From f312e1f59064b375d884d2968c200c17bbe8794b Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Mon, 18 Oct 2021 16:21:19 +0200
Subject: [PATCH] Add xfel-calibrate option to skip report generation
---
bin/slurm_finalize.sh | 11 +++++++----
src/xfel_calibrate/calibrate.py | 11 +++++++++--
src/xfel_calibrate/finalize.py | 30 ++++++++++++++++++------------
3 files changed, 34 insertions(+), 18 deletions(-)
diff --git a/bin/slurm_finalize.sh b/bin/slurm_finalize.sh
index 9eaf9a735..461d7cdd1 100755
--- a/bin/slurm_finalize.sh
+++ b/bin/slurm_finalize.sh
@@ -6,6 +6,7 @@ set -euo pipefail
python_path=$1
temp_dir=$2
finalize_script=$3
+report_to=$4
echo "Running with the following parameters:"
echo "Python path: $python_path"
@@ -23,9 +24,11 @@ export MPLBACKEND=AGG
# Ensure Python uses UTF-8 for files by default
export LANG=en_US.UTF-8
-shopt -s failglob # Fail fast if there are no notebooks found
-echo "Converting notebooks"
-${python_path} -m nbconvert --to rst --TemplateExporter.exclude_input=True "$temp_dir"/*.ipynb
-shopt -u failglob # Restore default glob behaviour
+if [ -n "$report_to" ]; then
+ shopt -s failglob # Fail fast if there are no notebooks found
+ echo "Converting notebooks"
+ ${python_path} -m nbconvert --to rst --TemplateExporter.exclude_input=True "$temp_dir"/*.ipynb
+ shopt -u failglob # Restore default glob behaviour
+fi
${python_path} "$finalize_script"
diff --git a/src/xfel_calibrate/calibrate.py b/src/xfel_calibrate/calibrate.py
index e83c60a41..e0ec92e71 100755
--- a/src/xfel_calibrate/calibrate.py
+++ b/src/xfel_calibrate/calibrate.py
@@ -83,6 +83,9 @@ def make_initial_parser(**kwargs):
help='Filename (and optionally path) for output'
' report')
+ parser.add_argument('--skip-report', action='store_true',
+ help='Skip report generation in finalize step.')
+
parser.add_argument('--concurrency-par', type=str,
help='Name of concurrency parameter.'
'If not given, it is taken from configuration.')
@@ -642,6 +645,7 @@ def run_finalize(fmt_args, temp_path, job_list, sequential=False):
sys.executable, # Python with calibration machinery installed
temp_path,
finalize_script,
+ fmt_args['report_to']
]
output = check_output(cmd, input=b'').decode('utf8')
@@ -1057,7 +1061,9 @@ def run():
out_path.mkdir(parents=True, exist_ok=True)
# Use given report name, falling back to notebook title
- if args["report_to"] is None:
+ if args['skip_report']:
+ report_to = ''
+ elif args["report_to"] is None:
report_to = out_path / title.replace(" ", "")
print(f"report_to not specified, will use {report_to}")
else:
@@ -1086,7 +1092,8 @@ def run():
parm_subdict[name] = p.value
metadata["pycalibration-version"] = version
- metadata["report-path"] = f"{report_to}.pdf"
+ metadata["report-path"] = f"{report_to}.pdf" if report_to \
+ else '# REPORT SKIPPED #'
metadata["concurrency"] = {
'parameter': concurrency_par,
'default': concurrency_defval,
diff --git a/src/xfel_calibrate/finalize.py b/src/xfel_calibrate/finalize.py
index 368306301..0c3ef4cdc 100644
--- a/src/xfel_calibrate/finalize.py
+++ b/src/xfel_calibrate/finalize.py
@@ -397,8 +397,6 @@ def finalize(joblist, finaljob, run_path, out_path, version, report_to, data_pat
request_time='', submission_time=''):
run_path = Path(run_path)
- prepare_plots(run_path)
-
# Archiving files in slurm_tmp
if finaljob:
joblist.append(str(finaljob))
@@ -427,13 +425,21 @@ def finalize(joblist, finaljob, run_path, out_path, version, report_to, data_pat
metadata.save()
metadata.save_copy(run_path)
- sphinx_path = combine_report(run_path, title)
- make_titlepage(sphinx_path, title, data_path, version)
- make_report(
- Path(sphinx_path),
- run_path,
- title,
- author,
- version,
- Path(report_to),
- )
+ if report_to:
+ prepare_plots(run_path)
+
+ sphinx_path = combine_report(run_path, title)
+ make_titlepage(sphinx_path, title, data_path, version)
+ make_report(
+ Path(sphinx_path),
+ run_path,
+ title,
+ author,
+ version,
+ Path(report_to),
+ )
+ else:
+ # If there is no report location, simply copy the slurm_out_
+ # directory to the output.
+ slurm_archive_dir = Path(out_path) / f"slurm_out_{run_path.name}"
+ move(str(run_path), str(slurm_archive_dir))
--
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