#67 Add formatter. make format.

.gitignore

@@ -10,4 +10,5 @@ alloc-profile.pb.gz
 profile.pb.gz
 
 *.ipynb
-.ipynb_checkpoints
+.ipynb_checkpoints
+*Manifest.toml

Makefile

@@ -4,9 +4,13 @@
 DOCSRC = docs
 DOCTARGET = $(DOCSRC)/build
 
+SCRIPTSRC = scripts
+FORMATTER = $(SCRIPTSRC)/formatter.jl
+
 JULIA ?= julia
 JULIAFLAGS ?= --project=.
 JULIAFLAGSDOCS ?= --project=$(DOCSRC)
+JULIAFLAGSSCRIPTS ?= --project=$(SCRIPTSRC)
 
 # Colors for terminal output
 ifdef NO_COLOR
@@ -38,7 +42,10 @@ help:
 	@echo '${GREEN}Development commands:${RESET}'
 	@echo '  ${YELLOW}deps${RESET}                 Install project dependencies'
 	@echo '  ${YELLOW}deps-docs${RESET}            Install documentation dependencies'
+	@echo '  ${YELLOW}deps-scripts${RESET}         Install script dependencies'
 	@echo '  ${YELLOW}test${RESET}                 Run project tests'
+	@echo '  ${YELLOW}format${RESET}               Format Julia code'
+	@echo '  ${YELLOW}check-format${RESET}         Check Julia code formatting (does not modify files)'
 	@echo '  ${YELLOW}clean${RESET}                Clean all generated files'
 	@echo ''
 	@echo '${GREEN}Help:${RESET}'
@@ -68,8 +75,17 @@ deps: ## Install project dependencies
 deps-docs: ## Install documentation dependencies
 	$(JULIA) $(JULIAFLAGSDOCS) -e 'using Pkg; Pkg.develop(path="."); Pkg.instantiate()'
 
+deps-scripts: ## Install script dependencies
+	$(JULIA) $(JULIAFLAGSSCRIPTS) -e 'using Pkg; Pkg.instantiate()'
+
 test: deps ## Run project tests
 	$(JULIA) $(JULIAFLAGS) -e 'using Pkg; Pkg.test(test_args = split("$(test_args)") .|> string)'	
 
+format: deps-scripts ## Format Julia code
+	$(JULIA) $(JULIAFLAGSSCRIPTS) $(FORMATTER) --overwrite
+
+check-format: deps-scripts ## Check Julia code formatting (does not modify files)
+	$(JULIA) $(JULIAFLAGSSCRIPTS) $(FORMATTER)
+
 clean: docs-clean ## Clean all generated files
 	rm -rf .julia/compiled

docs/make.jl

@@ -16,7 +16,7 @@ makedocs(;
         canonical = "https://reactivebayes.github.io/ExponentialFamilyProjection.jl",
         edit_link = "main",
         assets = String[],
-        repolink="https://github.com/ReactiveBayes/ExponentialFamilyProjection.jl"
+        repolink = "https://github.com/ReactiveBayes/ExponentialFamilyProjection.jl",
     ),
     pages = ["Home" => "index.md"],
 )

scripts/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d"

scripts/formatter.jl

@@ -0,0 +1,26 @@
+using JuliaFormatter
+using ArgParse
+
+s = ArgParseSettings()
+
+@add_arg_table s begin
+    "--overwrite"
+    help = "Overwrite the files with the formatted code"
+    action = :store_true
+    default = false
+end
+
+args = parse_args(ARGS, s)
+overwrite = args["overwrite"]
+projectroot = joinpath(@__DIR__, "..")
+
+passed = format(projectroot; verbose = true, overwrite = overwrite)
+
+if !passed && !overwrite
+    @error "JuliaFormatter check has failed. Run `make format` from the main directory and commit your changes to fix code style."
+    exit(1)
+elseif !passed && overwrite
+    @info "JuliaFormatter has overwritten files according to style guidelines"
+elseif passed
+    @info "Codestyle from JuliaFormatted checks have passed"
+end

src/jacobians.jl

@@ -3,65 +3,121 @@ function jacobian_nat_to_manifold!(::AbstractManifold, X_p, X_nat)
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.NormalMeanVariance}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{
+        F,
+        ExponentialFamily.NormalMeanVariance,
+    },
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= X_nat[1]
     X_p[2:2] .= -X_nat[2]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.Gamma}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{F,ExponentialFamily.Gamma},
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= X_nat[1]
     X_p[2:2] .= -X_nat[2]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.Rayleigh}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{F,ExponentialFamily.Rayleigh},
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= -X_nat[1]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.Geometric}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{F,ExponentialFamily.Geometric},
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= -X_nat[1]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.GammaInverse}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{
+        F,
+        ExponentialFamily.GammaInverse,
+    },
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= -X_nat[1]
     X_p[2:2] .= -X_nat[2]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.Exponential}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{F,ExponentialFamily.Exponential},
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= -X_nat[1]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.Weibull}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{F,ExponentialFamily.Weibull},
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= -X_nat[1]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.Laplace}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{F,ExponentialFamily.Laplace},
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= -X_nat[1]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.LogNormal}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    ::ExponentialFamilyManifolds.NaturalParametersManifold{F,ExponentialFamily.LogNormal},
+    X_p,
+    X_nat,
+) where {F}
     X_p[1:1] .= X_nat[1]
     X_p[2:2] .= -X_nat[2]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(M::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.MvNormalMeanScalePrecision}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    M::ExponentialFamilyManifolds.NaturalParametersManifold{
+        F,
+        ExponentialFamily.MvNormalMeanScalePrecision,
+    },
+    X_p,
+    X_nat,
+) where {F}
     k = first(ExponentialFamilyManifolds.getdims(M))
     X_p[1:k] .= X_nat[1:k]
-    X_p[k+1:k+1] .= -X_nat[k+1:k+1]
+    X_p[(k+1):(k+1)] .= -X_nat[(k+1):(k+1)]
     return X_p
 end
 
-function jacobian_nat_to_manifold!(M::ExponentialFamilyManifolds.NaturalParametersManifold{F, ExponentialFamily.MvNormalMeanCovariance}, X_p, X_nat) where {F}
+function jacobian_nat_to_manifold!(
+    M::ExponentialFamilyManifolds.NaturalParametersManifold{
+        F,
+        ExponentialFamily.MvNormalMeanCovariance,
+    },
+    X_p,
+    X_nat,
+) where {F}
     k = first(ExponentialFamilyManifolds.getdims(M))
     X_p[1:k] .= X_nat[1:k]
-    X_p[(k + 1):(k + k^2)] .= -X_nat[(k + 1):(k + k^2)]
+    X_p[(k+1):(k+k^2)] .= -X_nat[(k+1):(k+k^2)]
     return X_p
-end
+end

src/manopt/bounded_norm_update_rule.jl

@@ -29,7 +29,10 @@ function init_direction_rule(d::BoundedNormUpdateRule, ::Any)
     return d
 end
 
-function init_direction_rule(bounded_direction::BoundedNormUpdateRule{L,D}, M) where {L, D <: Manopt.ManifoldDefaultsFactory}
+function init_direction_rule(
+    bounded_direction::BoundedNormUpdateRule{L,D},
+    M,
+) where {L,D<:Manopt.ManifoldDefaultsFactory}
     inner_direction = bounded_direction.direction(M)
     return BoundedNormUpdateRule(bounded_direction.limit, inner_direction)
 end
@@ -54,4 +57,3 @@ function (b::BoundedNormUpdateRule)(
     end
     return step, d
 end
-

src/manopt/projection_objective.jl

@@ -31,7 +31,12 @@ get_supplementary_η(obj::ProjectionCostGradientObjective) = obj.supplementary_
 get_strategy(obj::ProjectionCostGradientObjective) = obj.strategy
 get_strategy_state(obj::ProjectionCostGradientObjective) = obj.strategy_state
 
-function call_objective(objective::ProjectionCostGradientObjective, M::AbstractManifold, X, p)
+function call_objective(
+    objective::ProjectionCostGradientObjective,
+    M::AbstractManifold,
+    X,
+    p,
+)
     current_ef = convert(ExponentialFamilyDistribution, M, p)
     current_η = copyto!(get_current_η(objective), getnaturalparameters(current_ef))
 
@@ -89,5 +94,3 @@ end
 function (objective::ProjectionCostGradientObjective)(M::AbstractManifold, X, p)
     return call_objective(objective, M, X, p)
 end
-
-

src/projected_to.jl

@@ -205,7 +205,13 @@ end
 
 using Manopt
 
-function check_inputs(prj::ProjectedTo, projection_argument::F, supplementary...; initialpoint = nothing, kwargs...) where {F}
+function check_inputs(
+    prj::ProjectedTo,
+    projection_argument::F,
+    supplementary...;
+    initialpoint = nothing,
+    kwargs...,
+) where {F}
     if isnothing(initialpoint)
         return
     end
@@ -214,7 +220,7 @@ function check_inputs(prj::ProjectedTo, projection_argument::F, supplementary...
             lazy"The initial point must be on the manifold `$(get_projected_to_manifold(prj))`, got `$(typeof(initialpoint))`",
         )
     end
-end 
+end
 """
     project_to(to::ProjectedTo, argument::F, supplementary..., initialpoint, kwargs...)
 
@@ -294,8 +300,15 @@ function project_to(
         getstrategy(projection_parameters),
         projection_argument,
     )
-    current_iteration_point = preprocess_initialpoint(initialpoint, strategy, M, projection_parameters)
-    check_inputs(prj, projection_argument, supplementary...; initialpoint = current_iteration_point, kwargs...)
+    current_iteration_point =
+        preprocess_initialpoint(initialpoint, strategy, M, projection_parameters)
+    check_inputs(
+        prj,
+        projection_argument,
+        supplementary...;
+        initialpoint = current_iteration_point,
+        kwargs...,
+    )
     current_ef = convert(ExponentialFamilyDistribution, M, current_iteration_point)
     state = create_state!(
         strategy,
@@ -424,4 +437,4 @@ end
 # Otherwise we just copy the initial point, since we use it for the optimization in place
 function preprocess_initialpoint(_, initialpoint::AbstractArray, strategy, M, parameters)
     return copy(initialpoint)
-end
+end