Use PythonCall to wrap Python ArviZ (#5)

* Add CondaPkg.toml

* Replace PyCall packages with PythonCall equivalents

* Add LazyHelp utility

* Use LazyHelp utility for docs

* Update imports

* Update utilities to use PythonCall

* Update conversion and styles

* Update conversions to ELPDData

* Update plotting functions to use PythonCall

* Update examples.md

* Update docs deps

* Update docs

* Remove PyCall-specific CI code

* Use simpler caching action

* Cache CondaPkg artifacts

* Remove futures workflow

* Run formatter

* Remove build fiile

* Remove prefix

* Index axes from 0

* Use pywith in example

* Overload Py methods

* Delete unused macro

* Add topytype

* Simplify plotting functions

* Don't import PyCall

* Run formatter

* Convert styles list

* Fixes for utils

* Update some tests

* Enable strict docs building

* Remove setup code

* Remove todataframes

* Remove frompytype

* Remove convert_result

* Remove unused topandas method

* Replace DataFrames with Tables

* Remove conversions from Py to InferenceObjects

* Simplify rcparams code

* Fix rcparams bugs

* Use topytype utility

* Run formatter

* Fix topytype

* Update tests

* Increment lower Julia version bound

* Bump lower Julia version bound

* Update docs

* Don't reexport ArviZ

* Update docs

* Increment ArviZ version bound

* Also run CI on nightly

.github/workflows/Invalidations.yml

@@ -9,9 +9,6 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-env:
-  PYTHON: "Conda" # use Julia's packaged Conda build for installing packages
-
 jobs:
   evaluate:
     # Only run on PRs to the default branch.
@@ -24,17 +21,6 @@ jobs:
         version: '1'
     - uses: actions/checkout@v3
     - uses: julia-actions/julia-buildpkg@v1
-    - name: Install Python ArviZ dependencies
-      run: |
-        using Pkg
-        Pkg.instantiate()
-        using Conda
-        # https://discourse.julialang.org/t/conda-not-installing-matplotlib-for-pyplot/96813/2
-        Conda.add("conda==23.1.0")
-        using ArviZPythonPlots
-        ArviZPythonPlots.initialize_arviz()
-        ArviZPythonPlots.initialize_pandas()
-      shell: julia --color=yes --project {0}
     - uses: julia-actions/julia-invalidations@v1
       id: invs_pr
 

.github/workflows/ci.yml

@@ -7,55 +7,38 @@ on:
   schedule:
     - cron: "0 0 * * *"
 
-env:
-  PYTHON: "Conda" # use Julia's packaged Conda build for installing packages
-
 jobs:
   test:
     name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ["1"]
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+        julia-version: ["1", "1.8", "nightly"]
+        os: [ubuntu-latest]
         include:
-          - julia-version: "1.6"
-            os: ubuntu-latest
+          - julia-version: "1"
+            os: windows-latest
+          - julia-version: "1"
+            os: macOS-latest
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
           arch: x64
-      - name: Cache Julia artifacts
-        uses: actions/cache@v2
+      - uses: julia-actions/cache@v1
+      - name: Cache CondaPkg
+        id: cache-condaPkg
+        uses: actions/cache@v3
         env:
-          cache-name: cache-artifacts
+          cache-name: cache-condapkg
         with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          path: .CondaPkg
+          key: ${{ runner.os }}-${{ env.cache-name }}-${{ hashFiles('docs/CondaPkg.toml') }}
           restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - name: Install wget for windows
-        if: matrix.os == 'windows-latest'
-        uses: crazy-max/ghaction-chocolatey@v2
-        with:
-          args: install wget
+            ${{ runner.os }}-${{ env.cache-name }}-
       - uses: julia-actions/julia-buildpkg@latest
-      - name: Install Python ArviZ dependencies
-        run: |
-          using Pkg
-          Pkg.instantiate()
-          using Conda
-          # https://discourse.julialang.org/t/conda-not-installing-matplotlib-for-pyplot/96813/2
-          Conda.add("conda==23.1.0")
-          using ArviZPythonPlots
-          ArviZPythonPlots.initialize_arviz()
-          ArviZPythonPlots.initialize_pandas()
-        shell: julia --color=yes --project {0}
       - uses: julia-actions/julia-runtest@latest
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1

.github/workflows/documenter.yml

@@ -5,25 +5,27 @@ on:
     tags: [v*]
   pull_request:
 
-env:
-  PYTHON: "Conda" # use Julia's packaged Conda build for installing packages
-
 jobs:
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - 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: |
+            .CondaPkg
+            docs/.CondaPkg
+          key: ${{ runner.os }}-${{ env.cache-name }}-${{ hashFiles('docs/CondaPkg.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-${{ env.cache-name }}-
       - uses: julia-actions/julia-buildpkg@latest
-      - name: Setup Conda
-        run: |
-          using Pkg
-          Pkg.instantiate()
-          using Conda
-          # https://discourse.julialang.org/t/conda-not-installing-matplotlib-for-pyplot/96813/2
-          Conda.add("conda==23.1.0")
-        shell: julia --color=yes --project {0}
       - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -6,3 +6,4 @@
 /docs/build
 /test/*.log
 .DS_Store
+.CondaPkg

CondaPkg.toml

@@ -0,0 +1,5 @@
+[deps]
+pandas = ""
+matplotlib = ""
+xarray = ""
+arviz = ">=0.14.0"

Project.toml

@@ -5,26 +5,27 @@ version = "0.1.0"
 
 [deps]
 ArviZ = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [compat]
-ArviZ = "0.9"
+ArviZ = "0.10"
 ArviZExampleData = "0.1.5"
-Conda = "1.0"
-DataFrames = "0.20, 0.21, 0.22, 1.0"
+CondaPkg = "0.2"
 DimensionalData = "0.23, 0.24"
 OrderedCollections = "1"
-PyCall = "1.91.2"
-PyPlot = "2.8.2"
+PythonCall = "0.9"
+PythonPlot = "1"
 Reexport = "1"
-julia = "1.6"
+Tables = "1"
+julia = "1.8"
 
 [extras]
 ArviZExampleData = "2f96bb34-afd9-46ae-bcd0-9b2d4372fe3c"

README.md

@@ -8,7 +8,7 @@
 [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org)
 
 ArviZPythonPlots.jl provides PyPlot-compatible plotting functions for exploratory analysis of Bayesian models using [ArviZ.jl](https://julia.arviz.org/).
-It provides an interface to use the plotting functions in [Python ArviZ](https://python.arviz.org/) with Julia types.
-It also re-exports all methods exported by both ArviZ.jl and [PyPlot.jl](https://github.com/JuliaPy/PyPlot.jl).
+It uses [PythonCall.jl](https://github.com/cjdoris/PythonCall.jl) to provide an interface for using the plotting functions in [Python ArviZ](https://python.arviz.org/) with Julia types.
+It also re-exports all methods exported by [PythonPlot.jl](https://github.com/JuliaPy/PythonPlot.jl).
 
 See the [documentation](https://julia.arviz.org/ArviZPythonPlots) for details.

docs/Project.toml

@@ -4,12 +4,9 @@ ArviZExampleData = "2f96bb34-afd9-46ae-bcd0-9b2d4372fe3c"
 ArviZPythonPlots = "4a6e88f0-2c8e-11ee-0601-e94153f0eada"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 
 [compat]
 ArviZExampleData = "0.1.5"
 Distributions = "0.25"
 Documenter = "0.27"
-PyCall = "1.0"
-PyPlot = "2.0"

docs/lazyhelp.jl

@@ -0,0 +1,47 @@
+using Documenter, Markdown, PythonCall
+
+# adapted from https://github.com/AtelierArith/Kyulacs.jl for PythonCall
+# MIT License
+# Copyright (c) 2022 Satoshi Terasaki <[email protected]> and contributors
+
+function get_signature(f)
+    inspect = pyimport("inspect")
+    try
+        return pyconvert(String, inspect.signature(f))
+    catch e
+        return ""
+    end
+end
+
+function gendocstr(h::LazyHelp)
+    o = h.o
+    for k in h.keys
+        o = pygetattr(o, k)
+    end
+    fname = pyhasattr(o, "__name__") ? pyconvert(String, o.__name__) : ""
+    sig = pyhasattr(o, "__call__") ? get_signature(o) : ""
+    fdoc = pyhasattr(o, "__doc__") ? pyconvert(String, o.__doc__) : ""
+
+    if isnothing(fdoc)
+        return """
+        $(fname)$(sig)
+        """
+    else
+        return """
+        $(fdoc)
+        """
+    end
+end
+
+function Documenter.Writers.HTMLWriter.mdconvert(h::LazyHelp, parent; kwargs...)
+    s = gendocstr(h)
+    # quote docstring `s` to prevent changing display result
+    m = Markdown.parse("""
+                       ```
+                       $s
+                       ```
+                       """)
+    return Documenter.Writers.HTMLWriter.mdconvert(m, parent; kwargs...)
+end
+
+Documenter.Utilities.MDFlatten.mdflatten(::IOBuffer, ::LazyHelp, ::Markdown.MD) = nothing

docs/make.jl

@@ -1,4 +1,7 @@
 using ArviZPythonPlots, Documenter
+using ArviZPythonPlots: LazyHelp
+
+include("lazyhelp.jl")
 
 makedocs(;
     modules=[ArviZPythonPlots],
@@ -17,7 +20,9 @@ makedocs(;
     format=Documenter.HTML(;
         prettyurls=haskey(ENV, "CI"), sidebar_sitename=false, canonical="stable"
     ),
+    doctest=false,
     linkcheck=true,
+    strict=true,
 )
 
 deploydocs(;