Use Ruff as linter and formatter and introduce git pre-commit hook (#759

)

.github/pull_request_template.md

@@ -4,7 +4,7 @@ Add a short description describing the pull request (PR) here.
 # Checklist before PR can be merged:
 - [ ] closes issue #xxxx
 - [ ] is documented
-- [ ] Format code with [Black formatting](https://black.readthedocs.io)
+- [ ] Format code with [ruff formatting](https://docs.astral.sh/ruff/)
 - [ ] type hints for functions and methods
 - [ ] tests added / passed
 - [ ] Example Notebook (for new features)

.github/workflows/test_benchmark_notebooks.yml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         include:
           - name: Test suite for benchmark Notebooks
-            python: "3.9"
+            python: "3.10"
             toxenv: notebooks
     env:
       # Color Output

.github/workflows/test_format_lint.yml

@@ -0,0 +1,49 @@
+name: CI RUFF
+
+on:
+  push:
+  pull_request:
+    branches:
+      - master
+      - dev
+
+jobs:
+  test:
+    name: ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Formatting and linting with ruff
+            python: "3.10"
+            toxenv: ruff
+    env:
+      # Color Output
+      # Rich (pip)
+      FORCE_COLOR: 1
+      # Tox
+      PY_COLORS: 1
+      # Pytest
+      PYTEST_ADDOPTS: "--color=yes"
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          check-latest: true
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Setup tox environment
+        run: tox -e ${{ matrix.toxenv }} --notest
+
+      - name: Test
+        run: tox -e ${{ matrix.toxenv }} --skip-pkg-install

.github/workflows/ci.yml → .github/workflows/test_unit_pytest.yml

@@ -1,4 +1,4 @@
-name: CI
+name: CI PYTEST
 
 on:
   push:
@@ -35,14 +35,6 @@ jobs:
             python: "3.12"
             toxenv: py312
             experimental: false
-          - name: Formatting with black + isort
-            python: "3.9"
-            toxenv: format
-            experimental: false
-          - name: Linting with flake8
-            python: "3.9"
-            toxenv: lint
-            experimental: false
           - name: Test suite for all unit tests including Notebooks
             python: "3.9"
             toxenv: all

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.4
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: ["--extend-select", "I", "--fix"]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]

doc/conf.py

@@ -9,15 +9,13 @@
 from datetime import date
 
 import requests
-
-year = date.today().strftime("%Y")
-
 from matplotlib import use
 
-use("agg")
-
 from pastas import __version__
 
+year = date.today().strftime("%Y")
+use("agg")
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # 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.

doc/developers/code_style.rst

@@ -2,25 +2,24 @@ Pastas Code Style
 =================
 This page provides information on the code style to use when writing code for Pastas.
 
-Black formatting
+Formatting and Linting
 ----------------
 To ensure high quality code that is easy to read and maintain we follow the
-`Black <https://black.readthedocs.io/en/stable/index.html>`_ code formatting standard.
-Please checkout the `Black Documentation <https://black.readthedocs.io/en/stable/index.html>`_
-on how to format Python code this way.
+`Ruff <https://docs.astral.sh/ruff/>`_ code standard. Please checkout the `Ruff
+Documentation <https://docs.astral.sh/ruff/>`_ on how to format Python code
+this way.
 
 Type Hints
 ----------
-Pastas uses TypeHinting, which is used to check user-provided input options. Please provide
-TypeHints when creating new methods and classes.
+Pastas uses Type Hinting, which is used to check user-provided input options.
+Please provide Type Hints when creating new methods and classes.
 
 Docstrings
 ----------
-Documentation is
-created using `Sphinxdoc <http://www.sphinx-doc.org>`_. Docstrings within
-the method or class need to be written in `NumPy docformat <https://numpydoc
-.readthedocs.io/en/latest/format.html#docstring-standard>`_ to enable
-automatic documentation on this website.
+Documentation is created using `Sphinxdoc <http://www.sphinx-doc.org>`_.
+Docstrings within the method or class need to be written in `NumPy docformat
+<https://numpydoc .readthedocs.io/en/latest/format.html#docstring-standard>`_
+to enable automatic documentation on this website.
 
 Optimization
 ------------

doc/developers/contributing.rst

@@ -14,11 +14,11 @@ to commit code changes to GitHub open source projects. Let's start!
 
 0. Pick an Issue
 ----------------
-Before you start, it is a good idea to check if there are any issues that you can help 
-with. You can find a list of issues that are open on the `GitHub Issues page 
-<https://github.com/pastas/pastas/labels/good-first-issue>`_` with the tag 
-"good-first-issue". These issues are a good place to start if you are new to Pastas 
-and want to contribute to the project.
+Before you start, it is a good idea to check if there are any issues that you
+can help with. You can find a list of issues that are open on the `GitHub
+Issues page <https://github.com/pastas/pastas/labels/good-first-issue>`_` with
+the tag "good-first-issue". These issues are a good place to start if you are
+new to Pastas and want to contribute to the project.
 
 1. Create a GitHub Issue
 ------------------------
@@ -27,63 +27,77 @@ propose to make and why these are necessary. This is an easy way to inform
 the Pastas community in an early stage of any issues that needs to be solved
 and allows others to help you work out a solution.
 
-2. Fork Pastas
---------------
-To start making changes to the original code, you need to make a local copy
-of the Pastas, called "Forking" in git-language. You can read how to fork a
-GitHub repository `here <https://help.github
-.com/en/github/getting-started-with-github/fork-a-repo>`_.
+2. Fork and install Pastas
+--------------------------
+To start making changes to the original code, you need to make a local copy of
+the Pastas, called "Forking" in git-language. You can read how to fork a GitHub
+repository `here
+<https://help.github.com/en/github/getting-started-with-github/fork-a-repo>`_.
+To use all the development tools; install Pastas in development mode by running
+`pip install -e .[dev]` in the root of the repository. This will install all
+development dependencies such as `tox`, `ruff`, `pre=commit` and `pytest`.
 
 .. note::
-    Make sure to make changes in the make changes in your local Development
-    branch (Dev) or start an entirely new branch that branches of the
-    Dev-branch.
+    Make sure to make changes in the make changes in a new branch that branches
+    of the Dev-branch. This way you can easily create a Pull Request later on.
 
 3. Write Code
 -------------
 After you forked Pastas, you can start making changes to the code or add new
 features to it. To ensure high quality code that is easy to read and maintain
-we follow the `Black <https://black.readthedocs.io/en/stable/index.html>`_ code
-formatting standard. Check out the Pastas Code Style section to learn
+we follow the `Ruff <https://docs.astral.sh/ruff/>`_ code
+formatting and linting standard. Check out the Pastas Code Style section to learn
 more about the formatting of code and docstrings.
 
+.. note::
+    To make sure your code is up to standards, you can run the following:
+    - `ruff check --extend-select I --fix`
+    - `ruff format`
+    or use tox:
+    - `tox -e ruff_fix`
+
+.. note::
+    If you want to make sure your code is formatted and linted on every commit:
+    consider using the git pre-commit hook by installing it with `pip install
+    pre-commit` and running `pre-commit install` in the root of the repository.
+
 4. Test Code
-------------
-The ensure a proper functioning of the Pastas, it is important to supply
-tests in the test-suite (`see here <https://github
+-----------
+The ensure a proper functioning of the Pastas, it is important to supply tests
+in the test-suite (`see here <https://github
 .com/pastas/pastas/tree/master/tests>`_). The ensure a proper functioning of
-the Pastas, the software is automatically tested using Github Actions when changes
-are made. Pastas uses `pytest <https://docs.pytest.org/en/stable/>`_ to run tests.
+the Pastas, the software is automatically tested using Github Actions when
+changes are made. Pastas uses `pytest <https://docs.pytest.org/en/stable/>`_ to
+run tests.
 
 5. Document Code
 ----------------
-When submitting a new function, method or class, docstrings are required
-before the new code will be pulled into the dev branch. Documentation is
-created using `Sphinxdoc <http://www.sphinx-doc.org>`_. Docstrings within
-the method or class need to be written in `NumPy docformat <https://numpydoc
-.readthedocs.io/en/latest/format.html#docstring-standard>`_ to enable
-automatic documentation on this website. In the case of a new module, the module
-needs to be added to `index.rst` in the api-folder.
+When submitting a new function, method or class, docstrings are required before
+the new code will be pulled into the dev branch. Documentation is created using
+`Sphinxdoc <http://www.sphinx-doc.org>`_. Docstrings within the method or class
+need to be written in `NumPy docformat <https://numpydoc
+.readthedocs.io/en/latest/format.html#docstring-standard>`_ to enable automatic
+documentation on this website. In the case of a new module, the module needs to
+be added to `index.rst` in the api-folder.
 
 A Jupyter Notebook explaining the use of your new code can be added the to
-examples folder. This Notebook will also be automatically converted and
-placed on the Examples page on this website.
+examples folder. This Notebook will also be automatically converted and placed
+on the Examples page on this website.
 
 6. Create a pull request
 ------------------------
 Once you have written, tested, and documented your code you can start a pull
-request on the development branch (dev) of Pastas. Pull requests can only
-be submitted to the dev-branch and need to be reviewed by one of the core
+request on the development branch (dev) of Pastas. Pull requests can only be
+submitted to the dev-branch and need to be reviewed by one of the core
 developers. When you start your Pull Request, you will automatically see a
-checklist to go through to check if your PR is up to standards. Pastas will
-run automatic code tests to ensure that the code works, is documented and
-has a good code style.
+checklist to go through to check if your PR is up to standards. Pastas will run
+automatic code tests to ensure that the code works, is documented and has a
+good code style.
 
 7. Share and enjoy your work!
 -----------------------------
-After you have create a Pull Request the Core Development Team will
-review your code and discuss potential improvements on GitHub before merging
-your code into the development branch. After a successful Pull Request your
-code will be included in the next release of Pastas when the master-branch is
-updated. Congratulations, you are now officially a contributor to the Pastas
-project!
+After you have create a Pull Request the Core Development Team will review your
+code and discuss potential improvements on GitHub before merging your code into
+the development branch. After a successful Pull Request your code will be
+included in the next release of Pastas when the master-branch is updated.
+Congratulations, you are now officially a contributor to the Pastas project!

pastas/dataset.py

@@ -136,6 +136,6 @@ def list_datasets(silent: bool = True) -> List[str]:
         for folder in data:
             print(f" - {folder}")
         print(
-            f"Use ps.load_dataset('folder_name') to load a dataset from the repository."
+            "Use ps.load_dataset('folder_name') to load a dataset from the repository."
         )
     return data

pastas/extensions/__init__.py

@@ -1,19 +1,21 @@
 import logging
 
-from pastas.extensions.accessor import register_model_accessor
+from pastas.extensions.accessor import (
+    register_model_accessor as register_model_accessor,
+)
 
 logger = logging.getLogger(__name__)
 
 
 def register_plotly():
     """Register Plotly extension for pastas.Model class for interactive plotting."""
-    from pastas.plotting.plotly import Plotly
+    from pastas.plotting.plotly import Plotly as Plotly
 
     logger.info("Registered plotly extension in Model class, e.g. `ml.plotly.plot()`.")
 
 
 def register_bokeh():
     """Register Bokeh extension for pastas.Model class for interactive plotting."""
-    from pastas.plotting.bokeh import Bokeh
+    from pastas.plotting.bokeh import Bokeh as Bokeh
 
     logger.info("Registered bokeh extension in Model class, e.g. `ml.bokeh.plot()`.")

pastas/extensions/accessor.py

@@ -57,7 +57,7 @@ def _register_accessor(name: str, cls):
 
     .. code-block:: python
 
-        def __init__(self, pastas_object):  # noqa: E999
+        def __init__(self, pastas_object):
             ...
 
     Examples

pastas/io/base.py

@@ -5,7 +5,6 @@
 from os import path
 
 from packaging import version
-from pandas import to_numeric
 
 import pastas as ps
 

pastas/io/pas.py

@@ -47,7 +47,8 @@ def pastas_hook(obj: dict):
         elif key == "series":
             try:
                 obj[key] = read_json(stringIO(value), typ="series", orient="split")
-            except:
+            except Exception as e:
+                logger.debug(e)
                 obj[key] = value
             if isinstance(obj[key], Series):
                 obj[key].index = obj[key].index.tz_localize(None)
@@ -64,7 +65,8 @@ def pastas_hook(obj: dict):
         else:
             try:
                 obj[key] = json.loads(value, object_hook=pastas_hook)
-            except:
+            except Exception as e:
+                logger.debug(e)
                 obj[key] = value
     return obj
 

pastas/model.py

@@ -25,7 +25,6 @@
 from pastas.decorators import get_stressmodel
 from pastas.io.base import _load_model, dump
 from pastas.modelstats import Statistics
-from pastas.noisemodels import ArNoiseModel
 from pastas.plotting.modelplots import Plotting, _table_formatter_stderr
 from pastas.rfunc import HantushWellModel
 from pastas.solver import LeastSquares
@@ -38,10 +37,9 @@
     get_sample,
 )
 from pastas.transform import ThresholdTransform
-from pastas.typing import ArrayLike
+from pastas.typing import ArrayLike, Solver, StressModel, TimestampType
 from pastas.typing import Model as ModelType
 from pastas.typing import NoiseModel as NoiseModelType
-from pastas.typing import Solver, StressModel, TimestampType
 from pastas.utils import validate_name
 from pastas.version import __version__
 
@@ -1820,7 +1818,8 @@ def _get_file_info(self) -> dict:
 
         try:
             file_info["owner"] = getlogin()
-        except:
+        except Exception as e:
+            logger.debug(e)
             file_info["owner"] = "Unknown"
 
         return file_info

pastas/objective_functions.py

@@ -1,5 +1,5 @@
-"""This module contains the objective functions that can be used with the pastas 
-`EmceeSolve` solver.   
+"""This module contains the objective functions that can be used with the pastas
+`EmceeSolve` solver.
 
 """