Setup rework (#228)

## v0.13.1 - Reworks the requirements to make install faster - Updates README to reflect changes - Re-adds the dLux logo - Removes some old files
LouisDesdoigts · May 30, 2023 · c540fa7 · c540fa7
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -21,9 +21,7 @@ jobs:
       - name: install environment
         run: |
           python -m pip install --upgrade pip
-          pip install --quiet pytest
-          pip install --quiet -r requirements.txt
-          pip install --quiet .
+          pip install --quiet ".[tests]"
 
       # ===== Tests =====
       - name: install tests

diff --git a/README.md b/README.md
@@ -36,11 +36,16 @@ The ∂Lux framwork is built in [Zodiax](https://github.com/LouisDesdoigts/zodia
 
 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/).
 
-Doccumentataion: [https://louisdesdoigts.github.io/dLux/](https://louisdesdoigts.github.io/dLux/)
+Documentation: [https://louisdesdoigts.github.io/dLux/](https://louisdesdoigts.github.io/dLux/)
+
+Requires: Python 3.8+, Jax 0.4.3+, Zodiax 0.4+
 
 Installation: ```pip install dLux```
 
-Requires: Python 3.8+, Jax 0.4.3+, Zodiax 0.4+
+Docs installation: ```pip install "dLux[docs]"```
+
+Test installation: ```pip install "dLux[tests]"```
+
 
 ## Collaboration & Development
 

diff --git a/dLux/__init__.py b/dLux/__init__.py
@@ -1,5 +1,5 @@
 name = "dLux"
-__version__ = "0.13.0"
+__version__ = "0.13.1"
 
 # Import as modules
 # Wavefronts and Optics

diff --git a/docs/assets/logo.jpg b/docs/assets/logo.jpg
diff --git a/docs/creating_a_layer.md b/docs/creating_a_layer.md
diff --git a/docs/notebooks/Core_classes.ipynb b/docs/notebooks/Core_classes.ipynb
diff --git a/docs/notebooks/HMC.ipynb b/docs/notebooks/HMC.ipynb
diff --git a/docs/notebooks/designing_a_mask.ipynb b/docs/notebooks/designing_a_mask.ipynb
diff --git a/docs/notebooks/fisher_information.ipynb b/docs/notebooks/fisher_information.ipynb
diff --git a/docs/notebooks/flatfield_calibration.ipynb b/docs/notebooks/flatfield_calibration.ipynb
diff --git a/docs/notebooks/phase_retrieval_demo.ipynb b/docs/notebooks/phase_retrieval_demo.ipynb
@@ -212,8 +212,8 @@
      "output_type": "stream",
      "text": [
       "Initial Loss: 144743.921875\n",
-      "CPU times: user 342 ms, sys: 18.8 ms, total: 361 ms\n",
-      "Wall time: 315 ms\n"
+      "CPU times: user 324 ms, sys: 15.3 ms, total: 339 ms\n",
+      "Wall time: 274 ms\n"
      ]
     }
    ],
@@ -241,7 +241,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "aaaa3c0c39c145f8b50bff2898343318",
+       "model_id": "fbbe389b4cc14ae0a4e16759cb4c7b10",
        "version_major": 2,
        "version_minor": 0
       },

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
 # Core
 jax
 jaxlib
-zodiax==0.4.0
+zodiax>=0.4.1
diff --git a/setup.py b/setup.py
@@ -18,14 +18,14 @@ def find_version(*file_paths):
     raise RuntimeError("Unable to find version string.")
 
 # DEPENDENCIES
-# 1. What are the required dependencies?
 with open('requirements.txt') as f:
     install_requires = f.read().splitlines()
-# 2. What dependencies required to run the unit tests? (i.e. `pytest --remote-data`)
 tests_require = ['pytest']
-docs_require = ['optax', 'matplotlib', 'jupyter', 'jupyterlab', 'tqdm', 
-    'chainconsumer', 'nummpyro']
-
+docs_require = ['matplotlib', 'jupyter', 'jupyterlab', 'tqdm', 
+    'chainconsumer', 'numpyro', 'dLuxToliman', "scikit-learn", "mkdocs", 
+    "mkdocs-jupyter", "mkdocs-same-dir", "mkdocs-autorefs",
+    "mkdocs-simple-plugin", "mkdocstrings-python",
+    "jupyter_contrib_nbextensions"]
 
 setuptools.setup(
     python_requires='>=3.7,<4.0',
@@ -43,13 +43,15 @@ def find_version(*file_paths):
     },
 
     install_requires=install_requires,
-    tests_require=tests_require,
-    extras_require={'docs': docs_require},
+    extras_require={
+        'docs': docs_require, 
+        'tests' : tests_require
+        },
 
     classifiers=[
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",
     ],
 
     packages = ["dLux", "dLux/utils"]
-)
+)