Merge branch 'docs_update_Dec2021' into 'master'

Documentation update Dec 2021

See merge request !417

.gitlab/merge_request_templates/Code Approval.md

 Issues: Closes #.... 
 
-The code approval procedure is described in the wiki: [Code approval procedure wiki](https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/-/wikis/Code-Approval-Procedure)
+The code approval procedure is described in the wiki: [Code approval procedure wiki](https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/-/wikis/Code-Approval-Procedure)
 
 - [ ] The MR is without `WIP/Draft` status
 - [ ] Make sure the most recent CI jobs (config, quality, build_test_example) all run fine with no failures

README.md

@@ -14,7 +14,7 @@ decision of the user must be performed at compile time. At run time
 model parameters can still be changed.
 
 CORSIKA 8 is by default released under the GPLv3 license. See [license
-file](https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/LICENSE)
+file](https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/LICENSE)
 which is part of every release and the source code.
 
 If you use, or want to refer to, CORSIKA 8 please cite ["Towards a Next
@@ -27,7 +27,7 @@ whole community.
 
 When you plan to contribute to CORSIKA 8 check the guidelines outlined here:
 [coding
-guidelines](https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/CONTRIBUTING.md). Code
+guidelines](https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/CONTRIBUTING.md). Code
 that fails the review by the CORSIKA author group must be improved
 before it can be merged in the official code base. After your code has
 been accepted and merged, you become a contributor of the CORSIKA 8
@@ -35,14 +35,14 @@ project (code author).
 
 IMPORTANT: Before you contribute, you need to read and agree to the
 [collaboration
-agreement](https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/COLLABORATION_AGREEMENT.md). The agreement can be discussed, and eventually improved.
+agreement](https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/COLLABORATION_AGREEMENT.md). The agreement can be discussed, and eventually improved.
 
 We also want to point you to the [MCnet
-guidelines](https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/MCNET_GUIDELINES), which are very useful also for us.
+guidelines](https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/MCNET_GUIDELINES), which are very useful also for us.
 
 
 ## Get in contact
-  * Connect to https://gitlab.ikp.kit.edu register yourself and join the "Air Shower Physics" group. Write to me (ralf.ulrich@kit.edu) only in case there are problems with that. 
+  * Connect to https://gitlab.iap.kit.edu register yourself and join the "Air Shower Physics" group. Write to me (ralf.ulrich@kit.edu) only in case there are problems with that. 
   * Connect to corsika-devel@lists.kit.edu (self-register at
     https://www.lists.kit.edu/sympa/subscribe/corsika-devel) to get in
     touch with the project.
@@ -88,7 +88,7 @@ pip install --user conan
 Once Conan is installed, follow these steps to download and install CORSIKA 8:
 
 ``` shell
-git clone --recursive git@gitlab.ikp.kit.edu:AirShowerPhysics/corsika.git
+git clone --recursive git@gitlab.iap.kit.edu:AirShowerPhysics/corsika.git
 mkdir corsika-build
 cd corsika-build
 cmake ../corsika -DCMAKE_INSTALL_PREFIX=../corsika-install
@@ -109,7 +109,7 @@ You only need docker, e.g. on Ubunut: `sudo apt-get install docker` and of cours
 
 Follow these steps to download and install CORSIKA 8, master development version
 ```shell
-git clone --recursive https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika.git
+git clone --recursive https://gitlab.iap.kit.edu/AirShowerPhysics/corsika.git
 sudo docker run -v $PWD:/corsika -it corsika/devel:clang-8 /bin/bash
 mkdir build
 cd build

README.rst

@@ -15,7 +15,7 @@ decision of the user must be performed at compile time. At run time
 model parameters can still be changed.
 
 CORSIKA 8 is by default released under the GPLv3 license. See `license
-file <https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/LICENSE>`_
+file <https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/LICENSE>`_
 which is part of every release and the source code.
 
 If you use, or want to refer to, CORSIKA 8 please cite `"Towards a Next
@@ -28,7 +28,7 @@ whole community.
 
 When you plan to contribute to CORSIKA 8 check the guidelines outlined here:
 `coding
-guidelines <https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/CONTRIBUTING.md>`_. Code
+guidelines <https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/CONTRIBUTING.md>`_. Code
 that fails the review by the CORSIKA author group must be improved
 before it can be merged in the official code base. After your code has
 been accepted and merged, you become a contributor of the CORSIKA 8
@@ -36,17 +36,17 @@ project (code author).
 
 IMPORTANT: Before you contribute, you need to read and agree to the
 `collaboration agreement
-<https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/COLLABORATION_AGREEMENT.md>`_. The
+<https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/COLLABORATION_AGREEMENT.md>`_. The
 agreement can be discussed, and eventually improved.
 
 We also want to point you to the `MCnet guidelines
-<https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/blob/master/MCNET_GUIDELINES>`_,
+<https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/blob/master/MCNET_GUIDELINES>`_,
 which are very useful also for us.
 
 
 Get in contact
 --------------
-  * Connect to https://gitlab.ikp.kit.edu register yourself and join the "Air Shower Physics" group. Write to me (ralf.ulrich@kit.edu) only in case there are problems with that. 
+  * Connect to https://gitlab.iap.kit.edu register yourself and join the "Air Shower Physics" group. Write to me (ralf.ulrich@kit.edu) only in case there are problems with that. 
   * Connect to corsika-devel@lists.kit.edu (self-register at
     https://www.lists.kit.edu/sympa/subscribe/corsika-devel) to get in
     touch with the project.
@@ -94,7 +94,7 @@ Compiling
 Once Conan is installed, follow these steps to download and install CORSIKA 8:
 ::
    
-  git clone --recursive git@gitlab.ikp.kit.edu:AirShowerPhysics/corsika.git
+  git clone --recursive git@gitlab.iap.kit.edu:AirShowerPhysics/corsika.git
   mkdir corsika-build
   cd corsika-build
   cmake ../corsika -DCMAKE_INSTALL_PREFIX=../corsika-install
@@ -118,7 +118,7 @@ Compiling
 Follow these steps to download and install CORSIKA 8, master development version
 ::
    
-  git clone --recursive https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika.git
+  git clone --recursive https://gitlab.iap.kit.edu/AirShowerPhysics/corsika.git
   sudo docker run -v $PWD:/corsika -it corsika/devel:clang-8 /bin/bash
   mkdir build
   cd build

corsika/detail/modules/energy_loss/BetheBlochPDG.inl

@@ -144,7 +144,7 @@ namespace corsika {
                                                             bool const) {
 
     // if this step was limiting the CORSIKA stepping, the particle is lost
-    /* see Issue https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/-/issues/389
+    /* see Issue https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/-/issues/389
     if (limitStep) {
       fillProfile(t, p.getEnergy());
       p.setEnergy(p.getMass());

corsika/detail/modules/pythia8/Interaction.inl

@@ -39,7 +39,7 @@ namespace corsika::pythia8 {
     Pythia8::Pythia::readString("Check:event = on");             // default: on
     Pythia8::Pythia::readString("Check:levelParticleData = 12"); // 1 is default
     /** \TODO: proper process initialization for MinBias needed, see
-        also Issue https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/-/issues/369 **/
+        also Issue https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/-/issues/369 **/
     Pythia8::Pythia::readString("HardQCD:all = on");
     Pythia8::Pythia::readString("ProcessLevel:resonanceDecays = off");
 

corsika/modules/ObservationPlane.hpp

@@ -27,7 +27,7 @@ namespace corsika {
    * The default output format is parquet.
    *
    * **Note/Limitation:** as discussed in
-   * https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/-/issues/397
+   * https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/-/issues/397
    * you cannot put two ObservationPlanes exactly on top of each
    * other. Even if one of them is "permeable". You have to put a
    * small gap in between the two plane in such a scenario, or develop

do-clang-format.py

 #!/usr/bin/env python3
+
+#
+# (c) Copyright 2020 CORSIKA Project, corsika-project@lists.kit.edu
+#
+# This software is distributed under the terms of the GNU General Public
+# Licence version 3 (GPL Version 3). See file LICENSE for a full version of
+# the license.
+#
+
 """
 Run clang-format with the style file in the CORSIKA repository.
 
-By default it finds new files and files with modifications with respect to the current master and prints the filenames which need clang-formatting. Returns 1 if there are files which need modifications and 0 otherwise, so it can be used as a test.
+By default it finds new files and files with modifications with respect 
+to the current master and prints the filenames which need clang-formatting. 
+Returns 1 if there are files which need modifications and 0 otherwise, 
+so it can be used as a test.
 """
+
 import argparse
 import subprocess as subp
 import os

do-copyright.py

 #!/usr/bin/env python3
 
+#
+# (c) Copyright 2020 CORSIKA Project, corsika-project@lists.kit.edu
+#
+# This software is distributed under the terms of the GNU General Public
+# Licence version 3 (GPL Version 3). See file LICENSE for a full version of
+# the license.
+#
+
+"""
+Script to crawl all files (hpp,inl,cpp) in a directory structure and
+check if there is an initial comment block within each file that
+resembles the CORSIKA 8 copyright notice.
+
+Exceptions can be specified in `excludeDirs` and `excludedFiles`.
+"""
+
+
 import os
 import sys, getopt
 import re

documentation/conf.py

+#
+# (c) Copyright 2020 CORSIKA Project, corsika-project@lists.kit.edu
+#
+# This software is distributed under the terms of the GNU General Public
+# Licence version 3 (GPL Version 3). See file LICENSE for a full version of
+# the license.
+#
+
+"""
+Readthedocs script to build documentation remotely.
+"""
+
 import sys
 import subprocess, os
 

documentation/corsika.dox

@@ -5,12 +5,12 @@
 Software documentatin and reference guide for the CORSIKA 8
 software framework for air shower simulations. CORSIKA 8 is developed
 at <a
-href="https://gitlab.ikp.kit.edu/AirShowerPhysics">https://gitlab.ikp.kit.edu</a>. If
+href="https://gitlab.iap.kit.edu/AirShowerPhysics">https://gitlab.iap.kit.edu</a>. If
 you got the code from somewhere else, consider to switch to the
 official development repository. If you want to report bugs, or want
 to suggest features or future development, please submit an "issue" on
 this gitlab server. We only accept Issues and discussion via our
-central development server https://gitlab.ikp.kit.edu.
+central development server https://gitlab.iap.kit.edu.
 
 Write to corsika-devel@lists.kit.edu, or even register yourself at
 https://www.lists.kit.edu/sympa/info/corsika-devel to get in contact

python/README.md

@@ -3,6 +3,6 @@
 To install this into your global environment using `pip` (not recommended), run
 
 ``` shell
-pip install --user git+https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/-/tree/master/python 
+pip install --user git+https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/-/tree/master/python 
 ```
 

python/setup.py

@@ -18,7 +18,7 @@ setup(
     description="A Python package for working with CORSIKA 8.",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    url="https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika",
+    url="https://gitlab.iap.kit.edu/AirShowerPhysics/corsika",
     author="CORSIKA 8 Collaboration",
     author_email="corsika-devel@lists.kit.edu",
     classifiers=[
@@ -46,6 +46,6 @@ setup(
         "pandas": ["pandas"],
     },
     scripts=[],
-    project_urls={"code": "https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika"},
+    project_urls={"code": "https://gitlab.iap.kit.edu/AirShowerPhysics/corsika"},
     include_package_data=False,
 )

src/corsika.hpp.in

@@ -26,11 +26,11 @@ namespace corsika {
    * Software documentatin and reference guide for the CORSIKA 8
    * software framework for air shower simulations. CORSIKA 8 is developed
    * at <a
-   * href="https://gitlab.ikp.kit.edu/AirShowerPhysics">https://gitlab.ikp.kit.edu</a>. If
+   * href="https://gitlab.iap.kit.edu/AirShowerPhysics">https://gitlab.iap.kit.edu</a>. If
    * you got the code from somewhere else, consider to switch to the official development
    * repository. If you want to report bugs, or want to suggest features or future
    * development, please submit an "issue" on this gitlab server. We only accept Issues
-   * and discussion via our central development server https://gitlab.ikp.kit.edu.
+   * and discussion via our central development server https://gitlab.iap.kit.edu.
    *
    * Write to corsika-devel@lists.kit.edu, or even register yourself at
    * https://www.lists.kit.edu/sympa/info/corsika-devel to get in contact

tests/modules/testSibyll.cpp

@@ -224,7 +224,7 @@ TEST_CASE("SibyllInterface", "modules") {
       See also:
 
       Issue 272 / MR 204
-      https://gitlab.ikp.kit.edu/AirShowerPhysics/corsika/-/merge_requests/204
+      https://gitlab.iap.kit.edu/AirShowerPhysics/corsika/-/merge_requests/204
 
     */