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Maximilian-Stefan-ErnstMaximilian-Stefan-Ernst
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Merge pull request #191 from StructuralEquationModels/reformat
Reformat
2 parents 57c2339 + ae6e408 commit 5963725

76 files changed

Lines changed: 2850 additions & 2037 deletions

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‎.JuliaFormatter.toml‎

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always_for_in = true
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align_assignment = true
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align_struct_field = true
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align_conditional = true
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align_pair_arrow = true
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align_matrix = true
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remove_extra_newlines = true
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whitespace_typedefs = true

‎.github/workflows/FormatCheck.yml‎

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name: Format suggestions
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on:
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pull_request:
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# this argument is not required if you don't use the `suggestion-label` input
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types: [ opened, reopened, synchronize, labeled, unlabeled ]
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jobs:
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code-style:
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runs-on: ubuntu-latest
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steps:
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- uses: julia-actions/julia-format@v2
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with:
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version: '1'
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suggestion-label: 'format-suggest'

‎docs/make.jl‎

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using Documenter, StructuralEquationModels
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makedocs(
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sitename="StructuralEquationModels.jl",
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sitename = "StructuralEquationModels.jl",
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pages = [
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"index.md",
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"Tutorials" => [
@@ -11,67 +11,62 @@ makedocs(
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"tutorials/specification/specification.md",
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"tutorials/specification/graph_interface.md",
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"tutorials/specification/ram_matrices.md",
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"tutorials/specification/parameter_table.md"
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"tutorials/specification/parameter_table.md",
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],
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"Model Construction" => [
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"tutorials/construction/construction.md",
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"tutorials/construction/outer_constructor.md",
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"tutorials/construction/build_by_parts.md"
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],
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"Optimization Backends" => [
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"tutorials/backends/optim.md",
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"tutorials/backends/nlopt.md"
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"tutorials/construction/build_by_parts.md",
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],
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"Optimization Backends" =>
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["tutorials/backends/optim.md", "tutorials/backends/nlopt.md"],
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"Model Fitting" => "tutorials/fitting/fitting.md",
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"Model Inspection" => "tutorials/inspection/inspection.md",
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"Mean Structures" => "tutorials/meanstructure.md",
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"Collections" => [
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"tutorials/collection/collection.md",
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"tutorials/collection/multigroup.md"
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"tutorials/collection/multigroup.md",
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],
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"Constraints" => "tutorials/constraints/constraints.md"
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"Constraints" => "tutorials/constraints/constraints.md",
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],
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"Developer documentation" => [
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"Extending the package" => "developer/extending.md",
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"Custom loss functions" => "developer/loss.md",
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"Custom imply types" => "developer/imply.md",
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"Custom optimizer types" => "developer/optimizer.md",
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"Custom observed types" => "developer/observed.md",
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"Custom model types" => "developer/sem.md"
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],
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"Advanced tutorials" => [
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"Regularization" => "tutorials/regularization/regularization.md"
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"Custom model types" => "developer/sem.md",
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],
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"Advanced tutorials" =>
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["Regularization" => "tutorials/regularization/regularization.md"],
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"Performance tips" => [
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"Model sorting" => "performance/sorting.md",
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"MKL" => "performance/mkl.md",
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"Simulation studies" => "performance/simulation.md",
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"Symbolic precomputation" => "performance/symbolic.md",
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"Starting values" => "performance/starting_values.md",
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"Parametric Types" => "performance/parametric.md"
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"Parametric Types" => "performance/parametric.md",
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],
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"Internals and design" => [
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"Internals and design" => "internals/internals.md",
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"files" => "internals/files.md",
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"types" => "internals/types.md"
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"types" => "internals/types.md",
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],
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"Complementary material" => [
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"Mathematical appendix" => "complementary/maths.md"
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]
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"Complementary material" => ["Mathematical appendix" => "complementary/maths.md"],
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],
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format = Documenter.HTML(
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prettyurls = get(ENV, "CI", nothing) == "true",
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assets = ["assets/favicon_zeta.ico"],
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ansicolor = true,
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collapselevel = 1
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collapselevel = 1,
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),
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doctest = false
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doctest = false,
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)
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# doctest(StructuralEquationModels, fix=true)
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deploydocs(
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repo = "github.com/StructuralEquationModels/StructuralEquationModels.jl",
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devbranch = "devel",
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push_preview = "push_preview=true" ∈ ARGS
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push_preview = "push_preview=true" ∈ ARGS,
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)

‎src/StructuralEquationModels.jl‎

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@@ -1,9 +1,18 @@
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module StructuralEquationModels
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3-
using LinearAlgebra, Optim,
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NLSolversBase, Statistics, SparseArrays, Symbolics,
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NLopt, FiniteDiff, PrettyTables,
6-
Distributions, StenoGraphs, LazyArtifacts, DelimitedFiles,
3+
using LinearAlgebra,
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Optim,
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NLSolversBase,
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Statistics,
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SparseArrays,
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Symbolics,
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NLopt,
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FiniteDiff,
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PrettyTables,
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Distributions,
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StenoGraphs,
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LazyArtifacts,
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DelimitedFiles,
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DataFrames
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import DataFrames: DataFrame
@@ -76,41 +85,90 @@ include("frontend/fit/fitmeasures/fit_measures.jl")
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include("frontend/fit/standard_errors/hessian.jl")
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include("frontend/fit/standard_errors/bootstrap.jl")
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export AbstractSem,
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AbstractSemSingle, AbstractSemCollection, Sem, SemFiniteDiff,
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SemEnsemble,
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SemImply,
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RAMSymbolic, RAMSymbolicZ, RAM, ImplyEmpty, imply,
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start_val,
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start_fabin3, start_simple, start_parameter_table,
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SemLoss,
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SemLossFunction, SemML, SemFIML, em_mvn, SemLasso, SemRidge,
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SemConstant, SemWLS, loss,
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SemOptimizer,
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SemOptimizerEmpty, SemOptimizerOptim, SemOptimizerNLopt, NLoptConstraint,
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optimizer, n_iterations, convergence,
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SemObserved,
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SemObservedData, SemObservedCovariance, SemObservedMissing, observed,
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sem_fit,
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SemFit,
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minimum, solution,
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sem_summary,
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objective!, gradient!, hessian!, objective_gradient!, objective_hessian!,
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gradient_hessian!, objective_gradient_hessian!,
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ParameterTable,
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EnsembleParameterTable, update_partable!, update_estimate!, update_start!,
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Fixed, fixed, Start, start, Label, label,
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get_identifier_indices,
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RAMMatrices,
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RAMMatrices!,
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identifier,
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fit_measures,
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AIC, BIC, χ², df, fit_measures, minus2ll, n_par, n_obs, p_value, RMSEA, n_man,
111-
EmMVNModel,
112-
se_hessian, se_bootstrap,
113-
example_data,
114-
swap_observed, update_observed,
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@StenoGraph, →, ←, ↔, ⇔
116-
end
88+
export AbstractSem,
89+
AbstractSemSingle,
90+
AbstractSemCollection,
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Sem,
92+
SemFiniteDiff,
93+
SemEnsemble,
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SemImply,
95+
RAMSymbolic,
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RAM,
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ImplyEmpty,
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imply,
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start_val,
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start_fabin3,
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start_simple,
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start_parameter_table,
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SemLoss,
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SemLossFunction,
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SemML,
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SemFIML,
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em_mvn,
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SemRidge,
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SemConstant,
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SemWLS,
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loss,
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SemOptimizer,
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SemOptimizerEmpty,
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SemOptimizerOptim,
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SemOptimizerNLopt,
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NLoptConstraint,
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optimizer,
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n_iterations,
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convergence,
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SemObserved,
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SemObservedData,
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SemObservedCovariance,
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SemObservedMissing,
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observed,
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sem_fit,
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SemFit,
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minimum,
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solution,
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sem_summary,
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objective!,
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gradient!,
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hessian!,
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objective_gradient!,
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objective_hessian!,
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gradient_hessian!,
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objective_gradient_hessian!,
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ParameterTable,
138+
EnsembleParameterTable,
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update_partable!,
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update_estimate!,
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update_start!,
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Fixed,
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fixed,
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Start,
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start,
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Label,
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label,
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get_identifier_indices,
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RAMMatrices,
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identifier,
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fit_measures,
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AIC,
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BIC,
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χ²,
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df,
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fit_measures,
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minus2ll,
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n_par,
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n_obs,
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p_value,
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RMSEA,
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n_man,
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EmMVNModel,
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se_hessian,
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se_bootstrap,
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example_data,
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swap_observed,
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update_observed,
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@StenoGraph,
170+
→,
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←,
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↔,
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⇔
174+
end

‎src/additional_functions/artifacts.jl‎

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Original file line numberDiff line numberDiff line change
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1919
data, header = readdlm(path, ',', header = true)
2020
data_raw = DataFrame(data, vec(header))
2121
for col in eachcol(data_raw)
22-
replace!(col,"NA" => missing)
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replace!(col, "NA" => missing)
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end
2424
data = identity.(data_raw)
2525
return data
@@ -31,11 +31,11 @@ function example_data(name)
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data, header = readdlm(path, ',', header = true)
3232
data_raw = DataFrame(data, vec(header))
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for col in eachcol(data_raw)
34-
replace!(col,"NA" => missing)
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replace!(col, "NA" => missing)
3535
end
3636
data = identity.(data_raw)
3737
push!(out, key => data)
3838
end
3939
return out
4040
end
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end
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end

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