fix: SyntaxWarnings due to non-raw regex pattern strings (#2359)

Fixes warnings of the form:

```
SyntaxWarning: invalid escape sequence '\['
```

Some of these warnings were causing linting test failures on Python
3.12.

### Description

Converts several regex pattern strings to raw strings (`r""`) in order
to avoid `SyntaxWarning` due to invalid backslash-escape sequences

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.

The changes in the first commit fix test failures on Python 3.12. It’s
not immediately clear how I would test the changes in the second commit,
although I confirm that they eliminate (non-failure) `SyntaxWarning`
messages when byte-compiling the modules.

* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).

No documentation changes are required.

snakemake/deployment/conda.py

@@ -747,7 +747,7 @@ def _check_version(self):
         version = shell.check_output(
             self._get_cmd("conda --version"), stderr=subprocess.PIPE, text=True
         )
-        version_matches = re.findall("\d+.\d+.\d+", version)
+        version_matches = re.findall(r"\d+.\d+.\d+", version)
         if len(version_matches) != 1:
             raise WorkflowError(
                 f"Unable to determine conda version. 'conda --version' returned {version}"

snakemake/linting/rules.py

@@ -111,7 +111,7 @@ def lint_long_run(self, rule):
                 links=[links.external_scripts, links.notebooks],
             )
 
-    def lint_iofile_by_index(self, rule, regex=re.compile("(input|output)\[[0-9]+\]")):
+    def lint_iofile_by_index(self, rule, regex=re.compile(r"(input|output)\[[0-9]+\]")):
         if rule.shellcmd and regex.search(rule.shellcmd):
             yield Lint(
                 title="Do not access input and output files individually by index in shell commands",

snakemake/linting/snakefiles.py

@@ -63,7 +63,7 @@ def lint_path_add(
     def lint_envvars(
         self,
         snakefile,
-        regex=re.compile("os.environ\[(?P<quote>['\"])(?P<name>.+)?(?P=quote)\]"),
+        regex=re.compile(r"os.environ\[(?P<quote>['\"])(?P<name>.+)?(?P=quote)\]"),
     ):
         for match in regex.finditer(snakefile):
             line = get_line(match, snakefile)

snakemake/remote/XRootD.py

@@ -151,7 +151,7 @@ def get_client(self, domain):
 
     def _parse_url(self, url):
         match = re.search(
-            "(?P<domain>(?:[A-Za-z]+://)[A-Za-z0-9:@\_\-\.]+\:?/)(?P<path>.+)", url
+            r"(?P<domain>(?:[A-Za-z]+://)[A-Za-z0-9:@\_\-\.]+\:?/)(?P<path>.+)", url
         )
         if match is None:
             return None

snakemake/sourcecache.py

@@ -343,7 +343,7 @@ def infer_source_file(path_or_uri, basedir: SourceFile = None):
 
 class SourceCache:
     cache_whitelist = [
-        "https://raw.githubusercontent.com/snakemake/snakemake-wrappers/\d+\.\d+.\d+"
+        r"https://raw.githubusercontent.com/snakemake/snakemake-wrappers/\d+\.\d+.\d+"
     ]  # TODO add more prefixes for uris that are save to be cached
 
     def __init__(self, runtime_cache_path=None):

snakemake/workflow.py

@@ -1325,7 +1325,7 @@ def register_envvars(self, *envvars):
         invalid_envvars = [
             envvar
             for envvar in envvars
-            if re.match("^\w+$", envvar, flags=re.ASCII) is None
+            if re.match(r"^\w+$", envvar, flags=re.ASCII) is None
         ]
         if invalid_envvars:
             raise WorkflowError(
@@ -1410,7 +1410,7 @@ def scattergather(self, **content):
         self._scatter.update(self.overwrite_scatter)
 
         # add corresponding wildcard constraint
-        self.global_wildcard_constraints(scatteritem="\d+-of-\d+")
+        self.global_wildcard_constraints(scatteritem=r"\d+-of-\d+")
 
         def func(key, *args, **wildcards):
             n = self._scatter[key]