Remove all no_type_check mark, fix new mypy error in 1.12.0 (#4110

)

* remove no_type_check mark

* remove no_type_check from plotter as it seems this have to go first

* remove mypy version pin

* take it slow and pin mypy for now

* fix io.lmto

* fix electronic structure plotter

* fix phase diagram

* fix pourbaix diagram

* migrate config

* bump pyright version

* fix pyright in io.lmto

* fix pyright in phase diagram

* remove mypy pin

* fix vis.structure_vtk

* fix core ptable

* pre-commit auto-fixes

* fix lobtser outputd

* fix typo in vasprun test

* handle converged_electronic for vasp ALGO=CHI

* fix another vasp.output error

* tweak code style a bit

* suppress overload error for now

* fix electronic structure plotter

* tweak code style a bit

* fix type

* fix incorrect type of cn

* use overload type

* bump pre-commit, mainly to get mypy 1.12

* fix incorrect return type of get_parameters

* fix most errors in local_env

* all done

* use set to check membership

* a bit more specific type for DEFAULT_OP_PARAMS

---------

Signed-off-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

.github/workflows/lint.yml

@@ -18,15 +18,14 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.x'
 
       - name: Install dependencies
         run: |
-          pip install --upgrade ruff 'mypy<1.12' pyright
+          pip install --upgrade ruff mypy pyright
 
       - name: ruff
         run: |
-          ruff --version
           ruff check .
           ruff format --check .
 

.pre-commit-config.yaml

@@ -8,29 +8,29 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.6.9
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.12.0
     hooks:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
       - id: codespell
-        stages: [commit, commit-msg]
+        stages: [pre-commit, commit-msg]
         exclude_types: [html]
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
         exclude: src/pymatgen/analysis/aflow_prototypes.json
@@ -43,12 +43,12 @@ repos:
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.0
     hooks:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.41.0
+    rev: v0.42.0
     hooks:
       - id: markdownlint
         # MD013: line too long
@@ -65,6 +65,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.379
+    rev: v1.1.384
     hooks:
       - id: pyright