CompatHelper: bump compat for MixedModels to 5, (keep existing compat) (#24)

* CompatHelper: bump compat for MixedModels to 5, (keep existing compat)

* style ci update

* CI update

* compat bumps

* fix with latest MM.jl patch release

* re-organize tests slightly, update Effects compat with an extension

* yas


---------

Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
Co-authored-by: Phillip Alday <me@phillipalday.com>

Author: 3 people

.github/workflows/ci.yml

@@ -21,19 +21,19 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.8'
+          - 'min'
           - '1'
           - 'nightly'
         os:
           - ubuntu-latest
-        arch:
-          - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v5
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+        with:
+          cache-compiled: "true"
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1

.github/workflows/documenter.yml

@@ -20,11 +20,11 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v5
+      - uses: julia-actions/setup-julia@v2
+      - uses: julia-actions/cache@v2
         with:
-          version: 1
-      - uses: julia-actions/cache@v1
+          cache-compiled: "true"
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-docdeploy@latest
         env:

.github/workflows/style.yml

@@ -1,38 +1,34 @@
-name: YASG-enforcer
+name: Style-Enforcer
 on:
-  push:
-    branches:
-      - 'main'
-    tags: '*'
   pull_request:
     types: [opened, synchronize, reopened, ready_for_review]
-    # note: keep in sync with `format/run.jl`
-    paths:
-      - 'src/**'
-      - 'test/**'
-      - 'docs/**'
-      - '.github/workflows/style.yml'
-      - 'format/**'
+    paths-ignore:
+      - 'README.md'
+      - '.gitignore'
 jobs:
   format-check:
-    name: YASG Enforcement (Julia ${{ matrix.julia-version }} - ${{ github.event_name }})
-    # Run on push's or non-draft PRs
-    if: (github.event_name == 'push') || (github.event.pull_request.draft == false)
+    name: Style Enforcement
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        julia-version: [1.7]
+        julia-version: [min]
     steps:
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.julia-version }}
-      - uses: actions/checkout@v1
-      - name: Instantiate `format` environment and format
+      - name: Install JuliaFormatter
+        shell: julia --project=@format --color=yes {0}
         run: |
-          julia --project=format -e 'using Pkg; Pkg.instantiate()'
-          julia --project=format 'format/run.jl'
+          using Pkg
+          Pkg.add(PackageSpec(; name="JuliaFormatter", version="1"))
+      - name: Check formatting
+        shell: julia --project=@format --color=yes {0}
+        run: |
+          using JuliaFormatter
+          format(".", YASStyle(); verbose=true) || exit(1)
+      # Add formatting suggestions to non-draft PRs even if "Check formatting" fails
       - uses: reviewdog/action-suggester@v1
-        if: github.event_name == 'pull_request'
+        if: ${{ !cancelled() && github.event.pull_request.draft == false }}
         with:
           tool_name: JuliaFormatter
-          fail_on_error: true

.gitignore

@@ -22,3 +22,4 @@ docs/site/
 # committed for packages, but should be committed for applications that require a static
 # environment.
 Manifest.toml
+Manifest-v*.toml

Project.toml

@@ -1,7 +1,7 @@
 name = "MixedModelsSerialization"
 uuid = "b32ace64-3998-4ca6-afd0-a0db4a0482b2"
 authors = ["Phillip Alday <me@phillipalday.com>"]
-version = "0.1.1"
+version = "0.2.0"
 
 [deps]
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
@@ -14,12 +14,32 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
+[weakdeps]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Effects = "8f03c58b-bd97-4933-a826-f71b64d2cca2"
+
+[extensions]
+MixedModelsSerializationEffectsExt = ["DataFrames", "Effects"]
+
 [compat]
+DataFrames = "1"
+Effects = "1"
 GLM = "1"
 JLD2 = "0.4.22"
-MixedModels = "4"
+MixedModels = "5.0.3"
 StatsAPI = "1"
 StatsBase = "0.33, 0.34"
 StatsFuns = "1"
 StatsModels = "0.7"
-julia = "1.8"
+julia = "1.10"
+
+[extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+Effects = "8f03c58b-bd97-4933-a826-f71b64d2cca2"
+MixedModelsDatasets = "7e9fb7ac-9f67-43bf-b2c8-96ba0796cbb6"
+Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestSetExtensions = "98d24dd4-01ad-11ea-1b02-c9a08f80db04"
+
+[targets]
+test = ["Aqua", "Effects", "MixedModelsDatasets", "Suppressor", "Test", "TestSetExtensions"]

ext/MixedModelsSerializationEffectsExt.jl

@@ -0,0 +1,15 @@
+module MixedModelsSerializationEffectsExt
+
+using DataFrames
+using Effects
+using MixedModels
+using MixedModelsSerialization
+using StatsBase
+
+function Effects.effects!(reference_grid::DataFrame, model::LinearMixedModelSummary;
+                          kwargs...)
+    # we don't want to use the MixedModel specific version since we don't store all the things
+    return @invoke effects!(reference_grid::DataFrame, model::RegressionModel; kwargs...)
+end
+
+end # module