From 910f9d79a467d131e7f30f80964ccf7673a96ce2 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Wed, 9 Sep 2020 16:30:37 +0100
Subject: [PATCH] Rely on path/to/python -m for IPython, ipyparallel &
nbconvert
---
README.rst | 8 --------
bin/activate.sh | 5 -----
bin/slurm_calibrate.sh | 32 +++++++++++++-------------------
xfel_calibrate/calibrate.py | 3 ---
xfel_calibrate/settings.py | 12 ++----------
5 files changed, 15 insertions(+), 45 deletions(-)
delete mode 100644 bin/activate.sh
diff --git a/README.rst b/README.rst
index b62b5285b..6328ee618 100644
--- a/README.rst
+++ b/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:$PATH
-
Install the package::
pip install -r requirements.txt
diff --git a/bin/activate.sh b/bin/activate.sh
deleted file mode 100644
index 8c8a0500e..000000000
--- a/bin/activate.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-source /etc/profile.d/modules.sh
-module load anaconda/3
-module load texlive/2019
-# export path to python environment
-export PATH=$HOME/.local/bin:$PATH
diff --git a/bin/slurm_calibrate.sh b/bin/slurm_calibrate.sh
index 44be0e93e..d5e87ebc3 100755
--- a/bin/slurm_calibrate.sh
+++ b/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
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index 8bdbdbe15..352c4ca3b 100755
--- a/xfel_calibrate/calibrate.py
+++ b/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"),
diff --git a/xfel_calibrate/settings.py b/xfel_calibrate/settings.py
index cbe4c21b6..78c3053e7 100644
--- a/xfel_calibrate/settings.py
+++ b/xfel_calibrate/settings.py
@@ -1,23 +1,15 @@
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())
--
GitLab