diff --git a/packages.yml b/packages.yml
index 645e93fb..772a89b1 100644
--- a/packages.yml
+++ b/packages.yml
@@ -12,7 +12,7 @@ embree:
   ignore: alpha,rc,beta,ploc
   include_v_prefix: false
   repository: https://github.com/embree/embree
-  version: 4.1.0
+  version: 4.2.0
 fresnel:
   ignore: alpha,rc,beta
   repository: https://github.com/glotzerlab/fresnel
@@ -20,7 +20,7 @@ fresnel:
 hoomd:
   ignore: beta,alpha,rc
   repository: https://github.com/glotzerlab/hoomd-blue
-  version: v4.0.1
+  version: v4.1.0
 osu_microbenchmark:
   repository: null
   version: 5.4.1
diff --git a/requirements.txt b/requirements.txt
index 0cfbc5af..8f418437 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 # glotzer tools
 freud-analysis==2.13.0
-gsd==3.1.0
+gsd==3.1.1
 garnett==0.7.1
 pythia-learn==0.3.0
 rowan==1.3.0.post1
@@ -13,9 +13,9 @@ signac-dashboard==0.5.0
 # commonly used packages
 h5py==3.9.0
 jupyter==1.0.0; platform_machine != 'ppc64le'
-jupyterlab==4.0.3; platform_machine != 'ppc64le'
+jupyterlab==4.0.4; platform_machine != 'ppc64le'
 matplotlib==3.7.2; platform_machine != 'ppc64le'
-notebook==7.0.1; platform_machine != 'ppc64le'
+notebook==7.0.2; platform_machine != 'ppc64le'
 opencv-python==4.8.0.74; platform_machine != 'ppc64le'
 pandas==2.0.3
 Pillow==10.0.0
@@ -27,7 +27,7 @@ statsmodels==0.14.0; platform_machine != 'ppc64le'
 
 
 # test requirements
-hypothesis==6.82.0
+hypothesis==6.82.2
 pytest==7.4.0
 miniball==1.2.0
 sympy==1.12
diff --git a/script/crusher/install.sh b/script/crusher/install.sh
index 3ef255ac..bbc2e084 100755
--- a/script/crusher/install.sh
+++ b/script/crusher/install.sh
@@ -87,8 +87,8 @@ fi
 # Embree
 if [ ! -f $ROOT/lib64/libembree4.so ]
 then
-curl -sSL https://github.com/embree/embree/archive/v4.1.0/embree-4.1.0.tar.gz | tar -xzC $BUILDDIR \
-    && cd $BUILDDIR/embree-4.1.0 \
+curl -sSL https://github.com/embree/embree/archive/v4.2.0/embree-4.2.0.tar.gz | tar -xzC $BUILDDIR \
+    && cd $BUILDDIR/embree-4.2.0 \
     && mkdir build && cd build \
     && cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOT -DCMAKE_INSTALL_LIBDIR=lib64/ -DCMAKE_BUILD_TYPE=Release -DEMBREE_TUTORIALS=OFF -DEMBREE_MAX_ISA="AVX2" -DEMBREE_ISPC_SUPPORT=OFF \
     && make install -j 32 \
@@ -160,7 +160,7 @@ then
     && mkdir -p build \
     && cd build \
     && export CFLAGS="-march=native" CXXFLAGS="-march=native" \
-    && cmake ../ -DENABLE_EMBREE=on -DENABLE_OPTIX=off -Dembree_DIR=/opt/embree-4.1.0.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-4.2.0.x86_64.linux -DCMAKE_INSTALL_PREFIX=`python3 -c "import site; print(site.getsitepackages()[0])"` \
     && make install -j32 \
     && cd ../../ \
     && rm -rf fresnel \
@@ -177,7 +177,7 @@ fi
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.0.1 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.1.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \
diff --git a/script/frontier/install.sh b/script/frontier/install.sh
index b6657a2c..b08ec069 100755
--- a/script/frontier/install.sh
+++ b/script/frontier/install.sh
@@ -88,8 +88,8 @@ fi
 # Embree
 if [ ! -f $ROOT/lib64/libembree4.so ]
 then
-curl -sSL https://github.com/embree/embree/archive/v4.1.0/embree-4.1.0.tar.gz | tar -xzC $BUILDDIR \
-    && cd $BUILDDIR/embree-4.1.0 \
+curl -sSL https://github.com/embree/embree/archive/v4.2.0/embree-4.2.0.tar.gz | tar -xzC $BUILDDIR \
+    && cd $BUILDDIR/embree-4.2.0 \
     && mkdir build && cd build \
     && cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOT -DCMAKE_INSTALL_LIBDIR=lib64/ -DCMAKE_BUILD_TYPE=Release -DEMBREE_TUTORIALS=OFF -DEMBREE_MAX_ISA="AVX2" -DEMBREE_ISPC_SUPPORT=OFF \
     && make install -j 32 \
@@ -161,7 +161,7 @@ then
     && mkdir -p build \
     && cd build \
     && export CFLAGS="-march=native" CXXFLAGS="-march=native" \
-    && cmake ../ -DENABLE_EMBREE=on -DENABLE_OPTIX=off -Dembree_DIR=/opt/embree-4.1.0.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-4.2.0.x86_64.linux -DCMAKE_INSTALL_PREFIX=`python3 -c "import site; print(site.getsitepackages()[0])"` \
     && make install -j32 \
     && cd ../../ \
     && rm -rf fresnel \
@@ -178,7 +178,7 @@ fi
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.0.1 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.1.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \
diff --git a/script/summit/install.sh b/script/summit/install.sh
index a06abec9..1adb652e 100755
--- a/script/summit/install.sh
+++ b/script/summit/install.sh
@@ -161,7 +161,7 @@ fi
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.0.1 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.1.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \