dumux issueshttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues2024-02-28T10:42:39Zhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1346[doc] fix as much typos as possible unto next release2024-02-28T10:42:39ZKai Wendel[doc] fix as much typos as possible unto next release**Description**
when one reads through the DuMux core codes comments and other documentation, one can find sometimes comments that are obviously not correctly describing the underlining code, or there are typos. It would be worth to try...**Description**
when one reads through the DuMux core codes comments and other documentation, one can find sometimes comments that are obviously not correctly describing the underlining code, or there are typos. It would be worth to try keeping this as tidy as we could as typos and incorrect comments are limiting the readability.
It is worth the effort, to fix as much obvious (and possbibly also some less obvious) typos or inconsistencies until the upcoming release.
Branch, that focuses on the `freeflow` part: [cleanup/smallCleanups](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/cleanup/smallCleanups?ref_type=heads). The changes are currently all limited to `freeflow`
Branch focusing on fluidsystems: [cleanup/fluidsAndFluidsystems](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/cleanup/fluidsAndFluidsystems?ref_type=heads)Kai WendelKai Wendelhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1337[doxygen] Erroneous processing of installation doc2024-01-09T09:00:28ZMaziar Veyskarami[doxygen] Erroneous processing of installation docIt seems that the script for cloning the DUNE modules on the website is displayed wrongly. It is
`for module in common geometry grid localfunctions istl; do
git clone -b releases/2.9 https://gitlab.dune-project.org/core/dune-\f$module...It seems that the script for cloning the DUNE modules on the website is displayed wrongly. It is
`for module in common geometry grid localfunctions istl; do
git clone -b releases/2.9 https://gitlab.dune-project.org/core/dune-\f$module.git
done`
It should be
`for module in common geometry grid localfunctions istl; do
git clone -b releases/2.9 https://gitlab.dune-project.org/core/dune-$module.git
done`
that means \f in front of $module is not necessary.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1314[doc][doxygen][pm] Effective diffusion2023-12-17T18:41:34ZTimo Kochtimokoch@math.uio.no[doc][doxygen][pm] Effective diffusionThe models with diffusion should explain that the diffusion coefficient is effective and refer to other places in the documentation that explains what type of laws are available. I think there could be a dedicated small page / doxygen gr...The models with diffusion should explain that the diffusion coefficient is effective and refer to other places in the documentation that explains what type of laws are available. I think there could be a dedicated small page / doxygen group for effective diffusion laws (take them out of the generic fluidmatrixinteraction)3.9Lars KaiserLars Kaiserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1313[doc][doxygen][pm] Time-dependent porosity2023-11-01T13:26:37ZTimo Kochtimokoch@math.uio.no[doc][doxygen][pm] Time-dependent porosityThe porous medium models are capable of handling evolving porosity. This should be reflected in the doxygen formulas.The porous medium models are capable of handling evolving porosity. This should be reflected in the doxygen formulas.3.9https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1312Better name for DualNetwork FancyFactor2023-10-30T15:06:50ZTimo Kochtimokoch@math.uio.noBetter name for DualNetwork FancyFactorThere is a type of heat conduction law called FancyFactor. We should find a better name.
Maybe HeatConductionWeighted or name it after the paper.
See !3682There is a type of heat conduction law called FancyFactor. We should find a better name.
Maybe HeatConductionWeighted or name it after the paper.
See !36823.8Anna Mareike KosteleckyAnna Mareike Kosteleckyhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1310Symbolic representation of div and grad2023-10-27T19:01:34ZIvan BunticSymbolic representation of div and gradIn our doxygen documentation, we use a written form of `grad` and `div`. Instead, symbolic representation of these operators would be nicer to look at. See [this equation](https://dumux.org/docs/doxygen/master/group___one_p_model.html) a...In our doxygen documentation, we use a written form of `grad` and `div`. Instead, symbolic representation of these operators would be nicer to look at. See [this equation](https://dumux.org/docs/doxygen/master/group___one_p_model.html) as an example.
!36753.8Leon KeimLeon Keimhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1307Update doxygen to 3.82023-10-27T20:40:04ZTimo Kochtimokoch@math.uio.noUpdate doxygen to 3.8For example, the installation instructions are now in doxygen and need updating:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/doc/doxygen/pages/installation.md?ref_type=headsFor example, the installation instructions are now in doxygen and need updating:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/doc/doxygen/pages/installation.md?ref_type=heads3.8Ivan BunticIvan Buntichttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1306Add variables description in equations2023-10-27T11:38:34ZYue Wangyue.wang@iws.uni-stuttgart.deAdd variables description in equationssee !3670see !36703.8Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1238Merge handbook into doxygen2023-06-28T23:07:28ZTimo Kochtimokoch@math.uio.noMerge handbook into doxygenIn order to have all documentation in one place, I suggest to merge the handbook into doxygen. This also allows to easily view everything online and improve searchability and cross-linking capabilities.
As far as I can see the handbook ...In order to have all documentation in one place, I suggest to merge the handbook into doxygen. This also allows to easily view everything online and improve searchability and cross-linking capabilities.
As far as I can see the handbook content is up-to-date and useful documentation. Currently, we have some sections doubled like the installation instructions. But also the advanced topic make sense for me in the doxygen documentation in the respective group, linked from the high-level documentation.
In case some people prefer PDF it is also possible to look into generating PDFs which doxygen from which the class docs could be excluded. Another possibility since all doc will be in markdown is to generate latex from selected markdown documents via pandoc. That way the sources are not doubled and the documentation will be easier to maintain and find.3.8https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1223Remove solver deprecation warnings2023-03-20T21:05:52ZTimo Kochtimokoch@math.uio.noRemove solver deprecation warnings* [ ] After merging !3386 there are deprecation warnings concerning the solvers for many test. The solvers should be updated to use the new IstlSolverBackend.* [ ] After merging !3386 there are deprecation warnings concerning the solvers for many test. The solvers should be updated to use the new IstlSolverBackend.3.7Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1204OpenSSF Best Practices2022-12-13T10:59:37ZBernd FlemischOpenSSF Best PracticesI added DuMux to OpenSSF Best practices: https://bestpractices.coreinfrastructure.org/en/projects/6768
Things look already quite good, but I didn't feel competent enough to address the criteria "Security" and "Analysis". We should
- [x...I added DuMux to OpenSSF Best practices: https://bestpractices.coreinfrastructure.org/en/projects/6768
Things look already quite good, but I didn't feel competent enough to address the criteria "Security" and "Analysis". We should
- [x] complete the evaluation form
- [x] add the badge to the repohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1194[examples] Review and improve new Example 9: Embedded network 1D-3D model2023-03-16T17:32:28ZTimo Kochtimokoch@math.uio.no[examples] Review and improve new Example 9: Embedded network 1D-3D modelSeveral sections are not super well documentation and some code snippets are fairly long. Not all files are documented (but this might be fine to not loose the focus on the main thing). The initial merge request has been merged without r...Several sections are not super well documentation and some code snippets are fairly long. Not all files are documented (but this might be fine to not loose the focus on the main thing). The initial merge request has been merged without review !3339 to make it immediately available. This issue is a reminder to complete the review.3.7Dennis GläserDennis Gläserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1184Improve doc of Riemann solver2023-12-13T11:13:10ZTimo Kochtimokoch@math.uio.noImprove doc of Riemann solverThere are some variables which use abbreviations. This might be justified to have it close to how the algorithm is described in a text book. But then all variablenames that are not self-explanatory shoild be documented for better maintai...There are some variables which use abbreviations. This might be justified to have it close to how the algorithm is described in a text book. But then all variablenames that are not self-explanatory shoild be documented for better maintainability of the code.
In case there is no correspondence to the textbook renaiming to self-explantory name is preferred (style guide)Leopold StadlerLeopold Stadlerhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1181Make doc on master fails2022-07-31T13:07:08ZDavid WernerMake doc on master fails**Bug report**
Running ``make doc`` to build the documentation fails.
**Problem description**:
The CI for building of the website failed, unfortunately I did not see any artifacts there,
which should be fixed too. I tried then subsequ...**Bug report**
Running ``make doc`` to build the documentation fails.
**Problem description**:
The CI for building of the website failed, unfortunately I did not see any artifacts there,
which should be fixed too. I tried then subsequently the build_documentation.sh from the CI in my local environment and
also manually ``make doc`` and also ``pdflatex`` direct onto ``0_dumux-handbook.tex`` in the ``dumux/doc/handbook`` directory.
**What you expected to happen**:
The pdf-file of the handbook should be build without errors. The return status of 'make doc' and 'pdflatex' should be 0.
For the ``make doc`` the process for building the doxygen-docs should be started after a clean build of the ``doc/handbook/0_dumux-handbook.pdf``.
**How to reproduce it**:
Checkout first appropriate dune-modules together with dumux master.
Do
```
./dune-common/bin/dunecontrol --opts=dumux/cmake.opts configure
cd dumux/build-cmake
make doc
echo $? # show the status of the last command in your shell.
```
Or a shortcut to see directly the latex problem do:
```
git clone https://git.iws.uni-stuttgart.de/dumux-repositories/dumux
cd dumux/doc/handbook
pdflatex 0_dumux-handbook.tex
```
**Anything else we need to know?**:
It looks like that ``dumux/build-cmake/doc/handbook/0_dumux-handbook.log`` indicates that there are latex-errors in
``dumux/doc/handbook/5_scripts.tex``. One can comment out the last section of this file and the 'make doc' succeeds to start doxygen.
**Environment**:
- Dune version: 2.8
- DuMux version: 81767483f9ed98b0468358d02c6ddbc0387c4095 (master from 2022-07-30)
- Others:
'pdfTeX 3.141592653-2.6-1.40.24 (TeX Live 2022/Arch Linux)'https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1149Documentation for flux headers2022-10-06T09:48:50ZTimo Kochtimokoch@math.uio.noDocumentation for flux headersAdd "physics" documentation (discretization-agnostic) for the fluxes (e.g. Darcy's law / Fick's law / ...).
This can then be referenced by the model documentation.
Todo:
- [x] Darcys law (!3177)
- [x] Ficks law (@leonidas, !3267 )
- [x]...Add "physics" documentation (discretization-agnostic) for the fluxes (e.g. Darcy's law / Fick's law / ...).
This can then be referenced by the model documentation.
Todo:
- [x] Darcys law (!3177)
- [x] Ficks law (@leonidas, !3267 )
- [x] Forchheimers law (@leonidas, !3231 )
- [x] Fouriers law (@leonidas, !3269 )
- [x] Hooks law (@leonidas, !3270 )
- [x] Maxwell Stefans law (@stefaniekiemle, !3297)
- [x] dispersion (@stefaniekiemle, !3299)
- [x] effective stress law (@leonidas, !3229 )
- [x] Shallowwater (@leopold.stadler , !3301 )
- [x] Shallowwaterviscous (@utz , !3301)
- [x] Fourierslaw non equilibrium (@stefaniekiemle, !3314 )3.6Theresa SchollenbergerTheresa Schollenbergerhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1144Cleanup model documentation2022-04-26T11:19:52ZTimo Kochtimokoch@math.uio.noCleanup model documentationThe doxygen model documentation (the part with the equations) shouldn't talk about discretization (or at least not a single discretization) because the discretization aspect is separate. If another discretization method becomes available...The doxygen model documentation (the part with the equations) shouldn't talk about discretization (or at least not a single discretization) because the discretization aspect is separate. If another discretization method becomes available updating the documentation is easily forgotten.
The following discussion from !3046 should be addressed:
- [ ] @timok started a [discussion](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/3046#note_74400): (+4 comments)
> ```suggestion:-0+0
> ```
> This is strictly speaking not part of the model, right?3.5Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1142Fix doxygen modules formatting2022-04-20T08:23:47ZMartin UtzFix doxygen modules formattingIn the doxygen documentation of the modules there is often a blank line missing between the `\brief` description and the rest of the description e.g.:
![Doxygen_modules](/uploads/e05205edfacf61396b7af220dcd66853/Doxygen_modules.PNG)
Wi...In the doxygen documentation of the modules there is often a blank line missing between the `\brief` description and the rest of the description e.g.:
![Doxygen_modules](/uploads/e05205edfacf61396b7af220dcd66853/Doxygen_modules.PNG)
Without the blank line doxygen takes the whole model description as `\brief`, which causes a duplication of the description and a missing full stop between the `\brief` description and the rest of the description:
![Doxygen](/uploads/870f463762d1829c2d753b7900228c20/Doxygen.PNG)3.5Martin UtzMartin Utzhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1140Improve documentation of shallow water model2022-04-19T14:51:54ZMartin UtzImprove documentation of shallow water modelThe documentation of the shallow water model (https://dumux.org/docs/doxygen/master/a18412.html) should be improved in the following points:
- [x] Add the viscous term to the documentation.
- [x] Improve the documentation of the source t...The documentation of the shallow water model (https://dumux.org/docs/doxygen/master/a18412.html) should be improved in the following points:
- [x] Add the viscous term to the documentation.
- [x] Improve the documentation of the source terms. Add units and explain the bottom friction term more comprehensively.3.5Martin UtzMartin Utzhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1139Geomechanics documentation is missing the equation overview2022-04-26T11:20:37ZTimo Kochtimokoch@math.uio.noGeomechanics documentation is missing the equation overviewThe current geomechanics models don't state the implemented equations in doxygen.The current geomechanics models don't state the implemented equations in doxygen.3.5Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1131Doxygen for 3.52022-03-02T08:05:39ZMelanie LippDoxygen for 3.5Todos:
* [x] empty doxyerr.log as much as possible
* [x] Anything interesting to fix in doxygen.log?
There is a warning "warning: Tag 'COLS_IN_ALPHA_INDEX' at line 114 of file 'Doxyfile' has become obsolete." However, this concerns dune-...Todos:
* [x] empty doxyerr.log as much as possible
* [x] Anything interesting to fix in doxygen.log?
There is a warning "warning: Tag 'COLS_IN_ALPHA_INDEX' at line 114 of file 'Doxyfile' has become obsolete." However, this concerns dune-common/doc/doxygen/Doxystyle, not dumux.
* [x] does doc/doxygen/modules.txt match the folder structure?
* [x] Check for missing ingroup
* [x] Check for wrong ingroup
* [x] check correct display of the equations
* [x] correct linking of the sites (see sanitizelinks.sh for previous fixes)
* [x] does work on the dumux website as well?
* [x] under Namespaces - Namespace List spot some undocumented classes
* [x] does the documentation make sense? spot mistakenly made copy& paste?
For possible reference of a future doxygen dude:
The documentation is built by running make doc in the dumux build folder.
One way to switch doxygen versions is to:
* download the doxygen git repository from https://github.com/doxygen/doxygen.git
* checkout the branch you want, e.g. Release_1_8_17
* the first time do: mkdir build, cd build, cmake -G "Unix Makefiles" ..
* always do in the doxygen build directory: make, sudo make install
* the first time do: export PATH=/usr/local/bin/doxygen:$PATH
* delete the dumux build folder and rerun dunecontrol for dumux ./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts --only=dumux all
After Changes in scr/doxygen.cpp delete the build folder an recreate it.
Related MRs: !3027, !30293.5Melanie LippMelanie Lipp