From 50f62c61fb90fc65f0412066138888034db06111 Mon Sep 17 00:00:00 2001
From: Thomas Holder <thomas.holder@rentschler.de>
Date: Sun, 10 Dec 2023 11:59:21 +0100
Subject: [PATCH] Refactor deprecated pkg_resources usage

- Locate resources relative to `__file__`
- Support egg/zip with `open_file_for_reading`
---
 propka/bonds.py     |  9 +++++----
 propka/input.py     | 19 +++++++++++++++----
 propka/lib.py       |  4 ++--
 tests/test_input.py | 29 +++++++++++++++++++++++++++++
 4 files changed, 51 insertions(+), 10 deletions(-)
 create mode 100644 tests/test_input.py

diff --git a/propka/bonds.py b/propka/bonds.py
index 10190db..396ec86 100644
--- a/propka/bonds.py
+++ b/propka/bonds.py
@@ -8,7 +8,7 @@
 import logging
 import math
 import json
-import pkg_resources
+from pathlib import Path
 import propka.calculations
 from typing import TYPE_CHECKING
 
@@ -35,6 +35,8 @@ class BondMaker:
     TODO - the documentation for this class needs to be improved.
     """
     def __init__(self):
+        from propka.input import open_file_for_reading
+
         # predefined bonding distances
         self.distances = {'S-S': DISULFIDE_DISTANCE,
                           'F-F': FLUORIDE_DISTANCE}
@@ -51,9 +53,8 @@ def __init__(self):
             + [self.default_dist_squared])
         self.max_sq_distance = max(distances)
         # protein bonding data
-        self.data_file_name = (
-            pkg_resources.resource_filename(__name__, 'protein_bonds.json'))
-        with open(self.data_file_name, 'rt') as json_file:
+        self.data_file_name = Path(__file__).parent / 'protein_bonds.json'
+        with open_file_for_reading(self.data_file_name) as json_file:
             self.protein_bonds = json.load(json_file)
         self.intra_residue_backbone_bonds = {'N': ['CA'], 'CA': ['N', 'C'],
                                              'C': ['CA', 'O'], 'O': ['C']}
diff --git a/propka/input.py b/propka/input.py
index c62ff84..e5658d8 100644
--- a/propka/input.py
+++ b/propka/input.py
@@ -10,10 +10,11 @@
    :func:`get_atom_lines_from_input`) have been removed.
 """
 import typing
-from typing import Iterator, Tuple
+from typing import Iterator, Tuple, Union
 import contextlib
+import io
+import zipfile
 from pathlib import Path
-from pkg_resources import resource_filename
 from propka.lib import protein_precheck
 from propka.atom import Atom
 from propka.conformation_container import ConformationContainer
@@ -34,6 +35,16 @@ def open_file_for_reading(
         input_file.seek(0)
         return contextlib.nullcontext(input_file)
 
+    input_file = Path(input_file)
+
+    if not input_file.is_file():
+        for p in input_file.parents:
+            if not zipfile.is_zipfile(p):
+                continue
+            zf = zipfile.ZipFile(p)
+            stream = zf.open(str(input_file.relative_to(p)))
+            return io.TextIOWrapper(stream)
+
     return contextlib.closing(open(input_file, 'rt'))
 
 
@@ -122,7 +133,7 @@ def read_molecule_file(filename: str, mol_container: MolecularContainer, stream=
     return mol_container
 
 
-def read_parameter_file(input_file, parameters: Parameters) -> Parameters:
+def read_parameter_file(input_file: Union[Path, str], parameters: Parameters) -> Parameters:
     """Read a parameter file.
 
     Args:
@@ -133,7 +144,7 @@ def read_parameter_file(input_file, parameters: Parameters) -> Parameters:
     """
     # try to locate the parameter file
     try:
-        ifile = resource_filename(__name__, input_file)
+        ifile = Path(__file__).parent / input_file
         input_ = open_file_for_reading(ifile)
     except (IOError, FileNotFoundError, ValueError, KeyError):
         input_ = open_file_for_reading(input_file)
diff --git a/propka/lib.py b/propka/lib.py
index 5a3d204..2140027 100644
--- a/propka/lib.py
+++ b/propka/lib.py
@@ -8,7 +8,7 @@
 import sys
 import logging
 import argparse
-import pkg_resources
+from pathlib import Path
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -246,7 +246,7 @@ def build_parser(parser=None):
         "--version", action="version", version=f"%(prog)s {propka.__version__}")
     group.add_argument(
         "-p", "--parameters", dest="parameters",
-        default=pkg_resources.resource_filename(__name__, "propka.cfg"),
+        default=str(Path(__file__).parent / "propka.cfg"),
         help="set the parameter file [{default:s}]")
     try:
         group.add_argument(
diff --git a/tests/test_input.py b/tests/test_input.py
new file mode 100644
index 0000000..af8ed5a
--- /dev/null
+++ b/tests/test_input.py
@@ -0,0 +1,29 @@
+import propka.input as m
+import zipfile
+
+
+def test_open_file_for_reading(tmp_path):
+    path = tmp_path / "tmp.txt"
+    path.write_text("One\nTwo\nThree\n")
+    # str
+    with m.open_file_for_reading(str(path)) as outer:
+        assert outer.read() == "One\nTwo\nThree\n"
+    assert outer.closed
+    # Path
+    with m.open_file_for_reading(path) as outer:
+        # TextIO
+        with m.open_file_for_reading(outer) as inner:
+            assert inner.readline() == "One\n"
+        assert not outer.closed
+        assert outer.readline() == "Two\n"
+    assert outer.closed
+
+
+def test_open_file_for_reading__zipfile(tmp_path):
+    zippath = tmp_path / "tmp.zip"
+    arcname = "foo/bar.txt"
+    with zipfile.ZipFile(zippath, "w") as ziphandle:
+        ziphandle.writestr(arcname, "One\nTwo\nThree\n")
+    with m.open_file_for_reading(zippath / arcname) as outer:
+        assert outer.readline() == "One\n"
+    assert outer.closed