Fix Lychee link failures from stack overflow (#3989)

* Starting to fix the link checks

* Remove remaining links

* style: pre-commit fixes

* Remove last link

* style: pre-commit fixes

* Minor comment fixes

* Code review fixes

* Code review fix

* Remove keras link

* Update .github/ISSUE_TEMPLATE/bug_report.yml

Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>

* Fix pre-commit

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Arjun Verma <arjunverma.oc@gmail.com>
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -34,7 +34,7 @@ body:
     id: reproduce
     attributes:
       label: Steps to Reproduce
-      description: Tell us how to reproduce this behaviour. Ideally, this should take the form of a [Minimum Workable Example](https://stackoverflow.com/help/minimal-reproducible-example)
+      description: Tell us how to reproduce this behaviour. Ideally, this should include a code block which produces the error. Strive to make this example as small and simple as possible. It should contain the code required to reproduce the error, and no additional code. For example, if your code includes lines to run a simulation, then lines to plot the results, and the lines to run the simulation fail, only include those lines (and not the plotting lines, which are irrelevant). Often, the act of simplifying code to pinpoint errors can help you find bugs in your own code. For more information, see [these references](https://en.wikipedia.org/wiki/Minimal_reproducible_example#External_links)
     validations:
       required: true
   - type: textarea

.readthedocs.yaml

@@ -1,8 +1,3 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
 # Build documentation in the docs/ directory with Sphinx
@@ -25,16 +20,11 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
   jobs:
     # Unshallow the git clone otherwise this may cause issues with Sphinx extensions
     post_checkout:
       - git fetch --unshallow
-    # Altered PDF build and upload job, attributed to
-    # https://stackoverflow.com/a/76992101/14001839
+    # Altered PDF build and upload job
     # This also runs on PR builds, but does not upload the PDF
     post_build:
       - mkdir --parents $READTHEDOCS_OUTPUT/pdf/

CONTRIBUTING.md

@@ -44,9 +44,12 @@ You now have everything you need to start making changes!
 
 ### B. Writing your code
 
-6. PyBaMM is developed in [Python](https://en.wikipedia.org/wiki/Python_(programming_language)), and makes heavy use of [NumPy](https://en.wikipedia.org/wiki/NumPy) (see also [NumPy for MatLab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) and [Python for R users](https://www.rebeccabarter.com/blog/2023-09-11-from_r_to_python)).
+6. PyBaMM is developed in [Python](https://www.python.org)), and makes heavy use of [NumPy](https://numpy.org/) (see also [NumPy for MatLab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) and [Python for R users](https://www.rebeccabarter.com/blog/2023-09-11-from_r_to_python)).
 7. Make sure to follow our [coding style guidelines](#coding-style-guidelines).
-8. Commit your changes to your branch with [useful, descriptive commit messages](https://chris.beams.io/posts/git-commit/): Remember these are publicly visible and should still make sense a few months ahead in time. While developing, you can keep using the GitHub issue you're working on as a place for discussion. [Refer to your commits](https://stackoverflow.com/questions/8910271/how-can-i-reference-a-commit-in-an-issue-comment-on-github) when discussing specific lines of code.
+8. Commit your changes to your branch with [useful, descriptive commit messages](https://chris.beams.io/posts/git-commit/): Remember these are
+   publicly visible and should still make sense a few months ahead in time.
+   While developing, you can keep using the GitHub issue you're working on
+   as a place for discussion.
 9. If you want to add a dependency on another library, or re-use code you found somewhere else, have a look at [these guidelines](#dependencies-and-reusing-code).
 
 ### C. Merging your changes with PyBaMM
@@ -87,7 +90,12 @@ Class names are CamelCase, and start with an upper case letter, for example `MyO
 While it's a bad idea for developers to "reinvent the wheel", it's important for users to get a _reasonably sized download and an easy install_. In addition, external libraries can sometimes cease to be supported, and when they contain bugs it might take a while before fixes become available as automatic downloads to PyBaMM users.
 For these reasons, all dependencies in PyBaMM should be thought about carefully, and discussed on GitHub.
 
-Direct inclusion of code from other packages is possible, as long as their license permits it and is compatible with ours, but again should be considered carefully and discussed in the group. Snippets from blogs and [stackoverflow](https://stackoverflow.com/) can often be included without attribution, but if they solve a particularly nasty problem (or are very hard to read) it's often a good idea to attribute (and document) them, by making a comment with a link in the source code.
+Direct inclusion of code from other packages is possible, as long as their
+license permits it and is compatible with ours, but again should be
+considered carefully and discussed in the group. Snippets from blogs and
+stackoverflow can often be included without attribution, but if they solve a
+particularly nasty problem (or are very hard to read) it's often a good idea to
+attribute (and document) them, by making a comment with a link in the source code.
 
 ### Separating dependencies
 

pybamm/callbacks.py

@@ -1,10 +1,3 @@
-#
-# Base class for callbacks and some useful callbacks for pybamm
-# Callbacks are used to perform actions (e.g. logging, saving)
-# at certain points in the simulation
-# Inspired by Keras callbacks
-# https://github.com/keras-team/keras/blob/master/keras/callbacks/callback.py
-#
 import pybamm
 import numpy as np
 import inspect
@@ -99,8 +92,7 @@ class CallbackList(Callback):
 
     This is done without having to redefine the method each time by using the
     `callback_loop_decorator` decorator, which is applied to every method that starts
-    with `on_`, using the `inspect` module. See
-    https://stackoverflow.com/questions/1367514/how-to-decorate-a-method-inside-a-class.
+    with `on_`, using the `inspect` module.
 
     If better control over how the callbacks are called is required, it might be better
     to be more explicit with the for loop.

pybamm/citations.py

@@ -59,7 +59,6 @@ def _caller_name():
         Returns the qualified name of classes that call :meth:`register` internally.
         Gets cached in order to reduce the number of calls.
         """
-        # Attributed to https://stackoverflow.com/a/53490973
         caller_name = _getframe().f_back.f_back.f_locals["self"].__class__.__qualname__
         return caller_name
 

pybamm/logger.py

@@ -1,11 +1,3 @@
-#
-# Logging class for PyBaMM
-# Includes additional logging levels inspired by verboselogs
-# https://pypi.org/project/verboselogs/#overview-of-logging-levels
-#
-# Implementation from stackoverflow
-# https://stackoverflow.com/questions/2183233/how-to-add-a-custom-loglevel-to-pythons-logging-facility
-#
 import logging
 
 

pybamm/solvers/base_solver.py

@@ -827,7 +827,7 @@ def solve(
                 )
             # It is assumed that when len(inputs_list) > 1, model set
             # up (initial condition, time-scale and length-scale) does
-            # not depend on input parameters. Thefore only `model_inputs[0]`
+            # not depend on input parameters. Therefore, only `model_inputs[0]`
             # is passed to `set_up`.
             # See https://github.com/pybamm-team/PyBaMM/pull/1261
             self.set_up(model, model_inputs_list[0], t_eval)

pybamm/solvers/solution.py

@@ -14,8 +14,9 @@
 
 class NumpyEncoder(json.JSONEncoder):
     """
-    Numpy serialiser helper class that converts numpy arrays to a list
-    https://stackoverflow.com/questions/26646362/numpy-array-is-not-json-serializable
+    Numpy serialiser helper class that converts numpy arrays to a list.
+    Numpy arrays cannot be directly converted to JSON, so the arrays are
+    converted to python list objects before encoding.
     """
 
     def default(self, obj):