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Switch to explicit imports of names from packages #748

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merged 8 commits into from
Mar 4, 2024
Merged

Switch to explicit imports of names from packages #748

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e956bb3
Switch to explicit imports
dmbates Mar 1, 2024
14bfeca
Committed the wrong file.
dmbates Mar 1, 2024
188f24b
Bump patch version number and add NEWS item.
dmbates Mar 1, 2024
1698bd2
Add imports from PrecompileTools; tests with ExplicitImports.
dmbates Mar 3, 2024
54707c5
Read and follow suggestion in ExplicitImports docs.
dmbates Mar 3, 2024
274a71a
Incorporate suggestions by palday and ericphanson
dmbates Mar 4, 2024
12da578
Update NEWS.md
dmbates Mar 4, 2024
d4ff897
Remove unused indirect dependency.
dmbates Mar 4, 2024
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7 changes: 7 additions & 0 deletions NEWS.md
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@@ -1,3 +1,8 @@
MixedModels v4.22.4 Release Notes
==============================
* Switch to explicit imports from all included packages (i.e. replace `using Foo` by `using Foo: Foo, bar, baz`) [#748]
* Reset parameter values before a `deepcopy` in an test (doesn't change test result) [#744]
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MixedModels v4.22.3 Release Notes
==============================
* Comment out calls to `@debug` [#733]
Expand Down Expand Up @@ -490,3 +495,5 @@ Package dependencies
[#715]: https://github.com/JuliaStats/MixedModels.jl/issues/715
[#717]: https://github.com/JuliaStats/MixedModels.jl/issues/717
[#733]: https://github.com/JuliaStats/MixedModels.jl/issues/733
[#744]: https://github.com/JuliaStats/MixedModels.jl/issues/744
[#748]: https://github.com/JuliaStats/MixedModels.jl/issues/748
8 changes: 6 additions & 2 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "MixedModels"
uuid = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
author = ["Phillip Alday <[email protected]>", "Douglas Bates <[email protected]>", "Jose Bayoan Santiago Calderon <[email protected]>"]
version = "4.22.3"
version = "4.22.4"

[deps]
Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"
Expand All @@ -20,6 +20,7 @@ ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
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since we already have StaticArrays, can we grab SVector from there? I know this doesn't increase our total dependency load, but it's another thing to track.

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filed ericphanson/ExplicitImports.jl#24 fyi. I think though if you do using StaticArrays: SVector, then it won't complain about the implicit import. But when it makes suggestions, it always does the "defining" module.

Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
StatsAPI = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
Expand All @@ -36,6 +37,7 @@ BSplineKit = "0.14, 0.15, 0.16, 0.17"
DataAPI = "1"
DataFrames = "1"
Distributions = "0.21, 0.22, 0.23, 0.24, 0.25"
ExplicitImports = "1.2"
GLM = "1.8.2"
InteractiveUtils = "1"
JSON3 = "1"
Expand All @@ -50,6 +52,7 @@ Random = "1"
SparseArrays = "1"
StableRNGs = "0.1, 1"
StaticArrays = "0.11, 0.12, 1"
StaticArraysCore = "1"
Statistics = "1"
StatsAPI = "1.5"
StatsBase = "0.31, 0.32, 0.33, 0.34"
Expand All @@ -65,10 +68,11 @@ julia = "1.8"
[extras]
Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Aqua", "DataFrames", "InteractiveUtils", "StableRNGs", "Suppressor", "Test"]
test = ["Aqua", "DataFrames", "ExplicitImports", "InteractiveUtils", "StableRNGs", "Suppressor", "Test"]
74 changes: 45 additions & 29 deletions src/MixedModels.jl
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@@ -1,35 +1,51 @@
module MixedModels

using Arrow
using BSplineKit
using DataAPI
using Distributions
using GLM
using JSON3
using LinearAlgebra
using Markdown
using NLopt
using Random
using PooledArrays
using ProgressMeter
using SparseArrays
using StaticArrays
using Statistics
using StatsAPI
using StatsBase
using StatsModels
using StructTypes
using Tables
using TypedTables

using LinearAlgebra: BlasFloat, BlasReal, HermOrSym, PosDefException, copytri!
using Arrow: Arrow
using Base: Ryu, require_one_based_indexing
using DataAPI: levels, refpool, refarray, refvalue
using GLM: Link, canonicallink, linkfun, linkinv, dispersion, dispersion_parameter
using BSplineKit: BSplineKit
using BSplineKit.BSplines: BSplineOrder
using BSplineKit.BoundaryConditions: Natural
using BSplineKit.DifferentialOps: Derivative
using BSplineKit.SplineInterpolations: SplineInterpolation, interpolate
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using DataAPI: DataAPI, levels, refpool, refarray, refvalue
using Distributions: Distributions, Bernoulli, Binomial, Chisq, Distribution, Gamma
using Distributions: InverseGaussian, Normal, Poisson, ccdf, estimate
using GLM: GLM, GeneralizedLinearModel, IdentityLink, InverseLink, LinearModel
using GLM: Link, LogLink, LogitLink, ProbitLink, SqrtLink
using GLM: canonicallink, glm, linkinv, dispersion, dispersion_parameter
using JSON3: JSON3
using LinearAlgebra: LinearAlgebra, Adjoint, BLAS, BlasFloat, ColumnNorm
using LinearAlgebra: Diagonal, Hermitian, HermOrSym, I, LAPACK, LowerTriangular
using LinearAlgebra: PosDefException, SVD, SymTridiagonal, Symmetric
using LinearAlgebra: UpperTriangular, cond, diag, diagind, dot, eigen, isdiag
using LinearAlgebra: ldiv!, lmul!, logdet, mul!, norm, normalize, normalize!, qr
using LinearAlgebra: rank, rdiv!, rmul!, svd, tr, tril!
using Markdown: Markdown
using MixedModelsDatasets: dataset, datasets
using NLopt: Opt
using StatsModels: TableRegressionModel
using NLopt: NLopt, Opt, ftol_abs, ftol_rel, initial_step, maxtime, xtol_abs, xtol_rel
using PooledArrays: PooledArrays, PooledArray
using PrecompileTools: PrecompileTools, @setup_workload, @compile_workload
using ProgressMeter: ProgressMeter, Progress, ProgressUnknown, finish!, next!
using Random: Random, AbstractRNG, randn!
using SparseArrays: SparseArrays, SparseMatrixCSC, SparseVector, dropzeros!, nnz
using SparseArrays: nonzeros, nzrange, rowvals, sparse
using StaticArrays: StaticArrays
using StaticArraysCore: SVector
using Statistics: Statistics, mean, quantile, std
using StatsAPI: StatsAPI, aic, aicc, bic, coef, coefnames, coeftable, confint, deviance
using StatsAPI: dof, dof_residual, fit, fit!, fitted, isfitted, islinear, leverage
using StatsAPI: loglikelihood, meanresponse, modelmatrix, nobs, predict, r2, residuals
using StatsAPI: response, responsename, stderror, vcov, weights
using StatsBase: StatsBase, CoefTable, model_response, summarystats
using StatsFuns: log2π, normccdf
using StatsModels: StatsModels, AbstractContrasts, AbstractTerm, CategoricalTerm
using StatsModels: ConstantTerm, DummyCoding, EffectsCoding, FormulaTerm, FunctionTerm
using StatsModels: HelmertCoding, HypothesisCoding, InteractionTerm, InterceptTerm
using StatsModels: MatrixTerm, SeqDiffCoding, TableRegressionModel, Term
using StatsModels: apply_schema, drop_term, formula, modelcols, term, @formula
using StructTypes: StructTypes
using Tables: Tables, columntable, rows
using TypedTables: TypedTables, DictTable, FlexTable, Table

export @formula,
AbstractReMat,
Expand Down Expand Up @@ -77,6 +93,8 @@ export @formula,
condVar,
condVartables,
confint,
dataset,
datasets,
deviance,
dispersion,
dispersion_parameter,
Expand Down Expand Up @@ -190,8 +208,6 @@ include("mimeshow.jl")
include("serialization.jl")
include("profile/profile.jl")

using PrecompileTools

@setup_workload begin
# Putting some things in `setup` can reduce the size of the
# precompile file and potentially make loading faster.
Expand Down
6 changes: 6 additions & 0 deletions test/runtests.jl
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@@ -1,4 +1,5 @@
using Aqua
using ExplicitImports
using GLM
using MixedModels
using Test
Expand All @@ -18,6 +19,11 @@ import LinearAlgebra: BLAS
piracies=(;treat_as_own=[GLM.wrkresp!, Base.:|]))
end

@testset "ExplicitImports" begin
@test check_no_implicit_imports(MixedModels) === nothing
@test check_no_stale_explicit_imports(MixedModels) === nothing
end

include("utilities.jl")
include("misc.jl")
include("pivot.jl")
Expand Down
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