doc: Fix master->main (#2904)

Update URLs - use the new main branch.

Author: dweindl

README.md

@@ -1,4 +1,4 @@
-<img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/banner.png" height="60" align="left" alt="AMICI logo">
+<img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/main/doc/gfx/banner.png" height="60" align="left" alt="AMICI logo">
 
 ## Advanced Multilanguage Interface for CVODES and IDAS
 
@@ -36,9 +36,9 @@ constrained optimization problems.
 <a href="https://github.com/AMICI-dev/AMICI/actions/workflows/test_pypi.yml">
   <img src="https://github.com/AMICI-dev/AMICI/actions/workflows/test_pypi.yml/badge.svg" alt="PyPI installation"></a>
 <a href="https://codecov.io/gh/AMICI-dev/AMICI">
-  <img src="https://codecov.io/gh/AMICI-dev/AMICI/branch/master/graph/badge.svg" alt="Code coverage"></a>
-<a href="https://sonarcloud.io/dashboard?id=ICB-DCM_AMICI&branch=master">
-  <img src="https://sonarcloud.io/api/project_badges/measure?branch=master&project=ICB-DCM_AMICI&metric=sqale_index" alt="SonarCloud technical debt"></a>
+  <img src="https://codecov.io/gh/AMICI-dev/AMICI/branch/main/graph/badge.svg" alt="Code coverage"></a>
+<a href="https://sonarcloud.io/dashboard?id=ICB-DCM_AMICI&branch=main">
+  <img src="https://sonarcloud.io/api/project_badges/measure?project=ICB-DCM_AMICI&metric=sqale_index" alt="SonarCloud technical debt"></a>
 <a href="https://zenodo.org/badge/latestdoi/43677177">
   <img src="https://zenodo.org/badge/43677177.svg" alt="Zenodo DOI"></a>
 <a href="https://amici.readthedocs.io/en/latest/?badge=latest">
@@ -73,7 +73,7 @@ are derived symbolically and C++ code is generated. This code is then
 compiled into a C++ library, a Python module, or a Matlab `.mex` file and
 is then used for model simulation.
 
-![AMICI workflow](https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/amici_workflow.png)
+![AMICI workflow](https://raw.githubusercontent.com/AMICI-dev/AMICI/main/doc/gfx/amici_workflow.png)
 
 ## Getting started
 
@@ -83,14 +83,14 @@ To install AMICI, first read the installation instructions for
 [C++](https://amici.readthedocs.io/en/latest/cpp_installation.html) or
 [Matlab](https://amici.readthedocs.io/en/latest/matlab_installation.html).
 There are also instructions for using AMICI inside
-[containers](https://github.com/AMICI-dev/AMICI/tree/master/container).
+[containers](https://github.com/AMICI-dev/AMICI/tree/main/container).
 
 To get you started with Python-AMICI, the best way might be checking out this
-[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/doc/examples/getting_started/GettingStarted.ipynb)
+[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/main/doc/examples/getting_started/GettingStarted.ipynb)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/main?labpath=doc%2Fexamples%2Fgetting_started%2FGettingStarted.ipynb).
 
 To get started with Matlab-AMICI, various examples are available
-in [matlab/examples/](https://github.com/AMICI-dev/AMICI/tree/master/matlab/examples).
+in [matlab/examples/](https://github.com/AMICI-dev/AMICI/tree/main/matlab/examples).
 
 Comprehensive documentation is available at
 [https://amici.readthedocs.io/en/latest/](https://amici.readthedocs.io/en/latest/).
@@ -149,11 +149,11 @@ When using AMICI in your project, please cite:
   ```
 
 When presenting work that employs AMICI, feel free to use one of the icons in
-[doc/gfx/](https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx),
+[doc/gfx/](https://github.com/AMICI-dev/AMICI/tree/main/doc/gfx),
 which are available under a
-[CC0](https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx/LICENSE.md)
+[CC0](https://github.com/AMICI-dev/AMICI/tree/main/doc/gfx/LICENSE.md)
 license:
 
 <p align="center">
-  <img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png" height="75" alt="AMICI Logo">
+  <img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/main/doc/gfx/logo_text.png" height="75" alt="AMICI Logo">
 </p>

doc/availability.rst

@@ -6,8 +6,8 @@ Source code
 
 The AMICI source code is available as
 
-- `tar archive <https://github.com/AMICI-dev/AMICI/tarball/master>`_
-- `zip archive <https://github.com/AMICI-dev/AMICI/zipball/master>`_
+- `tar archive <https://github.com/AMICI-dev/AMICI/tarball/main>`_
+- `zip archive <https://github.com/AMICI-dev/AMICI/zipball/main>`_
 - Git repository on `GitHub <https://github.com/AMICI-dev/AMICI>`_
 
 If AMICI was downloaded as an archive, it needs to be unpacked. If AMICI was

doc/how_to_cite.rst

@@ -32,12 +32,12 @@ When using AMICI in your project, please cite
      }
 
 When presenting work that employs AMICI, feel free to use one of the icons in
-`documentation/gfx/ <https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx>`_,
+`documentation/gfx/ <https://github.com/AMICI-dev/AMICI/tree/main/doc/gfx>`_,
 which are available under a
-`CC0 <https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx/LICENSE.md>`_
+`CC0 <https://github.com/AMICI-dev/AMICI/tree/main/doc/gfx/LICENSE.md>`_
 license:
 
-.. image:: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png
-   :target: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png
+.. image:: https://raw.githubusercontent.com/AMICI-dev/AMICI/main/doc/gfx/logo_text.png
+   :target: https://raw.githubusercontent.com/AMICI-dev/AMICI/main/doc/gfx/logo_text.png
    :height: 75
    :alt: AMICI LOGO

doc/index.rst

@@ -2,7 +2,7 @@ Welcome to AMICI's documentation!
 =================================
 
 
-.. image:: https://codecov.io/gh/AMICI-dev/AMICI/branch/master/graph/badge.svg
+.. image:: https://codecov.io/gh/AMICI-dev/AMICI/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/AMICI-dev/AMICI
    :alt: Code coverage
 .. image:: https://readthedocs.org/projects/amici/badge/?version=latest

doc/python_installation.rst

@@ -191,7 +191,7 @@ dependencies, you can run
 .. note::
 
    If you run into an error with above installation command, install all AMICI
-   dependencies listed in `setup.py <https://github.com/AMICI-dev/AMICI/blob/master/python/sdist/setup.py>`_
+   dependencies listed in `setup.py <https://github.com/AMICI-dev/AMICI/blob/main/python/sdist/setup.py>`_
    manually, and try again. (This is because ``pip`` ``--install-option`` is
    applied to *all* installed packages, including dependencies.)
 

doc/python_interface.rst

@@ -12,7 +12,7 @@ Model definition
 
 This document provides an overview of different interfaces to import models
 in AMICI. Further examples are available in the AMICI repository in the
-`python/examples <https://github.com/AMICI-dev/AMICI/tree/master/python/examples>`_
+`python/examples <https://github.com/AMICI-dev/AMICI/tree/main/python/examples>`_
 directory.
 
 SBML import