Merge pull request #2656 from jeromtom/issue-#2655-Updating-depreciated-link

Updated broken links.

Author: valentinsulzer

.all-contributorsrc

@@ -128,7 +128,7 @@
       "login": "dalonsoa",
       "name": "Diego",
       "avatar_url": "https://avatars1.githubusercontent.com/u/6095790?v=4",
-      "profile": "https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/research-software-engineering/",
+      "profile": "https://github.com/dalonsoa",
       "contributions": [
         "bug",
         "review",

.github/ISSUE_TEMPLATE/new_parameter_set.yml

@@ -6,7 +6,7 @@ body:
       value: |
         Third-party parameter sets can be added to PyBaMM by registering an entry
         point with `pybamm-parameter-sets` as described in our
-        [documentation](https://pybamm.readthedocs.io/en/latest/source/parameters/parameter_sets.html).
+        [documentation](https://pybamm.readthedocs.io/en/latest/source/api/parameters/parameter_sets.html).
   - type: input
     id: parameter-set-url
     attributes:

CONTRIBUTING.md

@@ -37,7 +37,7 @@ We use [GIT](https://en.wikipedia.org/wiki/Git) and [GitHub](https://en.wikipedi
 1. Create an [issue](https://guides.github.com/features/issues/) where new proposals can be discussed before any coding is done.
 2. Create a [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/) of this repo (ideally on your own [fork](https://help.github.com/articles/fork-a-repo/)), where all changes will be made
 3. Download the source code onto your local system, by [cloning](https://help.github.com/articles/cloning-a-repository/) the repository (or your fork of the repository).
-4. [Install](https://pybamm.readthedocs.io/en/latest/install/install-from-source.html) PyBaMM with the developer options.
+4. [Install](https://pybamm.readthedocs.io/en/latest/source/user_guide/installation/install-from-source.html) PyBaMM with the developer options.
 5. [Test](#testing) if your installation worked, using the test script: `$ python run-tests.py --unit`.
 
 You now have everything you need to start making changes!

docs/index.rst

@@ -18,12 +18,8 @@ PyBaMM documentation
 
 **Version**: |version|
 
-.. **Download documentation**:
-.. `PDF Version <https://numpy.org/doc/stable/numpy-user.pdf>`_ |
-.. `Historical versions of documentation <https://numpy.org/doc/>`_
-   
 **Useful links**:
-`Project Home Page <https://pybamm.org>`_ |
+`Project Home Page <https://www.pybamm.org>`_ |
 `Installation <source/user_guide/installation/index.html>`_ |
 `Source Repository <https://github.com/pybamm-team/pybamm>`_ |
 `Issue Tracker <https://github.com/pybamm-team/pybamm/issues>`_ |

docs/source/user_guide/installation/index.rst

@@ -37,8 +37,8 @@ Optional solvers
 
 Following GNU/Linux and macOS solvers are optionally available:
 
-*  `scikits.odes <https://scikits-odes.readthedocs.io/en/latest/>`_ -based solver, see `Optional - scikits.odes solver <https://pybamm.readthedocs.io/en/latest/install/GNU-linux.html#optional-scikits-odes-solver>`_.
-*  `jax <https://jax.readthedocs.io/en/latest/notebooks/quickstart.html>`_ -based solver, see `Optional - JaxSolver <https://pybamm.readthedocs.io/en/latest/install/GNU-linux.html#optional-jaxsolver>`_.
+*  `scikits.odes <https://scikits-odes.readthedocs.io/en/latest/>`_ -based solver, see `Optional - scikits.odes solver <https://pybamm.readthedocs.io/en/latest/source/user_guide/installation/GNU-linux.html#optional-scikits-odes-solver>`_.
+*  `jax <https://jax.readthedocs.io/en/latest/notebooks/quickstart.html>`_ -based solver, see `Optional - JaxSolver <https://pybamm.readthedocs.io/en/latest/source/user_guide/installation/GNU-linux.html#optional-jaxsolver>`_.
 
 Full installation guide
 -----------------------

examples/notebooks/Getting Started/Tutorial 4 - Setting parameter values.ipynb

@@ -42,10 +42,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "PyBaMM has a number of in-built parameter sets (check the list [here](https://pybamm.readthedocs.io/en/latest/source/parameters/parameter_sets.html)), which can be selected doing"
+    "PyBaMM has a number of in-built parameter sets (check the list [here](https://pybamm.readthedocs.io/en/latest/source/api/parameters/parameter_sets.html)), which can be selected doing"
    ]
   },
   {
@@ -554,7 +555,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.13 ('conda_jl')",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -585,7 +586,7 @@
   },
   "vscode": {
    "interpreter": {
-    "hash": "612adcc456652826e82b485a1edaef831aa6d5abc680d008e93d513dd8724f14"
+    "hash": "1a781583db2df3c2e87436f6d22cce842c2e50a5670da93a3bd820b97dc43011"
    }
   }
  },

examples/notebooks/Getting Started/Tutorial 7 - Model options.ipynb

@@ -28,10 +28,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this tutorial, we add a thermal model to the SPMe. From the [documentation](https://pybamm.readthedocs.io/en/latest/source/models/base_models/base_battery_model.html), we see that we have a choice of either a 'x-full' thermal model or a number of different lumped thermal models. For a deeper look at the thermal models see the [thermal models notebook](../models/thermal-models.ipynb). We choose the full thermal model, which solves the spatially-dependent heat equation on our battery geometry, and couples the temperature with the electrochemistry. We set the model options by creating a Python dictionary:"
+    "In this tutorial, we add a thermal model to the SPMe. From the [documentation](https://pybamm.readthedocs.io/en/latest/source/api/models/base_models/base_battery_model.html), we see that we have a choice of either a 'x-full' thermal model or a number of different lumped thermal models. For a deeper look at the thermal models see the [thermal models notebook](../models/thermal-models.ipynb). We choose the full thermal model, which solves the spatially-dependent heat equation on our battery geometry, and couples the temperature with the electrochemistry. We set the model options by creating a Python dictionary:"
    ]
   },
   {
@@ -108,10 +109,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this tutorial we have seen how to adjust the model options. To see all of the options currently available in PyBaMM, please take a look at the documentation [here](https://pybamm.readthedocs.io/en/latest/source/models/base_models/base_battery_model.html).\n",
+    "In this tutorial we have seen how to adjust the model options. To see all of the options currently available in PyBaMM, please take a look at the documentation [here](https://pybamm.readthedocs.io/en/latest/source/api/models/base_models/base_battery_model.html).\n",
     "\n",
     "In the [next tutorial](./Tutorial%208%20-%20Solver%20options.ipynb) we show how to change the solver options."
    ]
@@ -149,7 +151,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -163,7 +165,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.11.1"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "a06befff6f507b2769436dc41c340f64f62afa83086a8cd273928f468e329d0b"
+   }
   }
  },
  "nbformat": 4,

examples/notebooks/Getting Started/Tutorial 8 - Solver options.ipynb

@@ -32,10 +32,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Here we will change the absolute and relative tolerances, as well as the \"mode\" of the `CasadiSolver`. For a list of all the solver options  please consult the [documentation](https://pybamm.readthedocs.io/en/latest/source/solvers/index.html).\n",
+    "Here we will change the absolute and relative tolerances, as well as the \"mode\" of the `CasadiSolver`. For a list of all the solver options  please consult the [documentation](https://pybamm.readthedocs.io/en/latest/source/api/solvers/index.html).\n",
     "\n",
     "The `CasadiSolver` can operate in a number of modes, including \"safe\" (default) and \"fast\". Safe mode performs step-and-check integration and supports event handling (e.g. you can integrate until you hit a certain voltage), and is the recommended for simulations of a full charge or discharge. Fast mode performs direct integration, ignoring events, and is recommended when simulating a drive cycle or other simulation where no events should be triggered.\n",
     "\n",

examples/notebooks/README.md

@@ -63,8 +63,8 @@ Once you are comfortable with the expression tree structure, a good starting poi
 
 #### Lead-acid models
 
-- [Full porous-electrode](https://pybamm.readthedocs.io/en/latest/source/models/lead_acid/full.html)
-- [Leading-Order Quasi-Static](https://pybamm.readthedocs.io/en/latest/source/models/lead_acid/loqs.html)
+- [Full porous-electrode](https://pybamm.readthedocs.io/en/latest/source/api/models/lead_acid/full.html)
+- [Leading-Order Quasi-Static](https://pybamm.readthedocs.io/en/latest/source/api/models/lead_acid/loqs.html)
 
 ### Spatial Methods
 

examples/notebooks/callbacks.ipynb

@@ -19,15 +19,16 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "cb2ae3b6",
    "metadata": {},
    "source": [
     "Callbacks provide hooks for users to interact with the different parts of the PyBaMM pipeline, for example to log, save, or visualize outputs of intermediate functions. \n",
     "\n",
-    "A list of available callbacks can be found in the [API docs](https://pybamm.readthedocs.io/en/latest/source/callbacks.html). Any number of callbacks can be provided as a list, and they will each be called in turn in the order provided.\n",
+    "A list of available callbacks can be found in the [API docs](https://pybamm.readthedocs.io/en/latest/source/api/callbacks.html). Any number of callbacks can be provided as a list, and they will each be called in turn in the order provided.\n",
     "\n",
-    "The base class [`pybamm.callbacks.Callback`](https://pybamm.readthedocs.io/en/latest/source/citations.html#pybamm.callbacks.Callback) documents the available callback methods, at which point in the pipeline they are called, and what arguments are passed to them."
+    "The base class [`pybamm.callbacks.Callback`](https://pybamm.readthedocs.io/en/latest/source/api/callbacks.html#pybamm.callbacks.Callback) documents the available callback methods, at which point in the pipeline they are called, and what arguments are passed to them."
    ]
   },
   {