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@Fe-r-oz Fe-r-oz commented Sep 18, 2024

I noticed there was some errors with build. For the latest documentation to be deployed, all these errors needed to be fixed. The above two errors were causes by the references. I have updated them.

I will also fix all the others errors so that the build passes.

┌ Error: Entry tillich2009quantum is missing the year field(s).
└ @ BibInternal ~/.julia/packages/BibInternal/RsFF9/src/bibtex.jl:93
┌ Error: Entry kovalev1212quantum is missing the year field(s).
└ @ BibInternal ~/.julia/packages/BibInternal/RsFF9/src/bibtex.jl:93
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: skipped.
[ Info: ExpandTemplates: expanding markdown templates.
┌ Error: duplicate docs found for 'defining_set' in `@docs` block in src/Classical/cyclic_code.md:85-87```@docs
│ defining_set
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'set_distance_upper_bound!' in `@docs` block in src/Classical/linear_code.md:84-86```@docs
│ set_distance_upper_bound!
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'encode' in `@docs` block in src/Classical/linear_code.md:98-100```@docs
│ encode
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: unable to get the binding for 'CodingTheory.⊕' in `@docs` block in src/Classical/new_codes_from_old.md:25-27 from expression ':($(Expr(:incomplete, "incomplete: premature end of input")))' in module Main
│ ```@docs
│ CodingTheory.⊕
```
│   exception = `binding` cannot understand expression `$(Expr(:incomplete, "incomplete: premature end of input"))`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: unable to get the binding for 'CodingTheory.×' in `@docs` block in src/Classical/new_codes_from_old.md:30-32 from expression ':($(Expr(:incomplete, "incomplete: premature end of input")))' in module Main
│ ```@docs
│ CodingTheory.×
```
│   exception = `binding` cannot understand expression `$(Expr(:incomplete, "incomplete: premature end of input"))`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: unable to get the binding for 'CodingTheory.⊗' in `@docs` block in src/Classical/new_codes_from_old.md:35-37 from expression ':($(Expr(:incomplete, "incomplete: premature end of input")))' in module Main
│ ```@docs
│ CodingTheory.⊗
```
│   exception = `binding` cannot understand expression `$(Expr(:incomplete, "incomplete: premature end of input"))`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: unable to get the binding for 'CodingTheory./' in `@docs` block in src/Classical/new_codes_from_old.md:44-46 from expression ':($(Expr(:incomplete, "incomplete: premature end of input")))' in module Main
│ ```@docs
│ CodingTheory./
```
│   exception = `binding` cannot understand expression `$(Expr(:incomplete, "incomplete: premature end of input"))`.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'plot_EXIT_chart' in `@docs` block in src/LDPC/analysis.md:30-32```@docs
│ plot_EXIT_chart
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'multiplicative_gap' in `@docs` block in src/LDPC/analysis.md:35-37```@docs
│ multiplicative_gap
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'irregular_LDPC_code' in `@docs` block in src/LDPC/codes.md:39-41```@docs
│ irregular_LDPC_code
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'shortest_cycles' in `@docs` block in src/LDPC/codes.md:119-121```@docs
│ shortest_cycles
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'ACE_spectrum' in `@docs` block in src/LDPC/codes.md:124-126```@docs
│ ACE_spectrum
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'shortest_cycle_ACE' in `@docs` block in src/LDPC/codes.md:128-130```@docs
│ shortest_cycle_ACE
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'ACE_distribution' in `@docs` block in src/LDPC/codes.md:132-134```@docs
│ ACE_distribution
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'average_ACE_distribution' in `@docs` block in src/LDPC/codes.md:136-138```@docs
│ average_ACE_distribution
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'median_ACE_distribution' in `@docs` block in src/LDPC/codes.md:140-142```@docs
│ median_ACE_distribution
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'mode_ACE_distribution' in `@docs` block in src/LDPC/codes.md:144-146```@docs
│ mode_ACE_distribution
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'find_MP_schedule' in `@docs` block in src/LDPC/decoders.md:24-26```@docs
│ find_MP_schedule
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: undefined binding 'decoder_simulation' in `@docs` block in src/LDPC/decoders.md:36-38```@docs
│ decoder_simulation
```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
[ Info: CollectCitations
┌ Error: The @cite link text "" does not match required regex
│   ast =@ast MarkdownAST.Link("@cite", "")
│    
└ @ DocumenterCitations ~/.julia/packages/DocumenterCitations/OyiEp/src/citation_link.jl:151
┌ Error: Error collecting citations from "Tutorials/Message Passing.md"
...

@Fe-r-oz
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Fe-r-oz commented Sep 18, 2024

Please don't merge this yet. I am waiting the results from the build.

@Fe-r-oz Fe-r-oz changed the title fix ref doc error in build fix some doc errors in build and add ECC Zoo links for product codes Sep 18, 2024
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Fe-r-oz commented Sep 18, 2024

I think this is ready for review. I had added the ECC Zoo links for product codes as well. For the false positives errors mentioned in #40 (comment), I will look into it later. Thank you!

@esabo
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esabo commented Sep 19, 2024

I'll just review it when the false positives are done because it won't compile before then anyway.

@Fe-r-oz Fe-r-oz marked this pull request as draft September 20, 2024 11:01
@Fe-r-oz Fe-r-oz changed the title fix some doc errors in build and add ECC Zoo links for product codes fix documentation errors in build and add ECC Zoo links for product codes Sep 20, 2024
@Fe-r-oz Fe-r-oz marked this pull request as ready for review September 20, 2024 16:28
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Fe-r-oz commented Sep 20, 2024

Woohoo, documentation build passed. There is a way to suppress the errors using checkdocs in makedocs. Using @example block can be helpful than importing .png to message passing.md. In the next PRs, I will do that as well.

I think this is ready for review, Thank you!

@Fe-r-oz Fe-r-oz requested a review from esabo September 20, 2024 16:30
@esabo
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esabo commented Sep 20, 2024

There are a lot of deletions but I don't see things added back in?

@Fe-r-oz
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Fe-r-oz commented Sep 20, 2024

For some methods, docstrings are not defined, so called them in docs gives error. Namely: decoder_simulation, and find_MP_schedule. For some methods, docstring is defined, but calling it gives undefined binding. I will try to make sure to delete as less as possible. I can added the deleted methods using [[ ]](@ref) is possible. The assets don't have the images that's why build was throwing error as well. I think @example block can be used in place of manually inputting images.

@Fe-r-oz
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Fe-r-oz commented Sep 20, 2024

Thanks for your comment! I hope this is okay. There are no png images in assets as that was causing the documentation error in message passing.md tutorial. I have made sure to add the methods as See: or See also: so that user can refer to these methods. In the future, a lot more work on documentation can be done to revamp the message passing.md as well.

This PR make sure that we can deploy the docs by suppressing all the errors for methods for which docstrings are not defined! I think it's ready for review, Thank you!

P.S I used warnonly = [:missing_docs] instead of checkdocs as we want the entire documentation to be checked, we just want to suppress the errors such as method errors for which docstring is not defined and show them as warnings instead.

@esabo esabo merged commit f65d3eb into esabo:dev Oct 11, 2024
@Fe-r-oz Fe-r-oz deleted the fixdev branch October 11, 2024 15:40
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