From 8bf6fb7ef44e2add9d67123f79e9339f35c8552a Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Wed, 18 Aug 2021 10:21:33 +0100
Subject: [PATCH] Use CWD for notebook paths
---
src/xfel_calibrate/calibrate.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/src/xfel_calibrate/calibrate.py b/src/xfel_calibrate/calibrate.py
index f3f50120e..1aa2896f1 100755
--- a/src/xfel_calibrate/calibrate.py
+++ b/src/xfel_calibrate/calibrate.py
@@ -755,7 +755,7 @@ def prepare_job(
return JobArgs([
"{pkg_dir}/bin/slurm_calibrate.sh",
- "{run_tmp_path}/" + new_name,
+ new_name,
"{python}",
cluster_profile,
os.path.splitext(new_name)[0].upper(),
@@ -775,18 +775,18 @@ class JobArgs:
def __eq__(self, other):
return isinstance(other, JobArgs) and (self.args == other.args)
- def format_cmd(self, run_tmp_path, python):
+ def format_cmd(self, python):
return [a.format(
- run_tmp_path=run_tmp_path, python=python, pkg_dir=PKG_DIR
+ python=python, pkg_dir=PKG_DIR
) for a in self.args]
def run_direct(self, run_tmp_path, python) -> int:
- return call(self.format_cmd(run_tmp_path, python))
+ return call(self.format_cmd(python), cwd=run_tmp_path)
def submit_job(self, run_tmp_path, python, args, after_ok=(), after_any=()):
cmd = get_launcher_command(args, run_tmp_path, after_ok, after_any)
- cmd += self.format_cmd(run_tmp_path, python)
- output = check_output(cmd).decode('utf-8')
+ cmd += self.format_cmd(python)
+ output = check_output(cmd, cwd=run_tmp_path).decode('utf-8')
return output.partition(';')[0].strip() # job ID
--
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