Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

some more regex string fixes; and: use numpy.nan instead of numpy.NAN #288

Merged
merged 8 commits into from
Sep 14, 2024
Merged

some more regex string fixes; and: use numpy.nan instead of numpy.NAN #288

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
ed1ead7
some more regex string fixes
hsk17 Jul 10, 2024
4f6f79f
numpy.NAN dropped in numpy-2, use numpy.nan
hsk17 Jul 10, 2024
a75d155
Merge branch 'main' into my_branch
orbeckst Sep 13, 2024
071c108
Update gromacs/qsub.py
orbeckst Sep 13, 2024
b2d114a
make black happy
orbeckst Sep 13, 2024
e0b3560
add @hsk17 to AUTHORS and CHANGES
orbeckst Sep 13, 2024
5092ac5
Merge branch 'main' into my_branch
orbeckst Sep 14, 2024
51f9add
Update AUTHORS
orbeckst Sep 14, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion gromacs/fileformats/mdp.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@
default_extension = "mdp"
logger = logging.getLogger("gromacs.formats.MDP")

COMMENT = re.compile("""\s*;\s*(?P<value>.*)""") # eat initial ws
COMMENT = re.compile(r"""\s*;\s*(?P<value>.*)""") # eat initial ws

Check warning on line 58 in gromacs/fileformats/mdp.py

View check run for this annotation

Codecov / codecov/patch

gromacs/fileformats/mdp.py#L58 

Added line #L58 was not covered by tests
# see regex in cbook.edit_mdp()
PARAMETER = re.compile(
r"""
Expand Down
12 changes: 6 additions & 6 deletions gromacs/qsub.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -405,13 +405,13 @@ def write_script(template):
template,
[
("^ *DEFFNM=", "(?<==)(.*)", deffnm),
("^#.*(-J)", "((?<=-J\s))\s*\w+", jobname),
("^#.*(-J)", r"((?<=-J\s))\s*\w+", jobname),
(
"^#.*(-A|account_no)",
"((?<=-A\s)|(?<=account_no\s))\s*\w+",
r"((?<=-A\s)|(?<=account_no\s))\s*\w+",
budget,
),
("^#.*(-t)", "(?<=-t\s)(\d+:\d+:\d+)", walltime),
("^#.*(-t)", r"(?<=-t\s)(\d+:\d+:\d+)", walltime),
("^ *WALL_HOURS=", "(?<==)(.*)", wall_hours),
("^ *STARTDIR=", "(?<==)(.*)", startdir),
("^ *NPME=", "(?<==)(.*)", npme),
Expand All @@ -430,15 +430,15 @@ def write_script(template):
template,
[
("^ *DEFFNM=", "(?<==)(.*)", deffnm),
("^#.*(-N|job_name)", "((?<=-N\s)|(?<=job_name\s))\s*\w+", jobname),
("^#.*(-N|job_name)", r"((?<=-N\s)|(?<=job_name\s))\s*\w+", jobname),
orbeckst marked this conversation as resolved.
Show resolved Hide resolved
(
"^#.*(-A|account_no)",
"((?<=-A\s)|(?<=account_no\s))\s*\w+",
r"((?<=-A\s)|(?<=account_no\s))\s*\w+",
budget,
),
(
"^#.*(-l walltime|wall_clock_limit)",
"(?<==)(\d+:\d+:\d+)",
r"(?<==)(\d+:\d+:\d+)",
walltime,
),
("^ *WALL_HOURS=", "(?<==)(.*)", wall_hours),
Expand Down
Loading