dumux merge requestshttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests2020-03-31T07:42:11Zhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1925[examples] Add statement at the beginning of autogenerated files2020-03-31T07:42:11ZTimo Kochtimokoch@math.uio.no[examples] Add statement at the beginning of autogenerated filesPrevent people from editing the autogenerated files directly. This actually happened before, see !1784.Prevent people from editing the autogenerated files directly. This actually happened before, see !1784.3.2Dennis GläserDennis Gläserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1909[readme] Add new paper and section "how to cite"2020-03-26T21:41:35ZTimo Kochtimokoch@math.uio.no[readme] Add new paper and section "how to cite"Fixes #842Fixes #8423.2Dennis GläserDennis Gläserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1911[git] Amend mailmap to contain actual mapping entries2020-03-26T21:32:17ZTimo Kochtimokoch@math.uio.no[git] Amend mailmap to contain actual mapping entriesEach line should map the second argument (email address or name+email address) to the first name+email address. If I understood it correctly.
I sorted alphabetically.
Works for me to produce a nice list with unique names for `git s...Each line should map the second argument (email address or name+email address) to the first name+email address. If I understood it correctly.
I sorted alphabetically.
Works for me to produce a nice list with unique names for `git shortlog -esn`.
(tested with git version 2.21.0)3.2Dennis GläserDennis Gläserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1908[doc] Advertise [[deprecated(msg)]] instead of old Dune macro2020-03-26T14:14:59ZTimo Kochtimokoch@math.uio.no[doc] Advertise [[deprecated(msg)]] instead of old Dune macroSry @nedc I think my comment on this line didn't get sent. Thanks for the awesome description!Sry @nedc I think my comment on this line didn't get sent. Thanks for the awesome description!3.2Ned ColtmanNed Coltmanhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1906[contributionguide] Description of backwards compatibility policy2020-03-26T13:56:39ZNed Coltman[contributionguide] Description of backwards compatibility policyfixes #818.
* [x] Describe general rule
* [x] Give examples of deprecation methods
* [x] Have someone else check the psuedocode deprecation examples.
* [x] Describe what to do if backwards compatibility is not feasible.
* [x]...fixes #818.
* [x] Describe general rule
* [x] Give examples of deprecation methods
* [x] Have someone else check the psuedocode deprecation examples.
* [x] Describe what to do if backwards compatibility is not feasible.
* [x] Add short description in README.md3.2Kilian WeishauptKilian Weishaupthttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1907[Readme] fix url links2020-03-26T11:28:15ZNed Coltman[Readme] fix url links* [x] fix broken lh2 link
* [x] fix broken wiki update links
* [x] fix broken lh2 link
* [x] fix broken wiki update links
3.2Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1897feature/improve-tracer-example-doc2020-03-19T16:58:00ZDennis Gläserfeature/improve-tracer-example-docThis contains some edits on the description of the single-phase tracer example.This contains some edits on the description of the single-phase tracer example.3.2Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1885[doc] Doxygen.2020-03-19T16:54:47ZMelanie Lipp[doc] Doxygen.3.2Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1888Feature/examples automate readme2020-03-17T09:01:20ZTimo Kochtimokoch@math.uio.noFeature/examples automate readmeFixes #824Fixes #8243.2Kilian WeishauptKilian Weishaupthttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1793Feature/doc parallel direct solver2019-12-17T14:30:39ZTimo Kochtimokoch@math.uio.noFeature/doc parallel direct solverFixes #785Fixes #7853.2Martin SchneiderMartin Schneiderhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1809[doc] Improve example readme2019-11-25T14:10:19ZTimo Kochtimokoch@math.uio.no[doc] Improve example readme3.2https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1800[doc] Correct typos in comments2019-11-19T22:31:38ZKai Wendel[doc] Correct typos in comments3.2https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1758[doc] Update CHANGELOG.md2019-10-11T16:15:01ZTimo Kochtimokoch@math.uio.no[doc] Update CHANGELOG.md3.2Katharina HeckKatharina Heckhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1757[doc] Update dune.module to version 3.2-git2019-10-11T16:14:23ZTimo Kochtimokoch@math.uio.no[doc] Update dune.module to version 3.2-git3.2Katharina HeckKatharina Heckhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1736Docu/doxygen instructions2019-10-08T13:32:26ZSina AckermannDocu/doxygen instructionsCopied Simon's doxygen clean-up instructions from !1351 to a new README.md
The respective link in the styleguide points to the master branch and does not work right now.Copied Simon's doxygen clean-up instructions from !1351 to a new README.md
The respective link in the styleguide points to the master branch and does not work right now.3.1Katharina HeckKatharina Heckhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1690Feature/example shallow water2019-10-08T07:30:02ZMartin UtzFeature/example shallow water3.1Katharina HeckKatharina Heckhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1351Cleanup/doxygen for 3.02019-10-07T16:11:27ZSimon EmmertCleanup/doxygen for 3.0When checking doxygen, the doxygen should be built and the doxyerr.log should have as little lines/errors as possible. We currently have around 1800 lines of errors and want to reduce this to 1 to 7 lines.
The Doxygen for a **file** sh...When checking doxygen, the doxygen should be built and the doxyerr.log should have as little lines/errors as possible. We currently have around 1800 lines of errors and want to reduce this to 1 to 7 lines.
The Doxygen for a **file** should look like this:
```
/*!
* \file
* \ingroup Common
* \brief Manages the handling of time dependent problems
*/
```
It should always contain the `\file` first.
The `\ingroup` gives a Group that is as **precise** as possible and is part of the `modules.txt`
The `\brief` is a **short comment** on what happens in the file. Alternatively a `\copybrief` could be used. **Make sure the copybrief links to the correct section and is not ambigous!**
Additional text could be added similar to the function description.
A class could look like this:
```
/*!
* \ingroup Common
* \brief Manages the handling of time dependent problems.
*
* This class facilitates the time management of the simulation.
* It doesn't manage [...]
* [...]
* [...] index starting at 0.
*
* \note Time and time step sizes are in units of seconds
*/
```
The class should always have the proper `\ingroup` just like the file.
The `\brief` should always contain a **short description**, and only in very very rare occasions a class can have a `\copybrief`. In the end this is also documentation for users that do not build doxygen and `\copybriefs` from another file are most likely not very useful.
The main part should be an in depth explanation of what is done. This should contain math-expressions where applicable. They can look like the following:
```
* This class implements a spline \f$s(x)\f$ for which, given \f$n\f$ sampling
* points \f$x_1, \dots, x_n\f$, the following conditions hold
*\f{align*}{
s(x_i) & = y_i \quad \forall i \in \{1, \dots, n \}\\
s'(x_1) & = m_1 \\
s'(x_n) & = m_n
\f}
*
```
For a **function** in a file the Doxygen can look like this:
```
/*!
* \brief Set the current simulated time and the time step index.
*
* \param t The time \f$\mathrm{[s]}\f$ which should be jumped to
* \param stepIdx The new time step index
*/
void setTime(Scalar t, int stepIdx)
{ time_ = t; timeStepIdx_ = stepIdx; }
```
The function has a **short comment** with the `\brief`.
If there are **function-arguments** that are not self-explanatory, they should be described using `\param`.** Always explain all params or no params at all!** Otherwise Doxygen will throw an error.
Additional Doxygen-commands that might be useful are `\note` for giving an important note/hint on what the function does as well as `\return` which specifies the return value (if applicable).
We will go through the errors according to folders:
* [x] freeflow (262) @nedc
* [x] material (209) @ackerm
* [x] multidomain (168)
* [x] porousmediumflow (558) @scholz
* [x] common, discretization, geomechanics @hommel
* [ ] nonlinear,io,linear, material, nonlinear, parallel
Fix/Document everything according to the guideline. If there is a problem with a copybrief try to fix it or contact @scholz for help.
Closes #5963.0https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1547[examples] Set up problem for documentation (2p, adaptive, point source)2019-10-07T15:03:48ZSina Ackermann[examples] Set up problem for documentation (2p, adaptive, point source)3.1Katharina HeckKatharina Heckhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1721[doxygen] remove all sources of warnings, if easily possible2019-10-02T06:55:31ZBeatrix Becker[doxygen] remove all sources of warnings, if easily possibleChanges only affect documentation, should be possible to merge once todos are removed. @DennisGlaeser : I introduced 3-4 todos when I encountered variables that I don't know the purpose of. Could you clarify this or if you have no time p...Changes only affect documentation, should be possible to merge once todos are removed. @DennisGlaeser : I introduced 3-4 todos when I encountered variables that I don't know the purpose of. Could you clarify this or if you have no time point me to someone who can?
Note: This does not solve all problems with doxygen. I'm going to open an issue to ask for help with the rest of the warnings.3.1Katharina HeckKatharina Heckhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/1685[readme] Fix coverage link2019-08-06T08:46:28ZTimo Kochtimokoch@math.uio.no[readme] Fix coverage link3.1Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.no