From d6bf33b68754e63c0437e02291c0ca6d90554199 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Le=20Guyader?= <loic.le.guyader@xfel.eu>
Date: Mon, 19 Jun 2023 11:18:18 +0200
Subject: [PATCH] Switch from exfel_anaconda3 to exfel-python
---
doc/index.rst | 6 +++---
doc/maintainers.rst | 2 +-
doc/scripts/bin_dssc_module_job.sh | 3 +--
doc/scripts/boz_parameters_job.sh | 3 +--
doc/scripts/format_data.sh | 5 +++--
doc/scripts/start_job_single.sh | 3 +--
doc/scripts/start_processing_all.sh | 3 +--
src/toolbox_scs/detectors/dssc_data.py | 2 +-
src/toolbox_scs/test/README.rst | 4 ++--
9 files changed, 14 insertions(+), 17 deletions(-)
diff --git a/doc/index.rst b/doc/index.rst
index 0f08d2d..3a4249e 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -12,7 +12,7 @@ terminal on Maxwell:
.. code:: bash
- module load exfel exfel_anaconda3
+ module load exfel exfel-python
scs-activate-toolbox-kernel --proposal 2780
where in this example 2780 is the proposal number. After this and refreshing the
@@ -42,14 +42,14 @@ extra_data and the euxfel_bunch_pattern package, which are no official third
party python modules. Within environments where the latter are not present, they
need to be installed by hand.
-In most cases, you will want to install it in the *exfel_anaconda3* environment
+In most cases, you will want to install it in the *exfel_python* environment
which is the one corresponding to the *xfel* kernel on max-jhub.
To do so, first activate that environment:
.. code:: bash
- module load exfel exfel_anaconda3
+ module load exfel exfel-python
Then, check that the scs_toolbox is not already installed:
diff --git a/doc/maintainers.rst b/doc/maintainers.rst
index 4217dbd..3d87892 100644
--- a/doc/maintainers.rst
+++ b/doc/maintainers.rst
@@ -11,7 +11,7 @@ in Maxwell:
.. code:: shell
- module load exfel exfel_anaconda3
+ module load exfel exfel-python
scs-create-toolbox-env --proposal <PROPOSAL>
where ``<PROPOSAL>`` is the desired proposal number. This will create a Python
diff --git a/doc/scripts/bin_dssc_module_job.sh b/doc/scripts/bin_dssc_module_job.sh
index 7bec56b..e99e792 100644
--- a/doc/scripts/bin_dssc_module_job.sh
+++ b/doc/scripts/bin_dssc_module_job.sh
@@ -24,8 +24,7 @@ done
# Load xfel environment
source /etc/profile.d/modules.sh
-module load exfel
-module load exfel_anaconda3
+module load exfel exfel-python
echo processing run $RUN
PDIR=$(findxfel $PROPOSAL)
diff --git a/doc/scripts/boz_parameters_job.sh b/doc/scripts/boz_parameters_job.sh
index e8747f5..dd2cfef 100644
--- a/doc/scripts/boz_parameters_job.sh
+++ b/doc/scripts/boz_parameters_job.sh
@@ -30,8 +30,7 @@ done
# Load xfel environment
source /etc/profile.d/modules.sh
-module load exfel
-module load exfel_anaconda3/202301
+module load exfel exfel-python
echo processing run $RUN
PDIR=$(findxfel $PROPOSAL)
diff --git a/doc/scripts/format_data.sh b/doc/scripts/format_data.sh
index efc21f4..d2e1f74 100755
--- a/doc/scripts/format_data.sh
+++ b/doc/scripts/format_data.sh
@@ -7,8 +7,9 @@ RUN_DIR="../processed_runs/r_${RUN_NR}/"
if [ -d $RUN_DIR ]
then
echo creating formatted .h5 file for run $RUN_NR in $RUN_DIR
-# module load exfel
-# module load exfel_anaconda3
+ source /etc/profile.d/modules.sh
+ module load exfel exfel-python
+
python format_data.py --run-number $RUN_NR --run-folder $RUN_DIR
#chgrp -R 60002711-part $RUN_DIR
chmod -R 777 $RUN_DIR
diff --git a/doc/scripts/start_job_single.sh b/doc/scripts/start_job_single.sh
index d23a9ce..bd9b8e3 100755
--- a/doc/scripts/start_job_single.sh
+++ b/doc/scripts/start_job_single.sh
@@ -10,8 +10,7 @@ MODULES=$2
RUNTYPE=$3
source /etc/profile.d/modules.sh
-module load exfel
-module load exfel_anaconda3
+module load exfel exfel-python
echo processing modules $MODULES of run $RUN
python process_data_201007_23h.py --run-number $RUN --module ${MODULES} --runtype $RUNTYPE
diff --git a/doc/scripts/start_processing_all.sh b/doc/scripts/start_processing_all.sh
index a6f694b..a7ebe62 100755
--- a/doc/scripts/start_processing_all.sh
+++ b/doc/scripts/start_processing_all.sh
@@ -7,8 +7,7 @@ if [ $RUN ] && [ $RUNTYPE ]
then
echo processing run $RUN
source /etc/profile.d/modules.sh
- module load exfel
- module load exfel_anaconda3
+ module load exfel exfel-python
sbatch ./start_job_single.sh $RUN '0 1 2 3' $RUNTYPE
sbatch ./start_job_single.sh $RUN '4 5 6 7' $RUNTYPE
diff --git a/src/toolbox_scs/detectors/dssc_data.py b/src/toolbox_scs/detectors/dssc_data.py
index 94b2336..4822876 100644
--- a/src/toolbox_scs/detectors/dssc_data.py
+++ b/src/toolbox_scs/detectors/dssc_data.py
@@ -83,7 +83,7 @@ def load_xarray(fname, group='data', form='dataset'):
Load stored xarray Dataset.
Comment: This function exists because of a problem with the standard
netcdf engine that is malfunctioning due to related software installed
- in the exfel_anaconda3 environment. May be dropped at some point.
+ in the exfel-python environment. May be dropped at some point.
Parameters
----------
diff --git a/src/toolbox_scs/test/README.rst b/src/toolbox_scs/test/README.rst
index 2afe1d9..450a492 100644
--- a/src/toolbox_scs/test/README.rst
+++ b/src/toolbox_scs/test/README.rst
@@ -12,7 +12,7 @@ The test suites directly import the toolbox\_scs/ package. The idea is that prob
Requirements to run the code are:
-* loaded exfel_anaconda3 environment
+* loaded exfel-python environment
* local installation of toolbox\_scs using pip (pip install --user .)
*Comment*: During development, use the -e flag when installing via pip, such that changes become effective immediately.
@@ -71,4 +71,4 @@ Usage
----------------------------------------------------------------------
Ran 1 test in 0.616s
- OK
\ No newline at end of file
+ OK
--
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