runner.conda: Explicitly handle our package versions which are invali…

…d by PEP-440

Our nextstrain-base Conda package versions are not PEP-440 compliant, so
we inadvertently relied on packaging.version.parse_version() falling
back to its LegacyVersion class when it encountered an InvalidVersion
error.  LegacyVersion was dropped, however, in packaging 22.0 (December
2022).¹  This resulted in seeing the InvalidVersion error during runtime
update, e.g.:

    packaging.version.InvalidVersion: Invalid version: '20221019T172207Z'

To avoid that, we start handling InvalidVersion ourselves and produce a
valid proxy version instead with reasonable comparison semantics similar
to LegacyVersion.

The new version handling is more than strictly necessary for our current
package versions (which could just be simpler string comparisons), but
it allows us more leeway to change package versioning in the future if
need be without affecting existing installs of Nextstrain CLI.  I didn't
want to vendor LegacyVersion itself because it's fairly complex and
tangled with the implementation of packaging.version.

Resolves <#285>.

¹ <https://packaging.pypa.io/en/latest/changelog.html>

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