update paper branch with changes from main

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
     -   id: check-merge-conflict # Check for files that contain merge conflict strings.
     -   id: check-added-large-files # Prevent large files from being added to the repository.
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.11.0
+    rev: 25.12.0
     hooks:
     - id: black
   - repo: https://github.com/pycqa/isort

README.md

@@ -25,14 +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
@@ -41,7 +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`:
@@ -50,9 +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/).

docs/installation.rst

@@ -6,24 +6,37 @@ Installation
 Clone the repository and navigate to the root directory of the repository. Then run
 
 ```
-pip install .
+pip install .[cpu]
 ```
 
 If you want to contribute to the development of `RUBIX`, we recommend the following editable installation from this repository:
 
 ```
 git clone https://github.com/AstroAI-Lab/rubix
 cd rubix
-pip install -e .
+pip install -e .[cpu,tests,dev]
 ```
 Having done so, the test suit can be run unsing `pytest`:
 
 ```
 python -m pytest
 ```
 
-Note that if `JAX` is not yet installed, only the CPU version of `JAX` will be installed
+Note that if `JAX` is not yet installed, with the `cpu` option only the CPU version of `JAX` will be installed
 as a dependency. For a GPU-compatible installation of `JAX`, please refer to the
-[JAX installation guide](https://jax.readthedocs.io/en/latest/installation.html).
+[JAX installation guide](https://jax.readthedocs.io/en/latest/installation.html) or use the option `cuda`.
 
-Get started with this simple example notebooks/rubix_pipeline_single_function.ipynb.
+Get started with this simple example notebooks/rubix_pipeline_single_function_shard_map.ipynb.
+
+Configuration
+=============
+
+When you run the pipeline you provide a configuration dict that references the files in `rubix/config/`. The following sections are required for the default pipelines:
+
+- `pipeline.name`: Choose one of `calc_ifu`, `calc_dusty_ifu`, or another entry from `pipeline_config.yml`.
+- `galaxy`: Must include `dist_z` and a `rotation` block (`type` or explicit `alpha`, `beta`, `gamma`).
+- `telescope`: Needs `name`, a `psf` block (Gaussian kernel with both `size` and `sigma`), an `lsf` block with `sigma`, and `noise` containing `signal_to_noise` plus a `noise_distribution` (`normal` or `uniform`).
+- `ssp.dust`: Declares `extinction_model` and `Rv` before the dusty pipeline can produce an extincted datacube.
+- `data.args.particle_type`: Must include `"stars"` (add `"gas"` if you rely on the optional gas branch) so the filtering/rotation steps know which components to process.
+
+The telescopes in `rubix/telescope` currently only support square pixels, so every config should set `pixel_type: square` in the relevant telescope definition.

notebooks/cosmology.ipynb

@@ -75,8 +75,8 @@
     "from rubix.cosmology.utils import trapz\n",
     "import jax.numpy as jnp\n",
     "\n",
-    "x = jnp.array([0, 1, 2, 3])\n",
-    "y = jnp.array([0, 1, 4, 9])\n",
+    "x = jnp.array([0.0, 1.0, 2.0, 3.0])\n",
+    "y = jnp.array([0.0, 1.0, 4.0, 9.0])\n",
     "print(trapz(x, y))"
    ]
   },
@@ -102,7 +102,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "rubix",
+   "display_name": "publishrubix",
    "language": "python",
    "name": "python3"
   },
@@ -116,7 +116,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,