From 71d4ec04c95739c061d12b551d9cb9f86811134f Mon Sep 17 00:00:00 2001
From: Nicholas Devenish <ndevenish@gmail.com>
Date: Thu, 29 Jun 2023 22:24:38 +0100
Subject: [PATCH] Use importlib instead of pkg_resources (#643)

pkg_resources is now deprecated, as importlib has covered
most use-cases since python 3.8. This removes the code
causing warnings in downstream tests.

Also suppress numpy 'product' warnings when running pytest.
---
 libtbx_refresh.py                  | 11 +++--------
 newsfragments/643.misc             |  1 +
 pytest.ini                         |  1 +
 src/dxtbx/format/Registry.py       |  5 ++---
 src/dxtbx/model/experiment_list.py |  6 ++----
 src/dxtbx/model/profile.py         |  5 ++---
 6 files changed, 11 insertions(+), 18 deletions(-)
 create mode 100644 newsfragments/643.misc

diff --git a/libtbx_refresh.py b/libtbx_refresh.py
index f80786519..eef867e0f 100644
--- a/libtbx_refresh.py
+++ b/libtbx_refresh.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import contextlib
+import importlib
 import inspect
 import io
 import os
@@ -17,11 +18,6 @@
 except ModuleNotFoundError:
     pass
 
-try:
-    import pkg_resources
-except ModuleNotFoundError:
-    pkg_resources = None
-
 
 def _install_setup_readonly_fallback(package_name: str):
     """
@@ -67,9 +63,8 @@ def _install_setup_readonly_fallback(package_name: str):
     if import_path not in sys.path:
         sys.path.insert(0, import_path)
 
-    # ...and add to the existing pkg_resources working_set
-    if pkg_resources:
-        pkg_resources.working_set.add_entry(import_path)
+    # ...and make sure it is picked up by the import system
+    importlib.invalidate_caches()
 
     # This is already generated by this point, but will get picked up
     # on the second libtbx.refresh.
diff --git a/newsfragments/643.misc b/newsfragments/643.misc
new file mode 100644
index 000000000..0780b3d13
--- /dev/null
+++ b/newsfragments/643.misc
@@ -0,0 +1 @@
+Move from deprecated pkg_resources to importlib.
diff --git a/pytest.ini b/pytest.ini
index a3adf716c..a89237729 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -5,6 +5,7 @@ filterwarnings =
     ignore:numpy.dtype size changed:RuntimeWarning
     ignore:Datablocks are deprecated:UserWarning
     ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning
+    ignore:`product` is deprecated as of NumPy:DeprecationWarning:h5py|numpy
 junit_family = legacy
 markers =
     regression: dxtbx regression test
diff --git a/src/dxtbx/format/Registry.py b/src/dxtbx/format/Registry.py
index b7034a22e..03dc39e0d 100644
--- a/src/dxtbx/format/Registry.py
+++ b/src/dxtbx/format/Registry.py
@@ -5,12 +5,11 @@
 """
 from __future__ import annotations
 
+import importlib.metadata
 import os
 import typing
 from typing import Callable
 
-import pkg_resources
-
 from dxtbx.util import get_url_scheme
 
 if typing.TYPE_CHECKING:
@@ -35,7 +34,7 @@ def get_format_class_index() -> dict[str, tuple[Callable[[], type[Format]], list
     """
     if not hasattr(get_format_class_index, "cache"):
         class_index = {}
-        for e in pkg_resources.iter_entry_points("dxtbx.format"):
+        for e in importlib.metadata.entry_points()["dxtbx.format"]:
             if ":" in e.name:
                 format_name, base_classes_str = e.name.split(":", 1)
                 base_classes = tuple(base_classes_str.split(","))
diff --git a/src/dxtbx/model/experiment_list.py b/src/dxtbx/model/experiment_list.py
index 9770129ed..d415e1ccd 100644
--- a/src/dxtbx/model/experiment_list.py
+++ b/src/dxtbx/model/experiment_list.py
@@ -3,6 +3,7 @@
 import collections
 import copy
 import errno
+import importlib.metadata
 import itertools
 import json
 import logging
@@ -11,8 +12,6 @@
 import pickle
 from typing import Any, Callable, Generator, Iterable
 
-import pkg_resources
-
 import dxtbx.datablock
 from dxtbx.datablock import (
     BeamComparison,
@@ -323,7 +322,6 @@ def decode(self):
         # a sensible experiment.
         el = ExperimentList()
         for eobj in self._obj["experiment"]:
-
             # Get the models
             identifier = eobj.get("identifier", "")
             beam = self._lookup_model("beam", eobj)
@@ -467,7 +465,7 @@ def _lookup_model(self, name, experiment_dict):
     @staticmethod
     def _scaling_model_from_dict(obj):
         """Get the scaling model from a dictionary."""
-        for entry_point in pkg_resources.iter_entry_points("dxtbx.scaling_model_ext"):
+        for entry_point in importlib.metadata.entry_points()["dxtbx.scaling_model_ext"]:
             if entry_point.name == obj["__id__"]:
                 return entry_point.load().from_dict(obj)
 
diff --git a/src/dxtbx/model/profile.py b/src/dxtbx/model/profile.py
index 0fbb0434b..ba3852586 100644
--- a/src/dxtbx/model/profile.py
+++ b/src/dxtbx/model/profile.py
@@ -1,9 +1,8 @@
 from __future__ import annotations
 
+import importlib.metadata
 import logging
 
-import pkg_resources
-
 
 class ProfileModelFactory:
     """
@@ -17,7 +16,7 @@ def from_dict(obj):
         """
         if obj is None:
             return None
-        for entry_point in pkg_resources.iter_entry_points("dxtbx.profile_model"):
+        for entry_point in importlib.metadata.entry_points()["dxtbx.profile_model"]:
             if entry_point.name == obj["__id__"]:
                 return entry_point.load().from_dict(obj)
         logging.getLogger("dxtbx.model.profile").warn(