Merge branch 'master' into schema_cleanup

.github/workflows/docs.yml

@@ -54,7 +54,7 @@ jobs:
           init-shell: >-
             bash
             powershell
-          cache-environment: true
+          cache-environment: false
 
       - name: activate build env
         run: micromamba activate rtd

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
           - mdformat-config
   # ----- Python formatting -----
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.7
+    rev: v0.5.6
     hooks:
     # Run ruff linter.
     - id: ruff
@@ -39,7 +39,7 @@ repos:
     # Run ruff formatter.
     - id: ruff-format
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: 2.1.3
+    rev: 2.2.1
     hooks:
     - id: pyproject-fmt
   - repo: https://github.com/abravalheri/validate-pyproject
@@ -48,7 +48,7 @@ repos:
       - id: validate-pyproject
   # ----- Jupyter Notebooks -----
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.5
+    rev: 1.8.7
     hooks:
       - id: nbqa-black
       - id: nbqa-ruff  # ruff handles isort

.ruff.toml

@@ -77,5 +77,5 @@ required-imports = [
     "from __future__ import annotations",
 ]
 
-[flake8-import-conventions]
+[lint.flake8-import-conventions]
 extend-aliases = { xarray = "xr" }

CHANGELOG.md

@@ -5,10 +5,13 @@
 ### Fixes
 
 - rename (fix typo) argument to `lcs_child_in_parent` in `CoordinateSystemManager.add_cs`  \[{pull}`936`\].
+- replace usages of `pkg_resources` with `importlib.metadata` \[{pull}`941`\].
+- replace usages of `copy_arrays` with `memmap` for `asdf>=3.1.0` \[{pull}`940`\].
 
 ### Dependencies
 
 - pin `weldx-widgets>=0.2.3` for viz \[{pull}`939`\].
+- pin `pint>=0.21` \[{pull}`941`\].
 
 ## 0.6.8 (07.06.2024)
 

doc/rtd_environment.yml

@@ -32,5 +32,5 @@ dependencies:
   # pip packages
   - pip
   - pip:
-    - ../
-    - ./json_mime_render_plugin/
+    - weldx @ file:/../..//
+    - json_mime_render_plugin @ file:/..//json_mime_render_plugin

pyproject.toml

@@ -51,13 +51,23 @@ dependencies = [
   "networkx>=2.8.2",
   "numpy>=1.20,<2",
   "pandas>=1.5",
-  "pint>=0.18",
+  "pint>=0.21",
   "pint-xarray>=0.3",
   "psutil",
   "scipy>=1.6.2",
   "sympy>=1.6",
   "xarray>=2022.9",
 ]
+optional-dependencies.docs = [
+  "docutils>=0.19",
+  "numpydoc>=0.5",
+  "pydata-sphinx-theme<0.15",             # parallel-write-unsafe
+  "sphinx>=4.1.1,==7.2",
+  "sphinx-autodoc-typehints>=1.21.8,==2",
+  "sphinx-copybutton==0.5",
+  "typing-extensions",
+  "urllib3<2",
+]
 optional-dependencies.media = [
   "av",
   "dask-image",

weldx/asdf/file.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import copy
+import importlib.metadata
 import io
 import pathlib
 import warnings
@@ -42,12 +43,23 @@
 __all__ = [
     "WeldxFile",
     "DEFAULT_ARRAY_COMPRESSION",
-    "DEFAULT_ARRAY_COPYING",
+    "DEFAULT_MEMORY_MAPPING",
     "DEFAULT_ARRAY_INLINE_THRESHOLD",
     "_PROTECTED_KEYS",
 ]
 
 
+def asdf_open_memory_mapping_kwarg(memmap: bool) -> dict:
+    if tuple(importlib.metadata.version("asdf").split(".")) >= (
+        "3",
+        "1",
+        "0",
+    ):
+        return {"memmap": memmap}
+    else:
+        return {"copy_arrays": not memmap}
+
+
 @contextmanager
 def reset_file_position(fh: SupportsFileReadWrite):
     """Reset the internal position of the given file after leaving the context.
@@ -66,8 +78,8 @@ def reset_file_position(fh: SupportsFileReadWrite):
 DEFAULT_ARRAY_COMPRESSION = "input"
 """All arrays will be compressed using this algorithm, if not specified by user."""
 
-DEFAULT_ARRAY_COPYING = True
-"""Stored Arrays will be copied to memory, or not. If False, use memory mapping."""
+DEFAULT_MEMORY_MAPPING = False
+"""Stored Arrays will be memory-mapped, or not. If True, use memory mapping."""
 
 DEFAULT_ARRAY_INLINE_THRESHOLD = 10
 """Arrays with less or equal elements will be inlined (stored as string, not binary)."""
@@ -148,8 +160,8 @@ class WeldxFile(_ProtectedViewDict):
         - ``lz4``: Use lz4 compression.
         - ``input``: Use the same compression as in the file read.
           If there is no prior file, acts as None.
-    copy_arrays :
-        When `False`, when reading files, attempt to memory map (memmap) underlying data
+    memmap :
+        When `True`, when reading files, attempt to memory map (memmap) underlying data
         arrays when possible. This avoids blowing the memory when working with very
         large datasets.
     array_inline_threshold :
@@ -219,19 +231,19 @@ def __init__(
         ) = None,
         software_history_entry: Mapping = None,
         compression: str = DEFAULT_ARRAY_COMPRESSION,
-        copy_arrays: bool = DEFAULT_ARRAY_COPYING,
+        memmap: bool = DEFAULT_MEMORY_MAPPING,
         array_inline_threshold: int = DEFAULT_ARRAY_INLINE_THRESHOLD,
     ):
         if write_kwargs is None:
             write_kwargs = dict(all_array_compression=compression)
 
         if asdffile_kwargs is None:
-            asdffile_kwargs = dict(copy_arrays=copy_arrays)
+            asdffile_kwargs = asdf_open_memory_mapping_kwarg(memmap=memmap)
 
         # this parameter is now (asdf-2.8) a asdf.config parameter, so we store it here.
         self._array_inline_threshold = array_inline_threshold
 
-        # TODO: ensure no mismatching args for compression and copy_arrays.
+        # TODO: ensure no mismatching args for compression and memmap.
         self._write_kwargs = write_kwargs
         self._asdffile_kwargs = asdffile_kwargs
 

weldx/asdf/util.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import importlib.metadata
 from collections.abc import Callable, Hashable, Mapping, MutableMapping, Set
 from contextlib import contextmanager
 from io import BytesIO, TextIOBase
@@ -153,7 +154,7 @@ def read_buffer_context(
         Buffer containing ASDF file contents
     open_kwargs
         Additional keywords to pass to `asdf.AsdfFile.open`
-        Extensions are always set, ``copy_arrays=True`` is set by default.
+        Extensions are always set, ``memmap=False`` is set by default.
 
     Returns
     -------
@@ -162,7 +163,13 @@ def read_buffer_context(
 
     """
     if open_kwargs is None:
-        open_kwargs = {"copy_arrays": True, "lazy_load": False}
+        open_kwargs = {"memmap": False, "lazy_load": False}
+
+    if "memmap" in open_kwargs and tuple(
+        importlib.metadata.version("asdf").split(".")
+    ) < ("3", "1", "0"):
+        open_kwargs["copy_arrays"] = not open_kwargs["memmap"]
+        del open_kwargs["memmap"]
 
     buffer.seek(0)
 
@@ -194,7 +201,7 @@ def read_buffer(
         Buffer containing ASDF file contents
     open_kwargs
         Additional keywords to pass to `asdf.AsdfFile.open`
-        Extensions are always set, ``copy_arrays=True`` is set by default.
+        Extensions are always set, ``memmap=False`` is set by default.
 
     Returns
     -------
@@ -224,7 +231,7 @@ def write_read_buffer_context(
         Extensions are always set.
     open_kwargs
         Additional keywords to pass to `asdf.AsdfFile.open`
-        Extensions are always set, ``copy_arrays=True`` is set by default.
+        Extensions are always set, ``memmap=False`` is set by default.
 
     Returns
     -------
@@ -252,7 +259,7 @@ def write_read_buffer(
         Extensions are always set.
     open_kwargs
         Additional keywords to pass to `asdf.AsdfFile.open`
-        Extensions are always set, ``copy_arrays=True`` is set by default.
+        Extensions are always set, ``memmap=False`` is set by default.
 
     Returns
     -------

weldx/config.py

@@ -2,10 +2,11 @@
 
 from __future__ import annotations
 
+import importlib.metadata
+import sys
 from pathlib import Path
 
 import asdf
-import pkg_resources
 import yaml
 from asdf.config import ResourceMappingProxy
 from asdf.versioning import AsdfVersion, split_tag_version
@@ -175,7 +176,13 @@ def enable_quality_standard(name: str, version: AsdfVersion | str = None):
     @staticmethod
     def load_installed_standards():
         """Load all standards that are installed to the active virtual environment."""
-        for entry_point in pkg_resources.iter_entry_points("weldx.standard"):
+        if sys.version_info < (3, 10):
+            entry_points = importlib.metadata.entry_points().get("weldx.standard", [])
+        else:
+            entry_points = importlib.metadata.entry_points().select(
+                group="weldx.standard"
+            )
+        for entry_point in entry_points:
             standards = entry_point.load()()
             if not isinstance(standards, list):
                 standards = [standards]

weldx/constants.py

@@ -16,7 +16,6 @@
 
 WELDX_UNIT_REGISTRY = pint.UnitRegistry(
     preprocessors=[
-        lambda string: string.replace("%", "percent"),  # allow %-sign
         lambda string: string.replace("Δ°", "delta_deg"),  # parse Δ° for temperature
     ],
     force_ndarray_like=True,

weldx/tests/_helpers.py

@@ -4,7 +4,6 @@
 
 import numpy as np
 import pint
-from pkg_resources import get_distribution
 
 from weldx.constants import Q_
 from weldx.geometry import _vector_is_close as vector_is_close
@@ -130,7 +129,7 @@ def matrix_is_close(mat_a, mat_b, abs_tol=1e-9) -> bool:
         return False
 
     atol_unit = 1.0
-    if isinstance(mat_b, pint.Quantity) and get_distribution("pint").version >= "0.21":
+    if isinstance(mat_b, pint.Quantity):
         atol_unit = mat_b.u
 
     return np.all(np.isclose(mat_a, mat_b, atol=abs_tol * atol_unit)).__bool__()