pre-commit: sort imports / update contrib doc (AMICI-dev#2085)

* pre-commit: sort imports / update contrib doc

* sort imports

* fix circular import

.pre-commit-config.yaml

@@ -1,17 +1,23 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-        args: [--allow-multiple-documents]
-    -   id: check-added-large-files
-
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+    - id: isort
+      name: isort (python)
+      args: ["--profile", "black", "--filter-files"]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  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: 23.1.0
+  rev: 23.3.0
   hooks:
     - id: black
       # It is recommended to specify the latest version of Python

documentation/conf.py

@@ -10,17 +10,16 @@
 import re
 import subprocess
 import sys
-import typing
 
+# need to import before setting typing.TYPE_CHECKING=True, fails otherwise
+import amici
 import exhale.deploy
 import exhale_multiproject_monkeypatch
 import mock
-from exhale import configs as exhale_configs
-from sphinx.transforms.post_transforms import ReferencesResolver
-
-# need to import before setting typing.TYPE_CHECKING=True, fails otherwise
 import pandas as pd
 import sympy as sp
+from exhale import configs as exhale_configs
+from sphinx.transforms.post_transforms import ReferencesResolver
 
 exhale_multiproject_monkeypatch, pd, sp  # to avoid removal of unused import
 
@@ -60,7 +59,7 @@ def my_breathe_DomainDirectiveFactory_create(domain: str, args):
     if domain != "mat":
         return old_breathe_DomainDirectiveFactory_create(domain, args)
 
-    from sphinxcontrib.matlab import MATLABDomain, MatClassmember
+    from sphinxcontrib.matlab import MatClassmember, MATLABDomain
 
     matlab_classes = {k: (v, k) for k, v in MATLABDomain.directives.items()}
     matlab_classes["variable"] = (MatClassmember, "attribute")
@@ -125,12 +124,6 @@ def install_doxygen():
 # Required for matlab doxygen processing
 install_mtocpp()
 
-# Install AMICI if not already present
-typing.TYPE_CHECKING = True
-import amici
-
-typing.TYPE_CHECKING = False
-
 
 # -- Project information -----------------------------------------------------
 # The short X.Y version

documentation/development.rst

@@ -12,8 +12,8 @@ AMICI roughly follows the
 All new contributions are merged into ``develop``. These changes are
 regularly merged into ``master`` as new releases. For release versioning
 we are trying to follow `semantic versioning <https://semver.org/>`__.
-New releases are created on Github and are automatically deployed to
-`Zenodo <https://zenodo.org/record/3362453#.XVwJ9vyxVMA>`__ for
+New releases are created on GitHub and are automatically deployed to
+`Zenodo <https://doi.org/10.5281/zenodo.597928>`__ for
 archiving and to obtain a digital object identifier (DOI) to make them
 citable. Furthermore, our `CI pipeline <documentation/CI.md>`__ will
 automatically create and deploy a new release on
@@ -51,17 +51,11 @@ process described below:
 
 -  Submit a pull request to the ``develop`` branch
 
--  Make sure your code is documented appropriately
-
-   -  Run ``scripts/run-doxygen.sh`` to check completeness of your
-      documentation
-
--  Make sure your code is compatible with C++17, ``gcc`` and ``clang``
-   (our CI pipeline will do this for you)
+-  Ensure all tests pass
 
 -  When adding new functionality, please also provide test cases (see
-   ``tests/cpp/`` and
-   `documentation/CI.md <documentation/CI.md>`__)
+   ``tests/cpp/``, ``python/tests/``,
+   and `documentation/CI.md <documentation/CI.md>`__)
 
 -  Write meaningful commit messages
 
@@ -84,8 +78,8 @@ process described below:
 -  Wait for feedback. If you do not receive feedback to your pull
    request within a week, please give us a friendly reminder.
 
-Style guide
-~~~~~~~~~~~
+Style/compatibility guide
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
 General
 ^^^^^^^
@@ -105,12 +99,18 @@ Python
 -  For the Python code we want to follow
    `PEP8 <https://www.python.org/dev/peps/pep-0008/>`__. Although this
    is not the case for all existing code, any new contributions should
-   do so.
+   do so. We use `black <https://black.readthedocs.io/en/stable/index.html>`__
+   for code formatting.
+
+   To run black as pre-commit hook, install the
+   `pre-commit <https://pre-commit.com/>`_ package
+   (e.g. ``pip install pre-commit``), and enable AMICI-hooks by running
+   ``pre-commit install`` from within the AMICI directory.
 
 -  We use Python `type
    hints <https://docs.python.org/3/library/typing.html>`__ for all
    functions (but not for class attributes, since they are not supported
-   by the current Python doxygen filter). In Python code type hints
+   by the current Python doxygen filter). In Python code, type hints
    should be used instead of doxygen ``@type``.
 
    For function docstrings, follow this format:
@@ -135,15 +135,14 @@ Python
 C++
 ^^^
 
--  We use C++14
+-  We use C++17
 
--  We want to maintain compatibility with g++, clang and the Intel C++
+-  We want to maintain compatibility with g++, clang, and the Intel C++
    compiler
 
--  For code formatting, we use the settings from ``.clang-format`` in
-   the root directory
-
--  *Details to be defined*
+-  For code formatting, we use ``clang-format`` and ``cmake-format``. They can
+   be invoked by ``make clang-format cmake-format`` from the CMake build
+   directory.
 
 Matlab
 ^^^^^^

documentation/recreate_reference_list.py

@@ -8,12 +8,13 @@
 Requires pandoc
 """
 
-import biblib.bib
-import biblib.messages
-import biblib.algo
 import os
-import sys
 import subprocess
+import sys
+
+import biblib.algo
+import biblib.bib
+import biblib.messages
 
 
 def get_keys_by_year(bibfile):

python/benchmark/benchmark_pysb.py

@@ -5,17 +5,17 @@
 times are averages of N_REPEATS simulations at reference values.
 """
 
+import importlib
 import os
-import pysb
+import sys
+import timeit
+
 import amici
-from amici.pysb_import import pysb2amici
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import matplotlib.pyplot as plt
-import importlib
-import timeit
-import sys
-
+import pysb
+from amici.pysb_import import pysb2amici
 from pysb.simulator import ScipyOdeSimulator
 
 sys.path.insert(0, os.path.join("..", "tests"))

python/examples/example_presimulation/createModelPresimulation.py

@@ -1,7 +1,7 @@
-from pysb.core import Rule, Parameter, Model, Monomer, Expression, Initial, Observable
+import os
 
 import pysb.export
-import os
+from pysb.core import Expression, Initial, Model, Monomer, Observable, Parameter, Rule
 
 model = Model()
 

python/sdist/amici/__init__.py

@@ -14,7 +14,7 @@
 import sys
 from pathlib import Path
 from types import ModuleType as ModelModule
-from typing import Optional, Union, Callable, Any
+from typing import Any, Callable, Optional, Union
 
 
 def _get_amici_path():
@@ -52,7 +52,7 @@ def _get_commit_hash():
 def _imported_from_setup() -> bool:
     """Check whether this module is imported from `setup.py`"""
 
-    from inspect import getouterframes, currentframe
+    from inspect import currentframe, getouterframes
     from os import sep
 
     # in case we are imported from setup.py, this will be the AMICI package
@@ -107,18 +107,17 @@ def _imported_from_setup() -> bool:
         # has to be done before importing readSolverSettingsFromHDF5
         #  from .swig_wrappers
         hdf5_enabled = "readSolverSettingsFromHDF5" in dir()
-        from .swig_wrappers import *
-
         # These modules require the swig interface and other dependencies
-        from .numpy import ReturnDataView, ExpDataView
+        from .numpy import ExpDataView, ReturnDataView
         from .pandas import *
+        from .swig_wrappers import *
 
     # These modules don't require the swig interface
-    from .sbml_import import SbmlImporter, assignmentRules2observables
-    from .de_export import DEModel, DEExporter
-
     from typing import Protocol, runtime_checkable
 
+    from .de_export import DEExporter, DEModel
+    from .sbml_import import SbmlImporter, assignmentRules2observables
+
     @runtime_checkable
     class ModelModule(Protocol):
         """Type of AMICI-generated model modules.

python/sdist/amici/__init__.template.py

@@ -1,8 +1,9 @@
 """AMICI-generated module for model TPL_MODELNAME"""
 
-import amici
 from pathlib import Path
 
+import amici
+
 # Ensure we are binary-compatible, see #556
 if "TPL_AMICI_VERSION" != amici.__version__:
     raise amici.AmiciVersionError(

python/sdist/amici/__main__.py

@@ -1,9 +1,10 @@
 """Package-level entrypoint"""
 
-from . import __version__, compiledWithOpenMP, has_clibs, hdf5_enabled
 import os
 import sys
 
+from . import __version__, compiledWithOpenMP, has_clibs, hdf5_enabled
+
 
 def print_info():
     """Displays information on the current AMICI installation.

python/sdist/amici/conserved_quantities_demartino.py

@@ -2,7 +2,7 @@
 import math
 import random
 import sys
-from typing import List, MutableSequence, Sequence, Tuple, Union, Optional
+from typing import List, MutableSequence, Optional, Sequence, Tuple, Union
 
 from .logging import get_logger
 

python/sdist/amici/custom_commands.py

@@ -5,15 +5,14 @@
 import sys
 from pathlib import Path
 
+from amici.swig import fix_typehints
 from cmake_build_extension import BuildExtension, CMakeExtension
 from setuptools.command.build_py import build_py
 from setuptools.command.develop import develop
 from setuptools.command.install import install
 from setuptools.command.install_lib import install_lib
 from setuptools.command.sdist import sdist
 
-from amici.swig import fix_typehints
-
 
 class AmiciInstall(install):
     """Custom `install` command to handle extra arguments"""

python/sdist/amici/cxxcodeprinter.py

@@ -2,10 +2,10 @@
 import itertools
 import os
 import re
-from typing import Dict, List, Optional, Tuple, Iterable
+from typing import Dict, Iterable, List, Optional, Tuple
 
 import sympy as sp
-from sympy.codegen.rewriting import optimize, Optimization
+from sympy.codegen.rewriting import Optimization, optimize
 from sympy.printing.cxx import CXX11CodePrinter
 from sympy.utilities.iterables import numbered_symbols
 from toposort import toposort