Clean up environment and update pre-commit hooks (#14)

Author: pre-commit-ci[bot]

.envs/testenv.yml

@@ -12,14 +12,12 @@ dependencies:
   - jax
   - numpy
   - numba
-  - pandas
   - pyyaml
 
   # Testing infrastructure
   - pytest
   - pytest-cov
   - pytest-xdist
-
-  # Install locally
   - pip:
+      # Install locally
       - -e ../

.pre-commit-config.yaml

@@ -6,15 +6,15 @@ repos:
       - id: check-useless-excludes
     # -   id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
+    rev: v1.37.1
     hooks:
       - id: yamllint
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.16.0
+    rev: 1.17.0
     hooks:
       - id: yamlfix
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
         args:
@@ -42,7 +42,7 @@ repos:
       - id: python-use-type-annotations
       - id: text-unicode-replacement-char
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
         name: isort
@@ -55,17 +55,17 @@ repos:
   #       args:
   #         - --py37-plus
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.5.0
+    rev: v2.8.0
     hooks:
       - id: setup-cfg-fmt
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 25.1.0
     hooks:
       - id: black
-        language_version: python3.10
+        language_version: python3.11
         exclude: tests/utils/fast_upper_envelope_org.py
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.7
+    rev: v0.11.8
     hooks:
       - id: ruff
         # exclude: |
@@ -74,7 +74,7 @@ repos:
         #     docs/source/conf.py|
         #   )$
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+    rev: v1.7.7
     hooks:
       - id: docformatter
         args:
@@ -86,12 +86,12 @@ repos:
           - --blank
         exclude: tests/utils/fast_upper_envelope_org.py
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.5
+    rev: 1.9.1
     hooks:
       - id: nbqa-black
       - id: nbqa-ruff
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -102,7 +102,7 @@ repos:
           - '88'
         files: (README\.md)
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies:

environment.yml

@@ -4,27 +4,23 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.10
+  - python=3.11
   - pip
   - pytest
   - pytest-cov
   - pytest-xdist
 
   # Package dependencies
-  - estimagic
   - numpy
   - scipy
   - numba
-  - pandas
   - jax
-  - networkx
 
   # Misc
   - black
   - nb_black
   - flake8
   - jupyterlab
-  - matplotlib
   - pdbpp
   - pre-commit
   - setuptools_scm

setup.cfg

@@ -11,7 +11,6 @@ platforms = unix, linux, osx, cygwin, win32
 classifiers =
     Development Status :: 1 - Planning
     Intended Audience :: Science/Research
-    License :: OSI Approved :: MIT License
     Operating System :: MacOS :: MacOS X
     Operating System :: Microsoft :: Windows
     Operating System :: POSIX
@@ -24,7 +23,7 @@ project_urls =
 
 [options]
 packages = find:
-python_requires = >=3.8
+python_requires = >=3.9
 include_package_data = True
 package_dir =
     =src

tox.ini

@@ -21,7 +21,6 @@ conda_deps =
     jax
     numpy
     numba
-    pandas
     jax
 
     # Optional and test dependencies