Installation updates

BayesWaveUtils/bayeswave_pipe/bayeswave_pipe_utils.py

@@ -945,13 +945,20 @@ def condor_job_config(job_type, condor_job, config_parser):
 
     """
     valid_job_types=['bayeswave','bayeswave_post','bayeswave_fpeak','bayeswave_clean_frame','megaplot']
+    # When using default env, need to add capitalization etc in
+    executableNames = {'bayeswave':'BayesWave','bayeswave_post':'BayesWavePost','bayeswave_fpeak':'BayesWaveFpeak','bayeswave_clean_frame':'BayesWaveCleanFrame','megaplot':'megaplot.py'}
     try:
         job_index = valid_job_types.index(job_type)
     except ValueError:
         print("unrecognized job type", file=sys.stderr)
 
     # --- Set executable and choose singularity image
-    executable=config_parser.get('engine',job_type)
+    try:
+        executable=config_parser.get('engine',job_type)
+    except:
+        condaenv=sys.prefix+'/bin/'
+        executable=condaenv+executableNames[job_type]
+    print("Using executable...", executable)
     universe=config_parser.get('condor','universe')
     pipeline.CondorDAGJob.__init__(condor_job,universe,executable)
     pipeline.AnalysisJob.__init__(condor_job,config_parser)

CMakeLists.txt

 #
 # CMake packaging for BayesWave
-# Copyright 2019  James Alexander Clark <james.clark@ligo.org>
+# Copyright 2019  James Alexander Clark <james.clark@ligo.org>, Meg Millhouse <meg.millhouse@ligo.org>
 # Based on CMake packaging for libframe & Frv by Duncan MacLeod <duncan.macleod@ligo.org>
 #
 
@@ -21,6 +21,32 @@ find_package(PkgConfig)
 find_package(Git)
 find_package(OpenMP)
 
+#-----------------------------------------------------------------------
+# Set rpath so you don't have to set $LD_LIBRARY_PATH before running
+# instructions from:
+#   https://gitlab.kitware.com/cmake/community/-/wikis/doc/cmake/RPATH-handling
+
+IF(DEFINED ENV{CONDA_PREFIX})
+    MESSAGE(STATUS "CONDA_PREFIX: --[$ENV{CONDA_PREFIX}]--")
+ELSE()
+    MESSAGE(STATUS "Warning: could not find conda environment")
+ENDIF()
+
+
+# use, i.e. don't skip the full RPATH for the build tree
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+# In order to be able to install into a user specified directory, need to make sure the RPATH has the install directory first, and then the conda prefix.
+# So make sure to remove environment rpath, and then explicitly add conda library back in.
+# May be a more elegant way to do this
+set(CMAKE_INSTALL_REMOVE_ENVIRONMENT_RPATH TRUE)
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}:$ENV{CONDA_PREFIX}/lib") # 
+
+
 # -- build components -------
 
 # C library | enable/disable with -DENABLE_C={yes,no} (default yes)

build.sh

 #!/bin/bash
 set -e
 
-INSTALL_PREFIX=$1
+INSTALL_PREFIX=${1:-${CONDA_PREFIX}}
+
+echo ${INSTALL_PREFIX}
 
 # Get cmake
 if hash cmake 2>/dev/null; then

install.sh

@@ -17,16 +17,26 @@
 
 set -e
 
+# Allow user to specify install location, otherwise default to conda environment
 
-install_dir=${1}
+# check if user-defined installation location is set
+if [ -z $1 ] # if empty
+then
+    install_dir=${CONDA_PREFIX}
+    dir_flag=1
+else
+    install_dir=$1
+fi
 
 # Remove trailing slash if present
 install_dir=$(echo ${install_dir} | sed 's|/$||' )
 
-while [ $install_dir = "" ]
-do
-    read -p 'Specify install path: ' install_dir
-done
+# while [ $install_dir = "" ]
+# do
+#     read -p 'Specify install path: ' install_dir
+# done
+# echo "Installing to ${install_dir}"
+
 echo "Installing to ${install_dir}"
 
 #
@@ -53,11 +63,20 @@ popd
 mkdir -p ${install_dir}/etc
 sed "s|INSTALL_DIR|${install_dir}|g" etc/bayeswave-user-env.sh > ${install_dir}/etc/bayeswave-user-env.sh
 
-
-echo ""
-echo "*****************************************************************************"
-echo "  DONE: BayesWave built and installed to: "
-echo "      ${install_dir}"
-echo "  To use: "
-echo "      source ${install_dir}/etc/bayeswave-user-env.sh"
-echo "*****************************************************************************"
+# Tell user where BW was installed
+if [ -z $dir_flag ]
+then
+    echo ""
+    echo "*****************************************************************************"
+    echo "  DONE: BayesWave built and installed to: "
+    echo "      ${install_dir}"
+    echo "  To use: "
+    echo "      source ${install_dir}/etc/bayeswave-user-env.sh"
+    echo "*****************************************************************************"
+else
+    echo ""
+    echo "*****************************************************************************"
+    echo "  DONE: BayesWave built and installed into conda environment: "
+    echo "      ${CONDA_DEFAULT_ENV}"
+    echo "*****************************************************************************"
+fi
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