Prepare publish

.github/workflows/ci.yml

@@ -57,7 +57,7 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
-        python-version: "3.11"
+        python-version: "3.13"
 
     - name: Install Python package
       run: |

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+Tobias Buck, astroai@iwr.uni-heidelberg.de.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

Makefile

@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+SOURCEDIR     = docs
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".

README.md

@@ -6,7 +6,6 @@
 
 [![Contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/AstroAI-Lab/rubix/blob/main/docs/CONTRIBUTING.md)
 [![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/AstroAI-Lab/rubix/ci.yml?branch=main)](https://github.com/AstroAI-Lab/rubix/actions/workflows/ci.yml)
-[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/AstroAI-Lab/rubix/CI?label=build)](https://github.com/AstroAI-Lab/rubix/actions/workflows/ci.yml)
 [![Documentation Status](https://readthedocs.org/projects/rubix/badge/)](https://astro-rubix.web.app)
 [![codecov](https://codecov.io/gh/AstroAI-Lab/rubix/branch/main/graph/badge.svg)](https://codecov.io/gh/AstroAI-Lab/rubix)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
@@ -26,14 +25,16 @@ Key features include:
 
 ## Installation
 
-The Python package `rubix` can be downloades from git and can be installed:
+The Python package `rubix` is published on GitHub and can be installed alongside its runtime dependencies (including JAX) by choosing the relevant extras. For a CPU-only environment, install with:
 
 ```
 git clone https://github.com/AstroAI-Lab/rubix.git
 cd rubix
-pip install .
+pip install .[cpu]
 ```
 
+If you need GPU acceleration, replace `[cpu]` with `[cuda]` (or install `jax[cuda]` following the [JAX instructions](https://github.com/google/jax#installation) before installing Rubix). The plain `pip install .` command installs the minimal package without JAX and will raise `ImportError` if you try to import `rubix` before adding `jax` manually.
+
 ## Development installation
 
 If you want to contribute to the development of `rubix`, we recommend
@@ -42,7 +43,7 @@ the following editable installation from this repository:
 ```
 git clone https://github.com/AstroAI-Lab/rubix.git
 cd rubix
-python -m pip install --editable .[tests]
+python -m pip install --editable .[cpu,tests,dev]
 ```
 
 Having done so, the test suite can be run using `pytest`:
@@ -51,9 +52,21 @@ Having done so, the test suite can be run using `pytest`:
 python -m pytest
 ```
 
-This project depends on [jax](https://github.com/google/jax). It only installed for cpu computations with the testing dependencies. For installation instructions with gpu support,
-please refer to [here](https://github.com/google/jax?tab=readme-ov-file#installation).
+This project depends on [jax](https://github.com/google/jax). For the pytests we only test the `cpu` version.
+For installation instructions with gpu support,
+please refer to [here](https://github.com/google/jax?tab=readme-ov-file#installation) or simply use the `cuda` option when pip installing.
+
+## Configuration overview
+
+Rubix ships with two YAML files in `rubix/config/`: `rubix_config.yml` (constants, SSP templates, dust recipes, handler mappings, etc.) and `pipeline_config.yml` (pipeline graphs such as `calc_ifu` and `calc_dusty_ifu`). There is no configuration wizard — your runtime settings must supply a dictionary with the following blocks:
+
+- `pipeline.name`: Identifies the pipeline from `pipeline_config.yml` (e.g., `calc_ifu`, `calc_dusty_ifu`, or `calc_gradient`).
+- `galaxy`: Must provide `dist_z` and a `rotation` section (`type` or explicit `alpha`, `beta`, `gamma`).
+- `telescope`: Requires `name`, `psf` (currently only the `gaussian` kernel with `size` and `sigma`), `lsf` (`sigma`), and `noise` (`signal_to_noise` plus `noise_distribution`, choose from `normal` or `uniform`).
+- `ssp.dust`: Must declare `extinction_model` and `Rv` before calling the dusty pipeline (see `rubix/spectra/dust/extinction_models.py` for the supported models such as `Cardelli89`).
+- `data.args.particle_type`: Should include `"stars"` (and `"gas"` if you want the gas branch) so the filters and rotation functions know which components exist.
 
+The tutorials and notebooks assume square spaxels, so the default telescope factory currently only supports `pixel_type: square`. For a working example, inspect `notebooks/rubix_pipeline_single_function_shard_map.ipynb`, which runs the exact pipeline used in the tests.
 
 ## Documentation
 Sphinx Documentation of all the functions is currently available under [this link](https://astro-rubix.web.app/).
@@ -63,15 +76,16 @@ Sphinx Documentation of all the functions is currently available under [this lin
 Contributions to `rubix` are welcome and greatly appreciated!
 Whether you're fixing bugs, improving documentation, or suggesting new features, your help is valuable to us.
 
-Please see [here](source/CONTRIBUTING.md) for contribution guidelines.
+Please see [here](docs/CONTRIBUTING.md) for contribution guidelines.
 
 Thank you for helping improve `rubix`!
 
 ## Citation & Acknowledgement
 
 Please cite **both** of the following papers ([Cakir et al. 2024](https://arxiv.org/abs/2412.08265), [Schaible et al. 2025](https://arxiv.org/abs/2511.17110)) if you use Rubix in your research:
 
-@ARTICLE{2024arXiv241208265C,
+```
+  @ARTICLE{2024arXiv241208265C,
        author = {{{\c{C}}ak{\i}r}, Ufuk and {Schaible}, Anna Lena and {Buck}, Tobias},
         title = "{Fast GPU-Powered and Auto-Differentiable Forward Modeling of IFU Data Cubes}",
       journal = {arXiv e-prints},
@@ -81,14 +95,14 @@ Please cite **both** of the following papers ([Cakir et al. 2024](https://arxiv.
           eid = {arXiv:2412.08265},
         pages = {arXiv:2412.08265},
           doi = {10.48550/arXiv.2412.08265},
-archivePrefix = {arXiv},
+        archivePrefix = {arXiv},
        eprint = {2412.08265},
- primaryClass = {astro-ph.IM},
+        primaryClass = {astro-ph.IM},
        adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv241208265C},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
+  }
 
-@ARTICLE{2025arXiv251117110S,
+  @ARTICLE{2025arXiv251117110S,
        author = {{Schaible}, Anna Lena and {{\c{C}}ak{\i}r}, Ufuk and {Buck}, Tobias and {Mack}, Harald and {Obreja}, Aura and {Oguz}, Nihat and {Oliver}, William H. and {C{\u{a}}r{\u{a}}mizaru}, Horea-Alexandru},
         title = "{RUBIX: Differentiable forward modelling of galaxy spectral data cubes for gradient-based parameter estimation}",
       journal = {arXiv e-prints},
@@ -98,13 +112,13 @@ archivePrefix = {arXiv},
           eid = {arXiv:2511.17110},
         pages = {arXiv:2511.17110},
           doi = {10.48550/arXiv.2511.17110},
-archivePrefix = {arXiv},
+        archivePrefix = {arXiv},
        eprint = {2511.17110},
- primaryClass = {astro-ph.GA},
+      primaryClass = {astro-ph.GA},
        adsurl = {https://ui.adsabs.harvard.edu/abs/2025arXiv251117110S},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
+  }
+```
 
 
 
@@ -138,7 +152,7 @@ archivePrefix = {arXiv},
 
 ## Licence
 
-[GNU General Public License v3.0](https://github.com/synthesizer-project/synthesizer/blob/main/LICENSE.md)
+[MIT License](https://github.com/AstroAI-Lab/rubix/blob/main/LICENSE.md)
 
 ## Acknowledgments
 

source/Contributing.md → docs/CONTRIBUTING.md

@@ -49,6 +49,7 @@ at the root of the repo to activate the pre-commit hooks.
 
 If you would like to test whether it works you can run `pre-commit run --all-files` to run the pre-commit hook on the whole repo. You should see each stage complete without issue in a clean clone.
 
+
 ## Using Black
 
 We use [Black](https://black.readthedocs.io/en/stable/) for code formatting. Assuming you installed the development dependencies (if not you can install `black` with pip: `pip install black`), you can run the linting with `black {source_file_or_directory}`. For more details see the [Black documentation](https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html).
@@ -105,13 +106,13 @@ Adding content should be relatively simple if you follow the instructions below.
 
 To add Jupyter notebooks to the documentation:
 
-1. Add your Jupyter notebook to the `notebooks` directory under the `docs/source` folder. Make sure that you 'Restart Kernel and run all cells' to ensure that the notebook is producing up to date, consistent outputs.
-2. Add your notebook to the relevant toctree. See below for an example toctree. Each toctree is contained within a Sphinx `.rst` file in each documentation source directory. The top-level file is `source/index.rst`. If your file is in a subfolder, you need to update the `.rst` file in that directory.
+1. Add your Jupyter notebook to the `notebooks` directory under the `docs` folder. Make sure that you 'Restart Kernel and run all cells' to ensure that the notebook is producing up to date, consistent outputs.
+2. Add your notebook to the relevant toctree. See below for an example toctree. Each toctree is contained within a Sphinx `.rst` file in each documentation source directory. The top-level file is `docs/index.rst`. If your file is in a subfolder, you need to update the `.rst` file in that directory.
 
 - If you're creating a new sub-directory of documentation, you will need to carry out a couple more steps:
 
 1.  Create a new `.rst` file in that directory
-2.  Update `source/index.rst` with the path to that `.rst` file
+2.  Update `docs/index.rst` with the path to that `.rst` file
 3.  Currently we do not run pytests on jupyter notebooks. So please make sure your notebooks are actually working fine.
 
 Example toctree:
@@ -164,7 +165,7 @@ sphinx-quickstart
 
 #### Configuration and Content
 
-The core of the documentation setup resides in the source folder:
+The core of the documentation setup resides in the `docs` folder:
 
 - `conf.py`: This is the main configuration file where you define extensions (like myst_nb for notebooks), set the theme, and manage global build settings.
 

source/conf.py → docs/conf.py

@@ -11,9 +11,9 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "rubix"
-copyright = "2024, Ufuk, Tobias, Anna Lena"
-author = "Ufuk, Tobias, Anna Lena"
+project = "Rubix"
+copyright = "2025, Anna Lena Schaible, Ufuk Cakir, Tobias Buck"
+author = "Anna Lena Schaible, Ufuk Cakir, Tobias Buck"
 release = "0.1"
 
 # -- General configuration ---------------------------------------------------