fix: docs and env

quant-sci · Jun 18, 2024 · 779f146 · 779f146
1 parent 27bcb90
commit 779f146
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diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -14,4 +14,4 @@ sphinx-togglebutton
 pydata_sphinx_theme
 sphinx_design==0.5
 ipython==8.25.0
-optymus==0.2.0
+optymus==0.1.3
diff --git a/docs/source/examples/index.rst b/docs/source/examples/index.rst
@@ -8,7 +8,7 @@ This section contains examples of how to use the library.
 - `How to create a dashboard for optimizations <notebooks/3.optymus_dashboard.ipynb>`_
 - `Methods comparison <notebooks/4.methods_comparison.ipynb>`_
 - `Visualization with PCA <notebooks/5.visualization_with_pca.ipynb>`_
-- `Constraint optimization <notebooks/6.constraint_optmization.ipynb>`_
+- `Constraint optimization <notebooks/6.constraint_optimization.ipynb>`_
 
 Some applications are:
 
@@ -19,4 +19,16 @@ Some applications are:
 
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
+   :caption: Examples
+
+   notebooks/1.setup_functions
+   notebooks/2.optimize_a_function
+   notebooks/3.optymus_dashboard
+   notebooks/4.methods_comparison
+   notebooks/5.visualization_with_pca
+   notebooks/6.constraint_optimization
+   notebooks/optimization_in_deep_learning
+   notebooks/optimization_in_economics
+   notebooks/optimization_in_mechanical_engineering
+   notebooks/optimization_in_finance
diff --git a/docs/source/examples/notebooks/1.setup_functions.ipynb b/docs/source/examples/notebooks/1.setup_functions.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Setup objective function with `optymus.benchmark`"
+    "## Setup objective function (benchmark or custom)"
    ]
   },
   {

diff --git a/docs/source/examples/notebooks/2.optimize_a_function.ipynb b/docs/source/examples/notebooks/2.optimize_a_function.ipynb
diff --git a/docs/source/examples/notebooks/3.optymus_dashboard.ipynb b/docs/source/examples/notebooks/3.optymus_dashboard.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Create a results dashboard with `optymus.optimizer`"
+    "## Create a results dashboard"
    ]
   },
   {

diff --git a/docs/source/examples/notebooks/optimization_in_deep_learning.ipynb b/docs/source/examples/notebooks/optimization_in_deep_learning.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Optimization in Deep Learning"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -24,6 +31,13 @@
     "from optymus import Optimizer"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Simple neural network"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -53,17 +53,10 @@ To begin using `optymus`, follow these steps:
 
    opt.print_report()
 
-
-Explore the Documentation
--------------------------
-Visit the `official documentation <https://optymus.readthedocs.io/en/latest/?badge=latest>`_ to understand the available optimization methods and how to use them effectively.
-
-Refer to the documentation for detailed information on each method and its application.
-
 Contributions
 -------------
 
-Contributions to Optymus are highly appreciated. If you have additional optimization methods, improvements, or bug fixes, please submit a pull request following the [contribution guidelines](CONTRIBUTING.md).
+Contributions to Optymus are highly appreciated. If you have additional optimization methods, improvements, or bug fixes, please submit a pull request following the CONTRIBUTING.md on GitHub.
 
 How to cite
 ----

diff --git a/docs/source/reference/optimizer.rst b/docs/source/reference/optimizer.rst
@@ -1,7 +1,7 @@
 Optimizer
-=======
+=========
 
-`optymus.optim` provides a class to optimize a function using a selected optimization algorithm.
+`optymus` provides a class to optimize a function using a selected optimization algorithm.
 
 .. autosummary::
     :toctree: .generated/

diff --git a/notebooks/1.setup_functions.ipynb b/notebooks/1.setup_functions.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Setup objective function with `optymus.benchmark`"
+    "## Setup objective function (benchmark or custom)"
    ]
   },
   {

diff --git a/notebooks/2.optimize_a_function.ipynb b/notebooks/2.optimize_a_function.ipynb
diff --git a/notebooks/3.optymus_dashboard.ipynb b/notebooks/3.optymus_dashboard.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Create a results dashboard with `optymus.optimizer`"
+    "## Create a results dashboard"
    ]
   },
   {

diff --git a/notebooks/optimization_in_deep_learning.ipynb b/notebooks/optimization_in_deep_learning.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Optimization in Deep Learning"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -24,6 +31,13 @@
     "from optymus import Optimizer"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Simple neural network"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,

diff --git a/pyproject.toml b/pyproject.toml
@@ -23,16 +23,18 @@ classifiers = [
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dependencies = [
+  "dash==2.17.1",
+  "dash_bootstrap_components==1.6.0",
+  "dash_bootstrap_templates==1.1.2",
   "nbformat>=4.2.0",
   "jax>=0.4.28",
   "jaxlib>=0.4.28",
   "tqdm>=4.66.4",
   "pandas==2.0.3",
+  "numpy==1.26.4",
   "matplotlib>=3.9.0",
   "seaborn>=0.13.2",
-  "plotly==5.22.0",
   "scikit-learn>=1.5.0",
-  "numpy==1.26.4"
   ]
 
 
@@ -66,35 +68,39 @@ exclude_lines = ["no cov", "if __name__ == .__main__.:", "if TYPE_CHECKING:"]
 extend = "ruff_default.toml"
 exclude = ["docs/**", "tests/**", "tutorials/**"]
 
-[tool.hatch.envs.docs]
+[tool.hatch.envs.sphinx]
 dependencies = [
   "pydata-sphinx-theme==0.15.2",
   "sphinx_design==0.5.0",
   "sphinx_togglebutton==0.3.2",
   "sphinxcontrib.youtube==1.4.1",
-  "jax>=0.4.28",
-  "jaxlib>=0.4.28",
-  "plotly==5.22.0",
-  "ipython"
+  "sphinx_copybutton==0.5.2",
+  "myst_parser==3.0.1",
+  "nbsphinx==0.9.4",
+  "ipython==8.25.0"
 ]
 
-[tool.hatch.envs.docs.scripts]
+[tool.hatch.envs.sphinx.scripts]
 foo = ["which sphinx-build"]
 build = ["bash docs/source/build.sh"]
 
 
 [tool.hatch.envs.testing]
 dependencies = [
+  "dash==2.17.1",
+  "dash_bootstrap_components==1.6.0",
+  "dash_bootstrap_templates==1.1.2",
   "nbformat>=4.2.0",
   "jax>=0.4.28",
   "jaxlib>=0.4.28",
   "tqdm>=4.66.4",
-  "pandas>=2.2.2",
+  "pandas==2.0.3",
+  "numpy==1.26.4",
   "matplotlib>=3.9.0",
-  "plotly==5.22.0",
   "seaborn>=0.13.2",
   "scikit-learn>=1.5.0",
-]
+  ]
+
 paths = ["./src"]
 
 [tool.hatch.envs.testing.scripts]