some more regex string fixes; and: use numpy.nan instead of numpy.NAN (…

…#288)

* some more regex string fixes
* add @hsk17 to AUTHORS and CHANGES

AUTHORS

@@ -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

CHANGES

@@ -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

gromacs/fileformats/mdp.py

@@ -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"""

gromacs/qsub.py

@@ -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),
@@ -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),