runner.conda: Explicitly handle our package versions which are invalid by PEP-440

nextstrain/cli/runner/conda.py

@@ -46,7 +46,8 @@
 import subprocess
 import tarfile
 import traceback
-from packaging.version import parse as parse_version
+from functools import partial
+from packaging.version import Version, InvalidVersion
 from pathlib import Path, PurePosixPath
 from typing import Iterable, NamedTuple, Optional
 from urllib.parse import urljoin, quote as urlquote
@@ -596,6 +597,66 @@ def latest_package_label_version(channel: str, package: str, label: str) -> Opti
     return latest_file.get("version")
 
 
+def parse_version(version: str) -> Version:
+    """
+    Parse *version* into a PEP-440-compliant :cls:`Version` object, by hook or
+    by crook.
+
+    If *version* isn't already PEP-440 compliant, then it is parsed as a
+    PEP-440 local version label after replacing with ``.`` any characters not
+    matching ``a-z``, ``A-Z``, ``0-9``, ``.``, ``_``, or ``-``.  The comparison
+    semantics for local version labels amount to a string- and integer-based
+    comparison by parts ("segments"), which is super good enough for our
+    purposes here.  The full local version identifier produced for versions
+    parsed in this way always contains a public version identifier component of
+    ``0.dev0`` so it compares lowest against other public version identifiers.
+
+    >>> parse_version("1.2.3")
+    <Version('1.2.3')>
+    >>> parse_version("1.2.3-nope")
+    <Version('0.dev0+1.2.3.nope')>
+    >>> parse_version("20221019T172207Z")
+    <Version('0.dev0+20221019t172207z')>
+    >>> parse_version("@invalid+@")
+    <Version('0.dev0+invalid')>
+    >>> parse_version("not@@ok")
+    <Version('0.dev0+not.ok')>
+    >>> parse_version("20221019T172207Z") < parse_version("20230525T143814Z")
+    True
+    """
+    try:
+        return Version(version)
+    except InvalidVersion:
+        # Per PEP-440
+        #
+        # > …local version labels MUST be limited to the following set of
+        # > permitted characters:
+        # >
+        # >   ASCII letters ([a-zA-Z])
+        # >   ASCII digits ([0-9])
+        # >   periods (.)
+        # >
+        # > Local version labels MUST start and end with an ASCII letter or
+        # > digit.
+        #
+        # and
+        #
+        # > With a local version, in addition to the use of . as a separator of
+        # > segments, the use of - and _ is also acceptable. The normal form is
+        # > using the . character.
+        #
+        # and empty segments (x..z) aren't allowed either.
+        #
+        # c.f. <https://peps.python.org/pep-0440/#local-version-identifiers>
+        #      <https://peps.python.org/pep-0440/#local-version-segments>
+        remove_invalid_start_end_chars = partial(re.sub, r'^[^a-zA-Z0-9]+|[^a-zA-Z0-9]+$', '')
+        replace_invalid_with_separators = partial(re.sub, r'[^a-zA-Z0-9._-]+', '.')
+
+        as_local_segment = lambda v: replace_invalid_with_separators(remove_invalid_start_end_chars(v))
+
+        return Version(f"0.dev0+{as_local_segment(version)}")
+
+
 class PackageSpec(NamedTuple):
     name: str
     version_spec: Optional[str] = None