Update handling of Zlib by configure

.github/workflows/merge-gate.yml

@@ -131,42 +131,47 @@ jobs:
     steps:
     - name: Install prerequisite packages
       run: |
-        sudo apt-get install gfortran
-        sudo apt-get install libbz2-dev
-        sudo apt-get install libblas-dev liblapack-dev
-        sudo apt-get install libfftw3-dev
         sudo apt-get install clang
         sudo apt-get install cmake-data cmake    
     - uses: actions/checkout@v4
-    - name: Set up Python 3.10
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.12'
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install conda packages
       run: |
         which conda
-        conda install conda=24.11.0 python=3.10
+        conda install conda python=3.12
         conda --version
         conda env update --file devtools/ci/environment.yml --name base
     - name: Install cpptraj
       run: |
         export PATH=$HOME/bin:${PATH}
         export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}
+        export PATH=$CONDA/bin:${PATH}
+        export LD_LIBRARY_PATH=$CONDA/lib:${LD_LIBRARY_PATH}
+        echo $PATH
+        echo $LD_LIBRARY_PATH
+        ls $CONDA/lib
         export MAKE_COMMAND="make -j2"
-        ./configure --buildlibs -openmp -shared gnu
+        ./configure --buildlibs -openmp -shared --with-zlib=$CONDA --with-bzlib=$CONDA --with-hdf5=$CONDA --with-netcdf=$CONDA --with-fftw3=$CONDA gnu
         source cpptraj.sh
         make -j2 libcpptraj
     - name: Install pytraj
       run: |        
         git clone https://github.com/Amber-MD/pytraj.git
+        export PATH=$CONDA/bin:${PATH}
+        export LD_LIBRARY_PATH=$CONDA/lib:${LD_LIBRARY_PATH}
         source cpptraj.sh
         cd pytraj
         python setup.py install
         cd ..
     - name: Test with pytest
       run: |
+        export PATH=$CONDA/bin:${PATH}
+        export LD_LIBRARY_PATH=$CONDA/lib:${LD_LIBRARY_PATH}
         source cpptraj.sh && cd pytraj/tests && pytest -vs --ignore=test_parallel_pmap

configure

@@ -146,8 +146,8 @@ BZIP2_SRCDIR=''
 BZIP2_URL="https://www.sourceware.org/pub/bzip2/$BZIP2_SRCTAR"
 BZIP2_OPTS=''
 
-ZLIB_SRCTAR='zlib-1.2.11.tar.gz'
-ZLIB_SRCDIR='zlib-1.2.11'
+ZLIB_SRCTAR='zlib-1.3.1.tar.gz'
+ZLIB_SRCDIR='zlib-1.3.1'
 ZLIB_URL="https://zlib.net/$ZLIB_SRCTAR"
 ZLIB_OPTS=''
 
@@ -719,9 +719,15 @@ EOF
       TestProgram $BUILDTESTOPT "  Checking for bundled HDF5" "$CXX" "$CXXFLAGS ${LIB_INCL[$LHDF5]}" testp.cpp "${LIB_FLAG[$LHDF5]}"
       if [ $? -ne 0 ] ; then
         CheckRebuild "HDF5" "${LIB_FLAG[$LHDF5]}"
+	# If zlib was specified, pass that to hdf5
+        if [ "${LIB_STAT[$LZIP]}" = 'specified' ] ; then
+          hdf5zlib="--with-zlib=${LIB_HOME[$LZIP]}"
+	else
+          hdf5zlib=''
+	fi
         # See if user would like to get HDF5 
         PREFIX=$CPPTRAJHOME CC=$CC CFLAGS=$CFLAGS LIBNAME='hdf5' \
-            SRCDIR=$HDF5_SRCDIR SRCTAR=$HDF5_SRCTAR URL=$HDF5_URL ./get_library.sh $REBUILDOPT $HDF5_OPTS
+            SRCDIR=$HDF5_SRCDIR SRCTAR=$HDF5_SRCTAR URL=$HDF5_URL ./get_library.sh $REBUILDOPT $HDF5_OPTS $hdf5zlib
         if [ $? -ne 0 ] ; then
           ErrMsg "No HDF5 available. To build without HDF5 specify '-nohdf5'."
           exit 1

devtools/ci/environment.yml

@@ -1,11 +1,16 @@
 channels:
     - conda-forge
 dependencies:
-    - python=3.10
+    - python=3.12
     - pyflakes
     - numpy=2.0.0
     - cython=0.29.36
     - setuptools
     - pytest
     - mock
     - curl
+    - gcc_linux-64
+    - gxx_linux-64
+    - gfortran_linux-64
+    - netcdf4
+    - fftw

get_library.sh

@@ -196,7 +196,7 @@ if [ -z "$MAKE_COMMAND" ] ; then
   elif [ $NPROC -le 2 ] ; then
     MAKE_COMMAND='make'
   else
-    HALF=`echo "$NPROC / 2" | bc`
+    ((HALF = $NPROC / 2))
     MAKE_COMMAND="make -j$HALF"
   fi
   echo "    MAKE_COMMAND is not set; set to '$MAKE_COMMAND'"