Repository: pints-team/pints (language: python)

Issue:
Anyone mind if we rename `master` to `main` ?
@pints-team/devs ?

About time :D 


Discussion / hints:
Go for it.

Fix patch:
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index ca5b9faa8..3fe5562ff 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -43,7 +43,7 @@ You now have everything you need to start making changes!
 11. If you added a major new feature, perhaps it should be showcased in an [example notebook](#example-notebooks).
 12. When you feel your code is finished, or at least warrants serious discussion, run the [pre-commit checks](#pre-commit-checks) and then create a [pull request](https://help.github.com/articles/about-pull-requests/) (PR) on [PINTS' GitHub page](https://github.com/pints-team/pints).
 13. Update `CHANGELOG.md`, following the guidelines in the [changelog](#changelog) section.
-14. Once a PR has been created, it will be reviewed by any member of the community. Changes might be suggested which you can make by simply adding new commits to the branch. When everything's finished, someone with the right GitHub permissions will merge your changes into PINTS master repository.
+14. Once a PR has been created, it will be reviewed by any member of the community. Changes might be suggested which you can make by simply adding new commits to the branch. When everything's finished, someone with the right GitHub permissions will merge your changes into PINTS main repository.
 
 Finally, if you really, really, _really_ love developing PINTS, have a look at the current [project infrastructure](#infrastructure).
 
@@ -420,7 +420,7 @@ Configuration files:
 
 ### Binder
 
-Editable notebooks are made available using [Binder](mybinder.readthedocs.io) at https://mybinder.org/v2/gh/pints-team/pints/master?filepath=examples.
+Editable notebooks are made available using [Binder](mybinder.readthedocs.io) at https://mybinder.org/v2/gh/pints-team/pints/main?filepath=examples.
 
 Configuration files:
 
diff --git a/README.md b/README.md
index abfae4772..9c8b3bf07 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +1,17 @@
 [![Unit tests on multiple python versions](https://github.com/pints-team/pints/actions/workflows/unit-test-python-coverage.yml/badge.svg)](https://github.com/pints-team/pints/actions/workflows/unit-test-python-coverage.yml)
 [![Unit tests on multiple operating systems](https://github.com/pints-team/pints/actions/workflows/unit-test-os-coverage.yml/badge.svg)](https://github.com/pints-team/pints/actions/workflows/unit-test-os-coverage.yml)
-[![codecov](https://codecov.io/gh/pints-team/pints/branch/master/graph/badge.svg)](https://codecov.io/gh/pints-team/pints)
-[![Functional testing code](https://raw.githubusercontent.com/pints-team/functional-testing/master/badge-code.svg)](https://github.com/pints-team/functional-testing)
-[![Functional testing results](https://raw.githubusercontent.com/pints-team/functional-testing/master/badge-results.svg)](https://www.cs.ox.ac.uk/projects/PINTS/functional-testing)
-[![binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/pints-team/pints/master?filepath=examples)
+[![codecov](https://codecov.io/gh/pints-team/pints/branch/main/graph/badge.svg)](https://codecov.io/gh/pints-team/pints)
+[![Change-point testing code](https://raw.githubusercontent.com/pints-team/change-point-testing/main/badge-code.svg)](https://github.com/pints-team/change-point-testing)
+[![Change-point testing results](https://raw.githubusercontent.com/pints-team/change-point-testing/main/badge-results.svg)](https://www.cs.ox.ac.uk/projects/PINTS/functional-testing)
+[![binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/pints-team/pints/main?filepath=examples)
 [![readthedocs](https://readthedocs.org/projects/pints/badge/?version=latest)](http://pints.readthedocs.io/en/latest/?badge=latest)
 
 # What is Pints?
 
 PINTS (Probabilistic Inference on Noisy Time-Series) is a framework for optimisation and Bayesian inference on ODE models of noisy time-series, such as arise in electrochemistry and cardiac electrophysiology.
 
-PINTS is described in [this publication in JORS](http://doi.org/10.5334/jors.252), and can be cited using the information given in our [CITATION file](https://github.com/pints-team/pints/blob/master/CITATION).
-More information about PINTS papers can be found in the [papers directory](https://github.com/pints-team/pints/tree/master/papers).
+PINTS is described in [this publication in JORS](http://doi.org/10.5334/jors.252), and can be cited using the information given in our [CITATION file](https://github.com/pints-team/pints/blob/main/CITATION).
+More information about PINTS papers can be found in the [papers directory](https://github.com/pints-team/pints/tree/main/papers).
 
 
 ## Using PINTS
@@ -27,19 +27,19 @@ simulate(parameters, times) --> Returns a vector of model evaluations at
 ```
 
 Experimental data sets in PINTS are defined simply as lists (or arrays) of `times` and corresponding experimental `values`.
-If you have this kind of data, and if [your model (or model wrapper)](https://github.com/pints-team/pints/blob/master/examples/stats/custom-model.ipynb) implements the two methods above, then you are ready to start using PINTS to infer parameter values using [optimisation](https://github.com/pints-team/pints/blob/master/examples/optimisation/first-example.ipynb) or [sampling](https://github.com/pints-team/pints/blob/master/examples/sampling/first-example.ipynb).
+If you have this kind of data, and if [your model (or model wrapper)](https://github.com/pints-team/pints/blob/main/examples/stats/custom-model.ipynb) implements the two methods above, then you are ready to start using PINTS to infer parameter values using [optimisation](https://github.com/pints-team/pints/blob/main/examples/optimisation/first-example.ipynb) or [sampling](https://github.com/pints-team/pints/blob/main/examples/sampling/first-example.ipynb).
 
-A brief example is shown below:  
-![An example of using PINTS in an optimisation](https://raw.githubusercontent.com/pints-team/pints/master/example.svg)  
+A brief example is shown below:
+![An example of using PINTS in an optimisation](https://raw.githubusercontent.com/pints-team/pints/main/example.svg)
 _(Left)_ A noisy experimental time series and a computational forward model.
 _(Right)_ Example code for an optimisation problem.
-The full code can be [viewed here](https://github.com/pints-team/pints/blob/master/examples/sampling/readme-example.ipynb) but a friendlier, more elaborate, introduction can be found on the [examples page](https://github.com/pints-team/pints/blob/master/examples/README.md).
+The full code can be [viewed here](https://github.com/pints-team/pints/blob/main/examples/sampling/readme-example.ipynb) but a friendlier, more elaborate, introduction can be found on the [examples page](https://github.com/pints-team/pints/blob/main/examples/README.md).
 
 A graphical overview of the methods included in PINTS can be [viewed here](https://pints-team.github.io/pints-methods-overview/).
 
 ### Examples and documentation
 
-PINTS comes with a number of [detailed examples](https://github.com/pints-team/pints/blob/master/examples/README.md), hosted here on github.
+PINTS comes with a number of [detailed examples](https://github.com/pints-team/pints/blob/main/examples/README.md), hosted here on github.
 In addition, there is a [full API documentation](http://pints.readthedocs.io/en/latest/), hosted on readthedocs.io.
 
 
@@ -71,17 +71,17 @@ $ pip uninstall pints
 
 ## What's new in this version of PINTS?
 
-To see what's changed in the latest release, see the [CHANGELOG](https://github.com/pints-team/pints/blob/master/CHANGELOG.md).
+To see what's changed in the latest release, see the [CHANGELOG](https://github.com/pints-team/pints/blob/main/CHANGELOG.md).
 
 
 ## Contributing to PINTS
 
-If you'd like to help us develop PINTS by adding new methods, writing documentation, or fixing embarassing bugs, please have a look at these [guidelines](https://github.com/pints-team/pints/blob/master/CONTRIBUTING.md) first.
+If you'd like to help us develop PINTS by adding new methods, writing documentation, or fixing embarassing bugs, please have a look at these [guidelines](https://github.com/pints-team/pints/blob/main/CONTRIBUTING.md) first.
 
 
 ## License
 
-PINTS is fully open source. For more information about its license, see [LICENSE](https://github.com/pints-team/pints/blob/master/LICENSE.md).
+PINTS is fully open source. For more information about its license, see [LICENSE](https://github.com/pints-team/pints/blob/main/LICENSE.md).
 
 
 ## Get in touch
diff --git a/docs/source/conf.py b/docs/source/conf.py
index fad5c0cb3..9dd7a6ba5 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -50,8 +50,8 @@
 # source_suffix = ['.rst', '.md']
 source_suffix = '.rst'
 
-# The master toctree document.
-master_doc = 'index'
+# The main toctree document.
+main_doc = 'index'
 
 # General information about the project.
 project = u'Pints'
@@ -149,7 +149,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'Pints.tex', u'Pints Documentation',
+    (main_doc, 'Pints.tex', u'Pints Documentation',
      u'Pints Authors', 'manual'),
 ]
 
@@ -159,7 +159,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'pints', u'Pints Documentation',
+    (main_doc, 'pints', u'Pints Documentation',
      [author], 1)
 ]
 
@@ -170,7 +170,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'Pints', u'Pints Documentation',
+    (main_doc, 'Pints', u'Pints Documentation',
      author, 'Pints', 'One line description of project.',
      'Miscellaneous'),
 ]
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 6a9d00869..1a0cddbfe 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -1,7 +1,7 @@
 .. Root of all pints docs
 
 .. _GitHub: https://github.com/pints-team/pints
-.. _Detailed examples: https://github.com/pints-team/pints/blob/master/examples/README.md
+.. _Detailed examples: https://github.com/pints-team/pints/blob/main/examples/README.md
 
 Welcome to the pints documentation
 ==================================
diff --git a/examples/interfaces/stan.ipynb b/examples/interfaces/stan.ipynb
index 63be36d19..836623012 100644
--- a/examples/interfaces/stan.ipynb
+++ b/examples/interfaces/stan.ipynb
@@ -5881,7 +5881,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We now illustrate how to use the Stan interface to sample from the notorious hierarchical eight schools model (see the [eight schools](http://localhost:8888/notebooks/pints/examples/toy/distribution-eight-schools.ipynb) notebook for more on its notoriety). First, we use the PINTS [eight schools toy model](https://github.com/pints-team/pints/blob/master/examples/toy/distribution-eight-schools.ipynb) to give us the requisite data."
+    "We now illustrate how to use the Stan interface to sample from the notorious hierarchical eight schools model (see the [eight schools](http://localhost:8888/notebooks/pints/examples/toy/distribution-eight-schools.ipynb) notebook for more on its notoriety). First, we use the PINTS [eight schools toy model](https://github.com/pints-team/pints/blob/main/examples/toy/distribution-eight-schools.ipynb) to give us the requisite data."
    ]
   },
   {
diff --git a/examples/stats/autoregressive-moving-average-errors.ipynb b/examples/stats/autoregressive-moving-average-errors.ipynb
index c5d4af802..3659c80bc 100644
--- a/examples/stats/autoregressive-moving-average-errors.ipynb
+++ b/examples/stats/autoregressive-moving-average-errors.ipynb
@@ -8,7 +8,7 @@
     "\n",
     "A standard assumption in time series analysis is the presence of IID (independent and identically distributed) Gaussian noise, which is supported in Pints using the `pints.GaussianLogLikelihood` class. However, there are also more sophisticated noise models in which the noise terms depend on both a random term and on previous values. Two standard time series models which can be used as the error model in Pints are the autoregressive (AR) and autoregressive-moving-average (ARMA).\n",
     "\n",
-    "This example shows you how to perform Bayesian inference for a time series with AR(1) or ARMA(1,1) noise. It follows on from the [first sampling example](https://github.com/pints-team/pints/blob/master/examples/sampling/first-example.ipynb). Pints also includes some diagnostic plots which can help identify whether or not a correlated noise process such as AR(1) is appropriate, which are explained in [another example notebook](https://github.com/pints-team/pints/blob/master/examples/plotting/residuals-autocorrelation.ipynb)."
+    "This example shows you how to perform Bayesian inference for a time series with AR(1) or ARMA(1,1) noise. It follows on from the [first sampling example](https://github.com/pints-team/pints/blob/main/examples/sampling/first-example.ipynb). Pints also includes some diagnostic plots which can help identify whether or not a correlated noise process such as AR(1) is appropriate, which are explained in [another example notebook](https://github.com/pints-team/pints/blob/main/examples/plotting/residuals-autocorrelation.ipynb)."
    ]
   },
   {
@@ -623,4 +623,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
\ No newline at end of file
+}
diff --git a/examples/stats/constant-and-multiplicative-gaussian-error.ipynb b/examples/stats/constant-and-multiplicative-gaussian-error.ipynb
index c8b622b91..76b33a72a 100644
--- a/examples/stats/constant-and-multiplicative-gaussian-error.ipynb
+++ b/examples/stats/constant-and-multiplicative-gaussian-error.ipynb
@@ -130,7 +130,7 @@
     "\n",
     "We now try to recover the model parameters using pints' implementation of Haario's Adaptive Covariance MCMC, [`pints.HaarioACMC`](https://pints.readthedocs.io/en/latest/mcmc_samplers/haario_ac_mcmc.html).\n",
     "\n",
-    "In order to do that we need to construct a [`pints.LogPosterior`](https://pints.readthedocs.io/en/latest/log_pdfs.html#pints.LogPosterior) that incorporates the above simulated data, the logistic growth model and the error model. For a detailed introduction to how to do this in [pints](https://pints.readthedocs.io/en/latest/), please have a look at the dedicated [notebooks](https://github.com/pints-team/pints/blob/master/examples/sampling/first-example.ipynb).\n",
+    "In order to do that we need to construct a [`pints.LogPosterior`](https://pints.readthedocs.io/en/latest/log_pdfs.html#pints.LogPosterior) that incorporates the above simulated data, the logistic growth model and the error model. For a detailed introduction to how to do this in [pints](https://pints.readthedocs.io/en/latest/), please have a look at the dedicated [notebooks](https://github.com/pints-team/pints/blob/main/examples/sampling/first-example.ipynb).\n",
     "\n",
     "Let us simplify the inference by fixing the initial population size $f_0$ and the carrying capacity $k$ to the true values."
    ]


Test patch:
diff --git a/.github/workflows/copyright-test.yml b/.github/workflows/copyright-test.yml
index 60ccf2e5d..077203ad8 100644
--- a/.github/workflows/copyright-test.yml
+++ b/.github/workflows/copyright-test.yml
@@ -3,7 +3,7 @@ name: Copyright
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     # Run workflow when PR is changed, or when changed from draft to ready
     types: [opened, synchronize, reopened, ready_for_review]
diff --git a/.github/workflows/coverage-test.yml b/.github/workflows/coverage-test.yml
index 822c08c21..a1c916688 100644
--- a/.github/workflows/coverage-test.yml
+++ b/.github/workflows/coverage-test.yml
@@ -3,7 +3,7 @@ name: Coverage
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     # Run workflow when PR is changed, or when changed from draft to ready
     types: [opened, synchronize, reopened, ready_for_review]
diff --git a/.github/workflows/docs-test.yml b/.github/workflows/docs-test.yml
index b642785a3..cbf8fc878 100644
--- a/.github/workflows/docs-test.yml
+++ b/.github/workflows/docs-test.yml
@@ -3,7 +3,7 @@ name: Doctest
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     # Run workflow when PR is changed, or when changed from draft to ready
     types: [opened, synchronize, reopened, ready_for_review]
diff --git a/.github/workflows/style-test.yml b/.github/workflows/style-test.yml
index 27efe7ca5..3632b903e 100644
--- a/.github/workflows/style-test.yml
+++ b/.github/workflows/style-test.yml
@@ -3,7 +3,7 @@ name: Style tests (flake8)
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     # Run workflow when PR is changed, or when changed from draft to ready
     types: [opened, synchronize, reopened, ready_for_review]
diff --git a/.github/workflows/unit-test-os-coverage.yml b/.github/workflows/unit-test-os-coverage.yml
index aabcc1f83..aab0dc549 100644
--- a/.github/workflows/unit-test-os-coverage.yml
+++ b/.github/workflows/unit-test-os-coverage.yml
@@ -3,7 +3,7 @@ name: Unit tests (OS versions)
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     # Run workflow when PR is changed, or when changed from draft to ready
     types: [opened, synchronize, reopened, ready_for_review]
diff --git a/.github/workflows/unit-test-python-coverage.yml b/.github/workflows/unit-test-python-coverage.yml
index aa74f9d99..32eff5382 100644
--- a/.github/workflows/unit-test-python-coverage.yml
+++ b/.github/workflows/unit-test-python-coverage.yml
@@ -3,7 +3,7 @@ name: Unit tests (python versions)
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     # Run workflow when PR is changed, or when changed from draft to ready
     types: [opened, synchronize, reopened, ready_for_review]