Merge pull request #1 from jsaintvanne/master

Update for training material

.gitignore

@@ -3,7 +3,10 @@
 _site
 _pdf
 .directory
+Gemfile
+Gemfile.backup
 Gemfile.lock
+Gemfile.lock.backup
 build
 node_modules
 miniconda.sh

.travis.yml

@@ -1,7 +1,8 @@
 ---
 sudo: required
-language: python
-python: 3.6
+language: ruby
+rvm:
+  - 2.4.4
 branches:
   only:
     - gh-pages
@@ -72,6 +73,7 @@ script:
         make check-slides
       elif [ "$CHECK" == "site-build" ]
       then
+        make check-framework
         make build
       elif [ "$CHECK" == "pdf-generation" ]
       then
@@ -86,7 +88,15 @@ after_success:
       # update badges and instances and rebuild
       make annotate
       make build
+
+      # Publish to GH
       bin/publish
+
+      # monthly cron job to make release
+      if [ "$TRAVIS_EVENT_TYPE" == "cron" ]
+      then
+        python bin/make_release.py
+      fi
     elif [ "$TRAVIS_PULL_REQUEST" == "false" -a "$TRAVIS_TAG" != "" -a "$CHECK" == "site-build" ]
     then
       # Do not publish old versions live, and do not update badges since not pushing to gh-pages.

CODEOWNERS

@@ -1,22 +1,37 @@
 # See documentation here:
 # https://blog.github.com/2017-07-06-introducing-code-owners/
+#
+# Anybody is free to add their name here
 
-assets/*     @bebatut @shiltemann @erasche
-bin/*        @bebatut @shiltemann @erasche
-metadata/*   @bebatut @shiltemann @erasche
-badges/*     @erasche
-_layouts/*   @bebatut @shiltemann @erasche
-_includes/*  @bebatut @shiltemann @erasche
-_plugins/*   @bebatut @erasche
+assets/     @bebatut @shiltemann @erasche
+bin/        @bebatut @shiltemann @erasche
+metadata/   @bebatut @shiltemann @erasche
+badges/     @erasche
+_layouts/   @bebatut @shiltemann @erasche
+_includes/  @bebatut @shiltemann @erasche
+_plugins/   @bebatut @erasche
 
-# Topics
-topics/dev/*               @erasche @shiltemann @abretaud @lecorguille
-topics/admin/*             @erasche
-topics/instructors/*       @erasche
-topics/transcriptomics/*   @mblue9
-topics/genome-annotation/* @abretaud
-topics/metabolomics/*      @lecorguille
-topics/assembly/*          @Slugger70
+# Topic maintainers are placed in github teams @galaxyproject/training-<topic-name>
+topics/admin/                      @galaxyproject/training-admin
+topics/assembly/                   @galaxyproject/training-assembly
+topics/chip-seq/                   @galaxyproject/training-chip-seq
+topics/computational-chemistry/    @galaxyproject/training-computational-chemistry
+topics/contributing/               @galaxyproject/training-contributing
+topics/dev/                        @galaxyproject/training-dev @abretaud
+topics/ecology/                    @galaxyproject/training-ecology
+topics/epigenetics/                @galaxyproject/training-epigenetics
+topics/galaxy-data-manipulation/   @galaxyproject/training-galaxy-data-manipulation
+topics/galaxy-ui/                  @galaxyproject/training-galaxy-ui
+topics/genome-annotation/          @galaxyproject/training-genome-annotation
+topics/instructors/                @galaxyproject/training-instructors
+topics/introduction/               @galaxyproject/training-introduction
+topics/metabolomics/               @galaxyproject/training-metabolomics
+topics/metagenomics/               @galaxyproject/training-metagenomics
+topics/proteomics/                 @galaxyproject/training-proteomics
+topics/sequence-analysis/          @galaxyproject/training-sequence-analysis
+topics/statistics/                 @galaxyproject/training-statistics
+topics/transcriptomics/            @galaxyproject/training-transcriptomics
+topics/variant-analysis/           @galaxyproject/training-variant-analysis
 
 # Lines starting with '#' are comments.
 # # Order is important. The last matching pattern has the most precedence.

CONTRIBUTORS.yaml

@@ -32,6 +32,9 @@ afgane:
 aisanjiangw:
     name: Aisanjiang Wubuli
 
+almahmoud:
+    name: Alex Mahmoud
+
 andreasrichter:
     name: Andreas Richter
     github: false
@@ -54,6 +57,10 @@ anuprulez:
     email: [email protected]
     twitter: musafirtweetsz
 
+astrovsky01:
+    name: Alex Ostrovsky
+    email: [email protected]
+
 baberlevi:
     name: Levi Baber
 
@@ -107,12 +114,19 @@ cicozhang:
     maintainer_contact: https://hi-it.org
     twitter: CicoCN
 
+claraurf:
+    name: Clara Urfer
+
 claresloggett:
     name: Clare Sloggett
 
 cmonjeau:
     name: Cyril Monjeaud
 
+combesf:
+    name: Florence Combes
+    email: [email protected]
+
 cganote:
     name: Carrie Ganote
 
@@ -123,6 +137,9 @@ daltis20012009:
 dannon:
     name: Dannon Baker
 
+davidchristiany:
+    name: David Christiany
+
 delphine-l:
     name: Delphine Lariviere
     email: [email protected]
@@ -142,6 +159,9 @@ SanneAbeln:
 dyusuf:
     name: Dilmurat Yusuf
 
+emichn:
+    name: Elisa Michon
+
 erasche:
     name: Helena Rasche
     email: [email protected]
@@ -154,6 +174,10 @@ erxleben:
     email: [email protected]
     orcid: 0000-0002-7427-6478
 
+ethering:
+    name: Graham Etherington
+    orcid: 0000-0002-5003-1425
+
 fabio-cumbo:
     name: Fabio Cumbo
     email: [email protected]
@@ -165,12 +189,17 @@ fabio-cumbo:
 fidelram:
     name: Fidel Ramirez
 
-Florian-H-Lab:
-    name: Florian Heyl
-
 foellmelanie:
     name: Melanie Foell
 
+fpsom:
+    name: Fotis E. Psomopoulos
+    email: [email protected]
+    twitter: fopsom
+    gitter: fpsom
+    orcid: 0000-0002-0222-4273
+    linkedin: fpsom
+
 fmareuil:
     name: Fabien Mareuil
 
@@ -189,6 +218,9 @@ guerler:
 hdashnow:
     name: Harriet Dashnow
 
+heylf:
+    name: Florian Heyl
+
 hmenager:
     name: Hervé Ménager
 
@@ -200,6 +232,9 @@ hrhotz:
     orcid: 0000-0002-2799-424X
     linkedin: hans-rudolf-hotz-542b31
 
+ic4f:
+    name: Sergey Golitsynskiy
+
 igcbioinformatics:
     name: IGC Bioinformatics Unit
 
@@ -218,6 +253,9 @@ jennydg:
 jfallmann:
     name: Joerg Fallmann
 
+jfrancoismartin:
+    name: Jean-François Martin
+
 jgoecks:
     name: Jeremy Goecks
 
@@ -250,12 +288,22 @@ katrinleinweber:
     email: [email protected]
     orcid: 0000-0001-5135-5758
 
+khanteymoori:
+    name: Alireza Khanteymoori
+    email: [email protected]
+    orcid: 0000-0001-6811-9196
+
 lecorguille:
     name: Gildas Le Corguillé
 
 LeilyR:
     name: Leily Rabbani
 
+lldelisle:
+    name: Lucille Delisle
+    email: [email protected]
+    orcid: 0000-0002-1964-4960
+
 loraine-gueguen:
     name: Loraine Guéguen
 
@@ -291,6 +339,9 @@ mblue9:
 mccalluc:
     name: Chuck McCallum
 
+melpetera:
+    name: Mélanie Petera
+
 moffmade:
     name: Cory Maughmer
 
@@ -303,6 +354,7 @@ mritchie:
 
 mtekman:
     name: Mehmet Tekman
+    email: [email protected]
 
 mvdbeek:
     name: Marius van den Beek
@@ -329,6 +381,12 @@ NickSto:
 
 nsoranzo:
     name: Nicola Soranzo
+    gitter: nsoranzo
+    orcid: 0000-0003-3627-5340
+    twitter: NicolaSoranzo
+
+nuwang:
+    name: Nuwan Goonasekera
 
 nvk747:
     name: Vijay
@@ -342,6 +400,9 @@ pajanne:
 pavanvidem:
     name: Pavankumar Videm
 
+pcm32:
+    name: Pablo Moreno
+
 polkhe:
     name: Ekaterina Polkh
 
@@ -365,6 +426,11 @@ sanneabeln:
 sarah-peter:
     name: Sarah Peter
 
+sbenateau:
+    name: Simon Benateau
+    email: [email protected]
+    twitter: sbenateau
+
 Shians:
     name: Shian Su
 
@@ -400,6 +466,10 @@ tealiie:
 thomasmanke:
     name: Thomas Manke
 
+thomaswollmann:
+    name: Thomas Wollmann
+    orcid: 0000-0002-4741-3844
+
 timothygriffin:
     name: Timothy J. Griffin
     email: [email protected]
@@ -411,6 +481,13 @@ tizzir:
 tnabtaf:
     name: Dave Clements
 
+tobyhodges:
+    name: Toby Hodges
+    email: [email protected]
+    twitter: tbyhdgs
+    orcid: 0000-0003-1766-456X
+
+
 torhou:
     name: Torsten Houwaart
 
@@ -432,15 +509,30 @@ vdda:
 vivekbhr:
     name: Vivek Bhardwaj
 
+vloux:
+    name: Valentin Loux
+
 willdurand:
     name: William Durand
 
+willemdek11:
+    name: Willem de Koning
+
+workflow4metabolomics:
+    name: Workflow4Metabolomics core team
+
 wm75:
     name: Wolfgang Maier
 
+yguitton:
+    name: Yann Guitton
+
 yhoogstrate:
     name: Youri Hoogstrate
 
+yvandenb:
+    name: Yves Vandenbrouck
+
 yvanlebras:
     name: Yvan Le Bras
     email: [email protected]

Gemfile

@@ -0,0 +1,15 @@
+source "https://rubygems.org"
+gem "nokogiri", ">= 1.10.4"
+gem 'addressable'
+gem 'jekyll', '< 4'
+gem 'jekyll-feed'
+gem 'jekyll-environment-variables'
+gem 'jekyll-github-metadata'
+gem 'jekyll-scholar', '< 6'
+gem 'jekyll-redirect-from'
+gem 'jekyll-last-modified-at'
+gem 'csl-styles'
+gem 'awesome_bot'
+gem 'html-proofer'
+gem 'pkg-config'
+gem 'kwalify'