sdf-xarray 0.2.4__tar.gz → 0.4.0__tar.gz

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/.github/workflows/build_publish.yml

@@ -29,10 +29,10 @@ jobs:
     - name: Set up Python 3.12 and install dependencies
       run: |
         uv python install 3.12
-        uv sync --python 3.12 --extra test --extra build --frozen
+        uv sync --python 3.12 --frozen
 
     - name: Build
-      uses: pypa/cibuildwheel@v2.21.3
+      uses: pypa/cibuildwheel@v3.1.3
       env:
         CIBW_ARCHS_LINUX: auto
         CIBW_ARCHS_MACOS: x86_64 arm64

sdf_xarray-0.4.0/.github/workflows/lint.yml

@@ -0,0 +1,11 @@
+name: lint
+on: push
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Ruff
+        uses: astral-sh/ruff-action@v3
+      - name: Run Ruff
+        run: ruff check --output-format=github src tests

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/.github/workflows/tests.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v4
@@ -18,7 +18,7 @@ jobs:
 
     - name: Setup uv
       id: setup-uv
-      uses: astral-sh/setup-uv@v3
+      uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true
 
@@ -28,7 +28,7 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }} and install dependencies
       run: |
         uv python install ${{ matrix.python-version }}
-        uv sync --python ${{ matrix.python-version }} --extra test --extra build --frozen
+        uv sync --python ${{ matrix.python-version }} --frozen
 
     - name: Test with pytest
       run: uv run pytest

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/.gitignore

@@ -288,3 +288,6 @@ dkms.conf
 
 # Generated version file
 src/sdf_xarray/_version.py
+
+# Downloaded doc tutorial datasets
+docs/tutorial_*

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/.readthedocs.yaml

@@ -16,6 +16,16 @@ build:
     # rust: "1.55"
     # golang: "1.17"
 
+  jobs:
+    pre_create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    create_environment:
+      - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+    install:
+      - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py
@@ -23,11 +33,3 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF
 # formats:
 #    - pdf
-
-# Optionally declare the Python requirements required to build your docs
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/CITATION.cff

@@ -16,5 +16,13 @@ authors:
     given-names: Shaun
     orcid: 'https://orcid.org/0009-0005-0693-030X'
     affiliation: University of York
+  - family-names: Herdman
+    given-names: Chris
+    orcid: 'https://orcid.org/0000-0002-5159-0130'
+    affiliation: University of York
+  - family-names: Pattinson
+    given-names: Liam
+    orcid: 'https://orcid.org/0000-0001-8604-6904'
+    affiliation: University of York
 doi: 10.5281/zenodo.15351323
 date-released: '2024-07-25'

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/CONTRIBUTING.md

@@ -4,7 +4,7 @@ We welcome contributions to the BEAM ecosystem! Whether it's reporting issues,
 suggesting features, improving the documentation, or submitting pull requests,
 your input helps improve these tools for the community.
 
-## How to Contribute
+## How to contribute
 
 There are many ways to get involved:
 
@@ -20,6 +20,12 @@ There are many ways to get involved:
 
 ## Code
 
+```bash
+git clone --recursive https://github.com/epochpic/sdf-xarray.git
+cd sdf-xarray
+pip install .
+```
+
 ### Style
 
 We follow [PEP 8](https://peps.python.org/pep-0008/) and use the
@@ -29,26 +35,46 @@ following tools:
 - [black](https://black.readthedocs.io/en/stable/) for formatting
 - [isort](https://pycqa.github.io/isort/) for sorting imports
 
-To run these tools locally, install the optional dependencies and run:
+To run these tools locally, install the `lint` dependency group:
+
+```bash
+pip install --group lint
+```
+
+Ruff can then be run with:
 
 ```bash
-pip install "sdf-xarray[lint]"
-ruff check
+ruff check src tests
 ```
 
-### Running and Adding Tests
+Alternatively, `uv` users can do this in one step with `uv run`:
+
+```bash
+uv run ruff check src tests
+```
+
+### Running and adding tests
 
 We use [pytest](https://docs.pytest.org/en/stable/) to run tests.
 All new functionality should include relevant tests, placed in the `tests/`
 directory and following the existing structure.
 
+When running the tests for the first time you will need an internet connection
+in order to download the datasets.
+
 Before submitting code changes, ensure that all tests pass:
 
 ```bash
-pip install "sdf-xarray[test]"
+pip install --group test
 pytest
 ```
 
+Alternatively, `uv` users can use:
+
+```bash
+uv run pytest
+```
+
 ## Documentation
 
 ### Style
@@ -59,21 +85,30 @@ When contributing to the documentation:
 - Follow the format of existing `.rst` files.
 - Link to external functions or tools when possible.
 
-### Compiling and Adding Documentation
+### Compiling and adding documentation
+
+When compiling the documentation for the first time you will need an internet
+connection in order to download the datasets.
 
 To build the documentation locally, first install the required packages:
 
 ```bash
-pip install "sdf-xarray[docs]"
+pip install --group docs
 cd docs
 make html
 ```
+
+The documentation can be updated by changing any of the `*.rst` files located
+in the main `docs` directory. The existing documentation hopefully includes most
+of the snippets you'd need to write or update it, however if you are stuck
+please don't hesitate to reach out.
+
 Every time you make changes to the documentation or add a new page, you must
 re-run the `make html` command to regenerate the HTML files.
 
-### Previewing Documentation
+### Previewing documentation
 
-#### Using VS Code Extensions
+#### Using VS Code extensions
 
 Once the html web pages have been made you can review them installing the
 [Live Server](https://marketplace.visualstudio.com/items/?itemName=ritwickdey.LiveServer)
@@ -81,17 +116,17 @@ VS Code extension. Navigate to the `_build/html` folder, right-click the
 `index.html`, and select **"Open with Live Server"**. This
 will open a live preview of the documentation in your web browser.
 
-#### Using a Simple Python Server
+#### Using a simple python server
 
 Alternatively, if you're not using VS Code, you can start a simple local server with Python:
 
 ```bash
-python -m http.server -d _build/htm
+python -m http.server -d _build/html
 ```
 
 Then open http://localhost:8000 in your browser to view the documentation.
 
-## Continuous Integration
+## Continuous integration
 
 All pull requests are automatically checked using GitHub Actions for:
 

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/PKG-INFO

@@ -1,70 +1,24 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: sdf-xarray
-Version: 0.2.4
+Version: 0.4.0
 Summary: Provides a backend for xarray to read SDF files as created by the EPOCH plasma PIC code.
-Author-Email: Peter Hill <peter.hill@york.ac.uk>, Joel Adams <joel.adams@york.ac.uk>, Shaun Doherty <shaun.doherty@york.ac.uk>
-License: Copyright 2024, Peter Hill, Joel Adams, epochpic team
-         
-         Redistribution and use in source and binary forms, with or without
-         modification, are permitted provided that the following conditions are
-         met:
-         
-         1. Redistributions of source code must retain the above copyright
-         notice, this list of conditions and the following disclaimer.
-         
-         2. Redistributions in binary form must reproduce the above copyright
-         notice, this list of conditions and the following disclaimer in the
-         documentation and/or other materials provided with the distribution.
-         
-         3. Neither the name of the copyright holder nor the names of its
-         contributors may be used to endorse or promote products derived from
-         this software without specific prior written permission.
-         
-         THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-         “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-         LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-         A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-         HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-         SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-         LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-         DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-         THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-         (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-         
+Author-Email: Peter Hill <peter.hill@york.ac.uk>, Joel Adams <joel.adams@york.ac.uk>, Shaun Doherty <shaun.doherty@york.ac.uk>, Chris Herdman <chris.herdman@york.ac.uk>, Liam Pattinson <liam.pattinson@york.ac.uk>
+License-Expression: BSD-3-Clause
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Classifier: Intended Audience :: Science/Research
-Classifier: Topic :: Scientific/Engineering
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.10
 Requires-Dist: numpy>=2.0.0
 Requires-Dist: xarray>=2024.1.0
 Requires-Dist: dask>=2024.7.1
-Provides-Extra: docs
-Requires-Dist: sphinx>=5.3; extra == "docs"
-Requires-Dist: sphinx_autodoc_typehints>=1.19; extra == "docs"
-Requires-Dist: sphinx-book-theme>=0.4.0rc1; extra == "docs"
-Requires-Dist: sphinx-argparse-cli>=1.10.0; extra == "docs"
-Requires-Dist: sphinx-inline-tabs; extra == "docs"
-Requires-Dist: pickleshare; extra == "docs"
-Requires-Dist: ipython; extra == "docs"
-Requires-Dist: matplotlib; extra == "docs"
-Requires-Dist: pint; extra == "docs"
-Requires-Dist: pint-xarray; extra == "docs"
-Requires-Dist: myst-parser; extra == "docs"
-Provides-Extra: test
-Requires-Dist: pytest>=3.3.0; extra == "test"
-Requires-Dist: dask[complete]; extra == "test"
-Requires-Dist: matplotlib; extra == "test"
-Provides-Extra: lint
-Requires-Dist: ruff; extra == "lint"
-Provides-Extra: build
-Requires-Dist: cibuildwheel[uv]; extra == "build"
 Provides-Extra: jupyter
 Requires-Dist: dask[diagnostics]; extra == "jupyter"
 Requires-Dist: ipykernel>=6.29.5; extra == "jupyter"
@@ -90,23 +44,19 @@ Part of [BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules
 
 ## Installation
 
+> [!IMPORTANT]
+> To install this package make sure you are using one of the Python versions listed above.
+
 Install from PyPI with:
 
 ```bash
 pip install sdf-xarray
 ```
 
-> [!NOTE]
-> For use within jupyter notebooks, run this additional command after installation:
->
-> ```bash
-> pip install "sdf-xarray[jupyter]"
-> ```
-
-or from a local checkout:
+or download this code locally:
 
 ```bash
-git clone https://github.com/epochpic/sdf-xarray.git
+git clone --recursive https://github.com/epochpic/sdf-xarray.git
 cd sdf-xarray
 pip install .
 ```
@@ -115,6 +65,9 @@ We recommend switching to [uv](https://docs.astral.sh/uv/) to manage packages.
 
 ## Usage
 
+Below are some simple examples to get you started. Please read the full
+documentation here <https://sdf-xarray.readthedocs.io>.
+
 ### Single file loading
 
 ```python
@@ -135,15 +88,22 @@ print(df["Electric_Field_Ex"])
 
 ### Multi-file loading
 
-To open a whole simulation at once, pass `preprocess=sdf_xarray.SDFPreprocess()`
-to `xarray.open_mfdataset`:
+You can open all the SDF files for a given simulation by calling the `open_mfdataset`
+function from `sdf_xarray`. This will additionally add a time dimension using the `"time"`
+value stored in each files attributes.
+
+> [!IMPORTANT]
+> If your simulation has multiple `output` blocks so that not all variables are
+> output at every time step, then at the timesteps where those variables are not
+> present they will have have a value of nan. To clean your dataset by removing
+> these nan values we suggest using the `xarray.DataArray.dropna` function or
+> loading sparse data along separate time dimensions using `separate_times=True`.
 
 ```python
-import xarray as xr
-from sdf_xarray import SDFPreprocess
+from sdf_xarray import open_mfdataset
 
-with xr.open_mfdataset("*.sdf", preprocess=SDFPreprocess()) as ds:
-    print(ds)
+ds = open_mfdataset("*.sdf")
+print(ds)
 
 # Dimensions:
 # time: 301, X_Grid_mid: 128, ...
@@ -153,15 +113,6 @@ with xr.open_mfdataset("*.sdf", preprocess=SDFPreprocess()) as ds:
 # Attributes: (22) ...
 ```
 
-`SDFPreprocess` checks that all the files are from the same simulation, as
-ensures there's a `time` dimension so the files are correctly concatenated.
-
-If your simulation has multiple `output` blocks so that not all variables are
-output at every time step, then those variables will have `NaN` values at the
-corresponding time points.
-
-For more in depth documentation please visit: <https://sdf-xarray.readthedocs.io/>
-
 ## Citing
 
 If sdf-xarray contributes to a project that leads to publication, please acknowledge this by citing sdf-xarray. This can be done by clicking the "cite this repository" button located near the top right of this page.

{sdf_xarray-0.2.4 → sdf_xarray-0.4.0}/README.md

@@ -15,23 +15,19 @@ Part of [BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules
 
 ## Installation
 
+> [!IMPORTANT]
+> To install this package make sure you are using one of the Python versions listed above.
+
 Install from PyPI with:
 
 ```bash
 pip install sdf-xarray
 ```
 
-> [!NOTE]
-> For use within jupyter notebooks, run this additional command after installation:
->
-> ```bash
-> pip install "sdf-xarray[jupyter]"
-> ```
-
-or from a local checkout:
+or download this code locally:
 
 ```bash
-git clone https://github.com/epochpic/sdf-xarray.git
+git clone --recursive https://github.com/epochpic/sdf-xarray.git
 cd sdf-xarray
 pip install .
 ```
@@ -40,6 +36,9 @@ We recommend switching to [uv](https://docs.astral.sh/uv/) to manage packages.
 
 ## Usage
 
+Below are some simple examples to get you started. Please read the full
+documentation here <https://sdf-xarray.readthedocs.io>.
+
 ### Single file loading
 
 ```python
@@ -60,15 +59,22 @@ print(df["Electric_Field_Ex"])
 
 ### Multi-file loading
 
-To open a whole simulation at once, pass `preprocess=sdf_xarray.SDFPreprocess()`
-to `xarray.open_mfdataset`:
+You can open all the SDF files for a given simulation by calling the `open_mfdataset`
+function from `sdf_xarray`. This will additionally add a time dimension using the `"time"`
+value stored in each files attributes.
+
+> [!IMPORTANT]
+> If your simulation has multiple `output` blocks so that not all variables are
+> output at every time step, then at the timesteps where those variables are not
+> present they will have have a value of nan. To clean your dataset by removing
+> these nan values we suggest using the `xarray.DataArray.dropna` function or
+> loading sparse data along separate time dimensions using `separate_times=True`.
 
 ```python
-import xarray as xr
-from sdf_xarray import SDFPreprocess
+from sdf_xarray import open_mfdataset
 
-with xr.open_mfdataset("*.sdf", preprocess=SDFPreprocess()) as ds:
-    print(ds)
+ds = open_mfdataset("*.sdf")
+print(ds)
 
 # Dimensions:
 # time: 301, X_Grid_mid: 128, ...
@@ -78,15 +84,6 @@ with xr.open_mfdataset("*.sdf", preprocess=SDFPreprocess()) as ds:
 # Attributes: (22) ...
 ```
 
-`SDFPreprocess` checks that all the files are from the same simulation, as
-ensures there's a `time` dimension so the files are correctly concatenated.
-
-If your simulation has multiple `output` blocks so that not all variables are
-output at every time step, then those variables will have `NaN` values at the
-corresponding time points.
-
-For more in depth documentation please visit: <https://sdf-xarray.readthedocs.io/>
-
 ## Citing
 
 If sdf-xarray contributes to a project that leads to publication, please acknowledge this by citing sdf-xarray. This can be done by clicking the "cite this repository" button located near the top right of this page.

sdf_xarray-0.4.0/docs/_static/force_render_dark_xarray_objects.css

@@ -0,0 +1,7 @@
+/* workaround Pydata Sphinx theme using light colors for widget cell outputs in dark-mode */
+/* works for many widgets but not for Xarray html reprs */
+/* https://github.com/pydata/pydata-sphinx-theme/issues/2189 */
+html[data-theme="dark"] div.cell_output .text_html:has(div.xr-wrap) {
+    background-color: var(--pst-color-on-background) !important;
+    color: var(--pst-color-text-base) !important;
+}