Merged.

.flake8

@@ -1,3 +1,16 @@
 [flake8]
+extend-ignore =
+  # Don't be crazy if line too long
+  E501
+  # Missing docstring in __init__
+  D107
+  # black: blank lines after docstring for function/class
+  D202,D204
+  # Missing docstring in public module/class/method/function/package/magic method
+  D100,D101,D102,D103,D104,D105
 per-file-ignores =
     */__init__.py:F401,F403
+    tests/*:S101
+exclude =
+    amici_models
+    cache_fiddy

.github/workflows/setup.sh

@@ -0,0 +1,28 @@
+#!/bin/sh
+
+# Install CI dependencies, arguments specify what is required
+
+# Base packages
+pip install --upgrade pip
+pip install wheel setuptools
+
+# Used to create local test environments
+pip install tox
+
+# Update apt
+sudo apt-get update
+
+# Check arguments
+for par in "$@"; do
+  case $par in
+    doc)
+      # documentation
+      sudo apt-get install pandoc
+    ;;
+
+    *)
+      echo "Unknown argument: $par" >&2
+      exit 1
+    ;;
+  esac
+done

.github/workflows/test_suite.yml

@@ -1,8 +1,13 @@
 name: Test suite
 on:
   push:
+    branches:
+    - main
   pull_request:
   workflow_dispatch:
+  schedule:
+    # run Sunday at 01:23 UTC
+    - cron: '23 1 * * SUN'
 
 jobs:
   build:
@@ -12,7 +17,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.11']
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -37,15 +42,84 @@ jobs:
           swig \
           libatlas-base-dev
 
-    # TODO remove once released
-    - name: Install custom AMICI
-      run: |
-        pip install --upgrade --upgrade-strategy eager -e git+https://github.com/AMICI-dev/amici.git@develop#egg=amici\&subdirectory=python/sdist
-
     - name: Install package
       run: |
-        pip install --upgrade --upgrade-strategy eager -e .[tests,amici,pypesto]
+        pip install --upgrade --upgrade-strategy eager -e .[tests,amici]
 
     - name: Run tests
       run: |
         pytest tests/
+
+  quality:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-quality
+
+    - name: Install dependencies
+      run: pip install tox pre-commit
+
+    - name: Check repository size
+      run: tox -e size
+
+    - name: Run quality checks
+      timeout-minutes: 5
+      run: tox -e pyroma,flake8
+
+# failing on github
+#    - name: Run pre-commit hooks
+#      run: pre-commit run --all-files
+
+  docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-docs
+
+    - name: Install dependencies
+      run: .github/workflows/setup.sh doc
+
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+          swig \
+          libatlas-base-dev
+
+    - name: Install package
+      run: |
+        pip install --upgrade --upgrade-strategy eager -e .[doc]
+
+    - name: Build doc
+      timeout-minutes: 10
+      run: tox -e doc

.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+profile = black

.readthedocs.yaml

@@ -10,7 +10,10 @@ sphinx:
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
+  apt_packages:
+    - libatlas-base-dev
+    - swig
 
 python:
    install:

doc/conf.py

@@ -1,3 +1,6 @@
+import os
+import sys
+
 import mock
 
 # Configuration file for the Sphinx documentation builder.
@@ -12,8 +15,6 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
-import os
-import sys
 
 sys.path.insert(0, os.path.abspath(".."))
 

doc/rtd_requirements.txt

@@ -1 +1,2 @@
 petab
+urllib3<2

examples/derivative.ipynb

@@ -37,15 +37,14 @@
     "from fiddy.analysis import ApproximateCentral\n",
     "from fiddy.success import Consistency\n",
     "\n",
-    "\n",
-    "point = np.array([1,0,0])\n",
+    "point = np.array([1, 0, 0])\n",
     "sizes = [1e-10, 1e-5]\n",
     "derivative = get_derivative(\n",
     "    function=rosen,\n",
     "    point=point,\n",
     "    sizes=[1e-10, 1e-5],\n",
     "    method_ids=[MethodId.FORWARD, MethodId.BACKWARD],\n",
-    "    direction_ids=['x','y','z'],\n",
+    "    direction_ids=[\"x\", \"y\", \"z\"],\n",
     "    analysis_classes=[ApproximateCentral],\n",
     "    success_checker=Consistency(rtol=1e-2, atol=1e-15),\n",
     ")\n",
@@ -254,7 +253,7 @@
     }
    ],
    "source": [
-    "derivative.df.loc['x', 'computer_results']"
+    "derivative.df.loc[\"x\", \"computer_results\"]"
    ]
   },
   {
@@ -318,7 +317,7 @@
     }
    ],
    "source": [
-    "derivative.df.loc['x', 'analysis_results']"
+    "derivative.df.loc[\"x\", \"analysis_results\"]"
    ]
   },
   {

fiddy/__init__.py

@@ -1,12 +1,12 @@
 from .constants import *
+from .derivative import Derivative, get_derivative
+from .directional_derivative import methods
 
 # from . import difference
-from .function import Function, CachedFunction
+from .function import CachedFunction, Function
+from .numpy import fiddy_array
 
 # from . import quotient
 from .step import step
-from .derivative import Derivative, get_derivative
-from .directional_derivative import methods
-from .numpy import fiddy_array
 
 # from .gradient_check import gradient_check

fiddy/analysis.py

@@ -1,12 +1,11 @@
 import abc
-from typing import Any, List, Dict
 from dataclasses import dataclass, field
+from typing import Any, Dict
 
 import numpy as np
 
-from .constants import Type, MethodId
+from .constants import MethodId, Type
 from .directional_derivative import DirectionalDerivative
-from . import directional_derivative
 
 
 @dataclass

fiddy/constants.py

@@ -4,7 +4,6 @@
 import numpy as np
 from numpy.typing import NDArray
 
-
 __all__ = [
     "Type",
     "MethodId",
@@ -32,10 +31,8 @@ class Type:
     # TODO rename analysis and success to e.g.
     #      - "ANALYSE_DIRECTIONAL_DERIVATIVE_METHOD" and
     #      - "ANALYSE_DERIVATIVE_METHOD" and
-    ANALYSIS_METHOD = Callable[
-        ["directional_derivative.DirectionalDerivative"], Any
-    ]
-    SUCCESS_CHECKER = Callable[["derivative.Derivative"], Union[bool, Any]]
+    ANALYSIS_METHOD = Callable[["DirectionalDerivative"], Any]  # noqa: F821
+    SUCCESS_CHECKER = Callable[["Derivative"], Union[bool, Any]]  # noqa: F821
 
 
 # FIXME rename, since this can be the name of the base class in `derivative.py`
@@ -46,26 +43,9 @@ class MethodId(str, Enum):
     BACKWARD = "backward"
     CENTRAL = "central"
     FORWARD = "forward"
+    RICHARDSON = "richardson"
     # richardson
     # five point?
-    # TODO separate enum for "order" of method?
-    #      e.g. for higher-order derivatives?
-    HYBRID = "hybrid"
-
-
-# class AnalysisMethod(str, Enum):
-#    ABSOLUTE_ERROR = "absolute_error"
-#    RELATIVE_ERROR = "relative_error"
-# =======
-
-
-## TODO remove? redundant
-# class GradientCheckMethod(str, Enum):
-#    BACKWARD = MethodId.BACKWARD
-#    CENTRAL = MethodId.CENTRAL
-#    FORWARD = MethodId.FORWARD
-#    HYBRID = MethodId.HYBRID
-##>>>>>>> origin/main
 
 
 EPSILON = 1e-5

fiddy/derivative.py

@@ -1,29 +1,18 @@
-import abc
-from typing import Any, Callable, Dict, List, Union
-import warnings
-
-from dataclasses import dataclass
+from typing import Callable, Dict, List, Union
 
 import numpy as np
 import pandas as pd
 
-from .constants import (
-    MethodId,
-    Type,
-    EPSILON,
-)
-
 from .analysis import Analysis
+from .constants import MethodId, Type
 from .directional_derivative import (
-    methods,
-    get_directions,
     Computer,
     DirectionalDerivative,
+    get_directions,
+    methods,
 )
-
 from .success import Success
 
-
 # @dataclass
 # class Analysis:
 #    # Change to callable?
@@ -125,8 +114,8 @@ def df(self):
         df.index.rename("direction", inplace=True)
         return df
 
-    def print(self):
-        print(self.df)
+    # def print(self):
+    #     print(self.df)
 
 
 def get_derivative(