Enable JuliaFormatter

[nalimilan]

Add a JuliaFormatter style, apply it to the code base, and enable a GitHub workflow to add suggestions to PRs to follow the style. Inspired by discussions at JuliaStats/HypothesisTests.jl#299.

EDIT: the second commit shows what the default style looks like. It's a bit different from the majority of the current code regarding alignment of arguments.

[codecov]

Codecov Report

Attention: Patch coverage is 95.26627% with 8 lines in your changes missing coverage. Please review.

Project coverage is 94.82%. Comparing base (3d474b2) to head (77da751).
Report is 3 commits behind head on master.

Files with missing lines	Patch %	Lines
src/glmfit.jl	94.44%	3 Missing ⚠️
src/linpred.jl	93.02%	3 Missing ⚠️
src/glmtools.jl	91.66%	1 Missing ⚠️
src/negbinfit.jl	88.88%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #603      +/-   ##
==========================================
- Coverage   94.89%   94.82%   -0.07%     
==========================================
  Files           8        8              
  Lines        1038     1044       +6     
==========================================
+ Hits          985      990       +5     
- Misses         53       54       +1     

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[github-actions]

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/lm.jl

Line 246 in 3c7258a

ssqr = deviance(x.rr)/dofr

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/lm.jl

Line 263 in 3c7258a

levstr = isinteger(level*100) ? string(Integer(level*100)) : string(level*100)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/lm.jl

Line 266 in 3c7258a

hcat(cc, se, tt, p, cc+ci, cc-ci),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/lm.jl

Line 365 in 3c7258a

ret .= quantile(TDist(dofr), (1 - level)/2) .* sqrt.(ret)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/lm.jl

Line 368 in 3c7258a

upper .= prediction - + ret

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/lm.jl

Line 375 in 3c7258a

stderror(obj) * quantile(TDist(dof_residual(obj)), (1.0 - level)/2.0) * [1.0 -1.0]

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/lm.jl

Line 389 in 3c7258a

k = dof(obj)-1

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/negbinfit.jl

Line 9 in 3c7258a

tmp(yi, μi) = (yi+θ)/(μi+θ) + log(μi+θ) - 1 - log(θ) - digamma(θ+yi) + digamma(θ)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/negbinfit.jl

Line 14 in 3c7258a

tmp(yi, μi) = -(yi+θ)/(μi+θ)^2 + 2/(μi+θ) - 1/θ - trigamma(θ+yi) + trigamma(θ)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/src/negbinfit.jl

Line 155 in 3c7258a

@debug "NegativeBinomial dispersion optimization" iteration=i θ=θ

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 142 in 3c7258a

df.weights = repeat(1:5, Int(N/5))

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 155 in 3c7258a

88.02760245551447 -0.06772589439264813;

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 195 in 3c7258a

f = @formula(0 ~ 1 + G*H)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 622 in 3c7258a

y = logistic.(X*ones(2) + 1/10*randn(rng, n)) .> 1/2

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 964 in 3c7258a

@formula(Days ~ Eth+Sex+Age+Lrn),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 998 in 3c7258a

@formula(Days ~ Eth+Sex+Age+Lrn),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1075 in 3c7258a

halfn = round(Int, 0.5*size(quine, 1))

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1077 in 3c7258a

gm20a = negbin(@formula(Days ~ Eth+Sex+Age+Lrn), quine, LogLink(); wts = wts)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1102 in 3c7258a

gm20 = negbin(@formula(Days ~ Eth+Sex+Age+Lrn), quine, LogLink(); method = :qr)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1132 in 3c7258a

gm21 = negbin(@formula(Days ~ Eth+Sex+Age+Lrn), quine; method = dmethod)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Lines 1421 to 1422 in 3c7258a

	J = newX .* getindex.(GLM.inverselink.(LogitLink(), newX*coef(gm11)), 2)
	se_pred = sqrt.(diag(J*vcov(gm11)*J'))

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1589 in 3c7258a

se_pred = sqrt.(diag(newX*vcov(mm)*newX'))

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1601 in 3c7258a

pred2.prediction - quantile(TDist(dof_residual(mm)), 0.975)*se_pred ≈

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1610 in 3c7258a

pred2.prediction + quantile(TDist(dof_residual(mm)), 0.975)*se_pred ≈

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Lines 1637 to 1640 in 3c7258a

	quantile(
	TDist(dof_residual(mm)),
	0.975,
	)*sqrt.(diag(newX*vcov(mm)*newX') .+ deviance(mm)/dof_residual(mm)) ≈

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Lines 1650 to 1653 in 3c7258a

	quantile(
	TDist(dof_residual(mm)),
	0.975,
	)*sqrt.(diag(newX*vcov(mm)*newX') .+ deviance(mm)/dof_residual(mm)) ≈

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Lines 1842 to 1844 in 3c7258a

	@test preds_transformation.prediction ≈ ggplot_prediction atol=1e-3
	@test preds_transformation.lower ≈ ggplot_lower atol=1e-3
	@test preds_transformation.upper ≈ ggplot_upper atol=1e-3

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1846 in 3c7258a

@test preds_delta.upper .- preds_delta.lower ≈ 2 .* 1.96 .* R_glm_se atol=1e-3

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 1999 in 3c7258a

1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0;

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2019 in 3c7258a

Yc = RL\Y

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2021 in 3c7258a

Xc1 = RL\X[:, [1]]

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2024 in 3c7258a

Xc2 = RL\X

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Lines 2088 to 2090 in 3c7258a

	Matrix(qr(randn(rng, 100, 5)).Q)*Diagonal(10 .^ (-2.0:1.0:2.0))*Matrix(
	qr(randn(rng, 5, 5)).Q,
	)'

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2156 in 3c7258a

mod = lm(@formula(Result~Treatment), d)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2176 in 3c7258a

y = X*ones(2) + randn(10)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2288 in 3c7258a

@test stderror(mdl) ≈ [0.224095414423756, 0.003342439119757, 0.005838227761632] atol=1.0e-8

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2379 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2381 in 3c7258a

contrasts = Dict(:x=>DummyCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2383 in 3c7258a

mcat = lm(@formula(y~x), (y = 1:25, x = categorical(repeat(1:5, 5))))

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2385 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2389 in 3c7258a

contrasts = Dict(:x=>DummyCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2392 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2402 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2404 in 3c7258a

contrasts = Dict(:x=>DummyCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2406 in 3c7258a

mcat = fit(LinearModel, @formula(y~x), (y = 1:25, x = categorical(repeat(1:5, 5))))

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2409 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2413 in 3c7258a

contrasts = Dict(:x=>DummyCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2417 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2427 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2429 in 3c7258a

contrasts = Dict(:x=>EffectsCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2432 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2436 in 3c7258a

contrasts = Dict(:x=>EffectsCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2442 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2444 in 3c7258a

contrasts = Dict(:x=>EffectsCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2448 in 3c7258a

@formula(y~x),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2452 in 3c7258a

contrasts = Dict(:x=>EffectsCoding()),

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2578 in 3c7258a

-0.5493329715011036 0.26350316142056085;

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2593 in 3c7258a

f = @formula(0 ~ 1 + G*H)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2648 in 3c7258a

f = @formula(0 ~ 1 + G*H)

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2745 in 3c7258a

@test gvif(lm2; scale = true) ≈ [1.486330, 2.301648, 1.502666] atol=1e-4

---

[JuliaFormatter] _{reported by reviewdog 🐶}

GLM.jl/test/runtests.jl

Line 2749 in 3c7258a

@test gvif(gm2; scale = true) ≈ [1.486330, 2.301648, 1.502666] atol=1e-4

[devmotion]

Maybe even if we decide to use the default style, a .JuliaFormatter.toml file (in that case empty) should be added to the repo. JuliaFormatter.format traverses the file path upwards until it finds (or in the end doesn't find) a .JuliaFormatter.toml file: https://domluna.github.io/JuliaFormatter.jl/stable/config/ So in principle a configuration higher up in the file tree could cause the formatter to format GLM with a different style.