Added pretty printing for checks + option to error on failures + fixe…

…d docs (#13)

* added pretty printing of checks using PrettyTables.jl

* deprecate check_grads in favour of check

* proper depwarn for check_grads

* fixed depwarn message

* properly propagate kwargs from benchmark_model + updated docstringss

* added option of erroring on failed checks and/or backends

* bumped patch version

* renamed docuemnter yaml

* removed Manifest.toml from docs

* added preview cleanup action for docs

* fixed the url for docs + added preview of docs

* added back mistakenly removed line from previous commit

* fixed typo in args to deploydocs

* added some additional configuration for docs action

* added compat entry for PrettyTables.jl

* fixed ordering of adbackends in checks

* added an example in docs

* some minor style changes

* updated Project.toml for docs

* added compat entry for Documenter

.github/workflows/Docs.yml

@@ -0,0 +1,35 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+    branches:
+      - main
+  merge_group:
+    types: [checks_requested]
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          JULIA_DEBUG: Documenter # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955)
+        run: julia --project=docs/ docs/make.jl

.github/workflows/DocsPreivewCleanup.yml

@@ -0,0 +1,26 @@
+name: DocsPreviewCleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "documenter@juliadocs.github.io"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

Project.toml

@@ -1,13 +1,15 @@
 name = "TuringBenchmarking"
 uuid = "0db1332d-5c25-4deb-809f-459bc696f94f"
 authors = ["Tor Erlend Fjelde <tor.erlend95@gmail.com> and contributors"]
-version = "0.3.1"
+version = "0.3.2"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
 LogDensityProblemsAD = "996a588d-648d-4e1f-a8f0-a84b347e47b1"
+PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
@@ -25,6 +27,7 @@ BridgeStan = "2"
 DynamicPPL = "0.23"
 LogDensityProblems = "2"
 LogDensityProblemsAD = "1"
+PrettyTables = "2"
 Requires = "1"
 ReverseDiff = "1.14"
 Turing = "0.29"

docs/Project.toml

@@ -1,3 +1,7 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-TuringBenchmarking = "0db1332d-5c25-4deb-809f-459bc696f94f"
+Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
+
+[compat]
+Documenter = "1"
+Turing = "0.29"

docs/make.jl

@@ -6,11 +6,11 @@ DocMeta.setdocmeta!(TuringBenchmarking, :DocTestSetup, :(using TuringBenchmarkin
 makedocs(;
     modules=[TuringBenchmarking],
     authors="Tor Erlend Fjelde <torfjelde.github@gmail.com> and contributors",
-    repo="https://github.com/turinglang/TuringBenchmarking.jl/blob/{commit}{path}#{line}",
+    repo="https://github.com/TuringLang/TuringBenchmarking.jl/blob/{commit}{path}#{line}",
     sitename="TuringBenchmarking.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://turinglang.github.io/TuringBenchmarking.jl",
+        canonical="https://turinglang.org/TuringBenchmarking.jl",
         edit_link="main",
         assets=String[],
     ),
@@ -20,6 +20,7 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/turinglang/TuringBenchmarking.jl",
+    repo="github.com/TuringLang/TuringBenchmarking.jl",
     devbranch="main",
+    push_preview=true,
 )

docs/src/index.md

@@ -2,9 +2,35 @@
 CurrentModule = TuringBenchmarking
 ```
 
-# TuringBenchmarking
+# TuringBenchmarking.jl
 
-Documentation for [TuringBenchmarking](https://github.com/torfjelde/TuringBenchmarking.jl).
+A useful package for benchmarking and checking [Turing.jl](https://github.com/TuringLang/Turing.jl) models.
+
+## Example
+
+```@repl
+using TuringBenchmarking, Turing
+
+@model function demo(x)
+    s ~ InverseGamma(2, 3)
+    m ~ Normal(0, sqrt(s))
+    for i in 1:length(x)
+        x[i] ~ Normal(m, sqrt(s))
+    end
+end
+
+model = demo([1.5, 2.0]);
+
+benchmark_model(
+    model;
+    # Check correctness of computations
+    check=true,
+    # Automatic differentiation backends to check and benchmark
+    adbackends=[:forwarddiff, :reversediff, :reversediff_compiled, :zygote]
+)
+```
+
+## API
 
 ```@index
 ```