expire after 2 days. (847137f)
  • anchor with in anchor bug fix (45720f6)
  • annotation score calc updates (9eb6684)
  • applied filament excel patch (ece837e)
  • broken classification links fix (5ba0554)
  • bug fixes in schema and other updates to 3d rendering (ce4b9f9)
  • build deployment (6d15b0d)
  • cache and search filters update and bug fixes (fe82ab1)
  • cache applied to collection resource widgets (18aba41)
  • cannot access offset of type string on string bug fix (840404b)
  • changed molecule entry filed to text area and formatting changes (c7c842e)
  • citation introduction.md (df9d916)
  • class name "ImportSTOUTIUPACNames" update - build failure (eff9ac3)
  • classes are now made clickable which open corresponding searches in new tab (2d89b6b)
  • cleaned up spatie media remnants (a268a53)
  • code refactoring and performance improvements (8743bab)
  • collection image updates (ee160e9)
  • collections image override bug fix and auditables relation manager bug fix (a35bb25)
  • column altered to handle empty name (3b831eb)
  • composer_auth var added (4387da4)
  • compound details page updates, search updates and other minor changes (e53ddb7)
  • compound details page, header link updates and annotation score code formatting (ad443a0)
  • concatenating 0 to the cnp id (b32f65b)
  • conditional toolkit rendering enabled on molecular 2d views (0d225bb)
  • correct name for the command (d67dd04)
  • css updates fix (a35eac3)
  • dash widgets molecules count (3fa7a8d)
  • dashboard logo link is now pointed to homepage. fixes #157 (306510b)
  • database count introduction.md (589ff33)
  • database schema display (1795c15)
  • deactivation is only visible for super-admins (e18fc03)
  • default user avatar is now generated using first and last names (c9fd00c)
  • delete .DS_Store (158d94c)
  • delete organisms with no molecules and enables audit trail (7ca9c65)
  • details in about page are updated to be accurate. (dab0557)
  • DFG logo README.md (30e37c7)
  • disabled rest authorisation cache (61ad3bc)
  • display organisms list (e6763bc)
  • displaying revoked molecule details on the web page (df336a9)
  • download page css updates (104f17b)
  • drop shadow introduction.md (e010def)
  • enabled auditing (7a88fbe)
  • enabled edits of citations. (7837d5d)
  • enabled https redirect and also gzip compression (5c74027)
  • enabled lazy loading in the welcome page (57be610)
  • enabled tautomeric standardization, various import scripts and other updates (14b005a)
  • enforcing url https redirect (b0fdbc9)
  • filament route missing issue fix and composer update changes (edf2dbd)
  • file path missing bug fix (00aec98)
  • formatting updates (c6d9318)
  • formatting updates (8d836dc)
  • formatting updates and other changes (672f8fc)
  • gave view access to normal users for geolocations and organisms resources (aa4c86c)
  • header issue and other minor css changes (61606ad)
  • header issues resolved, tag line updates and other small bug fixes (644a319)
  • if the doi fetch fails to get data from the apis, it will also search coconut db (4b7eeeb)
  • import preset path fix (0cd86e9)
  • importer updates and formatting changes (d8bd65e)
  • imporved introduction and statistics (d07515e)
  • improve documentation visualization (6e7f3de)
  • improved readability of the event and affected columns (acb688c)
  • improved README.md (7e18df0)
  • improvements to the time line display in the compound details page (01ad02d)
  • include analysis (be5f0c6)
  • include licensing information (e241809)
  • introduced toggle buttons (583e295)
  • layout updates on 2d rendering (ef0ecdc)
  • list table and widgets of collection resource were pointed to the columns instead of cache (c71ccc8)
  • loading fonts locally (54b73fb)
  • logo path index.md (04bd35c)
  • logo shadow introduction.md (29c8d83)
  • made audits as the default tab for the report view after clicking on the button in the mail for status changes and removed unnecessary details in the mail templates. (df4a61d)
  • malformed auth.json bug fix (a669d6e)
  • merge conflicts from development (208e980)
  • minor molecule card updates (2ce5b9d)
  • minor updates (2ce527d)
  • minor updates and access panel logic added (346f292)
  • missing collection name in social card bug fix (9f63111)
  • missing file in the path bug fix (d4c856c)
  • missing files bug fix (d394a55)
  • missing identifiers now returns 404 and also added hasvariants logic to molecule details page (48c5a4d)
  • missing imports and can access panel (a64b2a0)
  • missing index.css file bug fix (b48fa4a)
  • molecule details page update, iupac names import command added, header changes (26fa0b7)
  • more lazy loading optimisations (9ebdd45)
  • more optimisation (6a19b77)
  • more updates (852e227)
  • more updates to header (535aa85)
  • nginx docker fail bug fix (cddf6ce)
  • nginx path update (0ab8a80)
  • now only the similar organism names with any molecules attached to them are displayed in the organism edit page's side panel (60a840d)
  • now report relations are shown according to the report type (492d700)
  • now users have to provide affiliation details (3645fc5)
  • npm security fix and other build files (91709a5)
  • npm update (1e2c4f0)
  • null synonymns bug fix (6e894b9)
  • OCL loading issue fix (ac18255)
  • organism name has to be unique in the table (4687194)
  • organisms in search listing updated (6f0cf24)
  • pagination dark mode css removed (40800c6)
  • parameterised the molecule in the frontend livewire view (48edf84)
  • path issues fix (2f4d64e)
  • performance improvement for dashboard widgets using raw queries. (9ae31bf)
  • performance improvement for widgets in collections, geolocations, molecules, organisms (6c00b12)
  • published assets, prod build and composer lock update (38530fd)
  • queries in collection and geolocation stats inline with app cache refresh (9506316)
  • query switched to unique cannonical smiles, other bug fixes and updates (319c64a)
  • ReadME (4c83bad)
  • reason from reports table is removed since there is a column comment that curators can use (37c1c50)
  • recent molecules filtering updates (465672a)
  • recent molecules max width and mobile nav bar missing links added (50dda62)
  • Redis not found bug fix (392080f)
  • remove SSL config since its configured using GKE ingress (bbcaa49)
  • removed avatar field for collections (259846e)
  • removed flush db command (ad22b40)
  • removed FLUSHDB (e448340)
  • removed python2 (56b0a45)
  • replaced the column molecular_weight with exact_molecular_weight and added a helper tool tip to mention the source of calculation (b880c46)
  • reset nginx conf (f47eac6)
  • reset previous commits (ffea98a)
  • resolved #117 issue and default query update (c6d24fc)
  • resolved #6 (3040e20)
  • resolved all text area import instances (90eb367)
  • resolved dark mode (19c52c2)
  • resolved molecule route issue (2c451b0)
  • resolved npm issues (5fc491c)
  • resolved structure editor overlap, other minor updates (ba43250)
  • resolves #169 (630a9a0)
  • resolves issue #136 (3f628d7)
  • search is now limited to specific columns and new formatting changes for php class instantiation (bf93081)
  • search organism by name query update (6e0d614)
  • search updates (f4d76be)
  • server error fix (9d75919)
  • similar organism display layout is altered (f033847)
  • slug is corrected (ea90d4c)
  • small screen optimisation (27c2b9c)
  • specifying social card image height (8c39777)
  • stream lined the form filed for molecules (f7f6b4a)
  • synonyms null check added (2792020)
  • tailwind config preset missing bug fix (0535511)
  • text area import issue fix (b1246e6)
  • text search ordering added (0ebb9b9)
  • the cache values are replaced with table columns filled using raw sql to improve performance (83f57fa)
  • the command is updated to handle organisms whose molecules have all been assigned to another organism (2a15149)
  • the curation process now updates the molecule counts after the re-association of the molecules (b8f8369)
  • to wrap the report tile in the table (a3da8b1)
  • turned the molecule query into raw and added info messages (96369f7)
  • two new commands for deduplicating the synonyms and updating the name with the first synonym where name is null (b1cad31)
  • typos and docs update (53de6c8)
  • undone few previous changes and fine tuned the DOI fetching and displaying the fields. (cc281d2)
  • update citations README.md (98ddf2e)
  • update doi CITATION.cff (e9f6808)
  • update release-please token (665e84c)
  • update to the fetch querry to avoid missing slugs (0907091)
  • updated about page (3224bde)
  • updated about page, details page corrections and added missing data - NPAtlas import command (aa7417d)
  • updated CD link and release notes in download page (9806d5c)
  • updated collections schema and also typo correction (1716888)
  • updated default collections filtering and ordering logic (0eab9a4)
  • updated docs content (2fa76dc)
  • updated docs links (5f209e4)
  • updated download links and other meta data (1ddc16b)
  • updated download page on coconut (383314d)
  • updated download page, removed bg pattern and other minor updates (68c7979)
  • updated downloads (new release added) (8f0c484)
  • updated favicon (221b67f)
  • updated header (84c3770)
  • updated landing page with search and other options, minor query updates (f6d2402)
  • updated links to report and request changes (edb02e2)
  • updated meta tags (37b5cbb)
  • updated molecule card and added counts to the molecules table (4752a2e)
  • updated package lock (bacc8f5)
  • updated search query (fd934d5)
  • updated smiles search with sort order (beba591)
  • updated the policies to allow user to create new reports and attach molecules, collections or citations to the report (017cf77)
  • updated the search placeholder and about texts (583bc04)
  • updated total molecules query (8f68374)
  • updated twitter card (ba5ccab)
  • users with any role can now deactivate (49b2afa)
  • various docs updates (4e85abd)
  • various landing page optimisations (3f1bdcf)
  • various landing page updates, search sorting implementation and other minor updates (f0ead1b)
  • various minor updates (1dd36fb)
  • various updates (7f31573)
  • various updates (c49023e)
  • view page is removed (dd14ff3)
  • vitepress build updates (4b7f0e1)
  • zenodo link introduction.md (0169c2b)

Miscellaneous Chores

This PR was generated with Release Please. See documentation.

v1.0.0-pre-release.1

What's Changed

New Contributors

Full Changelog: https://github.com/Steinbeck-Lab/coconut/commits/v1.0.0-pre-release.1

@CS76 CS76 merged commit d9f7da0 into main Sep 12, 2024
@Kohulan
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Kohulan commented Sep 12, 2024

🤖 Release is at https://github.com/Steinbeck-Lab/coconut/releases/tag/v1.0.0 🌻

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