From 349b558d09b1297c699fd82557c924b088e14c0b Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Thu, 9 Jul 2020 16:32:20 +0100
Subject: [PATCH] Use os.path functions instead of string formatting
---
xfel_calibrate/calibrate.py | 29 ++++++++++++++---------------
xfel_calibrate/settings.py | 2 +-
2 files changed, 15 insertions(+), 16 deletions(-)
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index 52470a648..030a8063b 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -163,7 +163,7 @@ def extract_title_author_version(nb):
# In case of a standard installation a version is stored
# in the _version.py file
try:
- git_dir = '{}/../.git'.format(os.path.dirname(__file__))
+ git_dir = os.path.join(PKG_DIR, '..', '.git')
FNULL = open(os.devnull, 'w')
version = check_output(['git',
'--git-dir={}'.format(git_dir),
@@ -276,7 +276,7 @@ def balance_sequences(in_folder, run, sequences, sequences_per_node,
import glob
import numpy as np
if sequences[0] == -1:
- path = "{}/r{:04d}/*{}-S*.h5".format(in_folder, run, path_inset)
+ path = os.path.join(in_folder, f"r{run:04d}", f"*{path_inset}-S*.h5")
sequence_files = glob.glob(path)
seq_nums = set()
for sf in sequence_files:
@@ -319,11 +319,9 @@ def make_extended_parser() -> argparse.ArgumentParser:
# The information is extracted from the first markdown cell of
# the notebook.
for caltype, notebook in det_notebooks.items():
- nbpath = os.path.abspath(
- "{}/{}".format(os.path.dirname(__file__), notebook["notebook"]))
- with open(nbpath, "r") as f:
- nb = nbformat.read(f, as_version=4)
- msg += make_epilog(nb, caltype=caltype)
+ nbpath = os.path.join(PKG_DIR, notebook["notebook"])
+ nb = nbformat.read(nbpath, as_version=4)
+ msg += make_epilog(nb, caltype=caltype)
return make_initial_parser(epilog=msg)
elif len(sys.argv) <= 3:
@@ -528,7 +526,7 @@ def create_finalize_script(fmt_args, temp_path, job_list):
''')
fmt_args['joblist'] = job_list
- f_name = "{}/finalize.sh".format(temp_path)
+ f_name = os.path.join(temp_path, "finalize.sh")
with open(f_name, "w") as finfile:
finfile.write(textwrap.dedent(tmpl.render(**fmt_args)))
@@ -546,7 +544,7 @@ def save_executed_command(run_tmp_path, version):
:parm version: git version of the pycalibration package
"""
- f_name = "{}/run_calibrate.sh".format(run_tmp_path)
+ f_name = os.path.join(run_tmp_path, "run_calibrate.sh")
with open(f_name, "w") as finfile:
finfile.write(f'# pycalibration version: {version}\n')
finfile.write(' '.join(sys.argv))
@@ -638,7 +636,7 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
new_name = "{}__{}__{}.ipynb".format(
os.path.basename(base_name), cparm, suffix)
- nbpath = "{}/{}".format(temp_path, new_name)
+ nbpath = os.path.join(temp_path, new_name)
with open(nbpath, "w") as f:
f.write(nbconvert.exporters.export(
nbconvert.NotebookExporter, new_nb)[0])
@@ -653,14 +651,14 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
srun_base = get_launcher_command(args, temp_path, dep_jids)
print(" ".join(srun_base))
- srun_base += [os.path.abspath("{}/bin/slurm_calibrate.sh".format(os.path.dirname(__file__))), # path to helper sh
+ srun_base += [os.path.join(PKG_DIR, "bin", "slurm_calibrate.sh"), # path to helper sh
os.path.abspath(nbpath), # path to notebook
python_path, # path to python
ipython_path, # path to ipython
jupyter_path, # path to jupyter
ipcluster_path, # path to ipcluster
# python activate path
- activate_path if activate_path!="" else "{}/bin/activate.sh".format(os.path.dirname(__file__)),
+ activate_path if activate_path!="" else os.path.join(PKG_DIR, "bin", "activate.sh"),
args.get("cluster_profile", "NO_CLUSTER"),
'"{}"'.format(base_name.upper()),
'"{}"'.format(args["detector"].upper()),
@@ -807,7 +805,7 @@ def run():
cluster_profile = "slurm_prof_{}".format(run_uuid)
# create a temporary output directory to work in
- run_tmp_path = "{}/slurm_out_{}_{}_{}".format(temp_path, detector, caltype, run_uuid)
+ run_tmp_path = os.path.join(temp_path, f"slurm_out_{detector}_{caltype}_{run_uuid}")
os.makedirs(run_tmp_path)
# Write all input parameters to rst file to be included to final report
@@ -816,8 +814,9 @@ def run():
save_executed_command(run_tmp_path, version)
# wait on all jobs to run and then finalize the run by creating a report from the notebooks
- out_path = "{}/{}/{}/{}".format(report_path, detector.upper(),
- caltype.upper(), datetime.now().isoformat())
+ out_path = os.path.join(
+ report_path, detector.upper(), caltype.upper(), datetime.now().isoformat()
+ )
if try_report_to_output:
if "out_folder" in args:
out_path = os.path.abspath(args["out_folder"])
diff --git a/xfel_calibrate/settings.py b/xfel_calibrate/settings.py
index fdf56f40c..cbe4c21b6 100644
--- a/xfel_calibrate/settings.py
+++ b/xfel_calibrate/settings.py
@@ -1,7 +1,7 @@
import os
# path into which temporary files from each run are placed
-temp_path = "{}/temp/".format(os.getcwd())
+temp_path = os.path.abspath("temp/")
# Path to use for calling Python. If the environment is correctly set, simply the command
python_path = "python"
--
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