sdf-xarray 0.6.0__tar.gz → 0.7.1__tar.gz

{sdf_xarray-0.6.0 → sdf_xarray-0.7.1}/.readthedocs.yaml

@@ -7,7 +7,7 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
 

{sdf_xarray-0.6.0 → sdf_xarray-0.7.1}/CONTRIBUTING.md

@@ -85,54 +85,78 @@ uv run pytest
 
 ## Documentation
 
-### Style
-
-When contributing to the documentation:
-
-- Wrap lines at 80 characters.
-- Follow the format of existing `.rst` files.
-- Link to external functions or tools when possible.
-
-### Compiling and adding documentation
-
+```{note}
 When compiling the documentation for the first time you will need an internet
 connection in order to download the datasets.
+```
+
+The documentation is stored under the `/docs` folder and is written in Markdown
+files following the [MyST-NB](https://myst-nb.readthedocs.io/en/latest/index.html)
+format.
 
 To build the documentation locally, first install the required packages:
 
 ```bash
 pip install --group docs
-cd docs
-make html
 ```
 
-The documentation can be updated by changing any of the `*.rst` files located
+The documentation can be updated by changing any of the `*.md` 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.
+### Building the documentation
+
+You can build the documentation using either auto-building (recommended for
+active development) or manual building.
 
-### Previewing documentation
+#### Auto-building
 
-#### Using VS Code extensions
+Run the following command from the `docs` folder in order to auto-rebuild the
+documentation when you save changes in any of the `docs/*.md`, `src/sdf_xarray/*.py`
+or update the `CONTRIBUTING.md` file:
+
+```bash
+make livehtml
+```
 
-Once the html web pages have been made you can review them installing the
+This should spin up a local server for the documentation which you can open in your
+browser. Example output including what changing a file should produce in the terminal:
+
+```bash
+[sphinx-autobuild] Starting initial build
+[sphinx-autobuild] > python -m sphinx build . _build/html --builder html --quiet
+[sphinx-autobuild] Serving on http://127.0.0.1:8000
+[sphinx-autobuild] Waiting to detect changes...
+[sphinx-autobuild] Detected changes (key_functionality.md)
+[sphinx-autobuild] Rebuilding...
+[sphinx-autobuild] > python -m sphinx build . _build/html --builder html --quiet
+[sphinx-autobuild] Serving on http://127.0.0.1:8000
+```
+
+#### Manual building
+
+If you prefer to rebuild the documentation manually, run the following
+command from the `docs` folder:
+
+```bash
+make html
+```
+
+Once the html web pages have been made you can review them by installing the
 [Live Server](https://marketplace.visualstudio.com/items/?itemName=ritwickdey.LiveServer)
-VS Code extension. Navigate to the `_build/html` folder, right-click the
+VS Code extension. Navigate to the `docs/_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
-
-Alternatively, if you're not using VS Code, you can start a simple local server with Python:
+Alternatively if you do not wish to install a VS Code extension run the following
+command from the `docs` folder:
 
 ```bash
 python -m http.server -d _build/html
 ```
 
-Then open http://localhost:8000 in your browser to view the documentation.
+Then open the link it gives you in the browser to view the documentation.
 
 ## Continuous integration
 

{sdf_xarray-0.6.0 → sdf_xarray-0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sdf-xarray
-Version: 0.6.0
+Version: 0.7.1
 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>, Chris Herdman <chris.herdman@york.ac.uk>, Liam Pattinson <liam.pattinson@york.ac.uk>, Sviatoslav Shekhanov <sviatoslav.shekhanov@york.ac.uk>
 License-Expression: BSD-3-Clause
@@ -27,7 +27,13 @@ Requires-Dist: pint; extra == "pint"
 Requires-Dist: pint-xarray; extra == "pint"
 Description-Content-Type: text/markdown
 
-# sdf-xarray
+<h1 align="center">
+    <picture>
+        <source media="(prefers-color-scheme: dark)" srcset="docs/_static/sdf-xarray-logo-dark.svg">
+        <source media="(prefers-color-scheme: light)" srcset="docs/_static/sdf-xarray-logo-light.svg">
+        <img alt="sdf-xarray logo" src="docs/_static/sdf-xarray-logo-dark.svg" width="400">
+    </picture>
+</h1><br>
 
 ![Dynamic TOML Badge](https://img.shields.io/badge/dynamic/toml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fepochpic%2Fsdf-xarray%2Frefs%2Fheads%2Fmain%2Fpyproject.toml&query=%24.project.requires-python&label=python&logo=python)
 [![Available on PyPI](https://img.shields.io/pypi/v/sdf-xarray?color=blue&logo=pypi)](https://pypi.org/project/sdf-xarray/)
@@ -37,10 +43,10 @@ Description-Content-Type: text/markdown
 [![Read the Docs](https://img.shields.io/readthedocs/sdf-xarray?logo=readthedocs&link=https%3A%2F%2Fsdf-xarray.readthedocs.io%2F)](https://sdf-xarray.readthedocs.io)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
-
-sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files as created by
-[EPOCH](https://epochpic.github.io) using the [SDF-C](https://github.com/epochpic/SDF_C) library.
-Part of [BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules).
+sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files
+as created by [EPOCH](https://epochpic.github.io) using the
+[SDF-C](https://github.com/epochpic/SDF_C) library. Part of
+[BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules).
 
 ## Installation
 
@@ -88,9 +94,9 @@ print(df["Electric_Field_Ex"])
 
 ### Multi-file loading
 
-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.
+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
@@ -115,37 +121,59 @@ print(ds)
 
 ## 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.
+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.
 
 ## Contributing
 
-We welcome contributions to the BEAM ecosystem! Whether it's reporting issues, suggesting features, or submitting pull requests, your input helps improve these tools for the community.
+We welcome contributions to the BEAM ecosystem! Whether it's reporting issues,
+suggesting features, or submitting pull requests, your input helps improve these
+tools for the community.
 
 ### How to Contribute
 
 There are many ways to get involved:
-- **Report bugs**: Found something not working as expected? Open an issue with as much detail as possible.
-- **Request a feature**: Got an idea for a new feature or enhancement? Open a feature request on [GitHub Issues](https://github.com/epochpic/sdf-xarray/issues)!
-- **Improve the documentation**: We aim to keep our docs clear and helpful—if something's missing or unclear, feel free to suggest edits.
-- **Submit code changes**: Bug fixes, refactoring, or new features are welcome.
 
+- **Report bugs**: Found something not working as expected? Open an issue with as
+much detail as possible.
+- **Request a feature**: Got an idea for a new feature or enhancement? Open a feature
+request on [GitHub Issues](https://github.com/epochpic/sdf-xarray/issues)!
+- **Improve the documentation**: We aim to keep our docs clear and helpful—if
+something's missing or unclear, feel free to suggest edits.
+- **Submit code changes**: Bug fixes, refactoring, or new features are welcome.
 
 All code is automatically linted, formatted, and tested via GitHub Actions.
 
-To run checks locally before opening a pull request, see [CONTRIBUTING.md](CONTRIBUTING.md) or [readthedocs documentation](https://sdf-xarray.readthedocs.io/en/latest/contributing.html)
+To run checks locally before opening a pull request, see
+[CONTRIBUTING.md](CONTRIBUTING.md) or [readthedocs documentation](https://sdf-xarray.readthedocs.io/en/latest/contributing.html)
 
 ## Broad EPOCH Analysis Modules (BEAM)
 
-![BEAM logo](./BEAM.png)
-
-**BEAM** is a collection of independent yet complementary open-source tools for analysing EPOCH simulations, designed to be modular so researchers can adopt only the components they require without being constrained by a rigid framework. In line with the **FAIR principles — Findable**, **Accessible**, **Interoperable**, and **Reusable** — each package is openly published with clear documentation and versioning (Findable), distributed via public repositories (Accessible), designed to follow common standards for data structures and interfaces (Interoperable), and includes licensing and metadata to support long-term use and adaptation (Reusable). The packages are as follows:
-
-- [sdf-xarray](https://github.com/epochpic/sdf-xarray): Reading and processing SDF files and converting them to [xarray](https://docs.xarray.dev/en/stable/).
+<h1 align="center">
+<img src="docs/_static/BEAM.png" width="400">
+</h1>
+
+**BEAM** is a collection of independent yet complementary open-source tools for
+analysing EPOCH simulations, designed to be modular so researchers can adopt only
+the components they require without being constrained by a rigid framework. In
+line with the **FAIR principles — Findable**, **Accessible**, **Interoperable**,
+and **Reusable** — each package is openly published with clear documentation and
+versioning (Findable), distributed via public repositories (Accessible), designed
+to follow common standards for data structures and interfaces (Interoperable), and
+includes licensing and metadata to support long-term use and adaptation (Reusable).
+The packages are as follows:
+
+- [sdf-xarray](https://github.com/epochpic/sdf-xarray): Reading and processing SDF
+files and converting them to [xarray](https://docs.xarray.dev/en/stable/).
 - [epydeck](https://github.com/epochpic/epydeck): Input deck reader and writer.
-- [epyscan](https://github.com/epochpic/epyscan): Create campaigns over a given parameter space using various sampling methods.
+- [epyscan](https://github.com/epochpic/epyscan): Create campaigns over a given
+parameter space using various sampling methods.
 
 ## PlasmaFAIR
 
-![PlasmaFAIR logo](PlasmaFAIR.svg)
+<h1 align="left">
+<img src="docs/_static/PlasmaFAIR.svg" width="400">
+</h1>
 
 Originally developed by [PlasmaFAIR](https://plasmafair.github.io), EPSRC Grant EP/V051822/1

{sdf_xarray-0.6.0 → sdf_xarray-0.7.1}/README.md

@@ -1,4 +1,10 @@
-# sdf-xarray
+<h1 align="center">
+    <picture>
+        <source media="(prefers-color-scheme: dark)" srcset="docs/_static/sdf-xarray-logo-dark.svg">
+        <source media="(prefers-color-scheme: light)" srcset="docs/_static/sdf-xarray-logo-light.svg">
+        <img alt="sdf-xarray logo" src="docs/_static/sdf-xarray-logo-dark.svg" width="400">
+    </picture>
+</h1><br>
 
 ![Dynamic TOML Badge](https://img.shields.io/badge/dynamic/toml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fepochpic%2Fsdf-xarray%2Frefs%2Fheads%2Fmain%2Fpyproject.toml&query=%24.project.requires-python&label=python&logo=python)
 [![Available on PyPI](https://img.shields.io/pypi/v/sdf-xarray?color=blue&logo=pypi)](https://pypi.org/project/sdf-xarray/)
@@ -8,10 +14,10 @@
 [![Read the Docs](https://img.shields.io/readthedocs/sdf-xarray?logo=readthedocs&link=https%3A%2F%2Fsdf-xarray.readthedocs.io%2F)](https://sdf-xarray.readthedocs.io)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
-
-sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files as created by
-[EPOCH](https://epochpic.github.io) using the [SDF-C](https://github.com/epochpic/SDF_C) library.
-Part of [BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules).
+sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files
+as created by [EPOCH](https://epochpic.github.io) using the
+[SDF-C](https://github.com/epochpic/SDF_C) library. Part of
+[BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules).
 
 ## Installation
 
@@ -59,9 +65,9 @@ print(df["Electric_Field_Ex"])
 
 ### Multi-file loading
 
-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.
+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
@@ -86,37 +92,59 @@ print(ds)
 
 ## 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.
+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.
 
 ## Contributing
 
-We welcome contributions to the BEAM ecosystem! Whether it's reporting issues, suggesting features, or submitting pull requests, your input helps improve these tools for the community.
+We welcome contributions to the BEAM ecosystem! Whether it's reporting issues,
+suggesting features, or submitting pull requests, your input helps improve these
+tools for the community.
 
 ### How to Contribute
 
 There are many ways to get involved:
-- **Report bugs**: Found something not working as expected? Open an issue with as much detail as possible.
-- **Request a feature**: Got an idea for a new feature or enhancement? Open a feature request on [GitHub Issues](https://github.com/epochpic/sdf-xarray/issues)!
-- **Improve the documentation**: We aim to keep our docs clear and helpful—if something's missing or unclear, feel free to suggest edits.
-- **Submit code changes**: Bug fixes, refactoring, or new features are welcome.
 
+- **Report bugs**: Found something not working as expected? Open an issue with as
+much detail as possible.
+- **Request a feature**: Got an idea for a new feature or enhancement? Open a feature
+request on [GitHub Issues](https://github.com/epochpic/sdf-xarray/issues)!
+- **Improve the documentation**: We aim to keep our docs clear and helpful—if
+something's missing or unclear, feel free to suggest edits.
+- **Submit code changes**: Bug fixes, refactoring, or new features are welcome.
 
 All code is automatically linted, formatted, and tested via GitHub Actions.
 
-To run checks locally before opening a pull request, see [CONTRIBUTING.md](CONTRIBUTING.md) or [readthedocs documentation](https://sdf-xarray.readthedocs.io/en/latest/contributing.html)
+To run checks locally before opening a pull request, see
+[CONTRIBUTING.md](CONTRIBUTING.md) or [readthedocs documentation](https://sdf-xarray.readthedocs.io/en/latest/contributing.html)
 
 ## Broad EPOCH Analysis Modules (BEAM)
 
-![BEAM logo](./BEAM.png)
-
-**BEAM** is a collection of independent yet complementary open-source tools for analysing EPOCH simulations, designed to be modular so researchers can adopt only the components they require without being constrained by a rigid framework. In line with the **FAIR principles — Findable**, **Accessible**, **Interoperable**, and **Reusable** — each package is openly published with clear documentation and versioning (Findable), distributed via public repositories (Accessible), designed to follow common standards for data structures and interfaces (Interoperable), and includes licensing and metadata to support long-term use and adaptation (Reusable). The packages are as follows:
-
-- [sdf-xarray](https://github.com/epochpic/sdf-xarray): Reading and processing SDF files and converting them to [xarray](https://docs.xarray.dev/en/stable/).
+<h1 align="center">
+<img src="docs/_static/BEAM.png" width="400">
+</h1>
+
+**BEAM** is a collection of independent yet complementary open-source tools for
+analysing EPOCH simulations, designed to be modular so researchers can adopt only
+the components they require without being constrained by a rigid framework. In
+line with the **FAIR principles — Findable**, **Accessible**, **Interoperable**,
+and **Reusable** — each package is openly published with clear documentation and
+versioning (Findable), distributed via public repositories (Accessible), designed
+to follow common standards for data structures and interfaces (Interoperable), and
+includes licensing and metadata to support long-term use and adaptation (Reusable).
+The packages are as follows:
+
+- [sdf-xarray](https://github.com/epochpic/sdf-xarray): Reading and processing SDF
+files and converting them to [xarray](https://docs.xarray.dev/en/stable/).
 - [epydeck](https://github.com/epochpic/epydeck): Input deck reader and writer.
-- [epyscan](https://github.com/epochpic/epyscan): Create campaigns over a given parameter space using various sampling methods.
+- [epyscan](https://github.com/epochpic/epyscan): Create campaigns over a given
+parameter space using various sampling methods.
 
 ## PlasmaFAIR
 
-![PlasmaFAIR logo](PlasmaFAIR.svg)
+<h1 align="left">
+<img src="docs/_static/PlasmaFAIR.svg" width="400">
+</h1>
 
 Originally developed by [PlasmaFAIR](https://plasmafair.github.io), EPSRC Grant EP/V051822/1

sdf_xarray-0.7.1/docs/_static/sdf-xarray-logo-dark.svg

@@ -0,0 +1,103 @@
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