remove rb-nokogiri from conda environment and pin ruby > 3

[valeriupredoi]

rb-nokogiri from conda forge is ancient (last uploaded more than 4 years ago) and it's holding up ruby to a very old version; removing it here, and pinning ruby >3 that'll pick up a modern version. If Nokogiri really needs installation (I don't know where it's used), a gem install nokogiri will most probably do the trick.

Nokogiri as a gem looks well maintained and released https://rubygems.org/gems/nokogiri/versions/1.18.10?locale=en

The issue manifests itself in a (rather poorly error coded) message seen by @rswamina in #359

Closes #359

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Closes {Link to the corresponding issue}

[valeriupredoi]

thanks @rswamina 🍺

[rswamina]

@valeriupredoi - Only one reviewer approval is required. If you are happy, I will merge.

[valeriupredoi]

ah sorry, old habit with @bouweandela in Core - I merged already 😁

[LisaBock]

Unfortunately, the new environment is not working for me. But the old one did. @valeriupredoi Do you know what the problem might be?

Output after make serve:

bundle install --path .vendor/bundle && bundle update && bundle exec jekyll serve
[DEPRECATED] The `--path` flag is deprecated because it relies on being remembered across bundler invocations, which bundler will no longer do in future versions. Instead please use `bundle config set path '.vendor/bundle'`, and stop using this flag
Bundler 2.6.9 is running, but your lockfile was generated with 1.17.2. Installing Bundler 1.17.2 and restarting using that version.
Fetching gem metadata from https://rubygems.org/.
Fetching bundler 1.17.2
Installing bundler 1.17.2
/athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/shared_helpers.rb:272:in 'Bundler::SharedHelpers#search_up': undefined method 'untaint' for an instance of String (NoMethodError)

      current  = File.expand_path(SharedHelpers.pwd).untaint
                                                    ^^^^^^^^
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/shared_helpers.rb:259:in 'Bundler::SharedHelpers#find_file'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/shared_helpers.rb:251:in 'Bundler::SharedHelpers#find_gemfile'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/shared_helpers.rb:27:in 'Bundler::SharedHelpers#root'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler.rb:234:in 'Bundler.root'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler.rb:246:in 'Bundler.app_config_path'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler.rb:273:in 'Bundler.settings'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/feature_flag.rb:21:in 'block in Bundler::FeatureFlag#settings_method'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/cli.rb:97:in '<class:CLI>'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/cli.rb:7:in '<module:Bundler>'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/cli.rb:6:in '<top (required)>'
        from <internal:/athome/bock_ls/mambaforge/envs/tutorial_test/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:136:in 'Kernel#require'
        from <internal:/athome/bock_ls/mambaforge/envs/tutorial_test/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:136:in 'Kernel#require'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/exe/bundle:23:in 'block in <top (required)>'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/lib/bundler/friendly_errors.rb:124:in 'Bundler.with_friendly_errors'
        from /athome/bock_ls/ESMVal/ESMValTool/ESMValTool_Tutorial_v2/.vendor/bundle/ruby/3.4.0/gems/bundler-1.17.2/exe/bundle:22:in '<top (required)>'
        from /athome/bock_ls/mambaforge/envs/tutorial_test/bin/bundle:31:in 'Kernel#load'
        from /athome/bock_ls/mambaforge/envs/tutorial_test/bin/bundle:31:in '<main>'
make: *** [Makefile:49: serve] Error 1

[valeriupredoi]

@LisaBock can you try with ruby==3.4.7 - that's the one it worked for me and Ranjini, if it does work, then I'll pin it in a PR - your conda/mamba may be a bit too old so it picked up 3.4.0

[LisaBock]

@valeriupredoi Sorry, this changed nothing... Same error.

[valeriupredoi]

your bundler is ancient, currently at 2.7.2 https://rubygems.org/gems/bundler/versions/2.7.2?locale=en - try updating that one as well - I am on 2.6.9 in the test I ran and found nokogiri being ancient

(esmvaltool_tutorial) [valeriu@sci-vm-01 esmvaltool]$ bundler --version
Bundler version 2.6.9

[valeriupredoi]

@LisaBock you really need to update your conda mamba base - your picking up some really ancient package versions, I just created the env on my local machine with:

(esmvaltool_tutorial) valeriu@valeriu-PORTEGE-Z30-C:~/ESMValTool_Tutorial$ conda -V                                                                      
conda 25.7.0                                                                                                                                             
(esmvaltool_tutorial) valeriu@valeriu-PORTEGE-Z30-C:~/ESMValTool_Tutorial$ mamba --version                                                               
2.3.2 

and my bundler is 2.6.9, with ruby

(esmvaltool_tutorial) valeriu@valeriu-PORTEGE-Z30-C:~/ESMValTool_Tutorial$ conda list ruby                                                               
# packages in environment at /home/valeriu/miniconda3/envs/esmvaltool_tutorial:                                                                          
#                                                                                                                                                        
# Name                     Version          Build            Channel                                                                                     
ruby                       3.4.7            h498564d_1       conda-forge

🍻

[LisaBock]

My versions are not old:

(base) bock_ls@lx001:~/ESMVal/ESMValTool/ESMValTool_Tutorial_v2> mamba --version
2.3.1
(base) bock_ls@lx001:~/ESMVal/ESMValTool/ESMValTool_Tutorial_v2> conda -V
conda 25.7.0

When typing mamba update --name base mamba conda, it's doing nothing:

(tutorial_test_4) bock_ls@lx001:~/ESMVal/ESMValTool/ESMValTool_Tutorial_v2> mamba update --name base mamba conda
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
ERROR: unknown command "inspect"

Pinned packages:
  - python=3.9

Transaction
  Prefix: /athome/bock_ls/mambaforge
  All requested packages already installed

Transaction starting
Transaction finished

[valeriupredoi]

ah they are not old at all! How are you creating the environment then?

[valeriupredoi]

it'd be good if you moved to eg Python 3.13 though, 3.9 is not supported anymore