Remove pkg_resources runtime usage

Mikado/configuration/configuration.py

@@ -15,7 +15,7 @@
 import toml
 import json
 from ..exceptions import InvalidConfiguration
-from pkg_resources import resource_filename
+from ..utilities.resources import resource_file
 try:
     from yaml import CSafeLoader as yLoader
 except ImportError:
@@ -118,7 +118,7 @@ def load_scoring(self, logger=None):
         options = [os.path.abspath(self.pick.scoring_file),
                    os.path.abspath(os.path.join(os.path.dirname(self.filename or ""),
                                                 self.pick.scoring_file)),
-                   os.path.abspath(os.path.join(resource_filename("Mikado.configuration", "scoring_files"),
+                   os.path.abspath(os.path.join(resource_file("Mikado.configuration", "scoring_files"),
                                                 self.pick.scoring_file))]
 
         if self.filename is not None:

Mikado/configuration/configurator.py

@@ -14,9 +14,9 @@
 from multiprocessing import get_start_method
 from logging import Logger
 import yaml
-from pkg_resources import resource_stream
 from ..exceptions import InvalidConfiguration
 from ..utilities.log_utils import create_default_logger
+from ..utilities.resources import resource_binary_stream
 import random
 import toml
 from .configuration import MikadoConfiguration
@@ -52,7 +52,7 @@ def create_cluster_config(config: Union[MikadoConfiguration, DaijinConfiguration
             cluster_config = args.cluster_config
         else:
             cluster_config = "daijin_hpc.yaml"
-        with open(cluster_config, "wb") as out, resource_stream("Mikado.daijin", "hpc.yaml") as original:
+        with open(cluster_config, "wb") as out, resource_binary_stream("Mikado.daijin", "hpc.yaml") as original:
             for pos, line in enumerate(original):
                 out.write(line)
                 if pos == 0:

Mikado/configuration/daijin_configurator.py

@@ -5,13 +5,13 @@
 import os
 import toml
 import yaml
-from pkg_resources import resource_stream
 from .configurator import create_cluster_config, load_and_validate_config
 from . import print_config
 from .daijin_configuration import DaijinConfiguration
 from .._transcripts.scoring_configuration import ScoringFile
 from ..exceptions import InvalidConfiguration
 from ..utilities.log_utils import create_default_logger
+from ..utilities.resources import resource_binary_stream
 import sys
 import pysam
 try:
@@ -208,9 +208,9 @@ def create_daijin_config(args: Namespace, config=None, level="ERROR", piped=Fals
     if args.scoring:
         if args.copy_scoring is not False:
             with open(args.copy_scoring, "wt") as out:
-                with resource_stream("Mikado", os.path.join("configuration",
-                                                            "scoring_files",
-                                                            args.scoring)) as original:
+                with resource_binary_stream("Mikado", os.path.join("configuration",
+                                                                    "scoring_files",
+                                                                    args.scoring)) as original:
                     for line in original:
                         print(line.decode(), file=out, end="")
             args.scoring = os.path.abspath(args.copy_scoring)

Mikado/daijin/__init__.py

@@ -13,21 +13,21 @@
 import time
 from snakemake.utils import min_version
 from ..configuration.daijin_configurator import create_daijin_config
-import pkg_resources
+from ..utilities.resources import resource_exists, resource_file, resource_listdir
 try:
     from yaml import CSafeLoader as yLoader
 except ImportError:
     from yaml import SafeLoader as yLoader
 
-system_hpc_yaml = pkg_resources.resource_filename("Mikado", os.path.join("daijin", "hpc.yaml"))
+system_hpc_yaml = resource_file("Mikado", os.path.join("daijin", "hpc.yaml"))
 
 min_version("3.6")
 
 TIME_START = time.time()
 NOW = datetime.datetime.fromtimestamp(TIME_START).strftime('%Y-%m-%d_%H:%M:%S')
 
-DAIJIN_DIR = pkg_resources.resource_filename("Mikado", "daijin")
-assert pkg_resources.resource_exists("Mikado", "daijin")
+DAIJIN_DIR = resource_file("Mikado", "daijin")
+assert resource_exists("Mikado", "daijin")
 
 
 # noinspection PyPep8Naming
@@ -197,7 +197,7 @@ def create_config_parser():
     scoring_file.add_argument("--scoring", type=str, default=None,
                          help="""Available scoring files. Either provide your own of choose from
                          one of the pre-packaged scoring files:
-                             {}""".format("\n".join(["- {}".format(_) for _ in pkg_resources.resource_listdir(
+                             {}""".format("\n".join(["- {}".format(_) for _ in resource_listdir(
                              "Mikado", os.path.join("configuration", "scoring_files"))]
                                                 )))
     scoring_file.add_argument("--custom-scoring", type=str, default=None,

Mikado/daijin/assemble.py

@@ -5,10 +5,10 @@
 import os
 from ..configuration import DaijinConfiguration
 from . import get_sub_commands, system_hpc_yaml, NOW
-import pkg_resources
 import shutil
 import sys
 import inspect
+from ..utilities.resources import resource_exists, resource_file
 try:
     import drmaa
     _ = drmaa.Session()
@@ -131,7 +131,7 @@ def assemble_transcripts_pipeline(args):
             os.symlink(os.path.abspath(lr_file), out)
 
     # Launch using SnakeMake
-    assert pkg_resources.resource_exists("Mikado", os.path.join("daijin", "assemble.smk"))
+    assert resource_exists("Mikado", os.path.join("daijin", "assemble.smk"))
 
     additional_config = {}
     if args.threads is not None:
@@ -207,7 +207,6 @@ def assemble_transcripts_pipeline(args):
         raise KeyError("No configfile key found")
 
     snakemake.snakemake(
-        pkg_resources.resource_filename("Mikado",
-                                        os.path.join("daijin", "assemble.smk")),
+        resource_file("Mikado", os.path.join("daijin", "assemble.smk")),
         **kwds
     )

Mikado/daijin/assemble.smk

@@ -2,8 +2,8 @@ import os
 import subprocess
 from shutil import which
 import functools
-import pkg_resources
 import re
+from Mikado.utilities.resources import resource_file
 from Mikado.utilities.file_type import filetype
 
 
@@ -15,7 +15,7 @@ except AttributeError:
 
 
 # Short read fields
-envdir = pkg_resources.resource_filename("Mikado.daijin", "envs")
+envdir = resource_file("Mikado.daijin", "envs")
 
 R1 = []
 R2 = []

Mikado/daijin/mikado.py

@@ -5,11 +5,11 @@
 import os
 from ..configuration import DaijinConfiguration
 from . import get_sub_commands, system_hpc_yaml, NOW
-import pkg_resources
 from dataclasses import asdict
 import shutil
 import sys
 import inspect
+from ..utilities.resources import resource_exists, resource_file
 try:
     import drmaa
     _ = drmaa.Session()
@@ -67,8 +67,7 @@ def mikado_pipeline(args):
         raise OSError("{} is not a directory!".format("daijin_logs"))
 
     # Launch using SnakeMake
-    assert pkg_resources.resource_exists("Mikado",
-                                         os.path.join("daijin", "mikado.smk"))
+    assert resource_exists("Mikado", os.path.join("daijin", "mikado.smk"))
 
     cluster_var = None
     if args.no_drmaa is True and sub_cmd:
@@ -147,7 +146,6 @@ def mikado_pipeline(args):
         raise KeyError("No configfile key found")
 
     snakemake.snakemake(
-        pkg_resources.resource_filename("Mikado",
-                                        os.path.join("daijin", "mikado.smk")),
+        resource_file("Mikado", os.path.join("daijin", "mikado.smk")),
         **kwds
     )

Mikado/daijin/mikado.smk

@@ -1,6 +1,6 @@
 import os
 from shutil import which
-import pkg_resources
+from Mikado.utilities.resources import resource_file
 from Bio.Data import CodonTable
 from Mikado.serializers.blast_serializer.tabular_utils import blast_keys
 import functools
@@ -41,7 +41,7 @@ try:
 except AttributeError:
     CFG=workflow.overwrite_configfile
 
-envdir = pkg_resources.resource_filename("Mikado.daijin", "envs")
+envdir = resource_file("Mikado.daijin", "envs")
 
 
 REF = config["reference"]["genome"]

Mikado/subprograms/configure.py

@@ -6,7 +6,6 @@
 import yaml
 import os
 import re
-from pkg_resources import resource_filename, resource_stream
 import glob
 import argparse
 import sys
@@ -17,6 +16,7 @@
 from ..exceptions import InvalidConfiguration
 from ..utilities import comma_split, percentage, merge_dictionaries
 from ..utilities.namespace import Namespace
+from ..utilities.resources import resource_binary_stream, resource_file
 from ..configuration.configurator import load_and_validate_config
 from ..configuration import print_config
 import tempfile
@@ -136,9 +136,9 @@ def create_config(args):
     if args.scoring is not None:
         if args.copy_scoring is not False:
             with open(args.copy_scoring, "wt") as out:
-                with resource_stream("Mikado", os.path.join("configuration",
-                                                            "scoring_files",
-                                                            args.scoring)) as original:
+                with resource_binary_stream("Mikado", os.path.join("configuration",
+                                                                    "scoring_files",
+                                                                    args.scoring)) as original:
                     for line in original:
                         print(line.decode().rstrip(), file=out)
             args.scoring = args.copy_scoring
@@ -224,7 +224,7 @@ def configure_parser():
     :rtype: argparse.ArgumentParser
     """
 
-    scoring_folder = resource_filename("Mikado", os.path.join("configuration", "scoring_files"))
+    scoring_folder = resource_file("Mikado", os.path.join("configuration", "scoring_files"))
     trailing = re.compile(r"^{}".format(os.path.sep))
     fold_path = re.compile(scoring_folder)
 

Mikado/utilities/resources.py

@@ -0,0 +1,31 @@
+"""Helpers for accessing package data files."""
+
+import os
+from importlib import resources
+
+
+def _resource_parts(*parts):
+    for part in parts:
+        for chunk in str(part).replace(os.sep, "/").split("/"):
+            if chunk not in ("", "."):
+                yield chunk
+
+
+def resource(package, *path_parts):
+    return resources.files(package).joinpath(*_resource_parts(*path_parts))
+
+
+def resource_file(package, *parts):
+    return str(resource(package, *parts))
+
+
+def resource_binary_stream(package, *parts):
+    return resource(package, *parts).open("rb")
+
+
+def resource_exists(package, *parts):
+    return resource(package, *parts).exists()
+
+
+def resource_listdir(package, *parts):
+    return [entry.name for entry in resource(package, *parts).iterdir()]

environment.yml

@@ -4,7 +4,7 @@ channels:
   - bioconda
 dependencies:
   - python>3.8,<3.11
-  - setuptools<80.9
+  - setuptools
   - cython==0.29.32
   - biopython==1.79
   - docutils==0.19

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools<80.9","wheel==0.37.1","Cython==0.29.32","numpy==1.23.3","scipy==1.11.1"]
+requires = ["setuptools","wheel==0.37.1","Cython==0.29.32","numpy==1.23.3","scipy==1.11.1"]
 build-backend = "setuptools.build_meta"
 
 [tool.pytest]

requirements.txt

@@ -1,4 +1,3 @@
-setuptools<80.9
 cython==0.29.32
 biopython==1.79
 docutils==0.19

sample_data/Snakefile

@@ -10,12 +10,12 @@ from Mikado.configuration.configuration import MikadoConfiguration
 import subprocess
 import gzip
 from snakemake import logger as snake_logger
-import pkg_resources
+from Mikado.utilities.resources import resource_file
 import Mikado
 import dataclasses
 import marshmallow_dataclass
 
-prod_conda = pkg_resources.resource_filename("Mikado.daijin", os.path.join("envs", "prodigal.yaml"))
+prod_conda = resource_file("Mikado.daijin", os.path.join("envs", "prodigal.yaml"))
 swissprot = "uniprot_sprot_plants.fasta.gz"
 swissprot_noat = "uniprot_sprot_plants.not_at.fasta"
 

setup.cfg

@@ -1,6 +1,6 @@
 [options]
 setup_requires =
-    setuptools<80.9
+    setuptools
 
 [aliases]
 test=pytest
@@ -34,4 +34,3 @@ markers =
 #     # See https://docs.python.org/3/library/warnings.html and
 #     # https://docs.pytest.org/en/latest/warnings.html
 #     #
-#     ignore:^Use of \.\. or absolute path in a resource path is not allowed and will raise exceptions in a future release\.$:DeprecationWarning:pkg_resources

setup.py

@@ -87,7 +87,7 @@
     author_email="lucventurini@gmail.com",
     license="LGPL-3.0-or-later",
     tests_require=["pytest"],
-    setup_requires=["setuptools<80.9"],
+    setup_requires=["setuptools"],
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Topic :: Scientific/Engineering :: Bio-Informatics",