Merge branch 'main' into fix-group-auto-groups-str

.github/workflows/coverage.yml

@@ -37,7 +37,7 @@ jobs:
           micromamba-version: 1.5.6-0
           environment-file: env.yml
           cache-environment: true
-          create-args: python=3.9
+          create-args: python=3.10
 
       - name: ccache
         uses: hendrikmuhs/ccache-action@v1.2.13

.github/workflows/docs.yml

@@ -45,7 +45,7 @@ jobs:
           fetch-depth: 0  # history required so cmake can determine version
       - uses: actions/setup-python@v3
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/ci.txt
       - run: |

.github/workflows/pr_and_main.yml

@@ -18,7 +18,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v3
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/ci.txt
       - run: tox -e static
@@ -40,7 +40,7 @@ jobs:
         - {os: ubuntu-22.04, cmake-preset: ci-linux}
         - {os: macos-11, cmake-preset: ci-macos}
         - {os: windows-2019, cmake-preset: ci-windows}
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/release-nightly.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-22.04]
-        build: [cp39, cp310]
+        build: [cp310]
     uses: ./.github/workflows/wheel.yml
     with:
       os: ${{ matrix.os }}
@@ -32,7 +32,7 @@ jobs:
           merge-multiple: true
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - run: python .github/workflows/rename-dev-wheels.py
       - uses: ncipollo/release-action@v1
         with:

.github/workflows/release.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v3
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/ci.txt
       - run: tox -e check-release
@@ -33,7 +33,7 @@ jobs:
           - {os: macos-11, target: osx_64}
           - {os: macos-11, target: osx_arm64}
           - {os: windows-2019, target: win_64}
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
     uses: ./.github/workflows/conda.yml
     with:
       os: ${{ matrix.variant.os }}
@@ -68,7 +68,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-22.04, macos-11, windows-2019]
-        build: [cp39, cp310, cp311, cp312]
+        build: [cp310, cp311, cp312]
     uses: ./.github/workflows/wheel.yml
     with:
       os: ${{ matrix.os }}
@@ -104,7 +104,7 @@ jobs:
           merge-multiple: true
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - run: conda install -c conda-forge --yes anaconda-client
       - run: anaconda --token ${{ secrets.ANACONDATOKEN }} upload --user scipp --label main $(ls conda-package-*/*/*.tar.bz2)
 
@@ -121,7 +121,7 @@ jobs:
           fetch-depth: 0  # history required so cmake can determine version
       - uses: actions/setup-python@v3
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/ci.txt
       - name: Set outputs

.github/workflows/weekly.yml

@@ -18,7 +18,7 @@ jobs:
       matrix:
         variant:
           - {os: ubuntu-22.04, target: linux_64}
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.10", "3.11"]
     uses: ./.github/workflows/conda.yml
     with:
       os: ${{ matrix.variant.os }}
@@ -29,7 +29,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04]
-        build: [cp39, cp312]
+        build: [cp310, cp312]
     uses: ./.github/workflows/wheel.yml
     with:
       os: ${{ matrix.os }}

.github/workflows/wheel.yml

@@ -23,7 +23,7 @@ jobs:
         submodules: true
         fetch-depth: 0  # history required so cmake can determine version
 
-    - uses: pypa/cibuildwheel@v2.17.0
+    - uses: pypa/cibuildwheel@v2.18.0
       env:
         CIBW_BUILD: ${{ inputs.build }}-*
         MACOSX_DEPLOYMENT_TARGET: "10.15"

docs/environments/developer.yml

@@ -10,7 +10,6 @@ dependencies:
   - cmake>=3.21
   - conan==1.59.0
   - conda-build
-  - graphlib-backport # for python < 3.9
   - h5py
   - hypothesis
   - ipympl
@@ -26,7 +25,7 @@ dependencies:
   - pooch
   - pre-commit
   - pytest
-  - python=3.8
+  - python=3.10
   - python-graphviz
   - pythreejs
   - pyyaml

docs/getting-started/installation.rst

@@ -3,7 +3,7 @@
 Installation
 ============
 
-Scipp requires Python 3.8 or above.
+Scipp requires Python 3.10 or above.
 
 Conda
 -----
@@ -64,7 +64,7 @@ To add Scipp to an existing conda environment:
 
 After installation the module, Scipp can be imported in Python.
 Note that only the bare essential dependencies are installed.
-If you wish to use plotting functionality you will also need to install ``plopp`` and ``ipywidgets``.
+If you wish to use plotting functionality you will also need to install ``plopp``, ``ipympl``, and ``pythreejs``.
 
 To update or remove Scipp use `conda update <https://docs.conda.io/projects/conda/en/latest/commands/update.html>`_ and `conda remove <https://docs.conda.io/projects/conda/en/latest/commands/remove.html>`_.
 
@@ -78,19 +78,19 @@ Scipp is available from `PyPI <https://pypi.org/>`_ via ``pip``:
    pip install scipp
 
 By default, this is only a minimal install without optional dependencies.
-To install components for additional submodules, use the ``all`` extras of the module:
+To install all optional dependencies, including libraries for interactive plotting in Jupyter, use:
 
 .. code-block:: sh
 
    pip install scipp[all]
 
-This will install everything that is needed, with the exception of plotting libraries for interactive use in Jupyter.
-These are available in the ``interactive`` extra.
-We recommend combining this with ``all``:
+
+You can also leave out the interactive tools and bring in only functional optional dependencies,
+such as ``h5py`` and ``scipy``, use ``extra`` instead of ``all``:
 
 .. code-block:: sh
 
-   pip install scipp[all,interactive]
+   pip install scipp[extra]
 
 From source
 -----------

docs/getting-started/tutorials/prepare_data_rhessi.py

@@ -13,7 +13,6 @@
 import re
 from datetime import date, datetime, time, timedelta
 from pathlib import Path
-from typing import Dict, Union
 
 import numpy as np
 import pooch
@@ -76,7 +75,7 @@ def parse_time(t) -> time:
     return time.fromisoformat(t)
 
 
-def parse_datetimes(d, start, peak, end) -> Dict[str, Union[np.datetime64, int]]:
+def parse_datetimes(d, start, peak, end) -> dict[str, np.datetime64 | int]:
     d = parse_date(d)
     start = parse_time(start)
     peak = parse_time(peak)

docs/user-guide/binned-data/binned-data.ipynb

@@ -73,7 +73,7 @@
     "    data=sc.array(dims=['row'], unit=sc.units.counts, values=values, variances=values),\n",
     "    coords={\n",
     "        'position': sc.array(\n",
-    "            dims=['row'], values=['site-{}'.format(i) for i in range(N)]\n",
+    "            dims=['row'], values=[f'site-{i}' for i in range(N)]\n",
     "        ),\n",
     "        'x': sc.array(dims=['row'], unit='m', values=np.random.rand(N)),\n",
     "        'y': sc.array(dims=['row'], unit='m', values=np.random.rand(N)),\n",
@@ -140,7 +140,7 @@
     "ax.set_xlabel('x [{}]'.format(table.coords['x'].unit))\n",
     "ax.set_ylabel('y [{}]'.format(table.coords['y'].unit))\n",
     "cbar = plt.colorbar(scatter)\n",
-    "cbar.set_label(\"[{}]\".format(table.unit))"
+    "cbar.set_label(f\"[{table.unit}]\")"
    ]
   },
   {
@@ -207,7 +207,7 @@
     "ax.set_yticks(binned.coords['y'].values)\n",
     "ax.grid()\n",
     "cbar = fig.colorbar(scatter)\n",
-    "cbar.set_label(\"[{}]\".format(table.unit))"
+    "cbar.set_label(f\"[{table.unit}]\")"
    ]
   },
   {

lib/cmake/.conan-recipes/pybind11/conandata.yml

@@ -1,4 +1,4 @@
 sources:
-  2.10.0:
-    sha256: eacf582fa8f696227988d08cfc46121770823839fe9e301a20fbce67e7cd70ec
-    url: https://github.com/pybind/pybind11/archive/v2.10.0.tar.gz
+  2.12.0:
+    sha256: bf8f242abd1abcd375d516a7067490fb71abd79519a282d22b6e4d19282185a7
+    url: https://github.com/pybind/pybind11/archive/v2.12.0.tar.gz

lib/cmake/.conan-recipes/pybind11/conanfile.py

@@ -65,18 +65,6 @@ def package(self):
             except RuntimeError:
                 pass
         if Version(self.version) >= "2.6.0":
-            replace_in_file(
-                self,
-                os.path.join(
-                    self.package_folder,
-                    "lib",
-                    "cmake",
-                    "pybind11",
-                    "pybind11Common.cmake",
-                ),
-                "if(TARGET pybind11::lto)",
-                "if(FALSE)",
-            )
             replace_in_file(
                 self,
                 os.path.join(

lib/cmake/scipp-conan.cmake

@@ -8,7 +8,7 @@ execute_process(
                     COMMAND_ECHO STDOUT
 )
 execute_process(
-  COMMAND conan export . 2.10.0@
+  COMMAND conan export . 2.12.0@
   WORKING_DIRECTORY "${CMAKE_CURRENT_LIST_DIR}/.conan-recipes/pybind11"
                     COMMAND_ECHO STDOUT
 )
@@ -58,7 +58,7 @@ conan_cmake_configure(
   eigen/3.4.0
   gtest/1.11.0
   LLNL-Units/0.9.1
-  pybind11/2.10.0
+  pybind11/2.12.0
   ${CONAN_ONETBB}
   OPTIONS
   benchmark:shared=False

lib/python/CMakeLists.txt

@@ -55,9 +55,6 @@ set_target_properties(
              "${CMAKE_INSTALL_RPATH}/${RELATIVE_LIB}/${CMAKE_INSTALL_LIBDIR}"
 )
 
-pybind11_strip(_scipp)
-pybind11_extension(_scipp)
-
 if(PRECOMPILED_HEADERS)
   target_precompile_headers(_scipp PRIVATE pybind11.h)
 endif()

pyproject.toml

@@ -18,7 +18,6 @@ classifiers = [
   "Natural Language :: English",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
@@ -28,7 +27,7 @@ classifiers = [
   "Topic :: Scientific/Engineering",
   "Typing :: Typed",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
   "numpy >= 1.20",
 ]
@@ -47,24 +46,23 @@ test = [
   "bs4",
   "ipython",
 ]
-all = [
+extra = [
   "h5py",
   "scipy>=1.7.0",
   "graphviz",
   "pooch",
   "plopp",
   "matplotlib"
 ]
-interactive = [
+all = [
+    "scipp[extra]",
     "ipympl",
     "ipython",
     "ipywidgets",
-    "matplotlib",
     "jupyterlab",
     "jupyterlab-widgets",
     "jupyter_nbextensions_configurator",
     "nodejs",
-    "plopp",
     "pythreejs",
 ]
 

src/scipp/compat/dict.py

@@ -190,7 +190,7 @@ def _dict_to_data_array(d):
     if "data" not in d:
         raise KeyError(
             "To create a DataArray, the supplied dict must contain "
-            "'data'. Got {}.".format(d.keys())
+            f"'data'. Got {d.keys()}."
         )
     out = {"coords": {}, "masks": {}, "attrs": {}}
     for key in out.keys():

src/scipp/compat/pandas_compat.py

@@ -3,7 +3,8 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Callable, Iterable, Literal, Optional, Tuple, Union
+from collections.abc import Callable, Iterable
+from typing import TYPE_CHECKING, Literal
 
 from ..core import DataArray, Dataset, Unit, UnitError, array
 from ..typing import VariableLike
@@ -56,7 +57,7 @@ def from_pandas_series(
 def from_pandas_dataframe(
     df: pd.DataFrame,
     *,
-    data_columns: Optional[Union[str, Iterable[str]]] = None,
+    data_columns: str | Iterable[str] | None = None,
     include_trivial_index: bool = False,
     header_parser: HeaderParserArg = None,
 ) -> Dataset:
@@ -85,9 +86,9 @@ def from_pandas_dataframe(
 
 
 def from_pandas(
-    pd_obj: Union[pd.DataFrame, pd.Series],
+    pd_obj: pd.DataFrame | pd.Series,
     *,
-    data_columns: Optional[Union[str, Iterable[str]]] = None,
+    data_columns: str | Iterable[str] | None = None,
     include_trivial_index: bool = False,
     header_parser: HeaderParserArg = None,
 ) -> VariableLike:
@@ -146,11 +147,11 @@ def from_pandas(
         raise ValueError(f"from_pandas: cannot convert type '{type(pd_obj)}'")
 
 
-HeaderParser = Callable[[str], Tuple[str, Optional[Unit]]]
-HeaderParserArg = Optional[Union[Literal["bracket"], HeaderParser]]
+HeaderParser = Callable[[str], tuple[str, Unit | None]]
+HeaderParserArg = Literal["bracket"] | HeaderParser | None
 
 
-def parse_bracket_header(head: str) -> Tuple[str, Optional[Unit]]:
+def parse_bracket_header(head: str) -> tuple[str, Unit | None]:
     """Parses strings of the form ``name [unit]``.
 
     ``name`` may be any string that does not contain the character ``[``.
@@ -207,7 +208,7 @@ def parse_bracket_header(head: str) -> Tuple[str, Optional[Unit]]:
 }
 
 
-def _parse_header(header: str, parser: HeaderParserArg) -> Tuple[str, Optional[Unit]]:
+def _parse_header(header: str, parser: HeaderParserArg) -> tuple[str, Unit | None]:
     if parser is None:
         return header, default_unit
     if callable(parser):