From 33ac9e40f4d658c6a72f1bb2c5e3283eb4484c9a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Le=20Guyader?= <loic.le.guyader@xfel.eu>
Date: Wed, 9 Feb 2022 10:11:07 +0100
Subject: [PATCH] Scripts moved and linked in documentation
---
doc/howtos.rst | 19 ++++++++++++++++---
.../scripts}/bin_dssc_module_job.sh | 0
.../scripts}/boz_parameters_job.sh | 0
{scripts => doc/scripts}/format_data.py | 0
{scripts => doc/scripts}/format_data.sh | 0
.../scripts}/process_data_201007_23h.py | 0
{scripts => doc/scripts}/start_job_single.sh | 0
.../scripts}/start_processing_all.sh | 0
8 files changed, 16 insertions(+), 3 deletions(-)
rename {scripts => doc/scripts}/bin_dssc_module_job.sh (100%)
rename {scripts => doc/scripts}/boz_parameters_job.sh (100%)
rename {scripts => doc/scripts}/format_data.py (100%)
rename {scripts => doc/scripts}/format_data.sh (100%)
rename {scripts => doc/scripts}/process_data_201007_23h.py (100%)
rename {scripts => doc/scripts}/start_job_single.sh (100%)
rename {scripts => doc/scripts}/start_processing_all.sh (100%)
diff --git a/doc/howtos.rst b/doc/howtos.rst
index d9ea91e..cc3f38f 100644
--- a/doc/howtos.rst
+++ b/doc/howtos.rst
@@ -41,7 +41,14 @@ which will be repeated. XGM data will also be binned similarly to the DSSC
data.
Since this data reduction step can be quite time consuming for large datasets,
-it is recommended to launch the notebook via a SLURM script:
+it is recommended to launch the notebook via a SLURM script. The script can be
+downloaded from :download:`scripts/bin_dssc_module_job.sh` and reads as:
+
+.. literalinclude:: scripts/bin_dssc_module_job.sh
+ :language: bash
+ :linenos:
+
+It is launched with the following:
.. code:: bash
@@ -101,8 +108,14 @@ non-linearity calculation by taking the JSON file as soon as it appears.
The determination of the non-linearity correction is a lot longer and can take
some 2 to 8 hours depending on the number of pulses in the
train. For this reason it is possible to use a script
-``scripts/boz_parameters_job.sh`` in the toolbox to launch the first notebook
-via slurm:
+that can be downloaded from :download:`scripts/boz_parameters_job.sh` and
+reads as:
+
+.. literalinclude:: scripts/boz_parameters_job.sh
+ :language: bash
+ :linenos:
+
+It uses the first notebook and is launched via slurm:
``sbatch ./boz_parameters_job.sh 615 614 3``
diff --git a/scripts/bin_dssc_module_job.sh b/doc/scripts/bin_dssc_module_job.sh
similarity index 100%
rename from scripts/bin_dssc_module_job.sh
rename to doc/scripts/bin_dssc_module_job.sh
diff --git a/scripts/boz_parameters_job.sh b/doc/scripts/boz_parameters_job.sh
similarity index 100%
rename from scripts/boz_parameters_job.sh
rename to doc/scripts/boz_parameters_job.sh
diff --git a/scripts/format_data.py b/doc/scripts/format_data.py
similarity index 100%
rename from scripts/format_data.py
rename to doc/scripts/format_data.py
diff --git a/scripts/format_data.sh b/doc/scripts/format_data.sh
similarity index 100%
rename from scripts/format_data.sh
rename to doc/scripts/format_data.sh
diff --git a/scripts/process_data_201007_23h.py b/doc/scripts/process_data_201007_23h.py
similarity index 100%
rename from scripts/process_data_201007_23h.py
rename to doc/scripts/process_data_201007_23h.py
diff --git a/scripts/start_job_single.sh b/doc/scripts/start_job_single.sh
similarity index 100%
rename from scripts/start_job_single.sh
rename to doc/scripts/start_job_single.sh
diff --git a/scripts/start_processing_all.sh b/doc/scripts/start_processing_all.sh
similarity index 100%
rename from scripts/start_processing_all.sh
rename to doc/scripts/start_processing_all.sh
--
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