PR to track changes on the dev branch

.github/workflows/documentation.yml

@@ -38,6 +38,9 @@ jobs:
           pip install mkdocstrings[python]
           pip install mkdocs-material
 
+      - name: build umls
+        run: docs/generate_umls.py
+
       - name: generate and deploy documentation
         run: mkdocs gh-deploy -d https://louisdesdoigts.github.io/dLux
 

.github/workflows/tests.yml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - name: checkout
@@ -25,50 +25,87 @@ jobs:
           pip install --quiet pytest
 
       # ===== Tests =====
-      - name: install tests
+      - name: tests install
         run: pytest --quiet tests/test_installation.py
-
-
-      - name: wavefront tests
-        run: pytest --quiet tests/test_wavefronts.py
-
-      - name: optical layer tests
-        run: pytest --quiet tests/test_optical_layers.py
-
-      - name: aperture tests
-        run: pytest --quiet tests/test_apertures.py
 
-      - name: aperture tests
-        run: pytest --quiet tests/test_aberrations.py
-
-      - name: propagator tests
-        run: pytest --quiet tests/test_propagators.py
-
-      - name: optics tests
-        run: pytest --quiet tests/test_optics.py
-
-
-      - name: image tests
-        run: pytest --quiet tests/test_images.py
+      - name: test utils array_ops
+        run: pytest --quiet tests/utils/test_array_ops.py
+
+      - name: test utils coordinates
+        run: pytest --quiet tests/utils/test_coordinates.py
+
+      - name: test utils geometry
+        run: pytest --quiet tests/utils/test_geometry.py
+
+      - name: test utils helpers
+        run: pytest --quiet tests/utils/test_helpers.py
+
+      - name: test utils interpolation
+        run: pytest --quiet tests/utils/test_interpolation.py
+
+      - name: test utils math
+        run: pytest --quiet tests/utils/test_math.py
 
-      - name: detector layer tests
-        run: pytest --quiet tests/test_detector_layers.py
+      - name: test utils optics
+        run: pytest --quiet tests/utils/test_optics.py
+
+      - name: test utils propagation
+        run: pytest --quiet tests/utils/test_propagation.py
+
+      - name: test utils source
+        run: pytest --quiet tests/utils/test_source.py
+
+      - name: test utils units
+        run: pytest --quiet tests/utils/test_units.py
+
+      - name: test utils zernike
+        run: pytest --quiet tests/utils/test_zernike.py
+
+      - name: test layers aberrations
+        run: pytest --quiet tests/layers/test_aberrations.py
+
+      - name: test layers apertures
+        run: pytest --quiet tests/layers/test_apertures.py
+
+      - name: test layers detector_layers
+        run: pytest --quiet tests/layers/test_detector_layers.py
+
+      - name: test layers optical_layers
+        run: pytest --quiet tests/layers/test_optical_layers.py
+
+      - name: test layers optics
+        run: pytest --quiet tests/layers/test_optics.py
+
+      - name: test layers propagators
+        run: pytest --quiet tests/layers/test_propagators.py
+
+      - name: test layers unified_layers
+        run: pytest --quiet tests/layers/test_unified_layers.py
 
-      - name: detector tests
+      - name: test transformations
+        run: pytest --quiet tests/test_transformations.py
+
+      - name: test detectors
         run: pytest --quiet tests/test_detectors.py
-
-
-      - name: spectra tests
-        run: pytest --quiet tests/test_spectra.py
-
-      - name: source tests
-        run: pytest --quiet tests/test_sources.py
-
-      - name: instrument tests
+
+      - name: test instruments
         run: pytest --quiet tests/test_instruments.py
+
+      - name: test optical_systems
+        run: pytest --quiet tests/test_optical_systems.py
+
+      - name: test psfs
+        run: pytest --quiet tests/test_psfs.py
+
+      - name: test sources
+        run: pytest --quiet tests/test_sources.py
+
+      - name: test spectra
+        run: pytest --quiet tests/test_spectra.py
+
+      - name: test wavefronts
+        run: pytest --quiet tests/test_wavefronts.py
+
+
 
-      - name: observations tests
-        run: pytest --quiet tests/test_observations.py
-
-      - name: utils tests
-        run: pytest --quiet tests/test_utils.py
+

.gitignore

@@ -1,6 +1,8 @@
 **/__pycache__/
 **/.ipynb_checkpoints/
 **.DS_Store
+**.ipynb
+**.npy
 dist/
 .vscode/
 build/

.pre-commit-config.yaml

@@ -3,9 +3,8 @@ repos:
     rev: 22.3.0
     hooks:
     - id: black
-      args: [--line-length=79]
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.0.278
     hooks:
     - id: ruff
-      args: [--fix]
+      args: [--fix, --line-length=88]

CHANGELOG.md

@@ -0,0 +1,4 @@
+
+# ChangeLog
+
+Project changes will be tracked here once the 1.0 version is released. We will not track changes during the development phase.

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contributing Guide
 
-dLux is an open-source framework and as such is very welcoming to contributions via pull requests! If you would like to contribute but are unfamiliar with any of this process, as I imagine many coming from a science background will be, please feel free to reach out to me at my [email]([email protected]) or on [twitter](https://twitter.com/gradientrider) and I will be happy to help you through the process!
+dLux is an open-source framework and as such is very welcoming to contributions via pull requests! If you would like to contribute but are unfamiliar with any of this process, as I imagine many coming from a science background will be, please feel free to reach out to me at my [email](mailto:[email protected]) or on [twitter](https://twitter.com/gradientrider) and I will be happy to help you through the process!
 
 ---
 

README.md

@@ -1,4 +1,4 @@
-![alt text](docs/assets/logo.jpg?raw=true)
+![alt text](assets/logo.jpg?raw=true)
 
 # ∂Lux
 
@@ -25,21 +25,21 @@ The ∂Lux framework is built in [Zodiax](https://github.com/LouisDesdoigts/zodi
 >
 > - [Automatic Vectorisation](https://jax.readthedocs.io/en/latest/jax-101/03-vectorization.html): Allows for simple parallelism across hardware and asynchronous execution
 >
-> - [Path-Based Pytree Interface](docs/usage.md): Path based indexing allows for easy interfacing with large and highly nested physical models
+<!-- > - [Path-Based Pytree Interface](usage.md): Path based indexing allows for easy interfacing with large and highly nested physical models -->
 
 For an overview of these capabilities and different optimisation methods in [Zodiax](https://github.com/LouisDesdoigts/zodiax), please go through this [Zodiax Tutorial](https://louisdesdoigts.github.io/zodiax/docs/usage/).
 
 Documentation: [https://louisdesdoigts.github.io/dLux/](https://louisdesdoigts.github.io/dLux/)
 
-Requires: Python 3.8+, Jax 0.4.3+, Zodiax 0.4+
+Requires: Python 3.10+, Jax 0.4.13+, Zodiax 0.4+
 
 Installation: ```pip install dLux```
 
 If you want to run the tutorials locally, you can install the 'extra' dependencies like so: ```pip install 'dLux[extras]'```
 
 ## Collaboration & Development
 
-We are always looking to collaborate and further develop this software! We have focused on flexibility and ease of development, so if you have a project you want to use ∂Lux for, but it currently does not have the required capabilities, have general questions, thoughts or ideas, don't hesitate to [email me]([email protected]) or contact me on [twitter](https://twitter.com/gradientrider)! More details about contributing can be found in our [contributing guide](CONTRIBUTING.md).
+We are always looking to collaborate and further develop this software! We have focused on flexibility and ease of development, so if you have a project you want to use ∂Lux for, but it currently does not have the required capabilities, have general questions, thoughts or ideas, don't hesitate to [email me](mailto:[email protected]) or contact me on [twitter](https://twitter.com/gradientrider)! More details about contributing can be found in our [contributing guide](CONTRIBUTING.md).
 
 ## Publications