Bump the python-dependencies group with 6 updates (#2098)

* Bump the python-dependencies group with 6 updates

Updates the requirements on [pydantic[email]](https://github.com/pydantic/pydantic), [pydantic-settings](https://github.com/pydantic/pydantic-settings), [numpy](https://github.com/numpy/numpy), [pymatgen](https://github.com/materialsproject/pymatgen), [jarvis-tools](https://github.com/usnistgov/jarvis) and [mkdocs-material](https://github.com/squidfunk/mkdocs-material) to permit the latest version.

Updates `pydantic[email]` from 2.7.3 to 2.7.4
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v2.7.3...v2.7.4)

Updates `pydantic-settings` from 2.3.2 to 2.3.3
- [Release notes](https://github.com/pydantic/pydantic-settings/releases)
- [Commits](pydantic/pydantic-settings@v2.3.2...v2.3.3)

Updates `numpy` to 2.0.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.22.0...v2.0.0)

Updates `pymatgen` from 2024.5.1 to 2024.6.4
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](materialsproject/pymatgen@v2024.5.1...v2024.6.4)

Updates `jarvis-tools` from 2024.4.10 to 2024.4.30
- [Release notes](https://github.com/usnistgov/jarvis/releases)
- [Commits](usnistgov/jarvis@v2024.4.10...v2024.4.30)

Updates `mkdocs-material` from 9.5.26 to 9.5.27
- [Release notes](https://github.com/squidfunk/mkdocs-material/releases)
- [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG)
- [Commits](squidfunk/mkdocs-material@9.5.26...9.5.27)

---
updated-dependencies:
- dependency-name: pydantic[email]
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: pydantic-settings
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: numpy
  dependency-type: direct:production
  dependency-group: python-dependencies
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: jarvis-tools
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: mkdocs-material
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
...

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

* Replace 'types-all' with individual stub libraries

* Exclude another pymatgen version and temporarily add tabulate as dep

* Bump ruff from 0.4.7 to 0.4.9

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.4.7 to 0.4.9.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.4.7...v0.4.9)

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

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

* Downgrade pymatgen further due to yanked release

* Downgrade jarvis-tools and add explicit pins

---------

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

.github/dependabot.yml

@@ -17,7 +17,9 @@ updates:
   - dependency-name: "elasticsearch*"
     versions: [ ">=8" ]
   - dependency-name: "pymatgen"
-    versions: [ "==2024.6.10" ]
+    versions: [ "==2024.6.10", "==2024.6.4" ]
+  - dependency-name: "jarvis-tools"
+    versions: [ "==2024.4.20", "==2024.4.30" ]
   groups:
     python-dependencies:
       applies-to: version-updates

.pre-commit-config.yaml

@@ -63,6 +63,6 @@ repos:
     hooks:
       - id: mypy
         name: "MyPy"
-        additional_dependencies: ["types-all", "pydantic~=2.0"]
+        additional_dependencies: ["types-requests", "types-pyyaml", "pydantic~=2.0"]
         exclude: ^tests/.*$
         args: [--check-untyped-defs]

pyproject.toml

@@ -81,9 +81,9 @@ http-client = [
 ]
 
 ase = ["ase~=3.22"]
-cif = ["numpy~=1.22"]
-pymatgen = ["pymatgen>=2022", "pandas~=2.2"]
-jarvis = ["jarvis-tools>=2023.1.8"]
+cif = ["numpy>=1.22,<3.0"]
+pymatgen = ["pymatgen>=2022,!=2024.6.10,!=2024.6.4", "tabulate~=0.8", "pandas~=2.2"]
+jarvis = ["jarvis-tools>=2023.1.8,!=2024.4.20,!=2024.4.30"]
 client = ["optimade[cif]"]
 
 # General

requirements-dev.txt

@@ -5,5 +5,5 @@ mypy==1.10.0
 pre-commit==3.7.1
 pytest==8.2.2
 pytest-cov==5.0.0
-ruff==0.4.7
+ruff==0.4.9
 types-all==1.0.0

requirements-docs.txt

@@ -1,5 +1,5 @@
 mike==2.1.1
 mkdocs==1.6.0
 mkdocs-awesome-pages-plugin==2.9.2
-mkdocs-material==9.5.26
+mkdocs-material==9.5.27
 mkdocstrings[python]==0.25.1

requirements.txt

@@ -1,6 +1,6 @@
 lark==1.1.9
-pydantic[email]==2.7.3
-pydantic_settings==2.3.2
+pydantic[email]==2.7.4
+pydantic_settings==2.3.3
 pyyaml==6.0.1
 requests==2.32.3
 uvicorn==0.30.1