Merge remote-tracking branch 'origin/some_improvements'

.github/workflows/ci.yml

@@ -0,0 +1,41 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+  pull_request:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          file: lcov.info
+

Project.toml

@@ -8,3 +8,11 @@ Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 InvertedIndices = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+
+
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

src/RecursiveCausalDiscovery.jl

@@ -18,7 +18,7 @@ Computes the Markov boundary matrix for all variables in-place.
 - `data::DataFrame`: DataFrame where each column is a variable.
 - `ci_test`: Conditional independence test to use.
 """
-function find_markov_boundary_matrix!(markov_boundary_matrix::BitMatrix, data::Matrix{Float64}, ci_test::Function)
+function find_markov_boundary_matrix!(markov_boundary_matrix::BitMatrix, data::AbstractMatrix, ci_test::Function)
     num_vars = size(data, 2)
 
     @threads for i in 1:(num_vars - 1)
@@ -38,18 +38,23 @@ RSL class for learning graph structure.
 - `markov_boundary_matrix`: Matrix indicating whether variable i is in the Markov boundary of j.
 - `skip_rem_check_vec`: Used to keep track of which variables to skip when checking for removability. Speeds up the algorithm.
 """
-struct RSL
-    data::Matrix{Float64}
-    ci_test::Function
+struct RSL{T, F}
+    data::Matrix{T}
+    ci_test::F
     markov_boundary_matrix::BitMatrix
     skip_rem_check_vec::BitVector
 
-    function RSL(data::Matrix{Float64}, ci_test::Function)
+    function RSL(data::Matrix{T}, ci_test::Function) where T
         num_vars = size(data, 2)
-        new(Float64.(data), ci_test, falses(num_vars, num_vars), falses(num_vars))
+        new{T, typeof(ci_test)}(data, ci_test, falses(num_vars, num_vars), falses(num_vars))
     end
 end
 
+
+_to_matrix(x) = Tables.matrix(x)
+_to_matrix(x::Matrix) = x
+
+
 """
     learn_and_get_skeleton(data, ci_test)::Graph
 
@@ -64,7 +69,7 @@ Runs the algorithm on the data to learn and return the learned skeleton graph.
 """
 function learn_and_get_skeleton(data, ci_test::Function; mkbd_ci_test::Function=ci_test)::SimpleGraph
     Tables.istable(data) || throw(ArgumentError("Argument does not support Tables.jl"))
-    data_mat = Tables.matrix(data)
+    data_mat = _to_matrix(data) 
     num_vars = size(data_mat, 2)
 
     rsl = RSL(data_mat, ci_test)
@@ -80,20 +85,20 @@ function learn_and_get_skeleton(data, ci_test::Function; mkbd_ci_test::Function=
 
     for i in 1:(num_vars - 1)
         # only consider variables that are left and have skip check set to False
-        var_to_check_arr = var_arr[var_left_bool_arr .& .!rsl.skip_rem_check_vec]
+        var_to_check_arr = @views var_arr[var_left_bool_arr .& .!rsl.skip_rem_check_vec]
 
         # sort the variables by the size of their markov boundary
-        mb_size = sum(rsl.markov_boundary_matrix[:, var_to_check_arr], dims = 1)[1, :]
+        mb_size = @views sum(rsl.markov_boundary_matrix[:, var_to_check_arr], dims = 1)[1, :]
         sort_indices = sortperm(mb_size)
-        sorted_var_arr = var_to_check_arr[sort_indices]
+        sorted_var_arr = @views var_to_check_arr[sort_indices]
 
         # find a removable variable
         removable_var = find_removable!(rsl, sorted_var_arr)
 
         if removable_var == REMOVABLE_NOT_FOUND
             # if no removable found, then pick the variable with the smallest markov boundary from var_left_bool_arr
             var_left_arr = findall(var_left_bool_arr)
-            mb_size_all = sum(rsl.markov_boundary_matrix[var_left_arr, :], dims = 2)
+            mb_size_all = @views sum(rsl.markov_boundary_matrix[var_left_arr, :], dims = 2)
             removable_var = var_left_arr[argmin(mb_size_all)]
 
             rsl.skip_rem_check_vec .= false
@@ -191,7 +196,7 @@ Find a removable variable in the given list of variables.
 # Returns
 - `Int`: Index of the removable variable.
 """
-function find_removable!(rsl::RSL, var_idx_list::Vector{Int})::Int
+function find_removable!(rsl::RSL, var_idx_list::AbstractVector{Int})::Int
     for var_idx in var_idx_list
         if is_removable(rsl, var_idx)
             return var_idx
@@ -208,7 +213,7 @@ Update the Markov boundary matrix after removing a variable.
 - `var_idx::Int`: Index of the variable to remove.
 - `var_neighbors::Vector{Int}`: Array containing the indices of the neighbors of var_idx.
 """
-function update_markov_boundary_matrix!(rsl::RSL, var_idx::Int, var_neighbors::Vector{Int})
+function update_markov_boundary_matrix!(rsl::RSL, var_idx::Int, var_neighbors::AbstractVector{Int})
     var_markov_boundary = findall(@view rsl.markov_boundary_matrix[:, var_idx])
 
     # For every variable in the Markov boundary of var_idx, remove it from the Markov boundary and update flag
@@ -225,10 +230,10 @@ function update_markov_boundary_matrix!(rsl::RSL, var_idx::Int, var_neighbors::V
             var_y_idx = var_neighbors[ne_idx_y]
             var_z_idx = var_neighbors[ne_idx_z]
 
-            var_y_markov_boundary = findall(rsl.markov_boundary_matrix[:, var_y_idx])
-            var_z_markov_boundary = findall(rsl.markov_boundary_matrix[:, var_z_idx])
+            var_y_markov_boundary = findall(@view rsl.markov_boundary_matrix[:, var_y_idx])
+            var_z_markov_boundary = findall(@view rsl.markov_boundary_matrix[:, var_z_idx])
 
-            if sum(rsl.markov_boundary_matrix[:, var_y_idx]) < sum(rsl.markov_boundary_matrix[:, var_z_idx])
+            if @views sum(rsl.markov_boundary_matrix[:, var_y_idx]) < sum(rsl.markov_boundary_matrix[:, var_z_idx])
                 cond_set = setdiff(var_y_markov_boundary, [var_z_idx])
             else
                 cond_set = setdiff(var_z_markov_boundary, [var_y_idx])

test/runtests.jl

@@ -0,0 +1,17 @@
+using RecursiveCausalDiscovery
+
+using Test
+
+
+# navigate with your shell in the main directory of the package
+# First run: using Pkg; Pkg.activate("."); using TestEnv; TestEnv.activate(); include("test/runtests.jl")
+# Second run: include("test/runtests.jl")
+
+
+@testset "Some unit tests" begin
+    @test 1 == SimpleGraph{Int64}(91, [Int64[], [50, 77], [63, 76, 97], [98], [21, 79, 82, 99], [29, 64], [16, 17, 45, 76, 96], [35, 45, 84], Int64[], [61], [60, 71], [30, 41, 73], [36], [24, 95], [54], [7, 43, 90], [7, 29, 97], [32], [33, 85], Int64[], [5], Int64[], [73], [14, 76], [100], Int64[], [70], [32, 62], [6, 17, 55], [12], Int64[], [18, 28], [19], [58], [8], [13, 48], [61, 86], Int64[], [99], [68, 88], [12, 46, 65], Int64[], [16, 53, 76, 84, 90], [55, 78, 97], [7, 8], [41, 71, 76], [73, 74, 77], [36], [59], [2], [68], Int64[], [43], [15], [29, 44, 76, 85, 98], [80], [70, 88], [34], [49, 87], [11, 88, 97], [10, 37], [28], [3, 90], [6], [41], Int64[], [69, 74], [40, 51, 85], [67], [27, 57], [11, 46], [100], [12, 23, 47], [47, 67, 82], Int64[], [3, 7, 24, 43, 46, 55, 89], [2, 47, 87], [44, 93], [5], [56], [82], [5, 74, 81], [87], [8, 43, 85], [19, 55, 68, 84, 89], [37], [59, 77, 83], [40, 57, 60], [76, 85], [16, 43, 63, 99], [95], Int64[], [78], Int64[], [14, 91], [7], [3, 17, 44, 60], [4, 55], [5, 39, 90], [25, 72]])
+end
+
+@testset "Some smaller finer tests" begin
+    @test true
+end