Compatibility fixes for unyt3.1.0

.github/workflows/lint_and_test.yml

@@ -44,22 +44,10 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Cache pip
-      uses: actions/cache@v4
-      with:
-        # This path is specific to Ubuntu
-        path: ~/.cache/pip
-        # Look to see if there is a cache hit for the corresponding requirements file
-        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-${{ runner.os }}-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        if [ -f optional_requirements.txt ]; then pip install -r optional_requirements.txt; fi
-        pip install -e .
+        pip install -e .[dev]
     - name: Test with pytest
       run: |
         pytest

.github/workflows/python-publish.yml

@@ -30,7 +30,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel build
-        pip install -r requirements.txt
         pip install .
     - name: Build
       run: |

.readthedocs.yaml

@@ -11,8 +11,7 @@ build:
     python: "3.12"
   jobs:
     post_create_environment:
-      - python3 -m pip install swiftsimio
-      - python3 -m pip install -r optional_requirements.txt
+      - python3 -m pip install .[docs]
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
@@ -22,11 +21,4 @@ sphinx:
 formats:
   - pdf
   - epub
-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-python:
-  install:
-    - requirements: docs/requirements.txt
 

CONTRIBUTING.md

@@ -33,9 +33,9 @@ Documentation
 
 The API documentation is built automatically from the docstrings of classes, functions, etc. in the source files. These follow the NumPy-style format. All public (i.e. not starting in `_`) modules, functions, classes, methods, etc. should have an appropriate docstring. Tests should also have descriptive docstrings, but full descriptions (e.g. of all parameters) are not required.
 
-In addition to this there is "narrative documentation" that should describe the features of the code. The docs are built with `sphinx` and use the "ReadTheDocs" theme. If you have the dependencies installed (check `/docs/requirements.txt`) you can build the documentation locally with `make html` in the `/docs` directory. Opening the `/docs/index.html` file with a browser will then allow you to browse the documentation and check your contributions.
+In addition to this there is "narrative documentation" that should describe the features of the code. The docs are built with `sphinx` and use the "ReadTheDocs" theme. If you have the dependencies installed (check `pyproject.toml` or use `pip install -e .[docs]` in the project root directory) you can build the documentation locally with `make html` in the `/docs` directory. Opening the `/docs/build/index.html` file with a browser will then allow you to browse the documentation and check your contributions.
 
 Docstrings
 ----------
 
-Ruff currently has limited support for [numpydoc](https://numpydoc.readthedocs.io/en/latest/index.html)-style docstrings. To run additional checks on docstrings use `numpydoc lint **/*.py` in the same directory as the `pyproject.toml` file. As more style rules become supported by `ruff` this will hopefully be phased out.
+Ruff currently has limited support for [numpydoc](https://numpydoc.readthedocs.io)-style docstrings. To run additional checks on docstrings use `numpydoc lint **/*.py` in the same directory as the `pyproject.toml` file. As more style rules become supported by `ruff` this will hopefully be phased out.

README.rst

@@ -15,7 +15,7 @@ SWIFTsimIO
    :target: https://github.com/SWIFTSIM/swiftsimio/actions/workflows/lint_and_test.yml
    :alt: Build status
 .. |Documentation status| image:: https://readthedocs.org/projects/swiftsimio/badge/?version=latest
-   :target: https://swiftsimio.readthedocs.io/en/latest/?badge=latest
+   :target: https://swiftsimio.readthedocs.io
    :alt: Documentation status
 .. |JOSS| image:: https://joss.theoj.org/papers/e85c85f49b99389d98f9b6d81f090331/status.svg
    :target: https://joss.theoj.org/papers/e85c85f49b99389d98f9b6d81f090331

docs/source/conf.py

@@ -109,7 +109,7 @@ def setup(app):  # numpydoc ignore=GL08
     numba=("https://numba.readthedocs.io/en/stable/", None),
     unyt=("https://unyt.readthedocs.io/en/stable/", None),
     scipy=("https://docs.scipy.org/doc/scipy/", None),
-    swiftgalaxy=("https://swiftsimio.readthedocs.io/en/latest/", None),
+    swiftgalaxy=("https://swiftgalaxy.readthedocs.io/en/stable/", None),
     velociraptor=("https://velociraptor-python.readthedocs.io/en/latest/", None),
     astropy=("https://docs.astropy.org/en/stable/", None),
 )

docs/source/getting_started/index.rst

@@ -30,19 +30,12 @@ To set up the code for development, first clone the latest master from GitHub:
 
    git clone https://github.com/SWIFTSIM/swiftsimio.git
 
-and install with ``pip`` using the ``-e`` ("editable") flag,
+and install with ``pip`` using the ``-e`` ("editable") flag, and specifying optional dependencies for development and building the documentation:
 
 .. code-block::
 
    cd swiftsimio
-   pip install -e .
-
-Then install the optioanl dependencies for the code and the documentation:
-
-.. code-block::
-
-   pip install -r optional_requirements.txt
-   pip install -r docs/requirements.txt
+   pip install -e .[dev,docs]
 
 .. include:: ../../../README.rst
    :start-after: COMMUNITY_START_LABEL

docs/source/soap/index.rst

@@ -38,4 +38,4 @@ swiftgalaxy
 
 The :mod:`swiftgalaxy` companion package to :mod:`swiftsimio` offers further integration with halo catalogues in SOAP, Caesar and Velociraptor formats (so far). It greatly simplifies efficient loading of particles belonging to an object from a catalogue, and additional tools that are useful when working with a galaxy or other localized collection of particles. Refer to the `swiftgalaxy documentation`_ for details.
 
-.. _swiftgalaxy documentation: https://swiftgalaxy.readthedocs.io/en/latest/
+.. _swiftgalaxy documentation: https://swiftgalaxy.readthedocs.io

pyproject.toml

@@ -38,21 +38,40 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "astropy>=5.0",
+    "astropy>=6.0",
     "numpy>=2.1.0",
     "h5py",
-    "unyt>=3.0.4",
+    "unyt>=3.1.0",
     "numba>=0.50.0",
 ]
 
 [project.urls]
 "Homepage" = "https://github.com/SWIFTSIM/swiftsimio"
 "Bug Tracker" = "https://github.com/SWIFTSIM/swiftsimio/issues"
-"Documentation" = "https://swiftsimio.readthedocs.io/en/latest"
+"Documentation" = "https://swiftsimio.readthedocs.io"
 
 [project.scripts]
 swiftsnap = "swiftsimio.swiftsnap:swiftsnap"
 
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "ruff",
+    "numpydoc",
+    "matplotlib",
+    "scipy",
+    "wily",
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "recommonmark",
+    "sphinx_design",
+]
+all = [
+    "swiftsimio[dev,docs]"
+]
+
 [tool.ruff]
 exclude = ["docs/source/conf.py"]
 line-length = 88

swiftsimio/_array_functions.py

@@ -93,7 +93,6 @@
     linalg_eigvalsh as unyt_linalg_eigvalsh,
     savetxt as unyt_savetxt,
     fill_diagonal as unyt_fill_diagonal,
-    isin as unyt_isin,
     place as unyt_place,
     put as unyt_put,
     put_along_axis as unyt_put_along_axis,
@@ -115,9 +114,13 @@
     array_repr as unyt_array_repr,
     linalg_outer as unyt_linalg_outer,
     trapezoid as unyt_trapezoid,
-    isin as unyt_in1d,
+    isin as unyt_isin,
     take as unyt_take,
 )
+from importlib.metadata import version
+from packaging.version import Version
+
+NUMPY_VERSION = Version(version("numpy"))
 
 _HANDLED_FUNCTIONS = {}
 
@@ -1271,39 +1274,8 @@ def wrapper(*args: tuple[Any], **kwargs: dict[str, Any]) -> Callable:
 
 
 @implements(np.array2string)
-def array2string(  # noqa numpydoc ignore=GL08
-    a,  # noqa: ANN001
-    max_line_width=None,  # noqa: ANN001
-    precision=None,  # noqa: ANN001
-    suppress_small=None,  # noqa: ANN001
-    separator=" ",  # noqa: ANN001
-    prefix="",  # noqa: ANN001
-    style=np._NoValue,  # noqa: ANN001
-    formatter=None,  # noqa: ANN001
-    threshold=None,  # noqa: ANN001
-    edgeitems=None,  # noqa: ANN001
-    sign=None,  # noqa: ANN001
-    floatmode=None,  # noqa: ANN001
-    suffix="",  # noqa: ANN001
-    *,
-    legacy=None,  # noqa: ANN001
-):
-    res = unyt_array2string(
-        a,
-        max_line_width=max_line_width,
-        precision=precision,
-        suppress_small=suppress_small,
-        separator=separator,
-        prefix=prefix,
-        style=style,
-        formatter=formatter,
-        threshold=threshold,
-        edgeitems=edgeitems,
-        sign=sign,
-        floatmode=floatmode,
-        suffix=suffix,
-        legacy=legacy,
-    )
+def array2string(a, *args, **kwargs):  # noqa numpydoc ignore=GL08
+    res = unyt_array2string(a, *args, **kwargs)
     if a.comoving:
         append = " (comoving)"
     elif a.comoving is False:
@@ -2262,14 +2234,46 @@ def trapezoid(y, x=None, dx=1.0, axis=-1):  # noqa numpydoc ignore=GL08
     return _return_helper(res, helper_result, ret_cf)
 
 
-implements(np.in1d)(_default_comparison_wrapper(unyt_in1d))
+implements(np.isin)(_default_comparison_wrapper(unyt_isin))
 implements(np.take)(_default_unary_wrapper(unyt_take, _preserve_cosmo_factor))
 
 # Now we wrap functions that unyt does not handle explicitly:
 
-implements(np.average)(
-    _propagate_cosmo_array_attributes_to_result(np.average._implementation)
-)
+
+@implements(np.average)
+def average(a, axis=None, weights=None, returned=False, *, keepdims=np._NoValue):  # noqa numpydoc ignore=GL08
+    # Average suffered from a bug
+    # (https://github.com/SWIFTSIM/swiftsimio/issues/285)
+    # Correct results depend on unyt>=3.1.0
+    # (https://github.com/yt-project/unyt/pull/611)
+    # There is also a fix in numpy>=3.4.1
+    # (https://github.com/numpy/numpy/pull/30522)
+    # that means we no longer need any special handling here, but to support older
+    # versions we need a patch.
+    helper_result = _prepare_array_func_args(
+        a, axis=axis, weights=weights, returned=returned, keepdims=keepdims
+    )
+    if NUMPY_VERSION < Version("2.4.1"):
+        from unyt._array_functions import average as super_average
+
+    else:
+        super_average = np.average._implementation
+
+    res = super_average(
+        a, axis=axis, weights=weights, returned=returned, keepdims=keepdims
+    )
+    ret_cf_avg = _preserve_cosmo_factor(helper_result["cfs"][0])
+    if returned:
+        avg, wsum = res
+        ret_cf_wsum = _preserve_cosmo_factor(helper_result["kw_cfs"]["weights"])
+        return (
+            _return_helper(avg, helper_result, ret_cf_avg),
+            _return_helper(wsum, helper_result, ret_cf_wsum),
+        )
+    else:
+        return _return_helper(res, helper_result, ret_cf_avg)
+
+
 implements(np.max)(_propagate_cosmo_array_attributes_to_result(np.max._implementation))
 implements(np.min)(_propagate_cosmo_array_attributes_to_result(np.min._implementation))
 implements(np.mean)(