Dependency update after v2.9.1 (#4089)

* Bump ruff from 0.12.8 to 0.12.9 (#4047)

* Bump ruff from 0.12.8 to 0.12.9

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.12.8 to 0.12.9.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.8...0.12.9)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.12.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

* Updated pre-commit

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Updated transient dependencies (#4048)

* Bump ruff from 0.12.9 to 0.12.10 (#4057)

* Bump ruff from 0.12.9 to 0.12.10

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.12.9 to 0.12.10.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.9...0.12.10)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.12.10
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

* Updated pre-commit

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump pybind11 from 3.0.0 to 3.0.1 (#4055)

* Bump pybind11 from 3.0.0 to 3.0.1

Bumps [pybind11](https://github.com/pybind/pybind11) from 3.0.0 to 3.0.1.
- [Release notes](https://github.com/pybind/pybind11/releases)
- [Changelog](https://github.com/pybind/pybind11/blob/master/docs/changelog.md)
- [Commits](pybind/pybind11@v3.0.0...v3.0.1)

---
updated-dependencies:
- dependency-name: pybind11
  dependency-version: 3.0.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pybind11-global from 3.0.0 to 3.0.1

Bumps [pybind11-global](https://github.com/pybind/pybind11) from 3.0.0 to 3.0.1.
- [Release notes](https://github.com/pybind/pybind11/releases)
- [Changelog](https://github.com/pybind/pybind11/blob/master/docs/changelog.md)
- [Commits](pybind/pybind11@v3.0.0...v3.0.1)

---
updated-dependencies:
- dependency-name: pybind11-global
  dependency-version: 3.0.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* ⬆️ Conda env

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: james <[email protected]>

* Updated transient dependencies (#4061)

* Bump ruff from 0.12.10 to 0.12.11 (#4067)

* Bump ruff from 0.12.10 to 0.12.11

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.12.10 to 0.12.11.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.10...0.12.11)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.12.11
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

* Updated pre-commit

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump matplotlib from 3.10.5 to 3.10.6 (#4065)

* Bump matplotlib from 3.10.5 to 3.10.6

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.10.5 to 3.10.6.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.10.5...v3.10.6)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-version: 3.10.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump pytools from 2025.2.2 to 2025.2.3 (#4064)

* Bump pytools from 2025.2.2 to 2025.2.3

Bumps [pytools](https://github.com/inducer/pytools) from 2025.2.2 to 2025.2.3.
- [Release notes](https://github.com/inducer/pytools/releases)
- [Commits](inducer/pytools@v2025.2.2...v2025.2.3)

---
updated-dependencies:
- dependency-name: pytools
  dependency-version: 2025.2.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* ⬆️ Conda env

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: james <[email protected]>

* Updated transient dependencies (#4068)

* Bump pytools from 2025.2.3 to 2025.2.4 (#4069)

* Bump pytools from 2025.2.3 to 2025.2.4

Bumps [pytools](https://github.com/inducer/pytools) from 2025.2.3 to 2025.2.4.
- [Release notes](https://github.com/inducer/pytools/releases)
- [Commits](inducer/pytools@v2025.2.3...v2025.2.4)

---
updated-dependencies:
- dependency-name: pytools
  dependency-version: 2025.2.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* ⬆️ Conda env file

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: james <[email protected]>

* Bump ruff from 0.12.11 to 0.12.12 (#4072)

* Bump ruff from 0.12.11 to 0.12.12

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.12.11 to 0.12.12.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.11...0.12.12)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.12.12
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

* Updated pre-commit

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Updated transient dependencies (#4073)

* Bump gmsh-interop from 2024.1 to 2025.1 (#4078)

Bumps [gmsh-interop](https://github.com/inducer/gmsh_interop) from 2024.1 to 2025.1.
- [Release notes](https://github.com/inducer/gmsh_interop/releases)
- [Commits](inducer/gmsh_interop@v2024.1...v2025.1)

---
updated-dependencies:
- dependency-name: gmsh-interop
  dependency-version: '2025.1'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump ruff from 0.12.12 to 0.13.0 (#4079)

* Bump ruff from 0.12.12 to 0.13.0

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.12.12 to 0.13.0.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.12...0.13.0)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.13.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

* Updated pre-commit

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Updated transient dependencies (#4080)

* Bump ruff from 0.13.0 to 0.13.1 (#4084)

* Bump ruff from 0.13.0 to 0.13.1

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.13.0 to 0.13.1.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.13.0...0.13.1)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.13.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

* Updated pre-commit

* Linter fixes

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump numba from 0.61.2 to 0.62.0 (#4082)

* Bump numba from 0.61.2 to 0.62.0

Bumps [numba](https://github.com/numba/numba) from 0.61.2 to 0.62.0.
- [Release notes](https://github.com/numba/numba/releases)
- [Commits](numba/numba@0.61.2...0.62.0)

---
updated-dependencies:
- dependency-name: numba
  dependency-version: 0.62.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated dependencies in requirements files

* 🐛 Numba lazy pformatting avoidance

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: james <[email protected]>

* Updated transient dependencies (#4088)

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: james <[email protected]>

Author: 3 people

.pre-commit-config.yaml

@@ -12,14 +12,14 @@ repos:
         exclude: test_data
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.8
+    rev: v0.13.1
     hooks:
       - id: ruff-check
         args: [--fix]
       - id: ruff-format
 
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.1.4
+    rev: v2.2.4
     hooks:
       - id: biome-format
         types: [json]

bluemira/base/logs.py

@@ -122,7 +122,8 @@ def _base(
     ):
         self._flushing = flush
         self._clean = _clean
-        msg = msg.strip()
+        if isinstance(msg, str):
+            msg = msg.strip()
         if (
             flush
             and get_log_level("bluemira", as_str=False) <= LogLevel(func.__name__).value

bluemira/codes/params.py

@@ -52,7 +52,7 @@ def from_defaults(
         new_param_dict = {}
         for bm_map_name, param_map in cls._mappings.items():
             new_param_dict[bm_map_name] = {
-                "value": data.get(param_map.name, None),
+                "value": data.get(param_map.name),
                 "unit": param_map.unit,
                 "source": source,
             }

conda/environment.yml

@@ -29,9 +29,9 @@ dependencies:
   - mpi4py
   - graphviz
   - h5py==3.13.0
-  - pybind11==3.0.0
-  - pybind11-global==3.0.0
-  - pytools==2025.2.2
+  - pybind11==3.0.1
+  - pybind11-global==3.0.1
+  - pytools==2025.2.4
   - vtk==9.3.1
   - libopenblas
   - pythonocc-core

pyproject.toml

@@ -18,7 +18,7 @@ dependencies = [
     "anytree>=2.5",
     "asteval>=1.0",
     "Babel>=2.17",
-    "click>=8.0",
+    "click>=8.0,!=8.3.0",
     "contourpy>=1.0",
     "CoolProp>=6.5",
     "eqdsk>=0.5.0, <0.6.0",
@@ -66,7 +66,7 @@ dev = [
     "pytest-html",
     "pytest-metadata",
     "pytest-json-report",
-    "ruff==0.12.8",
+    "ruff==0.13.1",
     "sphinx",
     "sphinx-autoapi",
     "sphinx_copybutton",
@@ -76,10 +76,10 @@ dev = [
 examples = ["notebook", "jupytext"]
 pinned = [
     "nlopt==2.7.1",
-    "numba==0.61.2",
+    "numba==0.62.0",
     "numba-scipy @ git+https://github.com/numba/numba-scipy@23c3b33440ea1fe0f84d05d269fb4a3df4b92787",
     "numpy==1.26.4",
-    "matplotlib==3.10.5",
+    "matplotlib==3.10.6",
     "scipy==1.15.3",
     "vtk==9.3.1",  # needed for uv resolution
 ]

requirements/conda.txt

@@ -1,6 +1,6 @@
-gmsh-interop==2024.1
+gmsh-interop==2025.1
 h5py==3.13.0
-pybind11==3.0.0
-pybind11-global==3.0.0
-pytools==2025.2.2
+pybind11==3.0.1
+pybind11-global==3.0.1
+pytools==2025.2.4
 vtk==9.3.1