Merge pull request #6184 from tjhei/fix-links

docs: fix links

CONTRIBUTING.md

@@ -65,7 +65,7 @@ planned, or that conflicts with other plans.
 To make a change to ASPECT you should:
 
 - Create a
-[fork](https://guides.github.com/activities/forking/#fork) (through GitHub) of
+[fork](https://guides.github.com/activities/forking) (through GitHub) of
 the code base.
 - Create a separate
 [branch](https://guides.github.com/introduction/flow/) (sometimes called a
@@ -124,7 +124,7 @@ When you add the bin directory to to your path, the indent command should find a
 
 If your new pull request creates a change that is noticeable to ASPECT users,
 please add an entry to our
-[changelog](http://aspect.geodynamics.org/doc/doxygen/changes_current.html). To
+[changelog](https://aspect.geodynamics.org/doc/doxygen/changes_current.html). To
 add such an entry, make a copy of one of the files in the
 [doc/modules/changes/](https://github.com/geodynamics/aspect/tree/main/doc/modules/changes)
 folder and modify it to explain
@@ -147,7 +147,7 @@ ways in which your contribution will be acknowledged by the ASPECT community:
   and merged pull requests, including an acknowledgment of the author of the
   issue/pull request.
 - For every release the most significant entries of our
-  [changelog](http://aspect.geodynamics.org/doc/doxygen/changes_current.html)
+  [changelog](https://aspect.geodynamics.org/doc/doxygen/changes_current.html)
   are selected to generate our release announcements. Additionally, all entries
   remain available for all previous releases of ASPECT inside the
   [repository](https://github.com/geodynamics/aspect/tree/main/doc/modules)

cookbooks/geomio/doc/geomio.md

@@ -16,7 +16,7 @@ generate the initial geometries of the materials as a drawing instead of by
 writing code. The MATLAB-based library geomIO
 (<https://bitbucket.org/geomio/geomio>, {cite}`bauville:baumann:2019` provides
 a convenient tool to convert a drawing generated with the vector graphics
-editor Inkscape (<https://inkscape.org/en/>) to a data file that can be read
+editor Inkscape (<https://inkscape.org>) to a data file that can be read
 into ASPECT. Here, we will demonstrate how this can be done for a 2D setup for a
 model with one compositional field, but geomIO also has the capability to
 create 3D volumes based on a series of 2D vector drawings using any number of
@@ -65,7 +65,7 @@ that you later want to use in your model (in m).
 :::
 
 After geomIO is initialized in MATLAB, we [run geomIO as described in the
-documentation](https://bitbucket.org/#assigning-phase-to-markers), loading the
+documentation](https://bitbucket.org/geomio/geomio/wiki/Basic2Dtutorial#markdown-header-assigning-phase-information-to-markers), loading the
 default options and then specifying all the
 option we want to change, such as the path to the input file, or the
 resolution:

cookbooks/multicomponent_steinberger/doc/multicomponent_steinberger.md

@@ -122,7 +122,7 @@ You may also notice that there is a `subsection Function` under `subsection Adia
 
 
 The complete input file can be found in
-[cookbooks/multicomponent_steinberger/doc/steinberger_thermochemical_plume.prm](https://www.github.com/geodynamics/aspect/blob/main/cookbooks/multicomponent_steinberger/doc/steinberger_thermochemical_plume.prm).
+[cookbooks/multicomponent_steinberger/doc/steinberger_thermochemical_plume.prm](https://github.com/geodynamics/aspect/blob/main/cookbooks/multicomponent_steinberger/steinberger_thermochemical_plume.prm).
 
 ## Results
 

cookbooks/steinberger/doc/steinberger.md

@@ -337,7 +337,7 @@ provides the values that should be interpolated onto the field.
 ```
 
 The complete input file can be found in
-[cookbooks/steinberger/doc/steinberger.prm](https://www.github.com/geodynamics/aspect/blob/main/cookbooks/steinberger/doc/steinberger.prm).
+[cookbooks/steinberger/doc/steinberger.prm](https://www.github.com/geodynamics/aspect/blob/main/cookbooks/steinberger/steinberger.prm).
 
 ## Results
 

doc/sphinx/conf.py

@@ -106,3 +106,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 html_last_updated_fmt = ""
+
+linkcheck_allowed_redirects = {r'https://doi.org/*': r'https://*',
+                               r'https://youtu.be/*': r'https://youtube.com/*',
+                               r'https://www.github.com/*': r'https://github.com/*'}

doc/sphinx/references.bib

@@ -12170,7 +12170,7 @@ @article{dannberg:grain:size
   pages={3034--3061},
   year={2017},
   publisher={Wiley Online Library},
-  doi = {https://doi.org/10.1002/2017GC006944},
+  doi = {10.1002/2017GC006944},
   url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017GC006944},
   eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2017GC006944}
 }
@@ -12282,7 +12282,7 @@ @article{tian_et_al_2019
 number = {12},
 pages = {5667-5690},
 keywords = {thermodynamic parameterization, dehydration, decarbonation, carbon transport, open systems, subduction zone},
-doi = {https://doi.org/10.1029/2019GC008488},
+doi = {10.1029/2019GC008488},
 year = {2019}
 }
 
@@ -12376,7 +12376,7 @@ @article{neuharth:etal:2022
 number = {3},
 pages = {e2021TC007166},
 keywords = {rifts, fault network, surface processes, geodynamics},
-doi = {https://doi.org/10.1029/2021TC007166},
+doi = {10.1029/2021TC007166},
 url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021TC007166},
 eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021TC007166},
 note = {e2021TC007166 2021TC007166},

doc/sphinx/user/answers.md

@@ -16,8 +16,8 @@ resources:
     library (the dependency on Trilinos and p4est is primarily through
     deal.II, and not directly visible in the
     ASPECT source code). If you have particular
-    questions about deal.II, contact the mailing lists described at
-    <https://www.dealii.org/mail.html>.
+    questions about deal.II, use the official mailing list
+    linked at <https://dealii.org/getting_help/contact/>.
 
 -   In case of more general questions about mantle convection, you can ask on
     the CIG mantle convection forum at

doc/sphinx/user/extending/index.md

@@ -95,7 +95,7 @@ which there is an extensive amount of documentation:
     deal.II does.
 
 -   A collection of modules at
-    <https://www.dealii.org/developer/doxygen/deal.II/modules.html> that give
+    <https://www.dealii.org/developer/doxygen/deal.II/topics.html> that give
     an overview of whole groups of classes and functions and how they work
     together to achieve their goal.
 

doc/sphinx/user/run-aspect/visualizing-results/index.md

@@ -10,10 +10,10 @@ latter, see {ref}`sec:extending:vis-postprocessors`).
 
 By default, the files that are generated are in VTU format, i.e., the
 XML-based, compressed format defined by the VTK library, see
-<http://vtk.org/>. This file format has become a broadly
+<https://vtk.org>. This file format has become a broadly
 accepted pseudo-standard that many visualization program support, including
 two of the visualization programs used most widely in computational science:
-VisIt (see <https://visit.llnl.gov/>) and ParaView (see
+VisIt (see <https://visit-dav.github.io/visit-website/>) and ParaView (see
 <http://www.paraview.org/>). The VTU format has a number of advantages beyond
 being widely distributed: