new release 2024.09.1 (#1831)

* adding jax to requirements-tests * Update way of installing cutax * Update requirements.txt * Update requirements.txt * downgrade astropy * adding jax to requirements-tests (#1789) * adding jax to requirements-tests * Update requirements.txt * Update requirements-tests.txt * downgrade nestpy * Monthly update Aug2024 (#1792) * downgrade jax * downgrade sphinx * Downgrade numpy * typo * downgrade dask * Install cutax with pip (#1793) * Update requirements-tests.txt (#1794) Bump xedocs to latest version. * Bump alea to v0.2.7 (#1795) * adding CONDA_OVERRIDE_GLIBC (#1796) There is a problem in loading cutax - https://xenonnt.slack.com/archives/C016DM0JPK9/p1721004131648269 solution source -https://blog.matteoferla.com/2022/11/glibc-236-vs-centos-7-tale-of-failure.html * Bump alea to 0.2.8 (#1797) * bump inference_interface to v0.0.3 (#1798) * cutax_bump (#1829) * Monthly update (#1828) * Monthly update * Update requirements.txt * Update requirements-tests.txt * Update requirements-tests.txt * Update requirements-tests.txt * debugging * Update requirements-tests.txt * Update requirements-tests.txt * Update requirements-tests.txt * downgrade dask * Update requirements.txt * Update requirements.txt * Minor fix of indent * Update cutax version (#1830) Manually updating cutax version to latest tag --------- Co-authored-by: Dacheng Xu <dx2227@columbia.edu> Co-authored-by: Ananthakrishnan RAVINDRAN <132569562+Ananthu-Ravindran@users.noreply.github.com> Co-authored-by: Robert Hammann <53221264+hammannr@users.noreply.github.com> Co-authored-by: Diego Ramírez García <diego.ramirez@physik.uzh.ch> Co-authored-by: Giovanni Volta <38431109+GiovanniVolta@users.noreply.github.com>
XENONnT · Sep 18, 2024 · e72e5d1 · e72e5d1
1 parent ad52649
commit e72e5d1
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Showing 6 changed files with 58 additions and 56 deletions.
diff --git a/.github/scripts/do_tests.sh b/.github/scripts/do_tests.sh
@@ -59,7 +59,7 @@ case "$1" in
     then
       git checkout $CUTAX_VERSION
     fi
-    python setup.py install --user
+    pip install -e ./ --user
     cd ..
     pytest cutax || { echo 'cutax tests failed' ; exit 1; }
   ;;

diff --git a/.github/scripts/update_context_wrapper.sh b/.github/scripts/update_context_wrapper.sh
@@ -12,6 +12,6 @@ CUTAX_VERSION=${CUTAX_VERSION//cutax_version=}
 if [ $CUTAX_VERSION = 'latest' ]; then echo "Dont upload for latest version" && exit 0; fi
 cd cutax
 git checkout $CUTAX_VERSION
-python setup.py install --user
+pip install ./ --user
 cd $HOME
 python .github/scripts/update-context-collection.py ${GITHUB_REF_NAME} ${GITHUB_REF_TYPE}
diff --git a/Dockerfile b/Dockerfile
@@ -7,6 +7,7 @@ LABEL opensciencegrid.category="Project"
 LABEL opensciencegrid.definition_url="https://github.com/XENONnT/base_environment"
 
 ARG XENONnT_TAG
+ENV CONDA_OVERRIDE_GLIBC=2.36
 
 RUN echo "Building Docker container for XENONnT_${XENONnT_TAG} ..."
 

diff --git a/create-env b/create-env
@@ -8,7 +8,7 @@ gfal2_bindings_version=1.12.2
 gfal2_util_version=1.8.1
 rucio_version=32.8.0
 ## REMEMBER THE 'v' IN CUTAX_VERSION!! (unless it is 'latest')
-cutax_version=v1.18.4
+cutax_version=v1.19.1
 #######################################################################
 
 set -e
@@ -97,9 +97,10 @@ wget -nv https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_
 tar xjf boost_1_74_0.tar.bz2
 rm -f boost_1_74_0.tar.bz2
 cd boost_1_74_0
-./bootstrap.sh --prefix=${target_dir}/anaconda/envs/${env_name} --show-libraries \
-               --with-libraries=atomic,chrono,date_time,exception,filesystem,graph,iostreams,locale,log,math,program_options,random,regex,serialization,system,test,thread,timer,wave,python \
-               --with-python=${target_dir}/anaconda/envs/${env_name}/bin/python3
+./bootstrap.sh \
+    --prefix=${target_dir}/anaconda/envs/${env_name} --show-libraries \
+    --with-libraries=atomic,chrono,date_time,exception,filesystem,graph,iostreams,locale,log,math,program_options,random,regex,serialization,system,test,thread,timer,wave,python \
+    --with-python=${target_dir}/anaconda/envs/${env_name}/bin/python3
 ./b2 install --prefix=${target_dir}/anaconda/envs/${env_name}
 cd ${target_dir}
 rm -rf boost_*
@@ -241,9 +242,9 @@ done
 config_path_midway2=/project2/lgrandi/xenonnt/xenon.config
 config_path_midway3=/project/lgrandi/xenonnt/xenon.config
 if [ -e \$config_path_midway2 ]; then
-   export XENON_CONFIG=\$config_path_midway2
+    export XENON_CONFIG=\$config_path_midway2
 elif [ -e \$config_path_midway3 ]; then
-   export XENON_CONFIG=\$config_path_midway3
+    export XENON_CONFIG=\$config_path_midway3
 fi
 
 # grab a local cutax installation if we have one
@@ -253,28 +254,28 @@ MIDWAY3_CUTAX_DIR=/project/lgrandi/xenonnt/software/cutax/${cutax_version}
 OSG_CUTAX_DIR=/ospool/uc-shared/project/xenon/xenonnt/software/cutax/${cutax_version}
 
 if [ "x\${CUTAX_LOCATION}" = "x" ]; then
-  for dir in \${DALI_CUTAX_DIR} \${MIDWAY2_CUTAX_DIR} \${MIDWAY3_CUTAX_DIR} \${OSG_CUTAX_DIR}; do
-    if [ -e \$dir ]; then
-       CUTAX_LOCATION=\$dir
-    fi
-  done
+    for dir in \${DALI_CUTAX_DIR} \${MIDWAY2_CUTAX_DIR} \${MIDWAY3_CUTAX_DIR} \${OSG_CUTAX_DIR}; do
+        if [ -e \$dir ]; then
+            CUTAX_LOCATION=\$dir
+        fi
+    done
 fi
 
 if [ "x\$INSTALL_CUTAX" = "x" ]; then
     export INSTALL_CUTAX=1
 fi
 
 if [ \$INSTALL_CUTAX -eq 1 ]; then
-  if [ -e "\${CUTAX_LOCATION}" ]; then
-    export CUTAX_LOCATION
-    export PYTHONPATH=\${CUTAX_LOCATION}:\$PYTHONPATH
-  fi
+    if [ -e "\${CUTAX_LOCATION}" ]; then
+        export CUTAX_LOCATION
+        export PYTHONPATH=\${CUTAX_LOCATION}:\$PYTHONPATH
+    fi
 fi
 
 # set env variable for matplotlib styles on Midway
 MPL_DIR='/dali/lgrandi/xenonnt/software/nton/mplconfigs/'
 if [ -e \$MPL_DIR ]; then
-   export MPLCONFIGDIR=\$MPL_DIR
+    export MPLCONFIGDIR=\$MPL_DIR
 fi
 
 EOF

diff --git a/extra_requirements/requirements-tests.txt b/extra_requirements/requirements-tests.txt
@@ -1,29 +1,30 @@
-awkward==2.6.6
+awkward==2.6.7
 blosc==1.11.2                                      # strax dependency
 bokeh==3.2.2                                       # panel 1.2.3 depends on bokeh<3.3.0 and >=3.1.1
 boltons==24.0.0
 commentjson==0.9.0                                 # straxen dependency
-coverage==7.5.4                                    
+coverage==7.6.1                                    
 coveralls==4.0.1
-dask==2024.6.2
-dask-jobqueue==0.8.5
-datashader==0.16.2
-deepdiff==7.0.1
+dask==2024.6.2                                     # 2024.7.0 depends on pandas>=2.0
+dask-jobqueue==0.8.5                               # 0.9.0 Requires-Python >=3.10
+datashader==0.16.3
+deepdiff==8.0.1
 dill==0.3.8                                        # strax dependency
 docutils==0.18.1                                   # don't update, straxen dependency
-flake8==7.1.0
+flake8==7.1.1
 GitPython==3.1.43                                  # Pegasus dependency
 graphviz==0.20.3
 holoviews==1.18.3                                  # Don't update, conflicts with xeauth 
-hypothesis==6.104.2
+hypothesis==6.111.2
 immutabledict== 4.2.0
-ipywidgets==8.1.3                                  # For online monitoring
+ipywidgets==8.1.5                                  # For online monitoring
+jax==0.4.30
 Jinja2==3.1.4
 jupyter-client==8.6.2
 keras==2.15.0                                      # tensorflow 2.15.0 depends on keras2.16 and=2.15.0
 lz4==4.3.3                                         # strax dependency
 m2r==0.2.1                                         # don't update, straxen dependency
-matplotlib==3.9.0
+matplotlib==3.9.2
 memory-profiler==0.61.0
 mistune==0.8.4                                     # nbconvert 6.5.4 requires mistune<2
 mongomock==4.1.2
@@ -38,18 +39,18 @@ panel==1.2.3                                       # upgrading it causes conflic
 pdmongo==0.3.4                                     # strax dependency
 psutil==5.9.8                                      # strax dependency
 pymongo==3.13.0                                    # don't upgrade it
-pytest==8.2.2
+pytest==8.3.2
 pytest-cov==5.0.0
 pytest-xdist==3.6.1
 rframe==0.2.21
 scikit-learn==1.2.2
 scipy==1.13.1                                     # 1.14.0 Requires-Python >=3.10
 tensorflow==2.15.0.post1
 typing-extensions==4.12.2                          # Tensorflow and bokeh dependency
-tqdm==4.66.4
-uproot==5.3.9
+tqdm==4.66.5
+uproot==5.3.12
 utilix==0.8.5                                      # dependency for straxen, admix
 xarray==2024.3.0                                   # xarray 2024.6.0 depends on pandas>=2.0
-xedocs==0.2.29
+xedocs==0.2.30
 zarr==2.18.2
 zstd==1.5.5.1                                      # strax dependency
diff --git a/requirements.txt b/requirements.txt
@@ -1,63 +1,62 @@
-alea-inference==0.2.6
+alea-inference==0.2.8
 appletree[cpu]==0.5.1
 astropy==6.0.1                                     # 6.1.x Requires-Python >=3.10
 atomicwrites==1.4.1
 axidence==0.3.2
-black==24.4.2
+black==24.8.0
 blueice==1.2.0
 codenamize==1.2.3                                  # for human-readable hashing
 comm==0.2.2
 corner==2.2.2
-cython==3.0.10
+cython==3.0.11
 emcee==3.1.6
 flamedisx==2.1.0
 future==1.0.0
 GOFevaluation==0.1.4
 h5py==3.11.0
-iminuit==2.26.0
-inference-interface==0.0.2
+iminuit==2.29.1
+inference-interface==0.0.3
 ipykernel==6.29.5                                  # For ipywidgets
 ipympl==0.9.4                                      # For online monitoring
 ipython==8.18.1                                    # >=8.19.0 Requires-Python >=3.10
 --find-links https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
-jax==0.4.30
 jedi==0.19.1                                       
-jupyter==1.0.0
+jupyter==1.1.1
 jupyterlab==4.0.12                                 # <4.1.0 for compatibility with xeauth 0.2.3
-jupyterlab-widgets==3.0.11
-jupyter-resource-usage==1.0.2                      # Memory viewer for notebooks
-lightgbm==4.4.0
+jupyterlab-widgets==3.0.13
+jupyter-resource-usage==1.1.0                      # Memory viewer for notebooks
+lightgbm==4.5.0
 line-profiler==4.1.3
 mergedeep==1.3.4
 ml-dtypes==0.2.0                                   # tensorflow 2.15.0.post1 requires ml-dtypes~=0.2.0
-nbsphinx==0.9.4
-nestpy==2.0.2
+nbsphinx==0.9.5
+nestpy==2.0.3
 notebook==7.0.8                                    # <7.1.0 for compatibility with jupyterlab 4.0.12
-numpy==1.26.4
-numpyro==0.15.0
-pandoc==2.3
+numpy==1.26.4                                      # tensorflow isn't compatible with 2.x.x
+numpyro==0.15.2
+pandoc==2.4
 parso==0.8.4                                       # upgrading to 0.8.0 breaks autocomplete in ipython
 pika==1.3.2                                        # Pegasus
-prettytable==3.10.0
-pre-commit==3.7.1
+prettytable==3.11.0
+pre-commit==3.8.0
 poetry==1.8.3
-pyarrow==15.0.2                                    # Necessary for pandas feather i/o
+pyarrow==17.0.0                                    # Necessary for pandas feather i/o
 pydantic==1.10.14                                    # rframe needs pydantic<2.0.0
 pytest-runner==6.0.1
 reprox==0.2.2
 requests==2.31.0                                   # rucio-clients 32.8.0 requires requests<=2.31.0
 seaborn==0.13.2
 simple-slurm==0.2.7
-#sharedarray==3.2.3
-sharedarray @ https://xenon.isi.edu/python/SharedArray-3.2.3.tar.gz   # workaround for numpy 2.0.0 build problem
+sharedarray==3.2.4
+#sharedarray @ https://xenon.isi.edu/python/SharedArray-3.2.3.tar.gz   # workaround for numpy 2.0.0 build problem
 snakeviz==2.2.0
-sphinx==7.3.7
+sphinx==7.3.7                                      # higher versions require python 3.10
 statsmodels==0.14.2
 strax==1.6.5
 straxen==2.2.4
-tables==3.9.2                                      # pytables, necessary for pandas hdf5 i/o
+tables==3.9.2                                      #higher versions require python 3.10; pytables, necessary for pandas hdf5 i/o
 tensorflow-probability==0.24.0
 timeout_decorator==0.5.0                           # needed by fuse
-uncertainties==3.2.1
+uncertainties==3.2.2
 xe-admix==1.0.15
-xgboost==2.1.0
+xgboost==2.1.1