Rely on path/to/python -m for IPython, ipyparallel & nbconvert

README.rst

@@ -50,14 +50,6 @@ Clone from git::
     git clone https://git.xfel.eu/gitlab/detectors/pycalibration.git
     cd pycalibration
 
-Edit path to the python environment in the bin/activate.sh file. Change::
-
-    export PATH=/home/${USER}/.local/bin:$PATH
-
-to::
-
-    export PATH=/path/to/new/virtual/environment/bin:$PATH
-
 Install the package::
 
     pip install -r requirements.txt

bin/activate.sh

-source /etc/profile.d/modules.sh
-module load anaconda/3
-module load texlive/2019
-# export path to python environment
-export PATH=$HOME/.local/bin:$PATH

bin/slurm_calibrate.sh

@@ -3,24 +3,18 @@
 # set paths to use
 nb_path=$1
 python_path=$2
-ipython_path=$3
-jupyter_path=$4
-ipcluster_path="${5}"
-activate_path=$6
-uuid=$7
-notebook=$8
-detector=$9
-caltype=${10}
-final=${11}
-finalize=${12}
-cluster_cores=${13}
+activate_path=$3
+uuid=$4
+notebook=$5
+detector=$6
+caltype=${7}
+final=${8}
+finalize=${9}
+cluster_cores=${10}
 
 echo "Running with the following parameters:"
 echo "Notebook path: $nb_path"
 echo "Python path: $python_path"
-echo "IPython path: $ipython_path"
-echo "Jupyter path: $jupyter_path"
-echo "IP-Cluster path: $ipcluster_path"
 echo "Environment activate: $activate_path"
 echo "IP-Cluster profile: $uuid"
 echo "notebook: $notebook"
@@ -45,20 +39,20 @@ export MPLBACKEND=AGG
 # start an ip cluster if requested
 if [ "${uuid}" != "NO_CLUSTER" ]
 then
-    ${ipython_path} profile create ${uuid} --parallel
-    ${ipcluster_path} start --n=${cluster_cores} --profile=${uuid} --daemon &
+    ${python_path} -m IPython profile create ${uuid} --parallel
+    ${python_path} -m ipyparallel.cluster start --n=${cluster_cores} --profile=${uuid} --daemon &
     sleep 15
 fi
 
 
 echo "Running script"
-${jupyter_path} nbconvert --to rst --ExecutePreprocessor.timeout=36000 --ExecutePreprocessor.allow_errors=True --TemplateExporter.exclude_input=True --execute ${nb_path}
+${python_path} -m nbconvert --to rst --ExecutePreprocessor.timeout=36000 --ExecutePreprocessor.allow_errors=True --TemplateExporter.exclude_input=True --execute ${nb_path}
 
 # stop the cluster if requested
 if [ "${uuid}" != "NO_CLUSTER" ]
 then
-    ${ipcluster_path} stop --profile=${uuid}
-    profile_path=`${ipython_path} locate profile ${uuid}`
+    ${python_path} -m ipyparallel.cluster stop --profile=${uuid}
+    profile_path=$(${python_path} -m IPython locate profile ${uuid})
     echo "Removing cluster profile from: $profile_path"
     rm -rf $profile_path
 fi

xfel_calibrate/calibrate.py

@@ -653,9 +653,6 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
     srun_base += [os.path.join(PKG_DIR, "bin", "slurm_calibrate.sh"),  # path to helper sh
                   os.path.abspath(nbpath),  # path to notebook
                   python_path,  # path to python
-                  ipython_path,  # path to ipython
-                  jupyter_path,  # path to jupyter
-                  ipcluster_path,  # path to ipcluster
                   # python activate path
                   activate_path if activate_path!="" else os.path.join(PKG_DIR, "bin", "activate.sh"),
                   args.get("cluster_profile", "NO_CLUSTER"),

xfel_calibrate/settings.py

 import os
+import sys
 
 # path into which temporary files from each run are placed
 temp_path = os.path.abspath("temp/")
 
 # Path to use for calling Python. If the environment is correctly set, simply the command
-python_path = "python"
-
-# Path to use for calling iPython. If the environment is correctly set, simply the command
-ipython_path = "ipython"
-
-# Path to use for calling Jupyter. If the environment is correctly set, simply the command
-jupyter_path = "jupyter"
+python_path = sys.executable
 
 # Path to find activate script
 activate_path = ""
 
-# Path to use for calling ipcluster. If the environment is correctly set, simply the command
-ipcluster_path = "ipcluster"
-
 # Path to store reports in
 report_path = "{}/calibration_reports/".format(os.getcwd())