Restore and update quickstart docs page (#296)

* Revert "Temporarily remove quickstart docs (#292)"

This reverts commit 2dc0ae2.

* Load ArviZPythonPlots before running notebook

* Add ArviZPythonPlots as docs dep

* Load ArviZPythonPlots in notebook

* Document use of ArviZPythonPlots

* Refer to ArviZ instead of ArviZ.jl

* Increment patch number

* Instantiate docs environment before resolving

* Use Conda Python

* Install Python deps manually

* Fix step

* Add ArviZPythonPlots docs compat

* Add back docs deps compats

* Remove SampleChains as unused docs dep

* Remove docs Manifest.toml

* Make docs-specific `.gitignore`

* Remove unneeded loads

* Increase ArviZ version bound

* Fix broken links

* Allow linkcheck to fail

* Increment patch number

* Cache CondaPkg artifacts for docs build

.github/workflows/CompatHelper.yml

@@ -13,4 +13,6 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia --color=yes -e 'using CompatHelper; CompatHelper.main()'
+        run: |
+          using CompatHelper
+          CompatHelper.main(; subdirs=["", "docs"])

.github/workflows/documenter.yml

@@ -7,6 +7,11 @@ on:
   schedule:
     - cron: "0 0 * * *"
 
+env:
+  CMDSTAN_VERSION: "2.25.0"
+  CMDSTAN_PATH: "${{ GITHUB.WORKSPACE }}/.cmdstan/"
+  JULIA_NUM_THREADS: 2
+
 jobs:
   docs:
     name: Documentation
@@ -15,12 +20,30 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
       - uses: julia-actions/cache@v1
+      - name: Cache CondaPkg
+        id: cache-condaPkg
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-condapkg
+        with:
+          path: docs/.CondaPkg
+          key: ${{ runner.os }}-${{ env.cache-name }}-${{ hashFiles('docs/CondaPkg.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-${{ env.cache-name }}-
+      - name: Download and build CmdStan
+        if: steps.cache-cmdstan.outputs.cache-hit != 'true'
+        run: |
+          wget -P ${{ env.CMDSTAN_PATH }} https://github.com/stan-dev/cmdstan/releases/download/v${{ env.CMDSTAN_VERSION }}/cmdstan-${{ env.CMDSTAN_VERSION }}.tar.gz
+          tar -xzpf ${{ env.CMDSTAN_PATH }}/cmdstan-${{ env.CMDSTAN_VERSION }}.tar.gz -C ${{ env.CMDSTAN_PATH }}
+          make -C ${{ env.CMDSTAN_PATH }}/cmdstan-${{ env.CMDSTAN_VERSION }}/ build
+        shell: bash
       - uses: julia-actions/julia-buildpkg@v1
       - name: Install dependencies
         run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - uses: julia-actions/julia-docdeploy@v1
         with:
           install-package: false
         env:
+          JULIA_CMDSTAN_HOME: ${{ env.CMDSTAN_PATH }}/cmdstan-${{ env.CMDSTAN_VERSION }}/ # required by CmdStan.jl
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -1,14 +1,6 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
-/deps/deps.jl
-/deps/build.log
-/docs/src/quickstart.md
-/docs/src/creating_custom_plots.md
-/docs/src/*.log
-/docs/src/assets/logo*.png
-/docs/src/assets/favicon.ico
-/docs/src/*.log
-/docs/build
 /test/*.log
 .DS_Store
+Manifest.toml

Project.toml

@@ -1,7 +1,7 @@
 name = "ArviZ"
 uuid = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
 authors = ["Seth Axen <[email protected]>"]
-version = "0.10.1"
+version = "0.10.2"
 
 [deps]
 InferenceObjects = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"

docs/.gitignore

@@ -0,0 +1,9 @@
+Manifest.toml
+.CondaPkg
+src/quickstart.md
+src/creating_custom_plots.md
+src/*.log
+src/assets/logo*.png
+src/assets/favicon.ico
+src/*.log
+build

docs/Project.toml

@@ -2,6 +2,7 @@
 AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
 ArviZ = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
 ArviZExampleData = "2f96bb34-afd9-46ae-bcd0-9b2d4372fe3c"
+ArviZPythonPlots = "4a6e88f0-2c8e-11ee-0601-e94153f0eada"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
@@ -11,14 +12,35 @@ Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5"
 InferenceObjects = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0"
 MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 MLJIteration = "614be32b-d00c-4edb-bd02-1eb411ab5e55"
 PSIS = "ce719bf2-d5d0-4fb9-925d-10a81b42ad04"
 PlutoStaticHTML = "359b1769-a58e-495b-9770-312e911026ad"
 PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
 PosteriorStats = "7f36be82-ad55-44ba-a5c0-b8b5480d7aa5"
-SampleChains = "754583d1-7fc4-4dab-93b5-5eaca5c9622e"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StanSample = "c1514b29-d3a0-5178-b312-660c88baa699"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
+
+[compat]
+AlgebraOfGraphics = "0.6.9"
+ArviZ = ">=0.10"
+ArviZExampleData = "0.1.5"
+ArviZPythonPlots = "0.1"
+CairoMakie = "0.8.9, 0.9, 0.10"
+DataFrames = "1"
+DimensionalData = "0.23, 0.24"
+Distributions = "0.25"
+Documenter = "0.27"
+EvoTrees = "0.14.8, 0.15"
+MCMCDiagnosticTools = "0.3"
+MLJBase = "0.21.6"
+MLJIteration = "0.5.1"
+PlutoStaticHTML = "4.0.5, 5, 6"
+PlutoUI = "0.7"
+PosteriorStats = "0.1.1"
+StanSample = "7.0.1"
+StatsBase = "0.32, 0.33, 0.34"
+Turing = "0.24.1, 0.25, 0.26, 0.27, 0.28"

docs/make.jl

@@ -1,6 +1,4 @@
 using Documenter, Downloads, ArviZ
-using MCMCChains: MCMCChains # make `from_mcmcchains` available for API docs
-using SampleChains: SampleChains # make `from_samplechains` available for API docs
 using PlutoStaticHTML: PlutoStaticHTML
 
 const DOCS_SRC_PATH = joinpath(@__DIR__, "src")
@@ -75,6 +73,7 @@ makedocs(;
     pages=[
         "Home" => "index.md",
         "Getting Started" => [
+            "Quickstart" => "quickstart.md",
             "Working with `InferenceData`" => "working_with_inference_data.md",
             "Creating custom plots" => "creating_custom_plots.md",
         ],
@@ -99,7 +98,8 @@ makedocs(;
     doctestfilters,
     linkcheck=true,
     analytics="G-W1G68W77YV",
-    strict=Documenter.except(:footnote, :missing_docs),
+    # allow linkcheck to fail so we can use pretty links to PlutoStaticHTML notebooks
+    strict=Documenter.except(:footnote, :linkcheck, :missing_docs),
 )
 
 deploydocs(; repo="github.com/arviz-devs/ArviZ.jl.git", devbranch="main", push_preview=true)

docs/src/index.md

@@ -25,7 +25,7 @@ pkg> add ArviZ
 
 ## [Usage](@id usage)
 
-See the [API Overview](@ref api) for description of functions.
+See the [Quickstart](./quickstart) for example usage and the [API Overview](@ref api) for description of functions.
 
 ## [Extending ArviZ.jl](@id extendingarviz)