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

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merged 8 commits into from
Sep 14, 2024
Merged

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

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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
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5 changes: 5 additions & 0 deletions AUTHORS
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Expand Up @@ -68,6 +68,11 @@ year of their first commit. GitHub handle is optional.
----

- Jinzhe Zeng (@njzjz)

2024
----

- Friedrich Haubensak (@hsk17)

We gratefully acknowledge code fixes contributed by
@quantifiedcode-bot from Quantified Code https://www.quantifiedcode.com
2 changes: 1 addition & 1 deletion CHANGES
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Expand Up @@ -3,7 +3,7 @@
==============================

2024-??-?? 0.9.1
orbeckst
orbeckst, hsk17

* templates in `config.templates` are now stored as
`importlib.resources.abc.Traversable` (PosixPath-like) objects instead of
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2 changes: 1 addition & 1 deletion gromacs/fileformats/mdp.py
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Expand Up @@ -55,7 +55,7 @@ class MDP(odict, utilities.FileUtils):
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
# see regex in cbook.edit_mdp()
PARAMETER = re.compile(
r"""
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16 changes: 10 additions & 6 deletions gromacs/qsub.py
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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 +430,19 @@ 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,
),
(
"^#.*(-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
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