Merge branch 'main' into add_mcc

README.md

@@ -36,8 +36,9 @@ python3 -m pip install pycyclops
 
 `cyclops` has many optional dependencies that are used for specific functionality. For
 example, the [monai](https://github.com/Project-MONAI/MONAI) library is used for loading
-DICOM images to create datasets. All optional dependencies can be installed with
-``pycyclops[all]``, and specific sets of dependencies are listed in the sections below.
+DICOM images to create datasets. Hence, `monai` can be installed using
+``python3 -m pip install pycyclops[monai]``. Specific sets of dependencies are listed
+below.
 
 
 | Dependency       | pip extra       | Notes                                                                                                        |
@@ -83,7 +84,7 @@ make html SPHINXOPTS="-D nbsphinx_allow_errors=True"
 ### Contributing
 
 Contributing to cyclops is welcomed.
-See [Contributing](https://vectorinstitute.github.io/cyclops/api/intro.html) for
+See [Contributing](https://vectorinstitute.github.io/cyclops/api/contributing.html) for
 guidelines.
 
 

docs/source/contributing.rst

@@ -22,19 +22,12 @@ Coding guidelines
 For code style, we recommend the `google style
 guide <https://google.github.io/styleguide/pyguide.html>`__.
 
-Pre-commit hooks apply the
-`black <https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html>`__
-code formatting.
-
 For docstrings we use `numpy
 format <https://numpydoc.readthedocs.io/en/latest/format.html>`__.
 
-We also use `flake8 <https://flake8.pycqa.org/en/latest/>`__ and
-`pylint <https://pylint.pycqa.org/en/stable/>`__ for further static code
-analysis. The pre-commit hooks show errors which you need to fix before
+We use `ruff <https://docs.astral.sh/ruff/>`__ for code formatting and static code
+analysis. Ruff checks various rules including `flake8 <https://docs.astral.sh/ruff/faq/#how-does-ruff-compare-to-flake8>`__. The pre-commit hooks show errors which you need to fix before
 submitting a PR.
 
 Last but not the least, we use type hints in our code which is then
 checked using `mypy <https://mypy.readthedocs.io/en/stable/>`__.
-Currently, mypy checks are not strict, but will be enforced more as the
-API code becomes more stable.

docs/source/installation.rst

@@ -8,7 +8,7 @@ Using pip
 
    python3 -m pip install pycyclops
 
-``cyclops`` has many optional dependencies that are used for specific functionality. For example, the `monai <https://github.com/Project-MONAI/MONAI>`__ library is used for loading DICOM images to create datasets. All optional dependencies can be installed with ``pycyclops[all]``, and specific sets of dependencies are listed in the sections below.
+``cyclops`` has many optional dependencies that are used for specific functionality. For example, the `monai <https://github.com/Project-MONAI/MONAI>`__ library is used for loading DICOM images to create datasets. Hence, `monai` can be installed using ``python3 -m pip install pycyclops[monai]``. Specific sets of dependencies are listed below.
 
 +-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+
 | Dependency                  | pip extra                | Notes                                                                                                         |