Merge branch 'master' into schema_cleanup

.github/workflows/build_pkg.yml

@@ -41,7 +41,7 @@ jobs:
           fetch-depth: 0 # Fetch all history for all tags and branches
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: ./devtools/conda.recipe/build_env.yml
           environment-name: build_env

.github/workflows/docs.yml

@@ -47,7 +47,7 @@ jobs:
           fetch-depth: 0 # Fetch all history for all tags and branches
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: ./doc/rtd_environment.yml
           environment-name: rtd

.github/workflows/pytest.yml

@@ -47,7 +47,7 @@ jobs:
           setup_requires: 'include'
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: ./environment.yml
           environment-name: weldx
@@ -120,7 +120,7 @@ jobs:
 
       - name: codecov.io
         if: matrix.py == '3.10'
-        uses: codecov/codecov-action@v3.1.5
+        uses: codecov/codecov-action@v4.1.0
 
   compat:
     name: pytest
@@ -147,7 +147,7 @@ jobs:
           setup_requires: 'include'
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: ./environment.yml
           environment-name: weldx

.github/workflows/pytest_asdf.yml

@@ -33,7 +33,7 @@ jobs:
           setup_requires: 'include'
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: ./environment.yml
           environment-name: weldx

.github/workflows/static_analysis.yml

@@ -20,7 +20,7 @@ jobs:
         with:
           python-version: 3.x
       - name: Lint
-        uses: pre-commit/action@v3.0.0
+        uses: pre-commit/action@v3.0.1
         with:
           extra_args: --all-files --show-diff-on-failure
 
@@ -49,7 +49,7 @@ jobs:
           key: ${{ runner.os }}-${{ hashFiles('./environment.yml') }}
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: ./environment.yml
           environment-name: weldx

.pre-commit-config.yaml

@@ -34,18 +34,18 @@ repos:
     - id: pyupgrade
       args: [--py39-plus]
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.1.1
     hooks:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.2.0
     hooks:
       - id: ruff
         args:
           - --quiet
           - --fix
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.15
+    rev: v0.16
     hooks:
       - id: validate-pyproject
   # ----- Jupyter Notebooks -----

CHANGELOG.md

@@ -1,10 +1,20 @@
 # Release Notes
 
+## 0.6.8 (unreleased)
+
+### Changes
+
+- use pandas.to_timedelta function to pass units to the TimeDeltaIndex object \[{pull}`918`\].
+
+### Dependencies
+
+- unpin nbval testing dependency.
+
 ## 0.6.7 (2023.08.24)
 
 ### Added
 
-- added `weldx.exceptions` module with `WeldxException` \[{pull}`871`\] .
+- added `weldx.exceptions` module with `WeldxException` \[{pull}`871`\].
 
 ### Fixes
 

conftest.py

@@ -1,4 +1,5 @@
 """PyTest configuration."""
+
 import pytest
 
 collect_ignore_glob = [

devtools/scripts/clean_notebooks.py

@@ -1,4 +1,5 @@
 """Clean up jupyter notebooks in main directory."""
+
 from __future__ import annotations
 
 import json

devtools/scripts/update_manifest.py

@@ -1,4 +1,5 @@
 """Update the manifest file with schema files found in this directory."""
+
 from pathlib import Path
 
 import yaml

doc/rtd_environment.yml

@@ -2,17 +2,18 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.9
+  - python=3.10
   - setuptools_scm
   # weldx base dependencies
   - numpy>=1.18
   - pandas>=1.0
   - xarray>=0.15
   - pint>=0.11
-  - scipy>=1.6.2
+  - scipy>=1.6.2,<1.12
   - sympy>=1.6
-  - asdf>=2.8
+  - asdf>=2.8,<3
   - bottleneck>=1.3
+  - matplotlib<3.8
   # notebook execution
   - myst-nb
   - ipykernel
@@ -24,7 +25,7 @@ dependencies:
   - urllib3<2
   #- jinja2=3.0
   - sphinx-copybutton
-  - pydata-sphinx-theme
+  - pydata-sphinx-theme<0.15 # parallel-write-unsafe
   - numpydoc>=0.5
   - sphinx-autodoc-typehints>=1.21.8
   - typing_extensions

doc/src/tutorials/util.py

@@ -1,4 +1,5 @@
 """Common util functions used in weldx tutorials."""
+
 from pathlib import Path
 
 tutorials_dir = Path(__file__).parent.absolute()

pyproject.toml

@@ -37,7 +37,7 @@ requires-python = ">=3.9"
 dependencies = [
     "numpy >=1.20",
     "asdf >=2.15.1",
-    "pandas >=1.0",
+    "pandas >=1.5",
     "xarray >=2022.9.0",
     "scipy >=1.6.2",
     "sympy >=1.6",
@@ -64,7 +64,7 @@ test = [
     "pytest >=6",
     "pytest-cov",
     "pytest-xdist",
-    "nbval <0.10",
+    "nbval",
 ]
 vis = [
     "weldx_widgets >=0.2",
@@ -125,6 +125,7 @@ filterwarnings = [
     "ignore::DeprecationWarning:traittypes.*:",
     "ignore:Passing method to :FutureWarning:xarray.*:",
     "error::pint.UnitStrippedWarning",
+    #"error::FutureWarning",  # todo: we want to enable this, as it notifies us about upcoming failures due to upstream changes.
 ]
 
 [tool.coverage.run]

weldx/__init__.py

@@ -116,6 +116,7 @@
     asdf.validators
 
 """
+
 # isort:skip_file
 import warnings
 

weldx/asdf/__init__.py

@@ -1,4 +1,5 @@
 """This submodule contains ASDF related weldx extensions and schemas."""
+
 # isort:skip_file
 
 from weldx import tags  # implement tags before the asdf extensions here just to be safe

weldx/asdf/cli/welding_schema.py

@@ -1,4 +1,5 @@
 """single_pass_weld schema."""
+
 from __future__ import annotations
 
 import sys

weldx/asdf/extension.py

@@ -1,4 +1,5 @@
 """ASDF-extensions for weldx types."""
+
 from __future__ import annotations
 
 from asdf.extension import ManifestExtension

weldx/asdf/file.py

@@ -1,4 +1,5 @@
 """`WeldxFile` wraps creation and updating of ASDF files and underlying files."""
+
 from __future__ import annotations
 
 import copy
@@ -211,8 +212,7 @@ def __init__(
         write_kwargs: Mapping = None,
         tree: Mapping = None,
         sync: bool = True,
-        custom_schema: None
-        | (
+        custom_schema: None | (
             types_path_like,
             tuple[None, types_path_like],
         ) = None,

weldx/asdf/util.py

@@ -1,4 +1,5 @@
 """Utilities for asdf files."""
+
 from __future__ import annotations
 
 from collections.abc import Callable, Hashable, Mapping, MutableMapping, Set

weldx/asdf/validators.py

@@ -1,4 +1,5 @@
 """ASDF-validators for weldx types."""
+
 from __future__ import annotations
 
 import re

weldx/config.py

@@ -1,4 +1,5 @@
 """Classes and functions to configure the WelDX package."""
+
 from __future__ import annotations
 
 from pathlib import Path

weldx/constants.py

@@ -1,4 +1,5 @@
 """Define constants for global library use."""
+
 from pathlib import Path as _Path
 
 import pint

weldx/core/__init__.py

@@ -1,4 +1,5 @@
 """Collection of common classes and functions."""
+
 # isort:skip_file
 from weldx.core.math_expression import MathematicalExpression
 from weldx.core.generic_series import GenericSeries

weldx/core/generic_series.py

@@ -1,4 +1,5 @@
 """Contains GenericSeries class."""
+
 from __future__ import annotations
 
 from collections.abc import Callable, Mapping

weldx/core/math_expression.py

@@ -1,4 +1,5 @@
 """Contains the MathematicalExpression class."""
+
 from __future__ import annotations
 
 from typing import Any, Union

weldx/core/spatial_series.py

@@ -1,4 +1,5 @@
 """Contains the SpatialSeries class."""
+
 from __future__ import annotations
 
 import pint

weldx/core/time_series.py

@@ -1,4 +1,5 @@
 """Contains TimeSeries class."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any

weldx/geometry.py

@@ -1,4 +1,5 @@
 """Provides classes to define lines and surfaces."""
+
 from __future__ import annotations
 
 import copy

weldx/schemas/weldx.bam.de/weldx/time/time-0.1.0.yaml

@@ -34,7 +34,7 @@ examples:
         values: !<asdf://weldx.bam.de/weldx/tags/time/datetimeindex-0.1.0>
           start: !<asdf://weldx.bam.de/weldx/tags/time/timestamp-0.1.0> '2021-01-01T00:00:00'
           end: !<asdf://weldx.bam.de/weldx/tags/time/timestamp-0.1.0> '2021-01-01T00:00:02'
-          freq: S
+          freq: s
           min: !<asdf://weldx.bam.de/weldx/tags/time/timestamp-0.1.0> '2021-01-01T00:00:00'
           max: !<asdf://weldx.bam.de/weldx/tags/time/timestamp-0.1.0> '2021-01-01T00:00:02'
         reference_time: !<asdf://weldx.bam.de/weldx/tags/time/timestamp-0.1.0> '2021-01-01T00:00:00'

weldx/schemas/weldx.bam.de/weldx/time/timedeltaindex-0.1.0.yaml

@@ -13,7 +13,7 @@ examples:
       !<asdf://weldx.bam.de/weldx/tags/time/timedeltaindex-0.1.0>
         start: !<asdf://weldx.bam.de/weldx/tags/time/timedelta-0.1.0> P0DT0H0M0S
         end: !<asdf://weldx.bam.de/weldx/tags/time/timedelta-0.1.0> P0DT0H0M10S
-        freq: 2S
+        freq: 2s
         min: !<asdf://weldx.bam.de/weldx/tags/time/timedelta-0.1.0> P0DT0H0M0S
         max: !<asdf://weldx.bam.de/weldx/tags/time/timedelta-0.1.0> P0DT0H0M10S
   -

weldx/tags/base_types.py

@@ -1,4 +1,5 @@
 """Module providing ASDF implementations for basic python types."""
+
 from uuid import UUID
 
 from asdf.asdf import SerializationContext

weldx/tags/core/data_array.py

@@ -1,4 +1,5 @@
 """Serialization for xarray.DataArray."""
+
 from __future__ import annotations
 
 import pint

weldx/tags/core/file.py

@@ -1,4 +1,5 @@
 """Contains classes for the asdf serialization of an external file."""
+
 from copy import deepcopy
 
 import numpy as np

weldx/tags/core/media_file.py

@@ -1,4 +1,5 @@
 """Contains classes for the asdf serialization of media files."""
+
 import pathlib
 
 from weldx.asdf.types import WeldxConverter

weldx/tags/core/time_series.py

@@ -1,4 +1,5 @@
 """Contains the serialization class for the weldx.core.TimeSeries."""
+
 from __future__ import annotations
 
 import pint

weldx/tags/time/timedeltaindex.py

@@ -8,6 +8,14 @@
 
 __all__ = ["TimedeltaIndexConverter"]
 
+PANDAS_OLD_UNIT_SUFFIXES = dict(H="h", T="min", S="s", L="ms", U="us", N="ns")
+
+
+def _handle_converted_pd_tdi_units(node: TaggedDict):
+    """Convert changed units in Pandas.Datetimeindex to valid values."""
+    for suf in PANDAS_OLD_UNIT_SUFFIXES:
+        node["freq"] = node["freq"].replace(suf, PANDAS_OLD_UNIT_SUFFIXES[suf])
+
 
 class TimedeltaIndexConverter(WeldxConverter):
     """A simple implementation of serializing pandas TimedeltaIndex."""
@@ -33,6 +41,7 @@ def to_yaml_tree(self, obj: pd.TimedeltaIndex, tag: str, ctx) -> dict:
     def from_yaml_tree(self, node: dict, tag: str, ctx):
         """Construct TimedeltaIndex from tree."""
         if "freq" in node:
+            _handle_converted_pd_tdi_units(node)
             return pd.timedelta_range(
                 start=node["start"], end=node["end"], freq=node["freq"]
             )
@@ -43,6 +52,7 @@ def from_yaml_tree(self, node: dict, tag: str, ctx):
     def shape_from_tagged(node: TaggedDict) -> list[int]:
         """Calculate the shape from static tagged tree instance."""
         if "freq" in node:
+            _handle_converted_pd_tdi_units(node)
             tdi_temp = pd.timedelta_range(
                 start=str(node["start"]),  # can't handle TaggedString directly
                 end=str(node["end"]),

weldx/tests/asdf_tests/test_asdf_aws_schema.py

@@ -1,4 +1,5 @@
 """Test ASDF serialization of AWS schema definitions."""
+
 import pytest
 
 from weldx.asdf.util import write_read_buffer_context

weldx/tests/asdf_tests/test_asdf_base_types.py

@@ -1,4 +1,5 @@
 """Tests asdf implementations of python base types."""
+
 import uuid
 
 import numpy as np