update doc + pre-commit

.github/workflows/deploy_release.yaml

@@ -9,7 +9,7 @@ jobs:
   pypi:
     name: Deploy PyPI
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
     - uses: actions/checkout@v1

.github/workflows/flake.yaml

@@ -23,4 +23,4 @@ jobs:
         with:
           checkName: 'flake8_py3'
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yaml

@@ -5,11 +5,11 @@ jobs:
   build:
     name: Python Version Matrix
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
 
@@ -32,4 +32,4 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.xml
-        fail_ci_if_error: true
+        fail_ci_if_error: true

.pre-commit-config.yaml

@@ -1,28 +1,21 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.14.4
   hooks:
-    - id: isort
-      name: isort (python)
-      args: ["--profile", "black", "--filter-files"]
+    # Run the linter
+    - id: ruff
+      args: [--fix]
+    # Run the formatter
+    - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v6.0.0
   hooks:
   - id: check-added-large-files
   - id: check-merge-conflict
   - id: check-yaml
     args: [--allow-multiple-documents]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.3.0
-  hooks:
-    - id: black
-      # It is recommended to specify the latest version of Python
-      # supported by your project here, or alternatively use
-      # pre-commit's default_language_version, see
-      # https://pre-commit.com/#top_level-default_language_version
-      language_version: python3.11
 exclude: '^(ThirdParty|models)/'

.readthedocs.yaml

@@ -21,9 +21,10 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
 
 build:
-  image: latest
+  os: "ubuntu-24.04"
+  tools:
+    python: "3.13"

CITATION.cff

@@ -24,4 +24,4 @@ preferred-citation:
   journal: "bioRxiv"
   month: 5
   title: "Fides: Reliable Trust-Region Optimization for Parameter Estimation of Ordinary Differential Equation Models"
-  year: 2021
+  year: 2021

README.md

@@ -20,8 +20,8 @@ reliability.
 
 Fides can be installed via `pip install fides`. Further documentation is
  available at [Read the Docs](https://fides-optimizer.readthedocs.io/).
- 
- 
+
+
 ## Features
 
 
@@ -31,4 +31,3 @@ Fides can be installed via `pip install fides`. Further documentation is
 * BFGS, DFP, SR1, Broyden (good and bad) and Broyden class iterative
  Hessian Approximation schemes
 * SSM, TSSM, FX, GNSBFGS and custom hybrid Hessian Approximations schemes
-

docs/_templates/autosummary/module.rst

@@ -40,4 +40,4 @@
 .. autofunction:: {{ function }}
 {% endfor %}
 
-{% endif %}
+{% endif %}

docs/about.rst

@@ -19,4 +19,3 @@ Features
 * Recursive Reflective and Truncated constraint management
 * Full and 2D subproblem solution solvers
 * BFGS, DFP and SR1 Hessian Approximations
-

docs/api.rst

@@ -13,6 +13,3 @@ Fides Python API
    fides.hessian_approximation
    fides.logging
    fides.constants
-
-
-

docs/requirements.txt

@@ -1,6 +1,6 @@
 # Requirements just for building the docs (used by readthedocs, but also
 # helpful for building docs locally).
-sphinx>=1.4
+sphinx>=7.2.0
 numpy>=1.19.2
 scipy>=1.5.2
 h5py>=3.5.0
@@ -10,4 +10,4 @@ recommonmark>=0.6.0
 sphinx_rtd_theme>=0.4.3
 sphinx-autodoc-typehints>=1.10.3
 sphinxcontrib-napoleon
-pygments==2.4.1
+pygments>=2.4.1

examples/Minimal.ipynb

@@ -48,9 +48,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import fides\n",
     "import numpy as np\n",
     "\n",
+    "import fides\n",
+    "\n",
     "opt = fides.Optimizer(\n",
     "    obj, ub=np.asarray([np.inf, 1.5]), lb=np.asarray([-1.5, -np.inf])\n",
     ")"

fides/constants.py

@@ -8,7 +8,6 @@
 import enum
 from numbers import Integral, Real
 from pathlib import PosixPath, WindowsPath
-from typing import Dict
 
 import numpy as np
 
@@ -43,6 +42,7 @@ class SubSpaceDim(str, enum.Enum):
     Defines the possible choices of subspace dimension in which the
     subproblem will be solved.
     """
+
     TWO = '2D'  #: Two dimensional Newton/Gradient subspace
     FULL = 'full'  #: Full :math:`\mathbb{R}^n`
     STEIHAUG = 'scg'  #: CG subspace via Steihaug's method
@@ -100,7 +100,7 @@ class ExitFlag(int, enum.Enum):
     GTOL = 3  #: Converged according to gradient norm
 
 
-def validate_options(options: Dict):
+def validate_options(options: dict):
     """Check if the chosen options are valid"""
     expected_types = {
         Options.MAXITER: Integral,
@@ -124,7 +124,9 @@ def validate_options(options: Dict):
         try:
             option = Options(option_key)
         except ValueError:
-            raise ValueError(f'{option_key} is not a valid options field.')
+            raise ValueError(
+                f'{option_key} is not a valid options field.'
+            ) from None
 
         if option_key is Options.SUBSPACE_DIM:
             option_value = SubSpaceDim(option_value)