# Documenter/CI

**URL:** <https://discourse.julialang.org/t/documenter-ci/114800>\
**Category:** New to Julia\
**Created:** [May 27, 2024, 8:06pm UTC](https://discourse.julialang.org/t/documenter-ci/114800 "2024-05-27T20:06:58Z")\
**Posts on this page:** 18\
**Page:** 1

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [May 27, 2024, 8:06pm UTC](https://discourse.julialang.org/t/documenter-ci/114800/1 "2024-05-27T20:06:58Z")

</div>

Hi,

First, let me say that Julia’s packaging (Pkg, PkgTemplates, etc…) is very impressive but also too difficult for dumb mortals like me to understand, unfortunately. I’ve got a package I’m trying to make conform a bit more to standard Julia things. I’ve already got docstrings everywhere. I’m trying to add Documenter to this. I thought I did it right, but now I’m getting error messages that I can’t fathom.

There is so much state to this thing (Documenter specifically, and all the configuration files for my project) that I have no idea what I should post here so that someone can help me. I’ve decided to push my broken thing to github and put the github link: [GitHub - sloisel/MultiGridBarrier.jl: MultiGrid Barrier method](https://github.com/sloisel/MultiGridBarrier.jl)

I’ll stick around for a little while and read replies, but I’m going to bed soon. I’m secretly hoping I did something really dumb and easy and someone will have posted the solution when I next check, but in case I only respond after I sleep, apologies.

Now for the error messages:

````julia
sebastienloisel@macbook-pro docs % julia --project make.jl       

[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
[ Info: ExpandTemplates: expanding markdown templates.
┌ Error: duplicate docs found for 'MultiGridBarrier.AMG' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.Barrier' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.amg' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.amgb' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.barrier' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.damped_newton' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.fem1d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.fem2d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.fem_interp1d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.fem_interp1d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.fem_plot_2d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.fem_solve_1d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.fem_solve_2d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.interp1d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.interp2d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.plot1d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.plot2d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.spectral_solve_1d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
┌ Error: duplicate docs found for 'MultiGridBarrier.spectral_solve_2d' in src/index.md:12-14
│ ```@autodocs
│ Modules = [MultiGridBarrier]
│ ```
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl:44
[ Info: CrossReferences: building cross-references.
[ Info: CheckDocument: running document checks.
[ Info: Populate: populating indices.
ERROR: LoadError: `makedocs` encountered an error [:autodocs_block] -- terminating build before rendering.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] runner(::Type{Documenter.Builder.RenderDocument}, doc::Documenter.Document)
   @ Documenter ~/.julia/packages/Documenter/CJeWX/src/builder_pipeline.jl:253
 [3] dispatch(::Type{Documenter.Builder.DocumentPipeline}, x::Documenter.Document)
   @ Documenter.Selectors ~/.julia/packages/Documenter/CJeWX/src/utilities/Selectors.jl:170
 [4] #86
   @ ~/.julia/packages/Documenter/CJeWX/src/makedocs.jl:248 [inlined]
 [5] withenv(::Documenter.var"#86#88"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}})
   @ Base ./env.jl:257
 [6] #85
   @ ~/.julia/packages/Documenter/CJeWX/src/makedocs.jl:247 [inlined]
 [7] cd(f::Documenter.var"#85#87"{Documenter.Document}, dir::String)
   @ Base.Filesystem ./file.jl:112
 [8] #makedocs#84
   @ ~/.julia/packages/Documenter/CJeWX/src/makedocs.jl:247 [inlined]
 [9] top-level scope
   @ ~/Dropbox/2023/Spectral Barrier Method/julia/MultiGridBarrier.jl/docs/make.jl:6
in expression starting at /Users/sebastienloisel/Dropbox/2023/Spectral Barrier Method/julia/MultiGridBarrier.jl/docs/make.jl:6
sebastienloisel@macbook-pro docs % 

````

---

<div class="post-metadata">

**Author:** ![gdalle](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/gdalle/32/27854_2.png) [@gdalle](https://discourse.julialang.org/u/gdalle)\
**Post date:** [May 27, 2024, 9:33pm UTC](https://discourse.julialang.org/t/documenter-ci/114800/2 "2024-05-27T21:33:02Z")

</div>

I’m not sure why you get that error message locally. Usually it means that you have included the same docstring twice, but I don’t see duplicates in your [`index.md`](https://github.com/sloisel/MultiGridBarrier.jl/blob/main/docs/src/index.md).  
In any case, the Documentation CI run [fails even earlier](https://github.com/sloisel/MultiGridBarrier.jl/actions/runs/9259899579/job/25472676692), when you try to install PyPlot.jl. If you want to avoid the struggle with Python dependencies, may I suggest switching to a pure-Julia solution like Makie.jl, or something that is easier to install like Plots.jl? The syntax is very similar.

As for the packaging tools in general, it is true that they are a bit daunting for beginners. Some friends and I wrote a blog to try and make sense of it all, hopefully it can help:

[https://modernjuliaworkflows.github.io/sharing/](https://modernjuliaworkflows.github.io/sharing/)

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [May 27, 2024, 9:48pm UTC](https://discourse.julialang.org/t/documenter-ci/114800/3 "2024-05-27T21:48:47Z")

</div>

Thanks for your reply.

I know that CI on github fails in an altogether different way, I wasn’t asking about that yet but your information is valuable. This code goes with a couple of papers and the choice of PyPlot was made after trying several plotting packages, this was the only suitable choice at the time. Unfortunately, if PyPlot is incompatible with CI, I will have to forgo CI. ☹

---

<div class="post-metadata">

**Author:** ![ufechner7](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/ufechner7/32/51363_2.png) [@ufechner7](https://discourse.julialang.org/u/ufechner7)\
**Post date:** [May 27, 2024, 11:06pm UTC](https://discourse.julialang.org/t/documenter-ci/114800/4 "2024-05-27T23:06:56Z")

</div>

As you can see here: [GitHub - aenarete/ControlPlots.jl: Create plots that can be saved and edited with Julia](https://github.com/aenarete/ControlPlots.jl) PyPlot works fine with CI …

---

<div class="post-metadata">

**Author:** ![kellertuer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kellertuer/32/220707_2.png) [@kellertuer](https://discourse.julialang.org/u/kellertuer)\
**Post date:** [May 28, 2024, 5:01am UTC](https://discourse.julialang.org/t/documenter-ci/114800/5 "2024-05-28T05:01:34Z")

</div>

For the PyPlot error, at first glance it seems to be missing from the environment in `docs/` where that should be present – and also loaded in the `make.jl`.

For the duplicate docs I would have to clone the repo, can try to do that later today and take a look, but at first glance I am surprised those errors to appear (and no worries, that is not a dumb question to ask for help with error messages!).

---

<div class="post-metadata">

**Author:** ![kellertuer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kellertuer/32/220707_2.png) [@kellertuer](https://discourse.julialang.org/u/kellertuer)\
**Post date:** [May 28, 2024, 6:05am UTC](https://discourse.julialang.org/t/documenter-ci/114800/6 "2024-05-28T06:05:21Z")

</div>

I cloned your repository. Had to change the first few lines of the docs to

```julia
using Pkg
Pkg.activate(@ __DIR__ )
# As long as it is not registered, this is nice, in general it locally always
# renders docs of the current version checked out in this repo.
Pkg.develop(PackageSpec(; path=(@ __DIR__ ) * "/../"))
using MultiGridBarrier
using Documenter, PyPlot

```

Since your package is not registered and this way documenter always takes the parent folder as the dev version of your package, so that way documenter always renders the docs belonging to the current state of the repo.

Without those lines I get the error that your package is unknown (sure, it is not registered). I also added `PyPlot` to the docs env.

My “problem” now is, that on my machine your docs just render fine

```julia
julia> include("make.jl")
  Activating project at `~/Repositories/Julia/MultiGridBarrier.jl/docs`
   Resolving package versions...
  No Changes to `~/Repositories/Julia/MultiGridBarrier.jl/docs/Project.toml`
  No Changes to `~/Repositories/Julia/MultiGridBarrier.jl/docs/Manifest.toml`
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
[ Info: ExpandTemplates: expanding markdown templates.
[ Info: CrossReferences: building cross-references.
[ Info: CheckDocument: running document checks.
[ Info: Populate: populating indices.
[ Info: RenderDocument: rendering document.
[ Info: HTMLWriter: rendering HTML pages.
[ Info: Automatic `version="1.0.0-DEV"` for inventory from ../Project.toml
┌ Warning: Documenter could not auto-detect the building environment. Skipping deployment.
└ @ Documenter ~/.julia/packages/Documenter/CJeWX/src/deployconfig.jl:76

```

which is what I expected from them. So could you provide a bit more details how you render the docs locally and which version of Documenter you are using?

For the above run, my environment in `docs` looks like

```julia
(docs) pkg> status
Status `~/Repositories/Julia/MultiGridBarrier.jl/docs/Project.toml`
  [e30172f5] Documenter v1.4.1
  [9e2c1f1d] MultiGridBarrier v1.0.0-DEV `~/Repositories/Julia/MultiGridBarrier.jl`
  [d330b81b] PyPlot v2.11.2

```

and I either run the docs like you with `julia --project make.jl ` (in the docs folder) or `include("make.jl")` (after activating the docs env manually). Both yield the output above.

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [May 28, 2024, 7:28am UTC](https://discourse.julialang.org/t/documenter-ci/114800/7 "2024-05-28T07:28:17Z")

</div>

Hi,

Thanks for spending time on my problem like this.

I’ve changed the first few lines of the docs to what you wrote, and also added PyPlot to the docs environment like you did, then reran `include("make.jl")` as you suggest, but I got the same error message as before.

First question: why do I have to add `PyPlot` to my environment, and also `using` it in `make.jl`? And why don’t I have to do that with other packages that are used by `MultiGridBarrier`, for example, `ProgressMeter`, `QuadratureRules`, `ForwardDiff`, `SparseArrays`, etc…?

I ran `status` as you requested, here it is:

```julia
(docs) pkg> status
Status `~/Dropbox/2023/Spectral Barrier Method/julia/MultiGridBarrier.jl/docs/Project.toml`
  [e30172f5] Documenter v1.4.1
  [9e2c1f1d] MultiGridBarrier v1.0.0-DEV `~/Dropbox/2023/Spectral Barrier Method/julia/MultiGridBarrier.jl`
  [d330b81b] PyPlot v2.11.2

```

---

<div class="post-metadata">

**Author:** ![kellertuer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kellertuer/32/220707_2.png) [@kellertuer](https://discourse.julialang.org/u/kellertuer)\
**Post date:** [May 28, 2024, 7:39am UTC](https://discourse.julialang.org/t/documenter-ci/114800/8 "2024-05-28T07:39:12Z")

</div>

Ehm, the `PyPlot was mainly in preparation because I thought that would fix the other error later on CI as well, but I am not sure about that yet. So that is maybe one step too far ahead trying to solve the other CI problem as well.

Hm, since the status the same, there must be something different in your `docs/src` folder that we haven’t found yet. Since it is working on my side (with the version on GitHub) – are you sure your local repository is _exactly the same_ as what is on GitHub?

(Btw I would not recommend to put a git repo in a Dropbox; dropbox sync can have troubles with the `.git` folder, yielding a sync conflict could invalidate your local repo)

_edit:_ Or to make the question more precise: Is there any other `.md` file locally present in your `docs/src`? All files present there will be rendered to HTML (processed by Documenter) – independent on whether they are listed in the menu or not. So if you have a list of functions in a `a_test.md` that will cause your errors.

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [May 28, 2024, 8:20am UTC](https://discourse.julialang.org/t/documenter-ci/114800/9 "2024-05-28T08:20:47Z")

</div>

Thanks again for your help.

From my previous experiences with Julia, and from your description that you could, in fact, build my documentation locally on your machine, I suspected that my Julia installation’s state got borked again. For background, in my ordinary use of Julia, I often find myself with a broken installation. For example, if I accidentally `]add MultiGridBarrier.jl` instead of `]dev`, I found it really hard to recover from this.

So I nuked everything and started from scratch. I did `brew uninstall julia` and `rm -rf ~/.julia` and then also `rm -rf MultiGridBarrier.jl`. I reinstalled everything. Now I can build my documentation locally.

So I don’t know exactly what it was, but something in the Julia state on my machine was broken.

Now I progress to the next thing that is broken for me: CI on github, for lack of a better name? Right now, github is failing to build docs. How do I get it to build docs?

This is what I’m seeing: [Merge pull request #2 from sloisel/dependabot/github\_actions/julia-ac… · sloisel/MultiGridBarrier.jl@f8c9cc6 · GitHub](https://github.com/sloisel/MultiGridBarrier.jl/actions/runs/9265815421/job/25488787322)

The error message is:

```julia
ERROR: LoadError: InitError: PyError (PyImport_ImportModule
The Python package matplotlib could not be imported by pyimport. Usually this means

```

What’s the fix for this?

Thanks,

S

---

<div class="post-metadata">

**Author:** ![kellertuer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kellertuer/32/220707_2.png) [@kellertuer](https://discourse.julialang.org/u/kellertuer)\
**Post date:** [May 28, 2024, 8:32am UTC](https://discourse.julialang.org/t/documenter-ci/114800/10 "2024-05-28T08:32:25Z")

</div>

`]add MultiGridBarrier.jl` should error, so should `]add MultiGridBarrier` (both are not registered packages, if it would be registered, the second is the right way to add it); in both `]rm MultiGridBarrier` resolves the issue.

But yeah you should be able to run locally (for me your first post even read like you did run it locally)

Yeah, it seems that maybe your dependencies are not loaded correctly (especially something related to Python). For that I do not see directly the solution – I could help with the _Documenter_ issue, but with Python? I am fighting quite a bit as well (and try to avoid it if possible), so I am sorry I can not provide much help on that.

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [May 28, 2024, 9:27am UTC](https://discourse.julialang.org/t/documenter-ci/114800/11 "2024-05-28T09:27:00Z")

</div>

Thanks again for all your help. I was finally able to get the documentation to build on GitHub, and also for the CI tests to run. For posterity, I am including the final steps of the solution.

So @kellertuer is the one who identified that my Julia installation was broken, so it was essential that I uninstall Julia and also `rm -rf ~/.julia`. I also nuked my local `MultiGridBarrier.jl` repository and re-cloned it from GitHub, for good measure.

It was @ufechner7 who gave the helpful suggestion to look at the following repository: [GitHub - aenarete/ControlPlots.jl: Create plots that can be saved and edited with Julia](https://github.com/aenarete/ControlPlots.jl)

In that repository’s `.github/workflows/CI.yml`, I discovered the following fragment:

```julia
...
    steps:
      - name: Install matplotlib
        run: if ["$RUNNER_OS" = "Linux"]; then sudo apt-get install -y python3-matplotlib; fi
        shell: bash
...

```

I added this to my `CI.yml` twice, once for the `test` “target”, and once for the `docs` “target”.

I’m not exactly sure what is so special about the GitHub environment that MatPlotLib, and only MatPlotLib, has to manually be installed.

Also, thank you to @kellertuer for your suggestion to `rm` my package, I had tried this and it had left my Julia installation in an inconsistent state. There were inconsistencies at minimum between the following files and folders, in `~/.julia`: `Manifest.toml` and `Project.toml`, and the `packages` directory all contained problematic data, after I had done `rm MultiGridBarrier`. I mention this for posterity, in case someone lands on this discussion through a Google search in the future, wondering why their Julia installation isn’t working after they accidentally `add`ed and `rm`ed a package they intended to `dev`.

Edit: also, @kellertuer suggested to add something to `docs/make.jl`, at the top, and I did this, and it may be important to do so, it does make sense to me:

```julia
using Pkg
Pkg.activate(@ __DIR__ )
# As long as it is not registered, this is nice, in general it locally always
# renders docs of the current version checked out in this repo.
Pkg.develop(PackageSpec(; path=(@ __DIR__ ) * "/../"))

```

There was no need to add `PyPlot` anywhere in the `docs/` subdirectory.

---

<div class="post-metadata">

**Author:** ![kellertuer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kellertuer/32/220707_2.png) [@kellertuer](https://discourse.julialang.org/u/kellertuer)\
**Post date:** [May 28, 2024, 9:37am UTC](https://discourse.julialang.org/t/documenter-ci/114800/12 "2024-05-28T09:37:54Z")

</div>

Great, that you solved it!  
As a remark, inconsistencies between the project and the manifest are often resolved … with `] resolve`.

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [May 28, 2024, 9:57am UTC](https://discourse.julialang.org/t/documenter-ci/114800/13 "2024-05-28T09:57:41Z")

</div>

Thanks for your suggestion. I had tried `]resolve`, and it does resolve some problems between `project.toml` and `manifest.toml` (although maybe sometimes not all problems?), but it did not resolve problems with the `packages` folder.

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [May 28, 2024, 12:16pm UTC](https://discourse.julialang.org/t/documenter-ci/114800/14 "2024-05-28T12:16:13Z")

</div>

OK one more for posterity.

`Documenter` looks recursively through the `docs/src` subdirectory for documentation to generate. Jupyter Lab created a hidden subdirectory `docs/src/.ipynb_checkpoints`, and I guess this subdirectory contained a backup of `docs/src/index.md`, and hence `Documenter` believed that all documentation had been emitted twice.

Long story short, Jupyter is incompatible with `Documenter`.

---

<div class="post-metadata">

**Author:** ![kellertuer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kellertuer/32/220707_2.png) [@kellertuer](https://discourse.julialang.org/u/kellertuer)\
**Post date:** [May 29, 2024, 7:04am UTC](https://discourse.julialang.org/t/documenter-ci/114800/15 "2024-05-29T07:04:02Z")

</div>

Oh! But that clarifies the duplicates that you had but I did not.

As I wrote above – yes, Documenter renders _all_ `.md` files in the source folder.  
I am not sure how Jupyter came to the idea to duplicate that, but that then was the origin of the errors this thread started with.

What did you use Jupyter for in the docs? I always write my Markdown in an editor directly.

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [June 2, 2024, 9:28pm UTC](https://discourse.julialang.org/t/documenter-ci/114800/16 "2024-06-02T21:28:04Z")

</div>

I just use Jupyter Lab. It’s not great but I had trouble with plots in VS code.

---

<div class="post-metadata">

**Author:** ![cgarling](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/cgarling/32/29278_2.png) [@cgarling](https://discourse.julialang.org/u/cgarling)\
**Post date:** [June 3, 2024, 2:34am UTC](https://discourse.julialang.org/t/documenter-ci/114800/17 "2024-06-03T02:34:03Z")

</div>

With respect to “what makes the github environment special”, the OS image you are probably running on CI has a default python installation. The apt-get command installs a version of matplotlib from ubuntu’s repositories into this default python installation.

You can have more control over this process (e.g., Python and matplotlib versions). I used the following steps on a project I set up recently. These steps install the most recent minor version of python `3.x`, update pip, and use pip to install the latest patch version of matplotlib 3.8. There is currently a bug with matplotlib 3.9 in PyPlot.jl which there is an open PR to fix. As Github runners have many python versions cached, the setup process is still very quick.

```julia
      - uses: actions/setup-python@v5
        with:
          python-version: '3.x'
      - run: python -m pip install --upgrade pip
      - run: pip install 'matplotlib==3.8.*'

```

I run this directly after checking out the repository, before building PyPlot.jl, so that it will find and use this new version instead of the OS default.

---

<div class="post-metadata">

**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [June 3, 2024, 8:04am UTC](https://discourse.julialang.org/t/documenter-ci/114800/18 "2024-06-03T08:04:55Z")

</div>

I’ve made this change. I don’t know if it helps anything, but it seemed less quirky than the apt-get I had. Thanks.