feat: add demes::ffi module (#339)

* add valgrind CI

.github/workflows/test_ffi.yml

@@ -38,12 +38,32 @@ jobs:
         with:
           crate: cbindgen
           version: "=0.24.3" 
-      - name: Run cmake
+      - name: Run cmake on demes-forward example
         run: |
             cmake -Sdemes-forward-capi/c_example -Bbuild
-      - name: Build
+      - name: Build demes-forward example
         run: |
             cmake --build build
-      - name: Run C example
+      - name: Run demes-forward C example
         run: |
            ./build/example demes-forward-capi/example_yaml/*.yaml
+      - name: cleanup
+        run: |
+            rm -rf build
+      - name: Run cmake on demes example
+        run: |
+            cmake -Sdemes/c_example -Bbuild
+      - name: Build demes example
+        run: |
+            cmake --build build
+      - name: Run demes C example
+        run: |
+           ./build/example demes/demes-spec/examples/browning_america.yaml
+      - run: sudo apt-get update -y
+        if: matrix.os == 'ubuntu-latest'
+      - run: sudo apt-get install -y valgrind
+        if: matrix.os == 'ubuntu-latest'
+      - name: Run demes C example through valgrind
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+           valgrind ./build/example demes/demes-spec/examples/browning_america.yaml

.github/workflows/valgrind.yaml

@@ -0,0 +1,40 @@
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+
+name: valgrind
+
+jobs:
+  cargo-valgrind:
+    name: Run valgrind
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        rust:
+          - stable
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          submodules: recursive
+      - uses: dtolnay/rust-toolchain@v1
+        with:
+          toolchain: ${{ matrix.rust }}
+          override: true
+      - uses: Swatinem/rust-cache@v2
+      - run: sudo apt-get update -y
+        if: matrix.os == 'ubuntu-latest'
+      - run: sudo apt-get install -y valgrind
+        if: matrix.os == 'ubuntu-latest'
+      - run: cargo install cargo-valgrind
+      - name: run cargo valgrind on demes::ffi
+        run: |
+            cargo valgrind test --manifest-path demes/Cargo.toml --all-features ffi
+

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "demes-forward-capi/corrosion"]
 	path = demes-forward-capi/c_example/corrosion
 	url = https://github.com/corrosion-rs/corrosion.git
+[submodule "demes/c_example/corrosion"]
+	path = demes/c_example/corrosion
+	url = https://github.com/corrosion-rs/corrosion.git

demes/Cargo.toml

@@ -9,12 +9,16 @@ homepage = "https://github.com/molpopgen/demes-rs"
 repository = "https://github.com/molpopgen/demes-rs"
 rust-version = "1.60.0"
 
+[lib]
+crate-type = ["lib", "staticlib"]
+
 [package.metadata.docs.rs]
 all-features = true
 rustdoc-args = ["--cfg", "doc_cfg"]
 
 [features]
 json = ["serde_json"]
+ffi = []
 
 [dependencies]
 thiserror = "~1"

demes/c_example/CMakeLists.txt

@@ -0,0 +1,26 @@
+# Usage from the workspace root:
+# cmake -S demes/c_example -B build
+# cmake --build build
+# cmake --build build --target clean
+cmake_minimum_required(VERSION 3.15)
+project(c_example LANGUAGES C)
+
+MESSAGE(${CMAKE_SOURCE_DIR} ${PROJECT_SOURCE_DIR})
+
+add_compile_options(-W -Wall -Werror -Wconversion)
+add_subdirectory(corrosion)
+
+# Specify to only build the demes crate and to use the ffi cargo feature of the crate
+corrosion_import_crate(MANIFEST_PATH ../Cargo.toml CRATES demes FEATURES ffi)
+# The header, demes.h, will be built in the root of the build dir
+get_filename_component(DEMES_HEADER_LOCATION ${CMAKE_BINARY_DIR} DIRECTORY CACHE)
+add_custom_target(header DEPENDS ${DEMES_HEADER_LOCATION}/demes.h)
+add_executable(example example.c)
+add_dependencies(example cargo-build_demes header)
+target_include_directories(example BEFORE PUBLIC ${DEMES_HEADER_LOCATION})
+target_link_directories(example PUBLIC ${CMAKE_BINARY_DIR})
+# We link the static C archive of demes and the C math lib to the binary
+target_link_libraries(example PUBLIC libdemes.a m)
+
+# Use cbindgen to build our header
+add_custom_command(OUTPUT ${DEMES_HEADER_LOCATION}/demes.h COMMAND cbindgen -l C -o ${DEMES_HEADER_LOCATION}/demes.h ${CMAKE_SOURCE_DIR}/..)

demes/c_example/example.c

@@ -0,0 +1,129 @@
+#define DEMES_FFI = 1
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <demes.h>
+
+void
+handle_error(int rv, FFIError *error, Graph *graph)
+{
+    char *error_msg = NULL;
+    if (rv != 0)
+        {
+            assert(demes_error_has_error(error));
+            assert((error_msg = demes_error_message(error)) != NULL);
+            fprintf(stderr, "%s\n", error_msg);
+            demes_c_char_deallocate(error_msg);
+            demes_error_deallocate(error);
+            if (graph != NULL)
+                {
+                    demes_graph_deallocate(graph);
+                }
+            exit(1);
+        }
+}
+
+void
+iterate_epochs(const Deme *deme)
+{
+    Epoch const *epoch;
+    size_t num_epochs = demes_deme_num_epochs(deme);
+    size_t i;
+    double midpoint, size_at_midpoint, start_time, end_time;
+    for (i = 0; i < num_epochs; ++i)
+        {
+            assert((epoch = demes_deme_epoch(deme, i)) != NULL);
+            start_time = demes_epoch_start_time(epoch);
+            end_time = demes_epoch_end_time(epoch);
+            midpoint = end_time + (start_time - end_time)/2.0;
+            assert(demes_epoch_size_at(epoch, midpoint, &size_at_midpoint) == 0);
+            fprintf(stdout, "\t\tstart time: %lf\n", start_time);
+            fprintf(stdout, "\t\tend time: %lf\n", end_time);
+            fprintf(stdout, "\t\tstart size: %lf\n", demes_epoch_start_size(epoch));
+            fprintf(stdout, "\t\tmidpoint size: %lf\n", size_at_midpoint);
+            fprintf(stdout, "\t\tend size: %lf\n", demes_epoch_end_size(epoch));
+        }
+}
+
+void
+iterate_ancestors_proportions(const Graph *graph, const Deme *deme)
+{
+    size_t const *ancestor_indexes;
+    Deme const *ancestor;
+    double const *ancestor_proportions;
+    double proportion;
+    char *ancestor_name;
+    size_t i, num_ancestors;
+
+    num_ancestors = demes_deme_num_ancestors(deme);
+    ancestor_indexes = demes_deme_ancestor_indexes(deme);
+    ancestor_proportions = demes_deme_proportions(deme);
+
+    for (i = 0; i < num_ancestors; ++i)
+        {
+            assert((ancestor = demes_graph_deme(graph, ancestor_indexes[i])) != NULL);
+            ancestor_name = demes_deme_name(deme);
+            proportion = ancestor_proportions[i];
+            fprintf(stdout, "\t \t%s %lf\n", ancestor_name, proportion);
+            demes_c_char_deallocate(ancestor_name);
+        }
+}
+
+void
+iterate_demes(Graph *graph, FFIError *error)
+{
+    size_t i, num_epochs;
+    Deme const *deme;
+    size_t num_demes;
+    char *deme_name = NULL;
+
+    assert(!demes_error_has_error(error));
+
+    num_demes = demes_graph_num_demes(graph);
+    for (i = 0; i < num_demes; ++i)
+        {
+            assert((deme = demes_graph_deme(graph, i)) != NULL);
+            num_epochs = demes_deme_num_epochs(deme);
+            assert((deme_name = demes_deme_name(deme)) != NULL);
+            fprintf(stdout, "deme %ld:\n", i);
+            fprintf(stdout, "\tname: %s\n", deme_name);
+            fprintf(stdout, "\tno. epochs: %ld\n", num_epochs);
+            fprintf(stdout, "\tstart time: %lf\n", demes_deme_start_time(deme));
+            fprintf(stdout, "\tend time: %lf\n", demes_deme_end_time(deme));
+            fprintf(stdout, "\tstart size: %lf\n", demes_deme_start_size(deme));
+            fprintf(stdout, "\tend size: %lf\n", demes_deme_end_size(deme));
+            demes_c_char_deallocate(deme_name);
+            fprintf(stdout, "\tancestor details:\n");
+            iterate_ancestors_proportions(graph, deme);
+            fprintf(stdout, "\tepoch details:\n");
+            iterate_epochs(deme);
+        }
+}
+
+int
+main(int argc, char **argv)
+{
+    FFIError *error = NULL;
+    Graph *graph = NULL;
+    int rv;
+
+    if (argc != 2)
+        {
+            fprintf(stderr, "usage: example filename\n");
+            exit(1);
+        }
+
+    error = demes_error_allocate();
+
+    rv = demes_graph_load_from_file(argv[1], error, &graph);
+    handle_error(rv, error, graph);
+
+    iterate_demes(graph, error);
+
+    demes_error_deallocate(error);
+    if (graph != NULL)
+        {
+            demes_graph_deallocate(graph);
+        }
+}

demes/cbindgen.toml

@@ -0,0 +1,3 @@
+[defines]
+"feature = ffi" = "DEMES_FFI"
+"feature = json" = "DEMES_JSON"

demes/src/error.rs

@@ -24,6 +24,7 @@ use thiserror::Error;
 /// ";
 /// assert!(matches!(demes::loads(yaml), Err(demes::DemesError::EpochError(_))));
 /// ```
+// cbindgen:no-export
 #[derive(Error, Debug)]
 #[non_exhaustive]
 pub enum DemesError {