conda -> uv and update readme and agents.md

Author: gonzalobenegas

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       # list of supported hooks: https://pre-commit.com/hooks.html
       - id: trailing-whitespace
@@ -19,58 +19,28 @@ repos:
 
   # python code formatting
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 25.11.0
     hooks:
       - id: black
         args: [--line-length, "99"]
 
   # python import sorting
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 7.0.0
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
 
   # python upgrading syntax to newer version
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
-        args: [--py38-plus]
-
-  # python docstring formatting
-  - repo: https://github.com/myint/docformatter
-    rev: v1.7.4
-    hooks:
-      - id: docformatter
-        args:
-          [
-            --in-place,
-            --wrap-summaries=99,
-            --wrap-descriptions=99,
-            --style=sphinx,
-            --black,
-          ]
-
-  # python docstring coverage checking
-  - repo: https://github.com/econchick/interrogate
-    rev: 1.5.0 # or master if you're bold
-    hooks:
-      - id: interrogate
-        args:
-          [
-            --verbose,
-            --fail-under=80,
-            --ignore-init-module,
-            --ignore-init-method,
-            --ignore-module,
-            --ignore-nested-functions,
-            -vv,
-          ]
+        args: [--py313-plus]
 
   # python check (PEP8), programming errors and code complexity
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
         args:
@@ -84,64 +54,21 @@ repos:
 
   # python security linter
   - repo: https://github.com/PyCQA/bandit
-    rev: "1.7.5"
+    rev: "1.9.1"
     hooks:
       - id: bandit
         args: ["-s", "B101"]
 
   # yaml formatting
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.6
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         types: [yaml]
         exclude: "environment.yaml"
 
   # shell scripts linter
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.9.0.2
+    rev: v0.11.0.1
     hooks:
       - id: shellcheck
-
-  # md formatting
-  - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
-    hooks:
-      - id: mdformat
-        args: ["--number"]
-        additional_dependencies:
-          - mdformat-gfm
-          - mdformat-tables
-          - mdformat_frontmatter
-          # - mdformat-toc
-          # - mdformat-black
-
-  # word spelling linter
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
-    hooks:
-      - id: codespell
-        args:
-          - --skip=logs/**,data/**,*.ipynb
-          # - --ignore-words-list=abc,def
-
-  # jupyter notebook cell output clearing
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
-    hooks:
-      - id: nbstripout
-
-  # jupyter notebook linting
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.3
-    hooks:
-      - id: nbqa-black
-        args: ["--line-length=99"]
-      - id: nbqa-isort
-        args: ["--profile=black"]
-      - id: nbqa-flake8
-        args:
-          [
-            "--extend-ignore=E203,E402,E501,F401,F841",
-            "--exclude=logs/*,data/*",
-          ]