docs: new illu and better style + sphinx book 1.1.0

lgrcia · Feb 12, 2024 · 8dbcdf0 · 8dbcdf0
2 parents a3d1118 + 9126207
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diff --git a/README.md b/README.md
@@ -1,14 +1,11 @@
-> Work in progress ...
-
 # nuance
 
-<p align="center" style="margin-top:20px">
-    <img src="docs/_static/nuance.svg" height="250">
+<p align="center">
+    <img src="docs/_static/illu_readme.png" height="350" style="margin:50px">
 </p>
 
 <p align="center">
-  A Python package to detect exoplanetary transits <br>in the presence of stellar variability and correlated noises
-  <br>
+  Efficient detection of planets transiting active stars
   <p align="center">
     <a href="./LICENSE"><img src="https://img.shields.io/badge/license-MIT-lightgray.svg?style=flat" alt="license"/></a>
     <a href="https://nuance.readthedocs.io"><img src="https://img.shields.io/badge/ReadThe-Doc-blue.svg?style=flat" alt="license"/></a>

diff --git a/docs/_static/favicon.png b/docs/_static/favicon.png
diff --git a/docs/_static/illu.png b/docs/_static/illu.png
diff --git a/docs/_static/illu_readme.png b/docs/_static/illu_readme.png
diff --git a/docs/_static/logo.png b/docs/_static/logo.png
diff --git a/docs/_static/style.css b/docs/_static/style.css
@@ -1,17 +1,11 @@
 :root {
     /* --pst-color-inline-code: 33, 125, 224; */
     --mystnb-source-margin-color: darkgrey;
+    --pst-color-primary: #6ca4df !important;
+    --pst-color-secondary: #b2b2b2 !important;
+    --pst-color-link-hover: var(--pst-color-secondary) !important;
 }
 
-
-/* Headings */
-
-h2 {
-    text-decoration: underline;
-    font-size: 22px;
-}
-
-
 /* Code cells */
 
 .highlight pre {
@@ -127,18 +121,19 @@ code span.pre {
     font-size: 2rem;
 } */
 
-.version-nb {
+/* .version-nb {
     margin-top: -5px;
     font-style: italic;
-    color: var(--pst-color-primary);
+    font-weight: bold;
+    color: lightgray;
 }
 
 .navbar-brand .logo__title {
     font-size: 2rem;
     white-space: normal;
     text-align: center;
     font-style: italic;
-    color: var(--pst-color-muted);
+    color: black;
     font-weight: 500;
     font-family: var(--pst-font-family-heading);
-}
+} */
diff --git a/docs/conf.py b/docs/conf.py
@@ -42,7 +42,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["jupyter_execute"]
+exclude_patterns = ["_build/*"]
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -64,8 +64,10 @@
 
 pyproject = toml.load("../pyproject.toml")
 version = pyproject["tool"]["poetry"]["version"]
-html_short_title = "nuance"
-html_title = f"{html_short_title}"
+# html_short_title = "nuance"
+# html_title = f"{html_short_title}"
+html_logo = "_static/logo.png"
+html_favicon = "_static/favicon.png"
 # -----
 
 source_suffix = {
@@ -79,7 +81,7 @@
 html_theme_options = {
     "repository_url": "https://github.com/lgrcia/nuance",
     "use_repository_button": True,
-    "show_navbar_depth": 2,
+    # "show_navbar_depth": 2,
 }
 
 nb_render_image_options = {"align": "center"}
@@ -93,4 +95,8 @@
 autodoc_typehints = "signature"
 autoclass_content = "both"
 
-nb_execution_excludepatterns = ["_build/*", "notebooks/tutorials/*"]
+nb_execution_excludepatterns = [
+    "_build/*",
+    "notebooks/tutorials/*",
+    "notebooks/_*.ipynb",
+]
diff --git a/docs/index.md b/docs/index.md
@@ -1,19 +1,18 @@
----
-sd_hide_title: true
+# *nuance*
+
+Efficient detection of planets transiting active stars
+
 ---
 
-# *nuance*
+<div style="margin: 100px"></div>
 
-```{image} _static/nuance.svg
-:height: 300px
+```{image} _static/illu.png
+:height: 200px
 :align: center
 ```
+<div style="margin: 100px"></div>
 
-```{warning}
-Documentation and code under development
-```
-
-A python package to search for planetary transits in light curves containing correlated noise (like instrumental systematics or stellar variability). Powered by [JAX](https://github.com/google/jax) and [tinygp](https://github.com/dfm/tinygp).
+*nuance* uses linear models and gaussian processes (using [JAX](https://github.com/google/jax)-based [tinygp](https://github.com/dfm/tinygp)) to simultaneously **search for planetary transits while modeling correlated noises** (e.g. stellar variability) in a tractable way.
 
 ```{toctree}
 :maxdepth: 1
@@ -40,5 +39,6 @@ notebooks/tutorials/ground_based.ipynb
 :maxdepth: 1
 :caption: Reference
 
+markdown/how
 markdown/API
 ```
diff --git a/docs/markdown/how.md b/docs/markdown/how.md
@@ -0,0 +1,5 @@
+# How it works
+
+<video width="320" height="240" autoplay loop muted>
+  <source src="notebooks/test.mp4" type="video/mp4">
+</video>
diff --git a/docs/notebooks/combined.ipynb b/docs/notebooks/combined.ipynb
diff --git a/docs/notebooks/exocomet.pdf b/docs/notebooks/exocomet.pdf
diff --git a/docs/notebooks/multi.ipynb b/docs/notebooks/multi.ipynb
diff --git a/docs/notebooks/periodic.ipynb b/docs/notebooks/periodic.ipynb
diff --git a/docs/notebooks/single.ipynb b/docs/notebooks/single.ipynb
@@ -19,35 +19,18 @@
               {
                      "cell_type": "code",
                      "execution_count": 1,
-                     "metadata": {},
-                     "outputs": [
-                            {
-                                   "data": {
-                                          "text/plain": [
-                                                 "[CpuDevice(id=0),\n",
-                                                 " CpuDevice(id=1),\n",
-                                                 " CpuDevice(id=2),\n",
-                                                 " CpuDevice(id=3),\n",
-                                                 " CpuDevice(id=4),\n",
-                                                 " CpuDevice(id=5),\n",
-                                                 " CpuDevice(id=6),\n",
-                                                 " CpuDevice(id=7),\n",
-                                                 " CpuDevice(id=8),\n",
-                                                 " CpuDevice(id=9)]"
-                                          ]
-                                   },
-                                   "execution_count": 1,
-                                   "metadata": {},
-                                   "output_type": "execute_result"
-                            }
-                     ],
+                     "metadata": {
+                            "tags": [
+                                   "hide-input"
+                            ]
+                     },
+                     "outputs": [],
                      "source": [
                             "# in order to run on all CPUs\n",
                             "import os\n",
                             "import jax\n",
                             "\n",
-                            "os.environ[\"XLA_FLAGS\"] = f\"--xla_force_host_platform_device_count={os.cpu_count()}\"\n",
-                            "jax.devices()"
+                            "os.environ[\"XLA_FLAGS\"] = f\"--xla_force_host_platform_device_count={os.cpu_count()}\""
                      ]
               },
               {
@@ -59,7 +42,7 @@
                                    "name": "stderr",
                                    "output_type": "stream",
                                    "text": [
-                                          "/Users/lgrcia/code/dev/nuance/nuance/combined.py:7: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
+                                          "/Users/lgarcia/mambaforge/envs/nuance/lib/python3.11/site-packages/nuance/combined.py:7: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
                                           "  from tqdm.autonotebook import tqdm\n"
                                    ]
                             },
@@ -107,12 +90,12 @@
                             {
                                    "data": {
                                           "application/vnd.jupyter.widget-view+json": {
-                                                 "model_id": "61fb5d6d76c048dfb2d842a437de8f10",
+                                                 "model_id": "ccd3be485d1b42e48896f25b36cf78c3",
                                                  "version_major": 2,
                                                  "version_minor": 0
                                           },
                                           "text/plain": [
-                                                 "  0%|          | 0/200 [00:00<?, ?it/s]"
+                                                 "  0%|          | 0/167 [00:00<?, ?it/s]"
                                           ]
                                    },
                                    "metadata": {},

diff --git a/docs/notebooks/single.pkl b/docs/notebooks/single.pkl
diff --git a/docs/notebooks/tutorials/exocomet.ipynb b/docs/notebooks/tutorials/exocomet.ipynb
@@ -10,37 +10,17 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "[CpuDevice(id=0),\n",
-       " CpuDevice(id=1),\n",
-       " CpuDevice(id=2),\n",
-       " CpuDevice(id=3),\n",
-       " CpuDevice(id=4),\n",
-       " CpuDevice(id=5),\n",
-       " CpuDevice(id=6),\n",
-       " CpuDevice(id=7),\n",
-       " CpuDevice(id=8),\n",
-       " CpuDevice(id=9),\n",
-       " CpuDevice(id=10),\n",
-       " CpuDevice(id=11)]"
-      ]
-     },
-     "execution_count": 1,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
+   "outputs": [],
    "source": [
     "# in order to run on all CPUs\n",
     "import os\n",
-    "import jax\n",
     "\n",
-    "os.environ[\"XLA_FLAGS\"] = f\"--xla_force_host_platform_device_count={os.cpu_count()}\"\n",
-    "jax.devices()"
+    "os.environ[\"XLA_FLAGS\"] = f\"--xla_force_host_platform_device_count={os.cpu_count()}\""
    ]
   },
   {
@@ -101,7 +81,7 @@
     {
      "data": {
       "text/plain": [
-       "[<matplotlib.lines.Line2D at 0x2be934310>]"
+       "[<matplotlib.lines.Line2D at 0x1124bcb10>]"
       ]
      },
      "execution_count": 4,
@@ -193,7 +173,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/lgarcia/code/dev/nuance/nuance/combined.py:7: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
+      "/Users/lgarcia/mambaforge/envs/nuance/lib/python3.11/site-packages/nuance/combined.py:7: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
       "  from tqdm.autonotebook import tqdm\n"
      ]
     },
@@ -310,7 +290,7 @@
     {
      "data": {
       "text/plain": [
-       "[<matplotlib.lines.Line2D at 0x2dffc0e90>]"
+       "[<matplotlib.lines.Line2D at 0x2c8fab550>]"
       ]
      },
      "execution_count": 9,
@@ -355,7 +335,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f363dd543b504b86850662f528cb9f49",
+       "model_id": "28b50c0a86984a8ba03d84f142fd63e6",
        "version_major": 2,
        "version_minor": 0
       },
@@ -414,7 +394,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 17458/17458 [00:25<00:00, 694.99it/s]\n"
+      "100%|██████████| 17458/17458 [00:18<00:00, 962.87it/s] \n"
      ]
     }
    ],

diff --git a/docs/notebooks/tutorials/exocomet.pdf b/docs/notebooks/tutorials/exocomet.pdf