Switch back to internal builds of igraph and HDF5.

.github/workflows/run-tests.yaml

@@ -6,57 +6,110 @@ on:
 
 name: Test JS bindings
 
+env:
+  IMAGE_VERSION: master
+
 jobs:
+  prepare-version:
+    runs-on: ubuntu-latest
+    steps:
+    - run: echo "null"
+    outputs:
+      version: ${{ env.IMAGE_VERSION }}
+
   # Building the RDS files for the various RDS-reading utilities.
-  build_rds:
+  create_rds:
     runs-on: ubuntu-latest
     container: rocker/r-base:latest
 
     steps:
     - name: Checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Build RDS files
       run: |
         cd tests/rds
         R -f generate.R
 
     - name: Upload RDS files
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: rds-files
         path: tests/rds/*.rds
 
-  check:
+  build_deps:
     runs-on: ubuntu-latest
-    needs: build_rds
-    container: ghcr.io/kanaverse/scran.js-docker/builder:master
-    defaults:
-      run:
-        working-directory: /scran.js
+    needs: [prepare-version]
+    container: ghcr.io/kanaverse/emcmake-docker/builder:${{ needs.prepare-version.outputs.version }}
 
     steps:
-    - name: Get to the right branch
+    - name: Checkout repo
+      uses: actions/checkout@v4
+
+    - name: Cache installed
+      id: installed
+      uses: actions/cache@v4
+      with:
+        path: extern/installed
+        key: deps-${{ hashFiles('**/extern/**/build.sh') }}-${{ env.IMAGE_VERSION }}
+
+    - name: Build HDF5
+      if: steps.installed.outputs.cache-hit != 'true'
+      run: |
+        cd extern/hdf5
+        ./build.sh
+
+    - name: Build igraph
+      if: steps.installed.outputs.cache-hit != 'true'
       run: |
-        git fetch --all
-        git checkout $GITHUB_SHA
+        cd extern/igraph
+        ./build.sh
+
+  test:
+    runs-on: ubuntu-latest
+    needs: [ create_rds, build_deps, prepare-version]
+    container: ghcr.io/kanaverse/emcmake-docker/builder:${{ needs.prepare-version.outputs.version }}
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v4
 
     - name: Set up Node
-      uses: actions/setup-node@v3
+      uses: actions/setup-node@v4
       with:
-        node-version: 16
+        node-version: 18
 
-    - name: Update node build 
-      run: bash build.sh main
+    - name: Cache Modules
+      uses: actions/cache@v4
+      with:
+        path: '**/node_modules'
+        key: npm-${{ hashFiles('**/package.json') }}
 
     - name: Update NPM packages
       run: npm i --include=dev
 
+    - name: Cache installed
+      uses: actions/cache@v4
+      with:
+        path: extern/installed
+        key: deps-${{ hashFiles('**/extern/**/build.sh') }}-${{ env.IMAGE_VERSION }}
+
+    - name: Cache node build
+      id: wasm-build
+      uses: actions/cache@v4
+      with:
+        path: js/wasm
+        key: wasm-${{ hashFiles('**/build.sh', '**/CMakeLists.txt', '**/src/*') }}-${{ env.IMAGE_VERSION }}
+
+    - name: Update node build 
+      if: steps.wasm-build.outputs.cache-hit != 'true'
+      run: bash build.sh main
+
     - name: Download RDS files
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: rds-files
-        path: /scran.js/tests/rds
+        path: tests/rds
 
     - name: Run tests
       run: |

.gitignore

@@ -1,3 +1,4 @@
+extern/installed
 build_*
 docs/html/
 docs/latex/

CMakeLists.txt

@@ -7,6 +7,10 @@ project(scran_wasm
 
 set(CMAKE_CXX_STANDARD 17)
 
+# Need the CMAKE_FIND_ROOT_PATH_BOTH to override Emscripten's overrides (see emscripten/issues#6595)
+find_package(igraph REQUIRED CONFIG CMAKE_FIND_ROOT_PATH_BOTH)
+find_package(HDF5 REQUIRED COMPONENTS C CXX CONFIG CMAKE_FIND_ROOT_PATH_BOTH)
+find_package(ZLIB REQUIRED)
 add_subdirectory(extern)
 
 add_executable(
@@ -66,8 +70,9 @@ target_link_libraries(
     mnncorrect
     qdtsne
     umappp
-    hdf5-wasm-cpp
-    igraph
+    hdf5-static
+    hdf5_cpp-static
+    igraph::igraph
     singlepp
     rds2cpp
 )

build.sh

@@ -45,7 +45,12 @@ if [ ! -e $builddir ]
 then
     mkdir $builddir
     echo "{}" > $builddir/package.json # avoid assuming ES6 syntax for igraph config scripts.
-    emcmake cmake -S . -B $builddir -DCOMPILE_NODE=${node_flag} -DCMAKE_BUILD_TYPE=Release
+    emcmake cmake \
+        -S . \
+        -B $builddir \
+        -DCOMPILE_NODE=${node_flag} \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_PREFIX_PATH=extern/installed
 fi
 
 cd $builddir

extern/CMakeLists.txt

@@ -15,7 +15,6 @@ endif()
 
 include(FetchContent)
 
-## TATAMI RELATED CONTENT ### 
 FetchContent_Declare(
   tatami 
   GIT_REPOSITORY https://github.com/tatami-inc/tatami
@@ -40,20 +39,6 @@ FetchContent_Declare(
   GIT_TAG 20ec1fb64e0419907d3094827b5d9134854a0119
 )
 
-## Prebuilt static libraries ### 
-FetchContent_Declare(
-  igraph 
-  URL https://github.com/kanaverse/igraph-wasm/releases/download/v0.2.1-pthreads_3.1.43/igraph-0.10.6-wasm.tar.gz # need the thread-aware version.
-  URL_HASH SHA256=a40595001e0b39ef715f4a84bb83f3bb668ee8eed3ac55bd206212d45d7c53f1
-)
-
-FetchContent_Declare(
-  h5wasm
-  URL https://github.com/kanaverse/libhdf5-wasm/releases/download/v0.3.0_3.1.43/libhdf5-1_12_2-wasm.tar.gz
-  URL_HASH SHA256=b2e58b102fe98326c77f1a160025c47a062c1a205818568680d5f5ed78df801c
-)
-
-## Other stuff ### 
 FetchContent_Declare(
   irlba
   GIT_REPOSITORY https://github.com/LTLA/CppIrlba
@@ -106,8 +91,6 @@ FetchContent_MakeAvailable(tatami)
 FetchContent_MakeAvailable(tatami_layered)
 FetchContent_MakeAvailable(tatami_mtx)
 FetchContent_MakeAvailable(tatami_hdf5)
-FetchContent_MakeAvailable(igraph)
-FetchContent_MakeAvailable(h5wasm)
 FetchContent_MakeAvailable(irlba)
 FetchContent_MakeAvailable(umappp)
 FetchContent_MakeAvailable(scran)

extern/hdf5/.gitignore

@@ -0,0 +1,3 @@
+hdf5*
+package.json
+build-*

extern/hdf5/build.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+set -e
+set -u
+
+HDF5_VERSION=1.14.5
+HDF5_HASH=ec2e13c52e60f9a01491bb3158cb3778c985697131fc6a342262d32a26e58e44
+SOURCE_DIR=hdf5-${HDF5_VERSION}
+
+if [[ ! -e ${SOURCE_DIR} ]]
+then
+    wget -q https://github.com/HDFGroup/hdf5/releases/download/hdf5_${HDF5_VERSION}/hdf5-${HDF5_VERSION}.tar.gz -O hdf5.tar.gz
+    OBSERVED_HASH=($(shasum -a 256 hdf5.tar.gz))
+    if [[ ${OBSERVED_HASH} != ${HDF5_HASH} ]]
+    then
+        echo "hash mismatch for ${HDF5_VERSION} (got ${OBSERVED_HASH})"
+        exit 1
+    fi
+    tar -xf hdf5.tar.gz
+
+    # Some source-editing shenanigans are required to deal with the lack of
+    # FE_INVALID in Emscripten, see emscripten-core/emscripten#22005. Hey,
+    # I don't make the rules.
+    offender=${SOURCE_DIR}/src/H5Tinit_float.c 
+    cat ${offender} | sed "s/feclearexcept(FE_INVALID)/0/" > tmp
+    mv tmp ${offender}
+fi
+
+BUILD_DIR=build-${HDF5_VERSION}
+if [ ! -e ${BUILD_DIR} ]
+then
+    mkdir -p ../installed
+    coreflags="-pthread" # propagating compile flags from the root scran.js CMakeLists.txt.
+    echo "{}" > package.json # avoid assuming ES6 module syntax from the root scran.js package.json.
+    emcmake cmake \
+        -S ${SOURCE_DIR} \
+        -B ${BUILD_DIR} \
+        -DCMAKE_C_FLAGS="${coreflags}" \
+        -DCMAKE_CXX_FLAGS="${coreflags}" \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=$(pwd)/../installed \
+        -DBUILD_SHARED_LIBS=OFF \
+        -DBUILD_TESTING=OFF \
+        -DHDF5_BUILD_EXAMPLES=OFF \
+        -DHDF5_BUILD_TOOLS=OFF \
+        -DHDF5_BUILD_UTILS=OFF \
+        -DHDF5_BUILD_CPP_LIB=ON \
+        -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
+        -DZLIB_USE_EXTERNAL=OFF \
+        -DHDF5_ENABLE_SZIP_SUPPORT=OFF
+fi
+
+cd ${BUILD_DIR}
+emmake make
+emmake make install

extern/igraph/.gitignore

@@ -0,0 +1,3 @@
+igraph*
+package.json
+build-*

extern/igraph/build.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+set -e
+set -u
+
+IGRAPH_VERSION=0.10.13
+IGRAPH_HASH=c6dc44324f61f52c098bedb81f6a602365d39d692d5068ca4fc3734b2a15e64c
+SOURCE_DIR=igraph-${IGRAPH_VERSION}
+
+if [[ ! -e ${SOURCE_DIR} ]]
+then
+    wget -q https://github.com/igraph/igraph/releases/download/${IGRAPH_VERSION}/igraph-${IGRAPH_VERSION}.tar.gz -O igraph.tar.gz
+    OBSERVED_HASH=($(shasum -a 256 igraph.tar.gz))
+    if [[ ${OBSERVED_HASH} != ${IGRAPH_HASH} ]]
+    then
+        echo "hash mismatch for ${IGRAPH_VERSION} (got ${OBSERVED_HASH})"
+        exit 1
+    fi
+    tar -xf igraph.tar.gz
+fi
+
+BUILD_DIR=build-${IGRAPH_VERSION}
+if [ ! -e ${BUILD_DIR} ]
+then
+    mkdir -p ../installed
+    coreflags="-pthread" # propagating compile flags from the root scran.js CMakeLists.txt.
+    echo "{}" > package.json # avoid assuming ES6 module syntax from the root scran.js package.json.
+    emcmake cmake \
+        -S ${SOURCE_DIR} \
+        -B ${BUILD_DIR} \
+        -DCMAKE_C_FLAGS="${coreflags}" \
+        -DCMAKE_CXX_FLAGS="${coreflags}" \
+        -DIGRAPH_WARNINGS_AS_ERRORS=OFF \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=$(pwd)/../installed
+fi
+
+cd ${BUILD_DIR}
+emmake make
+emmake make install