Merge pull request #323 from glotzerlab/update-packages-trunk

Update packages on trunk

.github/workflows/update-packages.yml

@@ -42,7 +42,7 @@ jobs:
       - name: Bump versions in requirements-mpi.txt
         run: pur -r requirements-mpi.txt
       - name: Bump versions in requirements-source.txt
-        run: pur -r requirements-source.txt --patch Cython
+        run: pur -r requirements-source.txt
       - name: Bump versions in requirements-cupy.txt
         run: pur -r requirements-cupy.txt
       - name: Bump versions in generated scripts

packages.yml

@@ -20,7 +20,7 @@ fresnel:
 hoomd:
   ignore: beta,alpha,rc
   repository: https://github.com/glotzerlab/hoomd-blue
-  version: v4.1.0
+  version: v4.2.0
 osu_microbenchmark:
   repository: null
   version: 5.4.1

requirements-source-summit.txt

@@ -1,4 +1,4 @@
-Cython==0.29.33
+Cython==3.0.2
 numpy==1.22.4
 pkgconfig==1.5.5
 pybind11==2.10.3

requirements-source.txt

@@ -1,5 +1,5 @@
-Cython==0.29.36
-numpy==1.25.2
+Cython==3.0.2
+numpy==1.26.0
 pkgconfig==1.5.5
 pybind11==2.11.1
 pythran==0.14.0

requirements.txt

@@ -1,33 +1,33 @@
 # glotzer tools
-freud-analysis==2.13.0
+freud-analysis==2.13.1
 gsd==3.1.1
 garnett==0.7.1
 pythia-learn==0.3.0
 rowan==1.3.0.post1
-coxeter==0.6.1
+coxeter==0.7.0
 plato-draw==1.12.0
 signac==2.1.0
-signac-flow==0.26.0
+signac-flow==0.26.1
 signac-dashboard==0.6.0
 
 # commonly used packages
 h5py==3.9.0
 jupyter==1.0.0; platform_machine != 'ppc64le'
-jupyterlab==4.0.5; platform_machine != 'ppc64le'
-matplotlib==3.7.3; platform_machine != 'ppc64le'
-notebook==7.0.3; platform_machine != 'ppc64le'
+jupyterlab==4.0.6; platform_machine != 'ppc64le'
+matplotlib==3.8.0; platform_machine != 'ppc64le'
+notebook==7.0.4; platform_machine != 'ppc64le'
 opencv-python==4.8.0.76; platform_machine != 'ppc64le'
-pandas==2.1.0
-Pillow==10.0.0
+pandas==2.1.1
+Pillow==10.0.1
 pyqt5==5.15.9; platform_machine != 'ppc64le'
 pyyaml==6.0.1
-scikit-learn==1.3.0
+scikit-learn==1.3.1
 scikit-image==0.21.0; platform_machine != 'ppc64le'
 statsmodels==0.14.0; platform_machine != 'ppc64le'
 
 
 # test requirements
-hypothesis==6.84.3
+hypothesis==6.86.2
 pytest==7.4.2
 miniball==1.2.0
 sympy==1.12

script/crusher/install.sh

@@ -180,7 +180,7 @@ fi
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.1.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.2.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \

script/frontier/install.sh

@@ -183,7 +183,7 @@ fi
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.1.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.2.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \

script/summit/install.sh

@@ -157,6 +157,7 @@ done <requirements-source-summit.txt
 
 
  export CFLAGS="-mcpu=power9 -mtune=power9" CXXFLAGS="-mcpu=power9 -mtune=power9" \
+    && python3 -m pip install cython==0.29.36
     && python3 -m pip install --no-build-isolation -r requirements-cupy.txt \
     || exit 1
 
@@ -170,7 +171,7 @@ done <requirements-source-summit.txt
 if [ ! -n "$(ls -d $ROOT/lib/python*/site-packages/hoomd)" ]
 then
 
- git clone --recursive --branch v4.1.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
+ git clone --recursive --branch v4.2.0 --depth 1 https://github.com/glotzerlab/hoomd-blue hoomd \
     && cd hoomd \
     && mkdir -p build \
     && cd build \

template/glotzerlab-software.jinja

@@ -12,7 +12,9 @@
 
 # build select packages from source with machine specific flags
 {{ RUN }} export CFLAGS="{{CFLAGS}}" CXXFLAGS="{{CFLAGS}}" \
-    && python3 -m pip install --no-build-isolation --no-binary freud-analysis,gsd -r requirements.txt -r requirements-cupy.txt \
+    && python3 -m pip install --no-build-isolation --no-binary freud-analysis,gsd -r requirements.txt \
+    && python3 -m pip install cython==0.29.36 \
+    && python3 -m pip install --no-build-isolation -r requirements-cupy.txt \
     && python3 -m pip cache purge
 
 {% else %}
@@ -41,6 +43,7 @@ done <requirements-source-summit.txt
 
 {% if system != 'crusher' and system != 'frontier' %}
 {{ RUN }} export CFLAGS="{{CFLAGS}}" CXXFLAGS="{{CFLAGS}}" \
+    && python3 -m pip install cython==0.29.36
     && python3 -m pip install --no-build-isolation -r requirements-cupy.txt \
     || exit 1
 {% endif %}