merge main into devel

Author: Maximilian-Stefan-Ernst

.github/workflows/CI.yml

@@ -33,6 +33,6 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           file: lcov.info

.github/workflows/CI_ecosystem.yml

@@ -36,6 +36,6 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           file: lcov.info

.github/workflows/CI_extended.yml

@@ -35,6 +35,6 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           file: lcov.info

Project.toml

@@ -1,7 +1,7 @@
 name = "StructuralEquationModels"
 uuid = "383ca8c5-e4ff-4104-b0a9-f7b279deed53"
 authors = ["Maximilian Ernst", "Aaron Peikert"]
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -39,6 +39,7 @@ ProximalAlgorithms = "0.7"
 StatsBase = "0.33, 0.34"
 Symbolics = "4, 5, 6"
 SymbolicUtils = "1.4 - 1.5, 1.7, 2, 3"
+StatsAPI = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -4,6 +4,9 @@
 |:-------------------------------------------------------------------------------:|:-----------------------------------------------------------------------------------------------:|:-----------------------------------------------------------------------------------------------:|
 | [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://structuralequationmodels.github.io/StructuralEquationModels.jl/) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://structuralequationmodels.github.io/StructuralEquationModels.jl/dev/) | [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Github Action CI](https://github.com/StructuralEquationModels/StructuralEquationModels.jl/workflows/CI_extended/badge.svg)](https://github.com/StructuralEquationModels/StructuralEquationModels.jl/actions/) [![codecov](https://codecov.io/gh/StructuralEquationModels/StructuralEquationModels.jl/branch/main/graph/badge.svg?token=P2kjzpvM4V)](https://codecov.io/gh/StructuralEquationModels/StructuralEquationModels.jl) | [![DOI](https://zenodo.org/badge/228649704.svg)](https://zenodo.org/badge/latestdoi/228649704) |
 
+> [!NOTE]  
+> Check out our [preprint](https://formal-methods-mpi.github.io/pkgmanuscript/manuscript.pdf) on the package!
+
 # What is this Package for?
 
 This is a package for Structural Equation Modeling.

docs/src/tutorials/collection/multigroup.md

@@ -81,8 +81,8 @@ model_ml_multigroup = SemEnsemble(
 We now fit the model and inspect the parameter estimates:
 
 ```@example mg; ansicolor = true
-fit = fit(model_ml_multigroup)
-update_estimate!(partable, fit)
+sem_fit = fit(model_ml_multigroup)
+update_estimate!(partable, sem_fit)
 details(partable)
 ```
 

docs/src/tutorials/inspection/inspection.md

@@ -117,6 +117,11 @@ Additional functions that can be used to extract information from a `SemFit` obj
 
 ```@docs
 SemFit
+params
+param_labels
+nparams
+nsamples
+nobserved_vars
 ```
 
 ## Fit measures
@@ -128,10 +133,6 @@ BIC
 χ²
 dof
 minus2ll
-nobserved_vars
-nsamples
-param_labels
-nparams
 p_value
 RMSEA
 ```

docs/src/tutorials/regularization/regularization.md

@@ -126,9 +126,9 @@ fit_lasso = fit(optimizer_lasso, model_lasso)
 and compare the solution to unregularizted estimates:
 
 ```@example reg
-fit = fit(model)
+sem_fit = fit(model)
 
-update_estimate!(partable, fit)
+update_estimate!(partable, sem_fit)
 
 update_partable!(partable, :estimate_lasso, param_labels(fit_lasso), solution(fit_lasso))
 
@@ -138,7 +138,7 @@ details(partable)
 Instead of explicitely defining a `SemOptimizerProximal` object, you can also pass `engine = :Proximal` and additional keyword arguments to `fit`:
 
 ```@example reg
-fit = fit(model; engine = :Proximal, operator_g = NormL1(λ))
+sem_fit = fit(model; engine = :Proximal, operator_g = NormL1(λ))
 ```
 
 ## Second example - mixed l1 and l0 regularization

src/frontend/specification/documentation.jl

@@ -29,6 +29,45 @@ model.
 """
 function latent_vars end
 
+latent_vars(spec::SemSpecification) =
+    error("latent_vars(spec::$(typeof(spec))) is not implemented")
+
+"""
+    param_labels(semobj) -> Vector{Symbol}
+
+Return the vector of parameter labels (in the same order as [`params`](@ref)).
+"""
+param_labels(spec::SemSpecification) = spec.param_labels
+
+"""
+    vars(semobj) -> Vector{Symbol}
+
+Return the vector of SEM model variables (both observed and latent)
+in the order specified by the model.
+"""
+function vars end
+
+vars(spec::SemSpecification) = error("vars(spec::$(typeof(spec))) is not implemented")
+
+"""
+    observed_vars(semobj) -> Vector{Symbol}
+
+Return the vector of SEM model observed variable in the order specified by the
+model, which also should match the order of variables in [`SemObserved`](@ref).
+"""
+function observed_vars end
+
+observed_vars(spec::SemSpecification) =
+    error("observed_vars(spec::$(typeof(spec))) is not implemented")
+
+"""
+    latent_vars(semobj) -> Vector{Symbol}
+
+Return the vector of SEM model latent variable in the order specified by the
+model.
+"""
+function latent_vars end
+
 latent_vars(spec::SemSpecification) =
     error("latent_vars(spec::$(typeof(spec))) is not implemented")
 

test/unit_tests/unit_tests.jl

@@ -33,3 +33,11 @@ selected_tests = isempty(ARGS) ? collect(keys(available_tests)) : ARGS
         end
     end
 end
+
+@safetestset "SemSpecification" begin
+    include("specification.jl")
+end
+
+@safetestset "Sem model" begin
+    include("model.jl")
+end