Merge pull request #372 from glotzerlab/update-packages-trunk

Update packages on trunk

packages.yml

@@ -12,15 +12,15 @@ embree:
   ignore: alpha,rc,beta,ploc
   include_v_prefix: false
   repository: https://github.com/embree/embree
-  version: 4.3.0
+  version: 4.3.1
 fresnel:
   ignore: alpha,rc,beta
   repository: https://github.com/glotzerlab/fresnel
   version: v0.13.5
 hoomd:
   ignore: beta,alpha,rc
   repository: https://github.com/glotzerlab/hoomd-blue
-  version: v4.4.1
+  version: v4.5.0
 osu_microbenchmark:
   repository: null
   version: 5.4.1

requirements-source.txt

@@ -1,5 +1,5 @@
 Cython==3.0.8
-numpy==1.26.3
+numpy==1.26.4
 pkgconfig==1.5.5
 pybind11==2.11.1
 pythran==0.15.0

requirements.txt

@@ -19,9 +19,9 @@ pyarrow==15.0.0
 # commonly used packages
 h5py==3.10.0
 jupyter==1.0.0
-jupyterlab==4.1.0
+jupyterlab==4.1.1
 matplotlib==3.8.2
-notebook==7.0.7
+notebook==7.1.0
 opencv-python==4.9.0.80
 pandas==2.2.0
 Pillow==10.2.0
@@ -33,13 +33,13 @@ statsmodels==0.14.1
 
 
 # test requirements
-hypothesis==6.98.1
+hypothesis==6.98.4
 pytest==8.0.0
 miniball==1.2.0
 sympy==1.12
 tables==3.9.2
 coverage==7.4.1
 click==8.1.7
 pytest-cov==4.1.0
-ruamel.yaml==0.18.5
+ruamel.yaml==0.18.6
 gitpython==3.1.41

script/crusher/install.sh

@@ -89,8 +89,8 @@ fi
 # Embree
 if [ ! -f $ROOT/lib64/libembree4.so ]
 then
-curl -sSL https://github.com/embree/embree/archive/v4.3.0/embree-4.3.0.tar.gz | tar -xzC $BUILDDIR \
-    && cd $BUILDDIR/embree-4.3.0 \
+curl -sSL https://github.com/embree/embree/archive/v4.3.1/embree-4.3.1.tar.gz | tar -xzC $BUILDDIR \
+    && cd $BUILDDIR/embree-4.3.1 \
     && mkdir build && cd build \
     && cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOT -DCMAKE_INSTALL_LIBDIR=lib64/ -DCMAKE_BUILD_TYPE=Release -DEMBREE_TUTORIALS=OFF -DEMBREE_MAX_ISA="AVX2" -DEMBREE_ISPC_SUPPORT=OFF \
     && make install -j 32 \
@@ -159,7 +159,7 @@ then
     && mkdir -p build \
     && cd build \
     && export CFLAGS="-march=native" CXXFLAGS="-march=native" \
-    && cmake ../ -DENABLE_EMBREE=on -DENABLE_OPTIX=off -Dembree_DIR=/opt/embree-4.3.0.x86_64.linux -DCMAKE_INSTALL_PREFIX=`python3 -c "import site; print(site.getsitepackages()[0])"` \
+    && cmake ../ -DENABLE_EMBREE=on -DENABLE_OPTIX=off -Dembree_DIR=/opt/embree-4.3.1.x86_64.linux -DCMAKE_INSTALL_PREFIX=`python3 -c "import site; print(site.getsitepackages()[0])"` \
     && make install -j32 \
     && cd ../../ \
     && rm -rf fresnel \
@@ -173,7 +173,7 @@ fi
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.4.1 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.5.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \

script/frontier/install.sh

@@ -117,8 +117,8 @@ fi
 # Embree
 if [ ! -f $ROOT/lib64/libembree4.so ]
 then
-curl -sSL https://github.com/embree/embree/archive/v4.3.0/embree-4.3.0.tar.gz | tar -xzC $BUILDDIR \
-    && cd $BUILDDIR/embree-4.3.0 \
+curl -sSL https://github.com/embree/embree/archive/v4.3.1/embree-4.3.1.tar.gz | tar -xzC $BUILDDIR \
+    && cd $BUILDDIR/embree-4.3.1 \
     && mkdir build && cd build \
     && cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOT -DCMAKE_INSTALL_LIBDIR=lib64/ -DCMAKE_BUILD_TYPE=Release -DEMBREE_TUTORIALS=OFF -DEMBREE_MAX_ISA="AVX2" -DEMBREE_ISPC_SUPPORT=OFF \
     && make install -j 32 \
@@ -187,7 +187,7 @@ then
     && mkdir -p build \
     && cd build \
     && export CFLAGS="-march=native" CXXFLAGS="-march=native" \
-    && cmake ../ -DENABLE_EMBREE=on -DENABLE_OPTIX=off -Dembree_DIR=/opt/embree-4.3.0.x86_64.linux -DCMAKE_INSTALL_PREFIX=`python3 -c "import site; print(site.getsitepackages()[0])"` \
+    && cmake ../ -DENABLE_EMBREE=on -DENABLE_OPTIX=off -Dembree_DIR=/opt/embree-4.3.1.x86_64.linux -DCMAKE_INSTALL_PREFIX=`python3 -c "import site; print(site.getsitepackages()[0])"` \
     && make install -j32 \
     && cd ../../ \
     && rm -rf fresnel \
@@ -201,7 +201,7 @@ fi
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.4.1 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.5.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \