Merge pull request #1249: Address pkg_resources deprecation warnings

LICENSE.nextstrain-cli

@@ -0,0 +1,27 @@
+This license applies to the original copy of resource functions from the
+Nextstrain CLI project into this project, incorporated in
+"augur/data/__init__.py". Any subsequent modifications to this project's copy of
+those functions are licensed under the license of this project, not of
+Nextstrain CLI.
+
+MIT License
+
+Copyright (c) 2018–2021 Trevor Bedford and Richard Neher
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

augur/data/__init__.py

@@ -0,0 +1,32 @@
+"""
+Resource files.
+"""
+# Originally copied from nextstrain/cli/resources/__init__.py in the Nextstrain
+# CLI project¹.
+#
+# ¹ <https://github.com/nextstrain/cli/blob/a5dda9c0579ece7acbd8e2c32a4bbe95df7c0bce/nextstrain/cli/resources/__init__.py>
+
+# We gate usage of the stdlib implementation on 3.11 because that's the first
+# version with a full adapter for making the new files() / Traversable API
+# backwards compatible with importers only providing the original path() /
+# ResourceReader API.  The PyPI backport, on the other hand, contains the full
+# adapter since 5.3.0, which we declare as our minimum version in setup.py, so
+# we use that even on 3.9 and 3.10.
+#
+# We're using the new API at all because the original one is being deprecated
+# and we want to avoid warnings both from the stdlib implementation on 3.11 and
+# from the PyPI backport implementation on older Python versions.
+#   -trs, 13 Sept 2022
+import sys
+
+if sys.version_info >= (3, 11):
+    from importlib.resources import files as _files, as_file as _as_file
+else:
+    from importlib_resources import files as _files, as_file as _as_file
+
+from pathlib import Path
+from typing import ContextManager
+
+
+def as_file(path: str) -> ContextManager[Path]:
+    return _as_file(_files(__name__) / path)

augur/util_support/color_parser.py

@@ -1,8 +1,7 @@
 from collections import defaultdict
-from io import TextIOWrapper
 import functools
-from pkg_resources import resource_stream
 
+from augur.data import as_file
 from augur.util_support.color_parser_line import ColorParserLine
 
 
@@ -17,8 +16,8 @@ def mapping(self):
         colors = {}
 
         if self.use_defaults:
-            with resource_stream("augur", "data/colors.tsv") as stream:
-                with TextIOWrapper(stream, "utf-8") as defaults:
+            with as_file("colors.tsv") as file:
+                with open(file, encoding="utf-8") as defaults:
                     colors = {**colors, **self.parse_file(defaults)}
 
         if self.mapping_filename:

augur/utils.py

@@ -5,10 +5,9 @@
 import os, json, sys
 import pandas as pd
 from collections import defaultdict, OrderedDict
-from pkg_resources import resource_stream
-from io import TextIOWrapper
 from .__version__ import __version__
 
+from augur.data import as_file
 from augur.io.file import open_file
 
 from augur.types import ValidationMode
@@ -243,8 +242,8 @@ def add_line_to_coordinates(line):
         else:
             print("WARNING: geo-coordinate file contains invalid line. Please make sure not to mix tabs and spaces as delimiters (use only tabs):",line)
     if use_defaults:
-        with resource_stream(__package__, "data/lat_longs.tsv") as stream:
-            with TextIOWrapper(stream, "utf-8") as defaults:
+        with as_file("lat_longs.tsv") as file:
+            with open(file, encoding="utf-8") as defaults:
                 for line in defaults:
                     add_line_to_coordinates(line)
     if overrides:

augur/validate.py

@@ -3,16 +3,15 @@
 """
 
 import sys
-import os
 from collections import defaultdict
 import json
 import jsonschema
 import jsonschema.exceptions
 import re
 from itertools import groupby
-from pkg_resources import resource_string
 from textwrap import indent
 from typing import Iterable, Union
+from augur.data import as_file
 from augur.io.print import print_err
 from augur.io.json import shorten_as_json
 from .validate_export import verifyMainJSONIsInternallyConsistent, verifyMetaAndOrTreeJSONsAreInternallyConsistent
@@ -31,7 +30,8 @@ def load_json_schema(path, refs=None):
     (located in augur/data)
     '''
     try:
-        schema = json.loads(resource_string(__package__, os.path.join("data", path)))
+        with as_file(path) as file, open(file, "r", encoding = "utf-8") as fh:
+            schema = json.load(fh)
     except json.JSONDecodeError as err:
         raise ValidateError("Schema {} is not a valid JSON file. Error: {}".format(path, err))
     # check loaded schema is itself valid -- see http://python-jsonschema.readthedocs.io/en/latest/errors/
@@ -43,7 +43,10 @@ def load_json_schema(path, refs=None):
 
     if refs:
         # Make the validator aware of additional schemas
-        schema_store = {k: json.loads(resource_string(__package__, os.path.join("data", v))) for k,v in refs.items()}
+        schema_store = dict()
+        for k, v in refs.items():
+            with as_file(v) as file, open(file, "r", encoding = "utf-8") as fh:
+                schema_store[k] = json.load(fh)
         resolver = jsonschema.RefResolver.from_schema(schema,store=schema_store)
         schema_validator = Validator(schema, resolver=resolver)
     else:

devel/release

@@ -88,9 +88,9 @@ assert-version-is-new() {
 version-is-gt() {
     python3 /dev/stdin "$1" "$2" <<<"$(cut -c 9- <<<'
         from sys import argv, exit
-        from pkg_resources import parse_version
+        from packaging.version import Version
 
-        version = list(map(parse_version, argv[1:3]))
+        version = list(map(Version, argv[1:3]))
 
         gt = version[1] > version[0]
 

setup.py

@@ -54,6 +54,7 @@
         "bcbio-gff >=0.7.0, ==0.7.*",
         "biopython >=1.67, !=1.77, !=1.78",
         "cvxopt >=1.1.9, ==1.*",
+        "importlib_resources >=5.3.0; python_version < '3.11'",
         "isodate ==0.6.*",
         "jsonschema >=3.0.0, ==3.*",
         "networkx >= 2.5, ==2.*",