Merge pull request CRPropa#420 from lukasmerten/documentation

Documentation

.github/workflows/testing.yml

@@ -15,13 +15,6 @@ jobs:
            fc: "gfortran-9"
            swig_builtin: "Off" #uses swig 4.0.1
            py: "/usr/bin/python3" #python 3.8
-         - name: "ubuntu-18_py2"
-           os: ubuntu-18.04
-           cxx: "g++-7"
-           cc: "gcc-7"
-           fc: "gfortran-7"
-           swig_builtin: "Off" #uses swig 3.x
-           py: "/usr/bin/python2"
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3

CHANGELOG.md

@@ -1,6 +1,7 @@
-# CRPropa NEXT
+# CRPropa vNext
 
 ### Bug fixes:
+* Re-added ToroidalHaloField and LogarithmicSpiralField models. Note, that the class name was also corrected in spelling: TorroidalHaloField --> ToroidalHaloField
 * Synchronized signature of ParticleSplitting constructor
 
 ### New features:
@@ -13,6 +14,8 @@
 * Weight column in hdf-Output is now called "W", which is the same as for TextOutput.
 
 ### Features that are deprecated and will be removed after this release
+* ObserverPoint will be renamed into Observer1D.
+* AMRMagenticField - underlying library (saga) is no longer supported.
 
 ### New plugins and resources linked on the webpages:
 

CMakeLists.txt

@@ -118,7 +118,7 @@ if(ENABLE_COVERAGE)
   find_program(LCOV_PATH lcov)
   find_program(GENHTML_PATH genhtml)
   if(LCOV_PATH AND GENHTML_PATH)
-    message("Enabling coverage report via $make coverage")
+    message("Enabling coverage report via $make test && make coverage")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
     list(APPEND CRPROPA_EXTRA_LIBRARIES "-lgcov")
     list(APPEND CRPROPA_EXTRA_LIBRARIES "-fprofile-arcs")

README.md

@@ -50,9 +50,9 @@ a mail with subject: subscribe crpropa-user to [email protected] from the address
 you wish to subscribe.
 
 ## How to cite CRPropa
-If you use CRPropa 3 for your research, please cite
+If you use CRPropa 3.2 for your research, please cite
 
-**JCAP 1605 (2016) no. 05, 038; [arXiv:1603.07142](https://arxiv.org/abs/1603.07142)**
+**JCAP (2022) no. 09, 035; [arXiv:2208.00107](https://arxiv.org/abs/2208.00107)**
 
 as well as [additional publications](https://crpropa.github.io/CRPropa3/pages/howto_cite_crpropa.html) dependent on the components you are using.
 

doc/conf.py

@@ -118,7 +118,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+#html_static_path = ['_static']
 html_js_files = [
         'js/breathe_fold.js',
 ]

doc/index.rst

@@ -24,7 +24,7 @@ Contents
 
    pages/Basic-concepts.md
    pages/Simulation-Modules.md
-   pages/example_notebooks/basics/basics.v4.ipynb
+   pages/example_notebooks/basics/basics.ipynb
    pages/extragalactic-simulations.rst
    pages/galactic_lensing.rst
    pages/galactic_cosmic_rays.rst

doc/pages/AdditionalResources.rst

@@ -2,24 +2,24 @@ Additional Resources
 --------------------
 
 -  The Galactic magnetic field lenses can be downloaded
-   `here <https://desycloud.desy.de/index.php/s/7sYqEWncD6Mp6cz>`__ .
+   `here <https://syncandshare.desy.de/index.php/s/ReEXpW7Lngbn2j3>`__ .
 -  The multi-resolution 'Dolag' extragalactic magnetic field, using
-   `Quimby <https://git.rwth-aachen.de/3pia/forge/quimby>`__, can be
+   `Quimby <https://github.com/CRPropa/Quimby>`__, can be
    downloaded
-   `here <https://desycloud.desy.de/index.php/s/Sf4NDbAsLs5wa7A>`__
+   `here <https://syncandshare.desy.de/index.php/s/StYK4jqcXMtgbZG>`__
 -  The 'Miniati', 'Dolag' and 'Benchmark' extragalactic magnetic field
-   models on regular grids are available
-   `here <https://desycloud.desy.de/index.php/s/Sf4NDbAsLs5wa7A>`__ and the
+   models on regular grids are available in the same directory
+   `here <https://syncandshare.desy.de/index.php/s/StYK4jqcXMtgbZG>`__ and the
    corresponding large-scale structure density fields can be downloaded
-   `here <https://desycloud.desy.de/index.php/s/tbtgxzwLzBLFxjZ>`__.
+   `here <https://syncandshare.desy.de/index.php/s/7a948NZT98fP77Q>`__.
 -  Data for the constrained `'Hackstein'
    models <https://arxiv.org/abs/1710.01353>`__ of the local Universe
    using initial conditions from the `CLUES
    project <https://arxiv.org/abs/1510.04900>`__ can be downloaded
-   `here <https://desycloud.desy.de/index.php/s/AZRNTZaPMZYsFAQ>`__.
+   `here <https://syncandshare.desy.de/index.php/s/6HbWrBZeQtQ5t4c>`__.
 -  Data for the strong extragalactic magnetic fields by `Alves Batista  et al. 
    <https://arxiv.org/abs/1704.05869>`__ can be downloaded
-   `here <https://desycloud.desy.de/index.php/s/fgbHxLtezwHcf33>`__.
+   `here <https://syncandshare.desy.de/index.php/s/Fo5xceXtwtk5Exo>`__.
 
 
 Note that these resources are completely external to CRPropa. We cannot supply any kind of additional information nor can we offer support on how to use them.

doc/pages/Code-Coverage.md

@@ -15,4 +15,4 @@ make test
 ```
 make coverage
 ```
-The final report is in ```coverageReport/index.html```
+The final report is in ```~/build/coverageReport/index.html```

doc/pages/Cpp-projects.md

@@ -23,7 +23,7 @@ int main(void) {
         sim.add(new MinimumEnergy(1*EeV));
 
         ref_ptr<Observer> obs = new Observer();
-        obs->add(new ObserverPoint());
+        obs->add(new Observer1D());
         obs->onDetection(new TextOutput("events.txt", Output::Event1D));
         obs->onDetection(new TextOutput());
         sim.add(obs);

doc/pages/Debugging.md

@@ -98,7 +98,7 @@ Valgrind is run as follows:
 valgrind --tool=callgrind python steering_card.py
 ```
 ### References
-* [KCachegrind Manual](https://docs.kde.org/stable4/en/kdesdk/kcachegrind/kcachegrind.pdf)
+* [KCachegrind Manual](https://docs.kde.org/stable5/en/kcachegrind/kcachegrind/kcachegrind.pdf)
 * [Callgrind manual](http://valgrind.org/docs/manual/cl-manual.html)
 * [GCC debugging options](https://gcc.gnu.org/onlinedocs/gcc-3.4.5/gcc/Debugging-Options.html)
 * [Python profiling](http://www.blog.pythonlibrary.org/2014/03/20/python-102-how-to-profile-your-code/)

doc/pages/FAQ.md

@@ -37,7 +37,7 @@ Out[20]: 0.37454011439684315
 ### How to define source positions from a matter density grid?
 
 ```python
-grid = ScalarGrid(Vector3d(0, 0, 0), 256, 256, 256, 100 * kpc)
+grid = Grid(Vector3d(0, 0, 0), 256, 100 * kpc)
 loadGridFromTxt(grid, 'some_density_grid.txt')
 #loadGrid(grid, 'some_density_grid.raw')
 density = crpropa.SourceDensityGrid(grid)