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Compatibility updates and online documentation (#9)
* add documentation + GH workflows * MixedModels 3.x compat * online documentation and examples * remove shrinkage2d from docs * sample plot tweaks * run CI on main * the null test * compat bounds * workflow lint * update readme
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name: continuous-integration | ||
on: | ||
push: | ||
branches: | ||
- master | ||
- main | ||
paths-ignore: | ||
- 'LICENSE.md' | ||
- 'README.md' | ||
- 'examples/**' | ||
pull_request: | ||
branches: | ||
- master | ||
- main | ||
paths-ignore: | ||
- 'LICENSE.md' | ||
- 'README.md' | ||
- 'examples/**' | ||
jobs: | ||
ci: | ||
runs-on: ${{ matrix.os }} | ||
strategy: | ||
matrix: | ||
version: [1.5, 1] | ||
arch: [x64] | ||
os: [ubuntu-18.04] # macos-10.15, windows-2019 | ||
steps: | ||
- name: Checkout | ||
uses: actions/checkout@v2 | ||
- name: Julia Setup | ||
uses: julia-actions/setup-julia@v1 | ||
with: | ||
version: ${{ matrix.version }} | ||
arch: ${{ matrix.arch }} | ||
- name: Cache | ||
uses: actions/cache@v1 | ||
env: | ||
cache-name: cache-artifacts | ||
with: | ||
path: ~/.julia/artifacts | ||
key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }} | ||
restore-keys: | | ||
${{ runner.os }}-test-${{ env.cache-name }}- | ||
${{ runner.os }}-test- | ||
${{ runner.os }}- | ||
- name: Build | ||
uses: julia-actions/julia-buildpkg@v1 | ||
- name: Test | ||
uses: julia-actions/julia-runtest@v1 | ||
env: | ||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
- name: Coverage Process | ||
uses: julia-actions/julia-processcoverage@v1 | ||
if: ${{ startsWith(matrix.os, 'ubuntu') && (matrix.version == '1') }} | ||
- name: Coverage Upload | ||
uses: codecov/codecov-action@v1 | ||
if: ${{ startsWith(matrix.os, 'ubuntu') && (matrix.version == '1') }} | ||
with: | ||
file: lcov.info |
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name: Documenter | ||
on: | ||
push: | ||
branches: | ||
- master | ||
- main | ||
tags: [v*] | ||
pull_request: | ||
branches: | ||
- master | ||
- main | ||
jobs: | ||
Documenter: | ||
name: Documentation | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- uses: julia-actions/julia-buildpkg@latest | ||
- uses: julia-actions/julia-docdeploy@latest | ||
env: | ||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} |
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# MixedModelsMakie | ||
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||
[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) | ||
[![Stable Docs][docs-stable-img]][docs-stable-url] | ||
[![Dev Docs][docs-dev-img]][docs-dev-url] | ||
[![Codecov](https://codecov.io/gh/palday/MixedModelsMakie.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/palday/MixedModelsMakie.jl) | ||
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[docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg | ||
[docs-dev-url]: https://palday.github.io/MixedModelsMakie.jl/dev | ||
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[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg | ||
[docs-stable-url]: https://palday.github.io/MixedModelsMakie.jl/stable | ||
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||
`MixedModelsMakie.jl` is a Julia package providing plotting capabilities for models fit with [MixedModels.jl](https://juliastats.org/MixedModels.jl/stable/). | ||
Plotting is performed using the [Makie ecoysystem](https://makie.juliaplots.org/stable/), with the interface defined using `AbstractPlotting.jl` for compatibility across all Makie backends. | ||
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||
Note that the functionality here is currently early alpha development and so breaking changes are expected as we refine the interface. | ||
Following [SemVer](https://semver.org/), these minor releases before 1.0 can introduce these breaking changes. | ||
The release of 1.0 will be indication that we believe the interface is reasonably stable. | ||
Minor refinements of graphical displays without changing the API are considered non-breaking. |
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[deps] | ||
CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" | ||
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" | ||
MixedModels = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316" | ||
MixedModelsMakie = "b12ae82c-6730-437f-aff9-d2c38332a376" | ||
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[compat] | ||
CairoMakie = "0.4.7" | ||
Documenter = "0.26" |
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using Documenter | ||
using MixedModelsMakie | ||
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makedocs(; | ||
root = joinpath(dirname(pathof(MixedModelsMakie)), "..", "docs"), | ||
sitename = "MixedModelsMakie", | ||
doctest = true, | ||
checkdocs = :exports, | ||
pages = [ | ||
"index.md", | ||
"api.md", | ||
], | ||
) | ||
|
||
deploydocs(repo = "github.com/palday/MixedModelsMakie.jl.git", push_preview = true) |
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```@meta | ||
CurrentModule = MixedModelsMakie | ||
DocTestSetup = quote | ||
using MixedModelsMakie | ||
end | ||
DocTestFilters = [r"([a-z]*) => \1", r"getfield\(.*##[0-9]+#[0-9]+"] | ||
``` | ||
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# MixedModelsMakie.jl API | ||
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## Caterpillar Plots | ||
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```@docs | ||
RanefInfo | ||
``` | ||
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```@docs | ||
ranefinfo | ||
``` | ||
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```@docs | ||
caterpillar | ||
``` | ||
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```@docs | ||
caterpillar! | ||
``` | ||
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```@example Caterpillar | ||
using CairoMakie | ||
CairoMakie.activate!(type = "svg") | ||
using MixedModels | ||
using MixedModelsMakie | ||
sleepstudy = MixedModels.dataset(:sleepstudy) | ||
fm1 = fit(MixedModel, @formula(reaction ~ 1 + days + (1 + days|subj)), sleepstudy) | ||
subjre = ranefinfo(fm1)[:subj] | ||
caterpillar!(Figure(; resolution=(800,600)), subjre) | ||
``` | ||
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```@example Caterpillar | ||
caterpillar!(Figure(; resolution=(800,600)), subjre; orderby=2) | ||
``` | ||
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## Shrinkage Plots | ||
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```@docs | ||
CoefByGroup | ||
``` | ||
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```@docs | ||
shrinkage | ||
``` | ||
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```@docs | ||
shrinkageplot | ||
``` | ||
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```@docs | ||
shrinkageplot! | ||
``` | ||
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```@example Shrinkage | ||
using CairoMakie | ||
using MixedModels | ||
using MixedModelsMakie | ||
sleepstudy = MixedModels.dataset(:sleepstudy) | ||
fm1 = fit(MixedModel, @formula(reaction ~ 1 + days + (1 + days|subj)), sleepstudy) | ||
shrink = shrinkage(fm1)[:subj] | ||
shrinkageplot!(Figure(; resolution=(800,600)), shrink) | ||
``` |
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# MixedModelsMakie.jl Documentation | ||
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```@meta | ||
CurrentModule = MixedModelsMakie | ||
``` | ||
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*MixedModelsMakie.jl* is a Julia package providing plotting capabilities for models fit with [MixedModels.jl](https://juliastats.org/MixedModels.jl/stable/). | ||
|
||
Note that the functionality here is currently early alpha development and so breaking changes are expected as we refine the interface. | ||
Following [SemVer](https://semver.org/), these minor releases before 1.0 can introduce these breaking changes. | ||
The release of 1.0 will be indication that we believe the interface is reasonably stable. | ||
|
||
```@contents | ||
Pages = [ | ||
"api.md", | ||
] | ||
Depth = 1 | ||
``` |
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using MixedModelsMakie | ||
using Test | ||
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@testset "MixedModelsMakie.jl" begin | ||
# Write your tests here. | ||
@testset "There are no tests" begin | ||
@test true | ||
end |
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@JuliaRegistrator register
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Registration pull request created: JuliaRegistries/General/36698
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via: