1. Deployment projects
  2. Deployment for Jalview Develop Builds
  3. Releases

Release: 2.11.2.3-alpha

Jalview Develop Build Deployments

Commits

Comparison is available only for releases created from the same branch as this release.

This release
Author Commit Message Commit date
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 135c826c69042c04c64cb8df30fdaef92eeb4ffc 135c826c69042c04c64cb8df30fdaef92eeb4ffc JAL-4004 Fix missing whatsNew.html when not building with RELEASE channel set
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> a7634a9f5f5f691a7bff7bb05ca21a340aa2f834 a7634a9f5f5f691a7bff7bb05ca21a340aa2f834 JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> efba321f20b819819c0b1cd9c9133d9d1a2ab314 efba321f20b819819c0b1cd9c9133d9d1a2ab314 Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> a9689ca54eaa10c839fafd5bb01c6ee6c17f5c9a a9689ca54eaa10c839fafd5bb01c6ee6c17f5c9a JAL-4004 add the autogenerated whatsNew.html and releases.html to .gitignore
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 599ce3ebcced809656e12ca0c0f69abd304f1577 599ce3ebcced809656e12ca0c0f69abd304f1577 JAL-4014 release notes for JAL-4026 patches
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 149754e206bd387ec23dff3eb3550073c62cec71 149754e206bd387ec23dff3eb3550073c62cec71 JAL-4026 increase timeouts for command line ops
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 1778cdd563831459f049be5864f04581c2f32187 1778cdd563831459f049be5864f04581c2f32187 JAL-4026 ignore StructureSelectionManager events if no viewer is available to act on them
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 986834f1db7bd344d067bb450970578acb32c10f 986834f1db7bd344d067bb450970578acb32c10f JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 99bfb1a08e5ceb3a3c990bb49dcd7433a0880558 99bfb1a08e5ceb3a3c990bb49dcd7433a0880558 JAL-4026 update the viewport’s wrapped width after calculating it
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 4ae3b020ccc351cc61130c9431f3a11dd7bc2995 4ae3b020ccc351cc61130c9431f3a11dd7bc2995 JAL-4014 release notes for JAL-4023 and JAL-4024
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> d1e20f6a5654ea6baf378afa3277b4e751c69a96 d1e20f6a5654ea6baf378afa3277b4e751c69a96 Merge branch 'improvement/JAL-4023_snotation_for_trees' into develop
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 5a0f398fd4bab96dd3cba085ffe77b010cfe24eb 5a0f398fd4bab96dd3cba085ffe77b010cfe24eb Merge branch 'patch/JAL-4024_jumpScrollHang' into develop
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 08bb9485b737ca84f223ea4ba92fc0873387fc0f 08bb9485b737ca84f223ea4ba92fc0873387fc0f JAL-4012 what’s new and release notes (in the new styleee!) for JAL-4004, JAL-3989 and JAL-3553
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> a1b8a79115a0ecf10ba395ec2dc8cf12c7063924 a1b8a79115a0ecf10ba395ec2dc8cf12c7063924 JAL-4004 delete temporary file mistakenly checked in
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 02f8e0098609a768e6a1a21c5c2928f81b5bf299 02f8e0098609a768e6a1a21c5c2928f81b5bf299 Merge branch 'issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop' into develop
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 71a3cc0202bd8b731f01e5706372e9bae047d592 71a3cc0202bd8b731f01e5706372e9bae047d592 JAL-4024 only render partially when new view overlaps with last rendered annotation panel view
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> dfc849311567b9764bf2984e22c683dc988ed5d7 dfc849311567b9764bf2984e22c683dc988ed5d7 JAL-4020 class formatting
Ben Soares Ben Soares cea2941f089e7d7a8dd94d4478ed711255eba75b cea2941f089e7d7a8dd94d4478ed711255eba75b JAL-4020 added the \Scripts\pymol.exe. to the pathList
Ben Soares Ben Soares e184f1c1dbdef0050cfd419a91c68ffd4638acfd e184f1c1dbdef0050cfd419a91c68ffd4638acfd JAL-4020 Added the +2 arg for PyMOLWin.exe allowing older versions of PyMOL
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> b49b2c492b12792c63178d195a7b14b8b9c8efa9 b49b2c492b12792c63178d195a7b14b8b9c8efa9 JAL-4020 updated tests
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 14e1f9dbb9c7a4535734fd3be7ddeee2a5ae72dc 14e1f9dbb9c7a4535734fd3be7ddeee2a5ae72dc JAL-4020 class reformatting
Ben Soares Ben Soares 2c1fabdc3d0b711ebcc844c846fefa61d4e58bd8 2c1fabdc3d0b711ebcc844c846fefa61d4e58bd8 JAL-4020 Added path search for global installation path and older version installation paths
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 20b5e49eaffdbc56b9d0274200a12204e362d5b1 20b5e49eaffdbc56b9d0274200a12204e362d5b1 JAL-4023 use %g for distances (scientific notation for very small or large values)
Ben Soares Ben Soares 483ecb5e4541537778844529cc93204f9124b68d 483ecb5e4541537778844529cc93204f9124b68d JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places starting with default install dir.  Added a new version (1.3) to ChimeraX
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> c6977851625f96831a95b45901aa1d84bd7774fe c6977851625f96831a95b45901aa1d84bd7774fe JAL-4023 store distances as doubles
Ben Soares Ben Soares 2319ef1a410ce35bf2ef1800fd0be4e779ee44eb 2319ef1a410ce35bf2ef1800fd0be4e779ee44eb Merge branch 'develop' into issues/JAL-3553+JAL-3978+JAL-3989+JAL-4014_merged_with_develop
Took Issues Resolved (1 issue) from releases.html 2.11.2.3 row and put
in help/markdown/releases/release-2_11_2_3.md
and regenerated releases.html with
gradle releasesTemplates
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 11346f873e4ecb2d191499fd1d52b8de07a65bf3 11346f873e4ecb2d191499fd1d52b8de07a65bf3 Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 2441f0e1e3afac23a73e3957b16c21b75ebfc62d 2441f0e1e3afac23a73e3957b16c21b75ebfc62d JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 094b06cac0d0e8f781462027ed2e4af5fe32d7c6 094b06cac0d0e8f781462027ed2e4af5fe32d7c6 JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !
Jalview Development Admin <jalview-dev-owner@jalview.org> Jalview Development Admin <jalview-dev-owner@jalview.org> 11c0c1e2426619039052264ce0f2b06a78cd9194 11c0c1e2426619039052264ce0f2b06a78cd9194 Merge branch 'releases/Release_2_11_2_Branch'
Ben Soares Ben Soares a8e52ab26dc6d12c8c18844ed29b9e604f6f4522 a8e52ab26dc6d12c8c18844ed29b9e604f6f4522 JAL-4004 cosmetic improvements for Java documentation renderer
Ben Soares Ben Soares 639bc5f3126d65cc1de8992b9a0fa0cfb993a9ff 639bc5f3126d65cc1de8992b9a0fa0cfb993a9ff JAL-4004 gradle task releasesTemplates now part of main build dependency tree. Improvements to releases.html.
Ben Soares Ben Soares 7f9536d5afb5f60359c827be09e97d0f22203130 7f9536d5afb5f60359c827be09e97d0f22203130 JAL-4004 working templates and generated whatsNew.html and releases.html file for both browser and Doc viewer
Ben Soares Ben Soares 2f0ae5beea0efcf3c40a7ebec33217ac34f90320 2f0ae5beea0efcf3c40a7ebec33217ac34f90320 JAL-4004 remove stray empty h3 headers
Ben Soares Ben Soares a1ad718d48d84b35e1e5e69ff34fc0ca7f69790e a1ad718d48d84b35e1e5e69ff34fc0ca7f69790e JAL-4004 gradle releasesTemplates builds releases.html
Ben Soares Ben Soares ff2fd741606ac49562f2cfb2b5b46059191feb35 ff2fd741606ac49562f2cfb2b5b46059191feb35 JAL-4004 Temporary mechanism to add JalviewJS link for selected versions to hugo website
Ben Soares Ben Soares 5e5545a5a719207cdab4c9b16baf7cd18c16bfba 5e5545a5a719207cdab4c9b16baf7cd18c16bfba JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time in release date header
Ben Soares Ben Soares 729e39d052a71602d82f7808fdb3862b9d893ce8 729e39d052a71602d82f7808fdb3862b9d893ce8 JAL-4004 Now generating hugo files from help/markdown/...
Ben Soares Ben Soares 07727bb7e06eb681af51a95e941cb035ac637d10 07727bb7e06eb681af51a95e941cb035ac637d10 JAL-4004 existing releases-VERSION.md files and releases.html template
Ben Soares Ben Soares ce916cd46bbe1ec0446d8672b7341f5af7471b6e ce916cd46bbe1ec0446d8672b7341f5af7471b6e JAL-4004 locations for markdown to go into whatsnew.html, releases.html and Version-VERSION/_index.md
Ben Soares Ben Soares a55b066dfc2bae86cf321b83a5a0731de9de16be a55b066dfc2bae86cf321b83a5a0731de9de16be JAL-3989 improved parsing and formatting now using flex CSS layout for columns
Ben Soares Ben Soares 567b80e2766af7104b626e8c01696cb76414d063 567b80e2766af7104b626e8c01696cb76414d063 JAL-1544 minor errors in releases.html and one missing version (2.8.2b1)
Ben Soares Ben Soares f0c00083746209028d075e5c7fe49e01e50f8644 f0c00083746209028d075e5c7fe49e01e50f8644 JAL-3989 small improvements to output markdown
Ben Soares Ben Soares f2e585f8dee5aba8522bbe622f4d6573648073b4 f2e585f8dee5aba8522bbe622f4d6573648073b4 JAL-3989 add in issue shortcodes to the archive version page changes list
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 9661db9ed56b5199c656b30005b892802ae49954 9661db9ed56b5199c656b30005b892802ae49954 JAL-1544 version number typo, probably copy and paste
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 7e58fdb919624619476a3c4389418889f1120209 7e58fdb919624619476a3c4389418889f1120209 JAL-3989 Populate template files for hugo build: archive version files including changes from releases.html, and installers data file
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> c67b28d36c11c8d5a7a25921c57f9c30f1855589 c67b28d36c11c8d5a7a25921c57f9c30f1855589 JAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build/website/docroot/old/VERSION and build/getdown/files, and files for hugo into build/website/hugo/...  This is better in multiple ways including collating files needed for the hugo website and website docroot.
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 01e95ae1be5ae83392de930dea48c531e2afa339 01e95ae1be5ae83392de930dea48c531e2afa339 JAL-3989 Independent creation of JSON installer sections
Ben Soares Ben Soares 8d46b6025f358a2642fb5996be91a75885f8fc88 8d46b6025f358a2642fb5996be91a75885f8fc88 JAL-3978 clean up unnecessary local variables for JALVIEW_VERSION_UNDERSCORES
Ben Soares Ben Soares 3f99b4c31e36e3f3eb277c65e5057c00977681b3 3f99b4c31e36e3f3eb277c65e5057c00977681b3 JAL-3989 Changed to using com.google.common.hash for SHA256 sum, for gradle 7 compatibility
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> ed8359e447a1f003c489ca79e9babbe6e3d40a95 ed8359e447a1f003c489ca79e9babbe6e3d40a95 Merge branch 'develop' into merge/JAL-3978+JAL-3553+develop+JAL-3989
Jim Procter <j.procter@dundee.ac.uk> Jim Procter <j.procter@dundee.ac.uk> 62fb9a3042bdc6daaad8218d47b12cb912907354 62fb9a3042bdc6daaad8218d47b12cb912907354 Merge branch 'develop' into releases/Release_2_11_2_Branch
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> db198a0eadd949de630aeef94c98321ffb6473f9 db198a0eadd949de630aeef94c98321ffb6473f9 JAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some commented out path changes to gradle.properties for future gathering of built files into more sensible places
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 41e0150abd0df895ce6fd849accde0d7c875bb06 41e0150abd0df895ce6fd849accde0d7c875bb06 JAL-3989 fix a build date once in build.gradle, not each time getDate() is called.
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> ecdae8027a9bad9e43f0ab12c54aec09fade15a1 ecdae8027a9bad9e43f0ab12c54aec09fade15a1 Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> a1cb36ade41d94aa93dd5b023e942c48f7e19de1 a1cb36ade41d94aa93dd5b023e942c48f7e19de1 Merge branch 'develop' into improvement/JAL-3978_add_gradle_task_to_make_getdown_archive_dir
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 993745a73b9f0660fb6d0fa263c13673158d1130 993745a73b9f0660fb6d0fa263c13673158d1130 JAL-3978 Using getdowninstanceappdir and getdowninstanceappbase to avoid conflict with getAppbaseBuildProperties(). Added an if around fetching build_properties to avoid failing to fetch local file appbase.
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> a9bc8da0124b22fde5d9e98b428e02f3338821b4 a9bc8da0124b22fde5d9e98b428e02f3338821b4 JAL-3978 Getdown add getdownappbase property to launched Jalview
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 32504ac62e27ce8849ab331a10b7cc3d0c2322b2 32504ac62e27ce8849ab331a10b7cc3d0c2322b2 JAL-3978 New tasks to build archive 'old' dir with appropriate getdown resources, JVL file and digest
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> eeb81bb516522a6a3fa4e246fc79ffddcc53bc67 eeb81bb516522a6a3fa4e246fc79ffddcc53bc67 JAL-3978 task stub and getdown splash screens
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 32359e95ca4259e224e6a93f793ab176b59c8184 32359e95ca4259e224e6a93f793ab176b59c8184 JAL-3553 added filesize to json
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> f550a2851efac4677abd69087245a3e74d966e98 f550a2851efac4677abd69087245a3e74d966e98 JAL-3553 now creating a json file for use on website.  It's easier to parse all the info here than on the website!
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 13944509925a0957ade80e195673c4fea1566d13 13944509925a0957ade80e195673c4fea1566d13 JAL-3553 copy sha256sums to a versioned filename too when created
Ben Soares <b.soares@dundee.ac.uk> Ben Soares <b.soares@dundee.ac.uk> 76b1f84db2be8f49de043a5d3f2c232aba33e37f 76b1f84db2be8f49de043a5d3f2c232aba33e37f JAL-3553 improve the labels in install4j's output.txt and make a versioned filename output-JALVIEW_VERSION.txt