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Issue on Windows: Undefined method `to_citeproc' for an instance of String #95

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jrs0 opened this issue Jan 24, 2024 · 8 comments
Closed

Issue on Windows: Undefined method `to_citeproc' for an instance of String #95

jrs0 opened this issue Jan 24, 2024 · 8 comments
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@jrs0
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jrs0 commented Jan 24, 2024

The asciidoctor-bibtex extension is great! However, I'm having an issue that is preventing it from working on Windows.

Minimal problem

On Windows, after installing asciidoctor (version 2.0.20), and asciidoctor-bibtex (0.8.0), create the following minimal bibtex file ref.bib:

@article{urban2021assessing,
  title={Assessing the risks of bleeding vs thrombotic events in patients at high bleeding risk after coronary stent implantation: the ARC--high bleeding risk trade-off model},
  author={Urban, Philip and Gregson, John and Owen, Ruth and Mehran, Roxana and Windecker, Stephan and Valgimigli, Marco and Varenne, Olivier and Krucoff, Mitchell and Saito, Shigeru and Baber, Usman and others},
  journal={JAMA cardiology},
  volume={6},
  number={4},
  pages={410--419},
  year={2021},
  publisher={American Medical Association}
}

and the following document test.adoc:

= Test

cite:[urban2021assessing]

bibliography::[]

On running asciidoctor -r asciidoctor-bibtex test.adoc, I get the following error:

asciidoctor: FAILED: C:/Users/john.scott/Documents/git/hbr_uhbw/docs/test.adoc: Failed to load AsciiDoc document - undefined method `to_citeproc' for an instance of String
  Use --trace to show backtrace

When adding --trace, I get:

C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `block in to_citeproc': asciidoctor: FAILED: C:/Users/john.scott/Documents/git/hbr_uhbw/docs/test.adoc: Failed to load AsciiDoc document - undefined method `to_citeproc' for an instance of String (NoMethodError)

      map { |n| n.to_citeproc(options) }
                 ^^^^^^^^^^^^
        from C:/Ruby33-x64/lib/ruby/3.3.0/forwardable.rb:240:in `each'
        from C:/Ruby33-x64/lib/ruby/3.3.0/forwardable.rb:240:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `map'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `to_citeproc'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:172:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:69:in `block 
in convert!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:132:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:132:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:68:in `convert!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:55:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:610:in `to_citeproc'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:407:in `block in to_citeproc'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:407:in `map'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:407:in `to_citeproc'     
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-bibtex-0.8.0/lib/asciidoctor-bibtex/processor.rb:76:in `initialize'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-bibtex-0.8.0/lib/asciidoctor-bibtex/extensions.rb:96:in `new'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-bibtex-0.8.0/lib/asciidoctor-bibtex/extensions.rb:96:in `process'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:545:in `[]'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:545:in `block in parse'        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:544:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:544:in `parse'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/load.rb:84:in `load'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:78:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:190:in `block in convert_file'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:190:in `open'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:190:in `convert_file'   
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/cli/invoker.rb:129:in `block in invoke!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/cli/invoker.rb:112:in `each'       
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/cli/invoker.rb:112:in `invoke!'    
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/bin/asciidoctor:15:in `<top (required)>'
        from C:/Ruby33-x64/bin/asciidoctor:32:in `load'
        from C:/Ruby33-x64/bin/asciidoctor:32:in `<main>'
C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `block in to_citeproc': undefined method `to_citeproc' for an instance of String (NoMethodError)

      map { |n| n.to_citeproc(options) }
                 ^^^^^^^^^^^^
        from C:/Ruby33-x64/lib/ruby/3.3.0/forwardable.rb:240:in `each'
        from C:/Ruby33-x64/lib/ruby/3.3.0/forwardable.rb:240:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `map'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `to_citeproc'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:172:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:69:in `block 
in convert!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:132:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:132:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:68:in `convert!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:55:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:610:in `to_citeproc'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:407:in `block in to_citeproc'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:407:in `map'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:407:in `to_citeproc'     
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-bibtex-0.8.0/lib/asciidoctor-bibtex/processor.rb:76:in `initialize'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-bibtex-0.8.0/lib/asciidoctor-bibtex/extensions.rb:96:in `new'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-bibtex-0.8.0/lib/asciidoctor-bibtex/extensions.rb:96:in `process'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:545:in `[]'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:545:in `block in parse'        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:544:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/document.rb:544:in `parse'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/load.rb:84:in `load'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:78:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:190:in `block in convert_file'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:190:in `open'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/convert.rb:190:in `convert_file'   
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/cli/invoker.rb:129:in `block in invoke!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/cli/invoker.rb:112:in `each'       
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/lib/asciidoctor/cli/invoker.rb:112:in `invoke!'    
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/asciidoctor-2.0.20/bin/asciidoctor:15:in `<top (required)>'
        from C:/Ruby33-x64/bin/asciidoctor:32:in `load'
        from C:/Ruby33-x64/bin/asciidoctor:32:in `<main>'

Versions

I obtained all the dependencies by running gem install asciidoctor-bibtex in the powershell, which gave the following log:

PS H:\> gem install asciidoctor-bibtex
Fetching asciidoctor-bibtex-0.8.0.gem
Fetching citeproc-ruby-1.1.14.gem
Fetching bibtex-ruby-5.1.6.gem
Successfully installed citeproc-ruby-1.1.14
Successfully installed bibtex-ruby-5.1.6
Successfully installed asciidoctor-bibtex-0.8.0
Parsing documentation for citeproc-ruby-1.1.14
Installing ri documentation for citeproc-ruby-1.1.14
Parsing documentation for bibtex-ruby-5.1.6
Installing ri documentation for bibtex-ruby-5.1.6
Parsing documentation for asciidoctor-bibtex-0.8.0
Installing ri documentation for asciidoctor-bibtex-0.8.0
Done installing documentation for citeproc-ruby, bibtex-ruby, asciidoctor-bibtex after 4 seconds
3 gems installed

More Testing

I thought initially the problem was with bibtex-ruby, because I was able to reproduce the same kind of issue by following the instructions on their readme page.

For example, running the following commands in irb (with bibtex-ruby version 5.1.6, as installed by asciidoctor-bibtex dependencies), I get:

require 'bibtex'
# => true
b = BibTeX.open('./ref.bib')
# => #<BibTeX::Bibliography data=[26]>
b['urban2021assessing'].title
# => "Assessing the risks of bleeding vs thrombotic events in patients at high bleeding risk after coronary stent implantation: the ARC--high bleeding risk trade-off model"

# Skipping down to the citeproc bit
require 'citeproc'
# => true
CiteProc.process b[:urban2021assessing].to_citeproc, :style => :apa

The final line produces the following error:

C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `block in to_citeproc': undefined method `to_citeproc' for an instance of String (NoMethodError)

      map { |n| n.to_citeproc(options) }
                 ^^^^^^^^^^^^
        from C:/Ruby33-x64/lib/ruby/3.3.0/forwardable.rb:240:in `each'
        from C:/Ruby33-x64/lib/ruby/3.3.0/forwardable.rb:240:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `map'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/names.rb:81:in `to_citeproc'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:172:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:69:in `block in convert!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:132:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:132:in `each'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:68:in `convert!'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry/citeproc_converter.rb:55:in `convert'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/bibtex-ruby-5.1.6/lib/bibtex/entry.rb:610:in `to_citeproc'
        from (irb):6:in `<main>'
        from <internal:kernel>:187:in `loop'
        from C:/Ruby33-x64/lib/ruby/gems/3.3.0/gems/irb-1.11.0/exe/irb:9:in `<top (required)>'
        from C:/Ruby33-x64/bin/irb:33:in `load'
        from C:/Ruby33-x64/bin/irb:33:in `<main>'

However, if I remove all my packages:

PS H:\> gem uninstall asciidoctor-bibtex bibtex-ruby citeproc-ruby cls-styles
Gem 'cls-styles' is not installed
Successfully uninstalled asciidoctor-bibtex-0.8.0
Successfully uninstalled citeproc-ruby-1.1.14
Successfully uninstalled bibtex-ruby-5.1.6

and then reinstall just bibtex-ruby and citeproc-ruby (getting the latest versions):

PS H:\> gem install bibtex-ruby citeproc-ruby
Fetching bibtex-ruby-6.1.0.gem
Successfully installed bibtex-ruby-6.1.0
Parsing documentation for bibtex-ruby-6.1.0
Installing ri documentation for bibtex-ruby-6.1.0
Done installing documentation for bibtex-ruby after 1 seconds
Fetching citeproc-ruby-2.0.0.gem
Successfully installed citeproc-ruby-2.0.0
Parsing documentation for citeproc-ruby-2.0.0
Installing ri documentation for citeproc-ruby-2.0.0
Done installing documentation for citeproc-ruby after 0 seconds
2 gems installed

the problem seems to go away (when I run the same commands as above in irb):

# ... same commands as above, ending with...

CiteProc.process b[:urban2021assessing].to_citeproc, :style => :apa
# => nil

Oddly, the command returns nil, when it should return a non-null entry (based on the bibtex-ruby readme). I haven't figured out the discrepancy, but my main thought was just that the to_citeproc error had gone. That made me think maybe there is some kind of version issue?

It works in Linux

Testing out using Linux Mint 21.1 Cinnamon, running:

# sudo gem install asciidoctor-bibtex
Fetching bibtex-ruby-5.1.6.gem
Fetching asciidoctor-bibtex-0.8.0.gem
Fetching csl-styles-1.0.1.11.gem
Fetching citeproc-ruby-1.1.14.gem
Successfully installed csl-styles-1.0.1.11
Successfully installed citeproc-ruby-1.1.14
Successfully installed bibtex-ruby-5.1.6
Successfully installed asciidoctor-bibtex-0.8.0
Parsing documentation for csl-styles-1.0.1.11
Installing ri documentation for csl-styles-1.0.1.11
Parsing documentation for citeproc-ruby-1.1.14
Installing ri documentation for citeproc-ruby-1.1.14
Parsing documentation for bibtex-ruby-5.1.6
Installing ri documentation for bibtex-ruby-5.1.6
Parsing documentation for asciidoctor-bibtex-0.8.0
Installing ri documentation for asciidoctor-bibtex-0.8.0
Done installing documentation for csl-styles, citeproc-ruby, bibtex-ruby, asciidoctor-bibtex after 0 seconds
4 gems installed

All the gem versions look the same as Windows to me (unless I missed something), but it does work on Linux (the minimal example above right at the top runs fine).

That made me think maybe it was a Ruby version issue -- on Linux, ruby --version gives ruby 3.0.2p107 (2021-07-07 revision 0db68f0233) [x86_64-linux-gnu], and on Windows it gives ruby 3.3.0 (2023-12-25 revision 5124f9ac75) [x64-mingw-ucrt]. Not sure if that would make any difference.

Conclusion

Not knowing anything about Ruby, I'm not really sure what the issue is, but it looked like some kind of dependency thing. I wondered if you would be able to offer any insight or any workarounds? (Or point out if I did anything obviously wrong, which would be ideal!)

Thanks in advance.
@marcelbaumann
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I would also be interested in information. I have a similar problem on macOS. From the downloaded gem dependencies, it seems a dependency problem.

@Seraphendipity
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Seraphendipity commented Jan 31, 2024 •
edited by mojavelinux
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Same issue. Which is unfortunate, as I was trying to give AsciiDoc a chance for documenting schoolwork this year to avoid the many Bibliography information errors I ran into with Pandoc...only to run into it yet again here ;-;

Guessing dependency error as well. Haven't quite figured out the RVM and Gem management stuff on Windows so probably will need to test when I have another free day to dive into that.

@mojavelinux
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mojavelinux commented Jan 31, 2024 •
edited
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These seems to be a compatibility error introduced by Ruby 3.3. All the tests work on Ruby 3.2.

FYI, you might want to give https://github.com/riboseinc/asciidoctor-bibliography a try.

@mojavelinux
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The error is actually coming from bibtex-ruby. The version this gem is using is not compatible with Ruby 3.3. However, the latest version is. So it's a matter of upgrading that gem.

mojavelinux added a commit to mojavelinux/asciidoctor-bibtex that referenced this issue Jan 31, 2024
@mojavelinux
resolves asciidoctor#95 upgrade bibtex-ruby to fix Ruby 3.3 compatibi…
bb81962 
…lity
mojavelinux added a commit to mojavelinux/asciidoctor-bibtex that referenced this issue Jan 31, 2024
@mojavelinux
resolves asciidoctor#95 upgrade bibtex-ruby to fix Ruby 3.3 compatibi…
d5b8bf9 
…lity
@mojavelinux
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I've fixed the main branch. We'll need @ProgramFan to publish a release in order for it to be included in the version from RubyGems.org.

@jrs0
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jrs0 commented Feb 2, 2024

Thanks very much @mojavelinux!

For anyone who wants a quick way to get started now, I found I can install directly from the main branch (now fixed for me) using:

# Remove everything to start from clean
gem uninstall asciidoctor-bibtex bibtex-ruby citeproc-ruby cls-styles

# Install directly from the main branch
gem install specific_install
gem specific_install -l https://github.com/asciidoctor/asciidoctor-bibtex

Would probably work on Mac and Linux too. Obviously best to install from the release when it's out, but this was useful for me to just get going quickly.

@mojavelinux
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Thanks for the tip!

There's also another way of using code directly from GitHub (or git for that matter) if you are using Bundler. Your Gemfile would look like this:

source 'https://rubygems.org'

gem 'asciidoctor'
gem 'asciidoctor-bibtex', github: 'asciidoctor/asciidoctor-bibtex'

Then run:

rm -rf .bundle/gems Gemfille.lock
bundle config set --local path .bundle/gems
bundle

You can then use bundle exec to instruct Ruby to use the locally installed gems.

bundle exec asciidoctor -r asciidoctor-bibtex doc.adoc

@jrs0
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jrs0 commented Feb 2, 2024

Nice, I'll keep those methods in mind. Thanks again!

@mojavelinux mojavelinux mentioned this issue Feb 5, 2024
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@mojavelinux @marcelbaumann @Seraphendipity @jrs0