Migrate doc links to GitHub pages instance

Author: sitic

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: Build docs
+name: docs
 
 on:
   push:

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: Build and test
+name: build and test
 
 on:
   push:

README.md

@@ -1,20 +1,20 @@
 # optimap
 
-[![docs](https://readthedocs.org/projects/optimap/badge/?version=latest&style=)](https://optimap.readthedocs.org)
+[![docs](https://github.com/cardiacvision/optimap/actions/workflows/docs.yml/badge.svg)](https://github.com/cardiacvision/optimap/actions/workflows/docs.yml)
 [![tests](https://github.com/cardiacvision/optimap/actions/workflows/main.yml/badge.svg)](https://github.com/cardiacvision/optimap/actions/workflows/main.yml)
 [![PyPI](https://img.shields.io/pypi/v/opticalmapping.svg)](https://pypi.org/project/opticalmapping/)
 [![Supported Python versions](https://img.shields.io/pypi/pyversions/opticalmapping.svg)](https://python.org)
 [![DOI](https://zenodo.org/badge/677528623.svg)](https://zenodo.org/badge/latestdoi/677528623)
 
-### optimap: An open-source library for the processing of fluorescence video data
+### optimap: An open-source library for processing fluorescence video data
 
-`optimap` is an open-source Python toolbox for exploring, visualizing, and analyzing high-speed fluorescence imaging data with a focus on cardiac optical mapping data. It includes modules for loading, processing and exporting videos, extracting and measuring optical traces, visualizing action potential or calcium waves, tracking motion and compensating motion artifacts, computing activation maps, conduction velocities, action potential durations, as well as measuring contractility and further analyzing and visualizing the results. Refer to the [Tutorials](https://optimap.readthedocs.io/en/latest/tutorials/) and the [Documentation](https://optimap.readthedocs.io/en/latest/) for more information about optimap's features.
+`optimap` is an open-source Python toolbox for exploring, visualizing, and analyzing high-speed fluorescence imaging data with a focus on cardiac optical mapping data. It includes modules for loading, processing and exporting videos, extracting and measuring optical traces, visualizing action potential or calcium waves, tracking motion and compensating motion artifacts, computing activation maps, conduction velocities, action potential durations, as well as measuring contractility and further analyzing and visualizing the results. Refer to the [Tutorials](https://cardiacvision.github.io/optimap/main/tutorials/) and the [Documentation](https://cardiacvision.github.io/optimap/) for more information about optimap's features.
 
 > ⚠️ optimap is currently in early development, expect breaking changes and bugs.
 
 ## Installation
 
-`optimap` is available for macOS, Windows and Linux, see the [Getting Started](https://optimap.readthedocs.io/en/latest/chapters/getting_started/) guide for more information.
+`optimap` is available for macOS, Windows and Linux, see the [Getting Started](https://cardiacvision.github.io/optimap/main/chapters/getting_started/) guide for more information.
 
 ### Installing pre-built binaries (macOS, Windows, Linux)
 
@@ -38,19 +38,19 @@ pip install --upgrade opticalmapping[all]
 
 ## About optimap
 
-`optimap` is an interactive, script or notebook-based software library created for cardiovascular scientists in particular, but might also be useful for scientists in other fields. For instance, when performing calcium imaging or physiological research with moving cells or tissues. It is designed to be a flexible and customizable analysis workflow toolkit, which allows for a wide range of analyses and visualizations. See the [Tutorials](https://optimap.readthedocs.io/en/latest/tutorials/) for examples and more information about the usage of `optimap`. The tutorials can be downloaded by clicking on the link in the green box at the top of each tutorial page.
+`optimap` is an interactive, script or notebook-based software library created for cardiovascular scientists in particular, but might also be useful for scientists in other fields. For instance, when performing calcium imaging or physiological research with moving cells or tissues. It is designed to be a flexible and customizable analysis workflow toolkit, which allows for a wide range of analyses and visualizations. See the [Tutorials](https://cardiacvision.github.io/optimap/main/tutorials/) for examples and more information about the usage of `optimap`. The tutorials can be downloaded by clicking on the link in the green box at the top of each tutorial page.
 
 `optimap` is developed by members of the [Cardiac Vision Laboratory](https://cardiacvision.ucsf.edu) at the [University of California, San Franicsco](https://www.ucsf.edu). It is open-source, freely available, and relies on open-source packages such as NumPy, SciPy, Matplotlib and OpenCV.
 
 ## Links
 
-- [Documentation](https://optimap.readthedocs.io)
+- [Documentation](https://cardiacvision.github.io/optimap/)
 - [Issue tracker](https://github.com/cardiacvision/optimap/issues)
 - [Source code](https://github.com/cardiacvision/optimap)
 
 ## Contributing
 
-We welcome bug reports, questions, ideas for new features and pull-requests to fix issues or add new features to optimap. See [Contributing](https://optimap.readthedocs.io/en/latest/chapters/contributing/) for more information.
+We welcome bug reports, questions, ideas for new features and pull-requests to fix issues or add new features to optimap. See [Contributing](https://cardiacvision.github.io/optimap/main/chapters/contributing/) for more information.
 
 ## License
 

docs/chapters/getting_started.md

@@ -1,7 +1,7 @@
 (installing)=
 # Installing optimap
 
-`optimap` is available for Windows, Mac OSX, and Linux. Pre-built binaries can be installed using `pip`, see below. You can find more detailed installation instructions in our [Installation Guide](https://optimap.readthedocs.io/en/latest/chapters/installation/). You can find the latest version of our sourcode here:
+`optimap` is available for Windows, Mac OSX, and Linux. Pre-built binaries can be installed using `pip`, see below. You can find more detailed installation instructions in our [Installation Guide](#installation). You can find the latest version of our source code here:
 
 [https://github.com/cardiacvision/optimap](https://github.com/cardiacvision/optimap).
 
@@ -16,13 +16,7 @@ optimap relies heavily on [NumPy](https://numpy.org) and [Matplotlib](https://ma
 The easiest way to install optimap is using `pip` in the command line:
 
 ```bash
-pip install opticalmapping[all]
-```
-
-If this command fails, please try the following:
-
-```bash
-python -m pip install opticalmapping\[all\]
+pip install "opticalmapping[all]"
 ```
 
 ```{note}
@@ -36,7 +30,7 @@ To use GPU-accelerated motion tracking algorithms a CUDA-enabled version of Open
 To update optimap to the latest version run
 
 ```bash
-pip install --upgrade opticalmapping[all]`
+pip install --upgrade "opticalmapping[all]"`
 ```
 
 #### Installing from source

docs/tutorials/example_files.ipynb

@@ -18,7 +18,7 @@
    "source": [
     "# Example Data Files\n",
     "\n",
-    "``optimap`` provides several optical mapping example videos, which are used throughout the [Tutorials](https://optimap.readthedocs.io/en/latest/tutorials/). The example files can be used to test optimap or to develop your own analysis scripts. They can be downloaded directly within a script while using ``optimap``:"
+    "``optimap`` provides several optical mapping example videos, which are used throughout the [Tutorials](https://cardiacvision.github.io/optimap/main/tutorials/). The example files can be used to test optimap or to develop your own analysis scripts. They can be downloaded directly within a script while using ``optimap``:"
    ]
   },
   {

optimap/__init__.py

@@ -6,7 +6,7 @@
     opencv_not_found_error = "\n\n" \
         "ERROR: Unable to import OpenCV, which we require. " \
         "Please install it, e.g. with `pip install opencv-python`. " \
-        "See https://optimap.readthedocs.io/en/latest/chapters/getting_started/ for details."  \
+        "See https://cardiacvision.github.io/optimap/main/chapters/getting_started/ for details."  \
         "\n\n"
     raise ImportError(opencv_not_found_error)