bring fides to 21st century

Author: FFroehlich

.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

@@ -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

@@ -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