Bump nokogiri from 1.13.10 to 1.15.4

Gemfile.lock

@@ -9,12 +9,11 @@ GEM
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
     eventmachine (1.2.7)
+    eventmachine (1.2.7-x64-mingw32)
     ffi (1.15.5)
-    ffi (1.15.5-x64-mingw-ucrt)
     forwardable-extended (2.6.0)
     gemoji (3.0.1)
-    google-protobuf (3.22.0-arm64-darwin)
-    google-protobuf (3.22.0-x64-mingw-ucrt)
+    google-protobuf (3.22.0)
     http_parser.rb (0.8.0)
     i18n (1.12.0)
       concurrent-ruby (~> 1.0)
@@ -61,28 +60,42 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
-    mini_portile2 (2.8.1)
-    nokogiri (1.13.10)
-      mini_portile2 (~> 2.8.0)
-      racc (~> 1.4)
-    nokogiri (1.13.10-arm64-darwin)
+    mini_portile2 (2.8.5)
+    nokogiri (1.15.4)
+      mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     posix-spawn (0.3.15)
     public_suffix (5.0.1)
-    racc (1.6.2)
+    racc (1.7.3)
     rainbow (3.1.1)
+    rake (13.1.0)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rexml (3.2.5)
     rouge (3.30.0)
     safe_yaml (1.0.5)
+    sass-embedded (1.58.3)
+      google-protobuf (~> 3.21)
+      rake (>= 10.0.0)
+    sass-embedded (1.58.3-aarch64-linux-gnu)
+      google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-arm-linux-gnueabihf)
+      google-protobuf (~> 3.21)
     sass-embedded (1.58.3-arm64-darwin)
       google-protobuf (~> 3.21)
     sass-embedded (1.58.3-x64-mingw-ucrt)
       google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x64-mingw32)
+      google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x86-linux-gnu)
+      google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x86_64-darwin)
+      google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x86_64-linux-gnu)
+      google-protobuf (~> 3.21)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     unicode-display_width (2.4.2)

_data/citations.yaml

@@ -2210,6 +2210,154 @@
   orcid: 0000-0003-1147-3666
   plugin: orcid.py
   file: orcid.yaml
+- title: Doublecortin domain containing protein 2 (DCDC2) genetic variants in primary
+    sclerosing cholangitis
+  authors:
+  - Angela C. Cheung
+  - Brian D. Juran
+  - Raymond M. Moore
+  - Nicholas F. LaRusso
+  - Konstantinos N. Lazaridis
+  publisher: Journal of Hepatology
+  date: '2017-09-01'
+  link: https://doi.org/gs3bbx
+  id: doi:10.1016/j.jhep.2017.02.036
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- title: Label-Free Proteomic Analysis of Protein Changes in the Striatum during Chronic
+    Ethanol Use and Early Withdrawal
+  authors:
+  - Jennifer R. Ayers-Ringler
+  - Alfredo Oliveros
+  - Yanyan Qiu
+  - Daniel M. Lindberg
+  - David J. Hinton
+  - Raymond M. Moore
+  - Surendra Dasari
+  - Doo-Sup Choi
+  publisher: Frontiers in Behavioral Neuroscience
+  date: '2016-03-11'
+  link: https://doi.org/gs3bbz
+  id: doi:10.3389/fnbeh.2016.00046
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- title: Prevalence of Pathogenic Mutations in Cancer Predisposition Genes among Pancreatic
+    Cancer Patients
+  authors:
+  - Chunling Hu
+  - Steven N. Hart
+  - William R. Bamlet
+  - Raymond M. Moore
+  - Kannabiran Nandakumar
+  - Bruce W. Eckloff
+  - Yean K. Lee
+  - Gloria M. Petersen
+  - Robert R. McWilliams
+  - Fergus J. Couch
+  publisher: Cancer Epidemiology, Biomarkers & Prevention
+  date: '2016-01-01'
+  link: https://doi.org/gs3bb2
+  id: doi:10.1158/1055-9965.EPI-15-0455
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- id: ':'
+  title: Accurate clinical detection of hemoglobin variants via combined top-down
+    and bottom-up proteomics
+  publisher: ASMS 63th Conference Proceedings
+  date: '2016-06-09'
+  link: http://www.asms.org/publications/abstracts-and-proceedings
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- id: eid:2-s2.0-84938820322
+  title: Bioinformatics strategies for identifying regions of epigenetic deregulation
+    associated with aberrant transcript splicing and RNA-editing
+  publisher: BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics
+    Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference
+    on Biomedical Engineering Systems and Technologies, BIOSTEC 2015
+  date: '2022-05-24'
+  link: http://www.scopus.com/inward/record.url?eid=2-s2.0-84938820322&partnerID=MN8TOARS
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- title: 'PANDA: pathway and annotation explorer for visualizing and interpreting
+    gene-centric data'
+  authors:
+  - Steven N. Hart
+  - Raymond M. Moore
+  - Michael T. Zimmermann
+  - Gavin R. Oliver
+  - Jan B. Egan
+  - Alan H. Bryce
+  - Jean-Pierre A. Kocher
+  publisher: PeerJ
+  date: '2015-05-19'
+  link: https://doi.org/gs3bb3
+  id: doi:10.7717/peerj.970
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- title: 'HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq
+    data'
+  authors:
+  - Huihuang Yan
+  - Jared Evans
+  - Mike Kalmbach
+  - Raymond Moore
+  - Sumit Middha
+  - Stanislav Luban
+  - Liguo Wang
+  - Aditya Bhagwate
+  - Ying Li
+  - Zhifu Sun
+  - Xianfeng Chen
+  - Jean-Pierre A Kocher
+  publisher: BMC Bioinformatics
+  date: '2014-08-15'
+  link: https://doi.org/f6rmzn
+  id: doi:10.1186/1471-2105-15-280
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- title: 'The Biological Reference Repository (BioR): a rapid and flexible system
+    for genomics annotation'
+  authors:
+  - Jean-Pierre A. Kocher
+  - Daniel J. Quest
+  - Patrick Duffy
+  - Michael A. Meiners
+  - Raymond M. Moore
+  - David Rider
+  - Asif Hossain
+  - Steven N. Hart
+  - Valentin Dinu
+  publisher: Bioinformatics
+  date: '2014-03-10'
+  link: https://doi.org/f59rz4
+  id: doi:10.1093/bioinformatics/btu137
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
+- title: 'SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints
+    of Structural Variations'
+  authors:
+  - Steven N. Hart
+  - Vivekananda Sarangi
+  - Raymond Moore
+  - Saurabh Baheti
+  - Jaysheel D. Bhavsar
+  - Fergus J. Couch
+  - Jean-Pierre A. Kocher
+  publisher: PLoS ONE
+  date: '2013-12-16'
+  link: https://doi.org/gnhp39
+  id: doi:10.1371/journal.pone.0083356
+  orcid: 0000-0003-4196-1804
+  plugin: orcid.py
+  file: orcid.yaml
 - title: Computational tumor stroma reaction evaluation led to novel prognosis-associated
     fibrosis and molecular signature discoveries in high-grade serous ovarian carcinoma
   authors: