Merge branch 'master' into py312

.github/dependabot.yml

@@ -10,3 +10,5 @@ updates:
       interval: "weekly"
       day: "sunday"
       timezone: "Europe/Berlin"
+    labels:
+      - "dependabot"

.github/release.yml

@@ -0,0 +1,7 @@
+# .github/release.yml
+
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.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@v1.8.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-file: ./devtools/conda.recipe/build_env.yml
           environment-name: build_env

.github/workflows/docs.yml

@@ -47,14 +47,14 @@ jobs:
           fetch-depth: 0 # Fetch all history for all tags and branches
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-file: ./doc/rtd_environment.yml
           environment-name: rtd
           init-shell: >-
             bash
             powershell
-          cache-environment: true
+          cache-environment: false
 
       - name: activate build env
         run: micromamba activate rtd

.github/workflows/pytest.yml

@@ -39,15 +39,15 @@ jobs:
         with:
           fetch-depth: '0' # Fetch all history for all tags and branches
 
-      - uses: CagtayFabry/pydeps2env@main
+      - uses: CagtayFabry/pydeps2env@v1.1.0
         with:
-          file: 'pyproject.toml'
+          files: 'pyproject.toml'
           channels: 'conda-forge defaults'
           extras: 'test vis media'
-          setup_requires: 'include'
+          build_system: 'include'
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         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@v4.3.0
+        uses: codecov/codecov-action@v4.5.0
 
   compat:
     name: pytest
@@ -139,15 +139,15 @@ jobs:
         with:
           fetch-depth: '0' # Fetch all history for all tags and branches
 
-      - uses: CagtayFabry/pydeps2env@main
+      - uses: CagtayFabry/pydeps2env@v1.1.0
         with:
-          file: 'pyproject.toml'
+          files: 'pyproject.toml'
           channels: 'conda-forge defaults'
           extras: 'test vis media'
-          setup_requires: 'include'
+          build_system: 'include'
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         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@v1.8.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-file: ./environment.yml
           environment-name: weldx

.github/workflows/static_analysis.yml

@@ -49,7 +49,7 @@ jobs:
           key: ${{ runner.os }}-${{ hashFiles('./environment.yml') }}
 
       - name: Setup Conda Environment
-        uses: mamba-org/setup-micromamba@v1.8.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-file: ./environment.yml
           environment-name: weldx

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ exclude: '.*.weldx$|.*.wx$|.*.asdf$'
 repos:
   # ----- general formatting -----
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
@@ -28,8 +28,8 @@ repos:
           - mdformat-black
           - mdformat-config
   # ----- Python formatting -----
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.3.5
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.6
     hooks:
     # Run ruff linter.
     - id: ruff
@@ -39,16 +39,16 @@ repos:
     # Run ruff formatter.
     - id: ruff-format
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: 1.7.0
+    rev: 2.2.1
     hooks:
     - id: pyproject-fmt
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.16
+    rev: v0.18
     hooks:
       - 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
@@ -63,7 +63,7 @@ repos:
           - --remove-kernel-metadata
   # ----- spellchecking -----
   - repo: https://github.com/codespell-project/codespell/
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         exclude: doc/src/legal-notice.md

.ruff.toml

@@ -0,0 +1,81 @@
+# Exclude a variety of commonly ignored directories.
+extend-exclude = [
+    "__init__.py",
+    "doc/src/conf.py",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+# Assume Python 3.9
+target-version = "py39"
+
+
+[lint]
+# TODO: should be the following list, but Ruff does not yet impl all of them.
+#    W503,W504
+#    E203
+#    C408
+ignore = [
+    "C408",
+    #"E203",
+    "E402",
+    #"W503",
+    #"W504",
+    "D203",
+    "D211",
+    "D213",
+    "UP006",
+    "UP007", # see ruff GH#4427
+]
+select = [
+    "B", # flake8-bugbear
+    "C", # flake8-comprehensions
+    #"D", # note: all relevant D's will be set by setting pydocstyle.convention=numpy!
+    "E",    # pycodestyles
+    "F",    # pyflakes
+    "W",    # pycodestyle warnings
+    "UP",   # pyupgrade
+    "T2",   # flake8-print
+    "I001", # isort
+    "ICN",  # import conventions, e.g. import numpy as np
+    #"B950",  # not yet implemented by Ruff.
+    "RUF100", # ensure 'noqa' declarations are still valid.
+]
+
+[lint.extend-per-file-ignores]
+# Allow pydocstyle violations in certain areas.
+"**/{tests,tags,asdf,devtools}/**" = [
+    "D",
+]
+"conftest.py" = [
+    "D",
+]
+"doc/src/tutorials/*" = [
+    "D",
+]
+"doc/src/conf.py" = [
+    "E501",   # ignore long lines.
+    "RUF100", # do no check if 'noqa' is needed (circular import workaround)
+]
+"**/{cli,tests,tutorials,devtools}/**/*{.py,ipynb}" = [
+    "T2",
+] # Allow prints in certain areas.
+
+[lint.pydocstyle]
+convention = "numpy"
+
+[lint.mccabe]
+max-complexity = 15 # max branches inside a function.
+
+[lint.isort]
+known-first-party = [
+    "weldx",
+]
+required-imports = [
+    "from __future__ import annotations",
+]
+
+[lint.flake8-import-conventions]
+extend-aliases = { xarray = "xr" }

CHANGELOG.md

@@ -1,6 +1,19 @@
 # Release Notes
 
-## 0.6.8 (unreleased)
+## 0.6.9 (unreleased)
+
+### 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)
 
 ### Changes
 
@@ -9,6 +22,7 @@
 ### Dependencies
 
 - unpin nbval testing dependency.
+- pin `python<3.12` \[{pull}`933`\].
 
 ## 0.6.7 (2023.08.24)
 

CITATION.cff

@@ -1,8 +1,8 @@
 # YAML 1.2
 ---
 title: weldx
-version: 0.6.7
-date-released: 2023-08-24
+version: 0.6.8
+date-released: 2024-07-06
 authors:
   - affiliation: "Bundesanstalt für Materialforschung und -prüfung (BAM)"
     email: cagtay.fabry@bam.de

doc/json_mime_render_plugin/pyproject.toml

@@ -1,5 +1,12 @@
 [project]
 name = "myst-nb-json-renderer"
 version = "1"
-[project.entry-points."myst_nb.mime_renderers"]
-json_mime = "myst_nb_json_render_plugin:MimeRenderPlugin"
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+]
+entry-points."myst_nb.mime_renderers".json_mime = "myst_nb_json_render_plugin:MimeRenderPlugin"

doc/rtd_environment.yml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.10
   - setuptools_scm
   # weldx base dependencies
-  - numpy>=1.18
+  - numpy>=1.18,<2
   - pandas>=1.0
   - xarray>=0.15
   - pint>=0.11
@@ -21,16 +21,16 @@ dependencies:
   - weldx_widgets>=0.2.1
   # documentation
   - docutils>=0.19
-  - sphinx>=4.1.1
+  - sphinx>=4.1.1,=7.2
   - urllib3<2
   #- jinja2=3.0
-  - sphinx-copybutton
+  - sphinx-copybutton=0.5
   - pydata-sphinx-theme<0.15 # parallel-write-unsafe
   - numpydoc>=0.5
-  - sphinx-autodoc-typehints>=1.21.8
+  - sphinx-autodoc-typehints>=1.21.8,=2.0
   - typing_extensions
   # pip packages
   - pip
   - pip:
-    - ../
-    - ./json_mime_render_plugin/
+    - weldx @ file:/../..//
+    - json_mime_render_plugin @ file:/..//json_mime_render_plugin

doc/src/tutorials.md

@@ -10,7 +10,7 @@ data processing and visualization.
 ```{toctree}
 :caption: Welding examples
 :maxdepth: 1
-:numbered: true
+:numbered:
 
 tutorials/01_01_introduction
 tutorials/01_02_time_dependent_data
@@ -27,7 +27,7 @@ related tasks.
 ```{toctree}
 :caption: Welding examples
 :maxdepth: 1
-:numbered: true
+:numbered:
 
 tutorials/welding_example_01_basics
 tutorials/custom_metadata
@@ -45,7 +45,7 @@ The API tutorials provide more detailed usages and examples of core
 ```{toctree}
 :caption: API tutorials
 :maxdepth: 1
-:numbered: true
+:numbered:
 
 tutorials/transformations_01_coordinate_systems
 tutorials/transformations_02_coordinate_system_manager

doc/src/tutorials/timeseries_01.ipynb

@@ -283,7 +283,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can also use `Quantites` with the appropriate dimension as Inputs for our interpolation:"
+    "We can also use `Quantities` with the appropriate dimension as Inputs for our interpolation:"
    ]
   },
   {