diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index c5870874700..bf6e8dd8302 100644 --- a/CONTRIBUTING.md +++ b/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) diff --git a/cookbooks/geomio/doc/geomio.md b/cookbooks/geomio/doc/geomio.md index 49d69a2e04c..a92556a9073 100644 --- a/cookbooks/geomio/doc/geomio.md +++ b/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 (, {cite}`bauville:baumann:2019` provides a convenient tool to convert a drawing generated with the vector graphics -editor Inkscape () to a data file that can be read +editor Inkscape () 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: diff --git a/cookbooks/multicomponent_steinberger/doc/multicomponent_steinberger.md b/cookbooks/multicomponent_steinberger/doc/multicomponent_steinberger.md index 9feaf25bbd4..52512608f9f 100644 --- a/cookbooks/multicomponent_steinberger/doc/multicomponent_steinberger.md +++ b/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 diff --git a/cookbooks/steinberger/doc/steinberger.md b/cookbooks/steinberger/doc/steinberger.md index 02093124f83..437f25f59d0 100644 --- a/cookbooks/steinberger/doc/steinberger.md +++ b/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 diff --git a/doc/sphinx/conf.py b/doc/sphinx/conf.py index f0a68b05a01..981031c514c 100644 --- a/doc/sphinx/conf.py +++ b/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/*'} diff --git a/doc/sphinx/references.bib b/doc/sphinx/references.bib index b3eda9e8c09..d5253c66cb2 100644 --- a/doc/sphinx/references.bib +++ b/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}, diff --git a/doc/sphinx/user/answers.md b/doc/sphinx/user/answers.md index 445e9456cc9..62f153e4c29 100644 --- a/doc/sphinx/user/answers.md +++ b/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 - . + questions about deal.II, use the official mailing list + linked at . - In case of more general questions about mantle convection, you can ask on the CIG mantle convection forum at diff --git a/doc/sphinx/user/extending/index.md b/doc/sphinx/user/extending/index.md index f7cd4c6564f..5729c445909 100644 --- a/doc/sphinx/user/extending/index.md +++ b/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 - that give + that give an overview of whole groups of classes and functions and how they work together to achieve their goal. diff --git a/doc/sphinx/user/run-aspect/visualizing-results/index.md b/doc/sphinx/user/run-aspect/visualizing-results/index.md index e703d9e6260..e98630d9a34 100644 --- a/doc/sphinx/user/run-aspect/visualizing-results/index.md +++ b/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 -. This file format has become a broadly +. 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 ) and ParaView (see +VisIt (see ) and ParaView (see ). The VTU format has a number of advantages beyond being widely distributed: