Merge pull request #120 from MouseLand/dev

Update window size, help windows and readthedocs
MouseLand · Aug 28, 2023 · 7a06276 · 7a06276
2 parents 9c4bb42 + 759e2e5
commit 7a06276
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -4,6 +4,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -18,12 +23,11 @@ formats:
 
 # specify dependencies
 python:
-   version: 3.8
    install:
       - requirements: docs/requirements.txt
-      #- method: pip
-        #path: .
-        #extra_requirements:
-        #  - docs
-        #  - gui
+      - method: pip
+        path: .
+        extra_requirements:
+          - docs
+          - gui
 
diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
-[![Downloads](https://pepy.tech/badge/facemap)](https://pepy.tech/project/facemap)
-[![Downloads](https://pepy.tech/badge/facemap/month)](https://pepy.tech/project/facemap)
+[![Downloads](https://static.pepy.tech/badge/facemap)](https://pepy.tech/project/facemap)
+[![Downloads](https://static.pepy.tech/badge/facemap/month)](https://pepy.tech/project/facemap)
 [![GitHub stars](https://badgen.net/github/stars/Mouseland/facemap)](https://github.com/MouseLand/facemap/stargazers)
 [![GitHub forks](https://badgen.net/github/forks/Mouseland/facemap)](https://github.com/MouseLand/facemap/network/members)
 [![](https://img.shields.io/github/license/MouseLand/facemap)](https://github.com/MouseLand/facemap/blob/main/LICENSE)
 [![PyPI version](https://badge.fury.io/py/facemap.svg)](https://badge.fury.io/py/facemap)
 [![Documentation Status](https://readthedocs.org/projects/ansicolortags/badge/?version=latest)](https://pypi.org/project/facemap/)
 [![GitHub open issues](https://badgen.net/github/open-issues/Mouseland/facemap)](https://github.com/MouseLand/facemap/issues)
 
-# Facemap <img src="https://raw.githubusercontent.com/MouseLand/facemap/main/facemap/mouse.png" width="200" title="facemap" alt="facemap" align="right" vspace = "50">
+# Facemap <img src="https://raw.githubusercontent.com/MouseLand/facemap/main/facemap/mouse.png" width="300" title="facemap" alt="facemap" align="right" vspace = "50">
 
 Facemap is a framework for predicting neural activity from mouse orofacial movements. It includes a pose estimation model for tracking distinct keypoints on the mouse face, a neural network model for predicting neural activity using the pose estimates, and also can be used compute the singular value decomposition (SVD) of behavioral videos.
 

diff --git a/docs/api.rst b/docs/api.rst
@@ -1,7 +1,6 @@
 Facemap API Guide
 ===================================
 
-
 Pose estimation 
 ~~~~~~~~~~~~~~~~
 .. autoclass:: facemap.pose.pose.Pose

diff --git a/docs/conf.py b/docs/conf.py
@@ -13,18 +13,22 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
+sys.path.insert(0, os.path.abspath('.'))
 
+""" 
+Use the following command to generate documentation 
+    sphinx-build -b html docs docs/build/html     
+"""
 # -- Project information -----------------------------------------------------
 
 project = "Facemap"
 copyright = "2023, Carsen Stringer & Atika Syeda"
 author = "Carsen Stringer & Atika Syeda"
 
 # The full version, including alpha/beta/rc tags
-release = "1.0.1"
+release = "1.0.2"
 
 
 # -- General configuration ---------------------------------------------------
@@ -39,7 +43,7 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
-    "nbsphinx"
+    "nbsphinx",
 ]
 # extensions = ['sphinx.ext.autodoc',
 #            'sphinx.ext.mathjax',
@@ -73,9 +77,10 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-"""
+
 html_theme = 'sphinx_rtd_theme'
 html_theme_path = ["_themes"]
+"""
 html_theme_options = {
     'canonical_url': '',
     'analytics_id': 'UA-XXXXXXX-1',  #  Provided by Google in your dashboard

diff --git a/docs/index.rst b/docs/index.rst
@@ -12,18 +12,9 @@ For more details, please see our `paper <https://www.biorxiv.org/content/10.1101
     gui
     inputs
     outputs
-
-.. toctree::
-    :maxdepth: 1
-    :caption: Tutorials
-
     notebooks/tutorials
 
 .. toctree::
    :caption: API Reference:
 
    api
-
-.. 
-    Use the following command to generate documentation 
-    sphinx-build -b html docs docs/build/html 
diff --git a/docs/notebooks/tutorials.rst b/docs/notebooks/tutorials.rst
@@ -1,5 +1,4 @@
-.. toctree::
-    :maxdepth: 1
+Tutorials
+===================================
 
-    process_keypoints
-    refine_keypoints_model
+See example tutorials for `processing keypoints <https://colab.research.google.com/github/MouseLand/facemap/blob/dev/docs/notebooks/process_keypoints.ipynb>`__ and `refining keypoints model <https://colab.research.google.com/drive/1mrlJVTiqndDQ_kWYXrx7GsPXDiIgpRSm?usp=sharing>`__. 
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,5 @@
 ipykernel
-nbsphinx
+nbsphinx
+sphinx==5.3.0
+sphinx_rtd_theme==1.1.1
+readthedocs-sphinx-search==0.1.1
diff --git a/facemap/__main__.py b/facemap/__main__.py
@@ -7,9 +7,9 @@
 
 import numpy as np
 
-from facemap import process
+from facemap import process, version_str
 from facemap.gui import gui
-from facemap import version_str
+
 
 def tic():
     return time.time()