From c7450f28e2e916cefc0542b6d195c525ad0e5e28 Mon Sep 17 00:00:00 2001 From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com> Date: Thu, 9 Jan 2025 07:17:05 +0000 Subject: [PATCH 1/9] Update Node.js to version 22.13.0 --- .nvmrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nvmrc b/.nvmrc index bb8c76c68..2c022021b 100644 --- a/.nvmrc +++ b/.nvmrc @@ -1 +1 @@ -v22.11.0 +v22.13.0 From ff5026b380d491f2e3ba2d51b1235f8863672af8 Mon Sep 17 00:00:00 2001 From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com> Date: Thu, 9 Jan 2025 18:54:08 +0000 Subject: [PATCH 2/9] Update @rails/ujs to version 7.1.501 --- package.json | 2 +- yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/package.json b/package.json index db0c80528..643a9d8a4 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "dependencies": { - "@rails/ujs": "^7.1.3", + "@rails/ujs": "^7.1.501", "axios": "^0.28.1", "bootstrap-vue": "^2.23.1", "cytoscape": "^3.30.2", diff --git a/yarn.lock b/yarn.lock index ae736f012..3539ec81b 100644 --- a/yarn.lock +++ b/yarn.lock @@ -619,10 +619,10 @@ resolved "https://registry.yarnpkg.com/@prettier/plugin-ruby/-/plugin-ruby-4.0.4.tgz#73d85fc2a1731a3f62b57ac3116cf1c234027cb6" integrity sha512-lCpvfS/dQU5WrwN3AQ5vR8qrvj2h5gE41X08NNzAAXvHdM4zwwGRcP2sHSxfu6n6No+ljWCVx95NvJPFTTjCTg== -"@rails/ujs@^7.1.3": - version "7.1.402" - resolved "https://registry.yarnpkg.com/@rails/ujs/-/ujs-7.1.402.tgz#5d4e7e5d1e2e22df081bf5693fc75f0725635130" - integrity sha512-q9dDlIR+anDtuGcV56rLnqHAxtWo8vkSnvfFt7juthvHc+97NEtGlnM++uhvnlDbR+7EGkX8nGqQIF8R93oWMQ== +"@rails/ujs@^7.1.501": + version "7.1.501" + resolved "https://registry.yarnpkg.com/@rails/ujs/-/ujs-7.1.501.tgz#e560a7b6885a12a659c4beb47f4336c8a9353056" + integrity sha512-7EDRGUlgns12IgP3SXVSaxA3CwRzbLOypPXn1EqEZiZ/NS/PwaQ/oa7Z2VRO4B46JifoVr0PYg+G5ERSGQJHxQ== "@rollup/rollup-android-arm-eabi@4.22.4": version "4.22.4" From 59d7a37e9df7799297139eb56239d52d855c8220 Mon Sep 17 00:00:00 2001 From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com> Date: Thu, 9 Jan 2025 20:11:50 +0000 Subject: [PATCH 3/9] Update vite-plugin-ruby to version 5.1.1 --- package.json | 2 +- yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/package.json b/package.json index 643a9d8a4..8c1858372 100644 --- a/package.json +++ b/package.json @@ -35,7 +35,7 @@ "sass": "^1.77.8", "typescript": "^4.6.3", "vite": "^5.4.10", - "vite-plugin-ruby": "^5.1.0", + "vite-plugin-ruby": "^5.1.1", "vitest": "^2.1.4", "vue-template-compiler": "^2.7.0" }, diff --git a/yarn.lock b/yarn.lock index 3539ec81b..892d480f4 100644 --- a/yarn.lock +++ b/yarn.lock @@ -3238,10 +3238,10 @@ vite-node@2.1.4: pathe "^1.1.2" vite "^5.0.0" -vite-plugin-ruby@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/vite-plugin-ruby/-/vite-plugin-ruby-5.1.0.tgz#489f2071ea6d86b5db735ea1fbbbe10e50e8e9bc" - integrity sha512-Dgd/dCvb/8GYxZx2NEgxygEoUpHz9vfad7itlO4fXqYwdfAEwFwwOohC630yf/+kxIGBZXI5yk+Y3WkL9VkwcA== +vite-plugin-ruby@^5.1.1: + version "5.1.1" + resolved "https://registry.yarnpkg.com/vite-plugin-ruby/-/vite-plugin-ruby-5.1.1.tgz#ecd72591ddb90a23613051005bd70a6410945129" + integrity sha512-I1dXJq2ywdvTD2Cz5LYNcYLujqQ3eUxPoCjruRdfm2QBtHBY15NEeb6x5HuPM3T5S+y8S3p9fwRsieQQCjk0gg== dependencies: debug "^4.3.4" fast-glob "^3.3.2" From 43e9d53dd032eee210c5470472c71073fe349484 Mon Sep 17 00:00:00 2001 From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com> Date: Thu, 9 Jan 2025 20:30:17 +0000 Subject: [PATCH 4/9] Update vite to version 5.4.11 --- package.json | 2 +- yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/package.json b/package.json index 8c1858372..9e6dc4de0 100644 --- a/package.json +++ b/package.json @@ -34,7 +34,7 @@ "prettier": "^3.0.0", "sass": "^1.77.8", "typescript": "^4.6.3", - "vite": "^5.4.10", + "vite": "^5.4.11", "vite-plugin-ruby": "^5.1.1", "vitest": "^2.1.4", "vue-template-compiler": "^2.7.0" diff --git a/yarn.lock b/yarn.lock index 892d480f4..ce49a4483 100644 --- a/yarn.lock +++ b/yarn.lock @@ -3257,10 +3257,10 @@ vite@^5.0.0: optionalDependencies: fsevents "~2.3.3" -vite@^5.4.10: - version "5.4.10" - resolved "https://registry.yarnpkg.com/vite/-/vite-5.4.10.tgz#d358a7bd8beda6cf0f3b7a450a8c7693a4f80c18" - integrity sha512-1hvaPshuPUtxeQ0hsVH3Mud0ZanOLwVTneA1EgbAM5LhaZEqyPWGRQ7BtaMvUrTDeEaC8pxtj6a6jku3x4z6SQ== +vite@^5.4.11: + version "5.4.11" + resolved "https://registry.yarnpkg.com/vite/-/vite-5.4.11.tgz#3b415cd4aed781a356c1de5a9ebafb837715f6e5" + integrity sha512-c7jFQRklXua0mTzneGW9QVyxFjUgwcihC4bXEtujIo2ouWCe1Ajt/amn2PCxYnhYfd5k09JX3SB7OYWFKYqj8Q== dependencies: esbuild "^0.21.3" postcss "^8.4.43" From dc39932a9c99617456838c65f938b3cfbd05a23d Mon Sep 17 00:00:00 2001 From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com> Date: Thu, 9 Jan 2025 21:27:00 +0000 Subject: [PATCH 5/9] Update cytoscape to version 3.30.4 --- package.json | 2 +- yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/package.json b/package.json index 9e6dc4de0..c14373e1c 100644 --- a/package.json +++ b/package.json @@ -3,7 +3,7 @@ "@rails/ujs": "^7.1.501", "axios": "^0.28.1", "bootstrap-vue": "^2.23.1", - "cytoscape": "^3.30.2", + "cytoscape": "^3.30.4", "cytoscape-elk": "^2.2.0", "cytoscape-popper": "^2.0.0", "devour-client": "^2.1.2", diff --git a/yarn.lock b/yarn.lock index ce49a4483..24234c538 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1242,10 +1242,10 @@ cytoscape-popper@^2.0.0: dependencies: "@popperjs/core" "^2.0.0" -cytoscape@^3.30.2: - version "3.30.2" - resolved "https://registry.yarnpkg.com/cytoscape/-/cytoscape-3.30.2.tgz#94149707fb6547a55e3b44f03ffe232706212161" - integrity sha512-oICxQsjW8uSaRmn4UK/jkczKOqTrVqt5/1WL0POiJUT2EKNc9STM4hYFHv917yu55aTBMFNRzymlJhVAiWPCxw== +cytoscape@^3.30.4: + version "3.30.4" + resolved "https://registry.yarnpkg.com/cytoscape/-/cytoscape-3.30.4.tgz#3404da0a159c00a1a3df2c85b2b43fdc66a0e28e" + integrity sha512-OxtlZwQl1WbwMmLiyPSEBuzeTIQnwZhJYYWFzZ2PhEHVFwpeaqNIkUzSiso00D98qk60l8Gwon2RP304d3BJ1A== data-urls@^5.0.0: version "5.0.0" From 506f77ea99fb620f43f2e887b71b34d90ae615b0 Mon Sep 17 00:00:00 2001 From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com> Date: Thu, 9 Jan 2025 22:48:18 +0000 Subject: [PATCH 6/9] Update ruby-units to version 4.1.0 --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 154695dab..e880e7b1b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -371,7 +371,7 @@ GEM rubocop (>= 1.33.0, < 2.0) rubocop-ast (>= 1.31.1, < 2.0) ruby-progressbar (1.13.0) - ruby-units (4.0.3) + ruby-units (4.1.0) ruby2_keywords (0.0.5) rubyzip (2.3.2) securerandom (0.4.1) From b961bad7dfc01280802e6926ac8d18b6ab901fec Mon Sep 17 00:00:00 2001 From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com> Date: Thu, 9 Jan 2025 23:35:20 +0000 Subject: [PATCH 7/9] Update vite_rails to version 3.0.19 --- Gemfile.lock | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index e880e7b1b..a7e42729f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -414,12 +414,13 @@ GEM tzinfo (2.0.6) concurrent-ruby (~> 1.0) unicode-display_width (2.5.0) - vite_rails (3.0.17) - railties (>= 5.1, < 8) + vite_rails (3.0.19) + railties (>= 5.1, < 9) vite_ruby (~> 3.0, >= 3.2.2) - vite_ruby (3.9.0) + vite_ruby (3.9.1) dry-cli (>= 0.7, < 2) logger (~> 1.6) + mutex_m rack-proxy (~> 0.6, >= 0.6.1) zeitwerk (~> 2.2) web-console (4.2.1) From fcf9c03dcb3401966bf3eb40deb328e6110dac84 Mon Sep 17 00:00:00 2001 From: Katy Taylor Date: Fri, 10 Jan 2025 13:30:20 +0000 Subject: [PATCH 8/9] Change the diluent volume, as requested by lab staff --- config/purposes/scrna_core_library_prep.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/purposes/scrna_core_library_prep.yml b/config/purposes/scrna_core_library_prep.yml index 53c27bfa8..87932d84e 100644 --- a/config/purposes/scrna_core_library_prep.yml +++ b/config/purposes/scrna_core_library_prep.yml @@ -47,7 +47,7 @@ LRC GEM-X 5p GE Dil: :creator_class: LabwareCreators::ConcentrationBinnedPlate :dilutions: :source_volume: 10 - :diluent_volume: 0 + :diluent_volume: 25 :bins: - max: 25.0 pcr_cycles: 15 From a31f222c18f432070737c2240bef4bc36bd844ad Mon Sep 17 00:00:00 2001 From: Katy Taylor Date: Fri, 10 Jan 2025 13:57:32 +0000 Subject: [PATCH 9/9] Changes to the binning ranges - requirement missed back in June --- config/purposes/scrna_core_library_prep.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/config/purposes/scrna_core_library_prep.yml b/config/purposes/scrna_core_library_prep.yml index 87932d84e..a56026550 100644 --- a/config/purposes/scrna_core_library_prep.yml +++ b/config/purposes/scrna_core_library_prep.yml @@ -49,26 +49,26 @@ LRC GEM-X 5p GE Dil: :source_volume: 10 :diluent_volume: 25 :bins: - - max: 25.0 + - max: 50.0 pcr_cycles: 15 colour: 1 - - min: 25.0 - max: 150.0 + - min: 50.0 + max: 250.0 pcr_cycles: 13 colour: 2 - - min: 150.0 - max: 500.0 + - min: 250.0 + max: 600.0 pcr_cycles: 11 colour: 3 - - min: 500.0 - max: 1000.0 + - min: 600.0 + max: 1_100.0 pcr_cycles: 9 colour: 4 - - min: 1000.0 - max: 1500.0 + - min: 1_100.0 + max: 1_500.0 pcr_cycles: 7 colour: 5 - - min: 1500.0 + - min: 1_500.0 pcr_cycles: 5 colour: 12 :file_links: