Switch from exfel_anaconda3 to exfel-python

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:
 

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

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)

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)

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

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

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

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
     ----------

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