matthewfeickert
commented
2 years ago These comments are a follow up to my review on 2022-01-17 (https://github.com/openjournals/joss-reviews/issues/3993#issuecomment-1015075303) and pertain to release v1.4.0 of the software.
Notes on completion of previous recommendations
- [x] Change the
Makefileto remove targeting/usr/localas a default. In many situations this is an unwritable location for users.
The change to CMake looks great and you have nice clean out-of-source builds now! :+1:
Example in Docker container:
```console $ docker run --rm -ti -v $PWD:$PWD -w $PWD atlasamglab/stats-base:root6.24.06 root@ce876ebc60e7:/tmp/JOSS# git clone --depth 1 https://github.com/villano-lab/nrCascadeSim.git --branch v1.4.0 --single-branch root@ce876ebc60e7:/tmp/JOSS# cmake -DCMAKE_INSTALL_PREFIX=/usr/local/venv -S nrCascadeSim -B build # Using /usr/local/venv as it is already on PATH root@ce876ebc60e7:/tmp/JOSS# cmake build -LH root@ce876ebc60e7:/tmp/JOSS# cmake \ --build build \ --clean-first \ --parallel $(($(nproc) - 1)) root@ce876ebc60e7:/tmp/JOSS# ls -lhtra build/ total 196K drwxrwxr-x 4 1000 1000 4.0K Feb 19 03:50 .. -rw-r--r-- 1 root root 19K Feb 19 03:50 CMakeCache.txt -rw-r--r-- 1 root root 5.7K Feb 19 03:50 cmake_install.cmake -rw-r--r-- 1 root root 23K Feb 19 03:50 Makefile -rwxr-xr-x 1 root root 25K Feb 19 03:50 regexPlayground drwxr-xr-x 2 root root 4.0K Feb 19 03:50 lib drwxr-xr-x 4 root root 4.0K Feb 19 03:50 . -rwxr-xr-x 1 root root 99K Feb 19 03:50 realizeCascades drwxr-xr-x 15 root root 4.0K Feb 19 03:50 CMakeFiles root@ce876ebc60e7:/tmp/JOSS# cmake --build build --target install root@ce876ebc60e7:/tmp/JOSS# command -v realizeCascades /usr/local/venv/bin/realizeCascades root@ce876ebc60e7:/tmp/JOSS# realizeCascades --help Usage: (null) options [ inputfile(s) ] -d, --seedSmall note: The v1.4.0 Download & Build docs suggest to use the legacy in source build pattern and to change to Make right away
mkdir -p /path/to/build
cd /path/to/build
cmake -DCMAKE_INSTALL_PREFIX=/path/to/install /path/to/source
makeWhile not wrong, the legacy pattern isn't needed and even on old/stability focused operating systems like CentOS 7 in almost every situation in which software development is happening you'll have access to devtoolset-7 or newer in which cmake(3) is available. So I'd recommend using the pattern of
$ cmake <options> -S <path to source> -B <path to build directory to make>
$ cmake <path to build directory> -LH # See all of the options you've selected in a human readable form before build
$ cmake --build <path to build directory> --clean-first --parallel $(($(nproc) - 1))as this gives the benefits of out-of-source builds, more transparency on what is happening, and allows for other build systems to be used other than Make (e.g. Ninja).
For more on this please see the book An Introduction to Modern CMake by Henry Schreiner.
c.f. https://github.com/villano-lab/nrCascadeSim/issues/101
- [x] Add removal of the
.gcnoand.gcdafiles generated during the build to thecleanMake target. - [x] Remove recommendations of use of
sudoto install software.
Note that the v1.4.0 Executables of nrCascadeSim docs still have one final instance of advocating for using sudo make that can be cleaned up. Otherwise great!
c.f. https://github.com/villano-lab/nrCascadeSim/issues/102
- [x] Add at least one regression test to the test suite and plan to add more in the future.
- [x] In the State of the Field section it would be beneficial to mention that
Geant4is open source software and to clarify ifFIFRELINis open source or not.
It would have been nice to clarify the FIFRELIN isn't an open source project, but I think the comparison that was done to Geant4 v10.7.3 is quite nice to have. :tada:
Summary
@lucydot I am very impressed with the work that the team has done and I would give my full recommendation for publication with JOSS. I have opened two final GitHub issues as suggestions to the team for work in the future, but they should not be considered as further work for them to address in the review. :+1:
villaa
lucydot
whedon
arfon
editorialbot
nuclearGoblin
Submitting author: !--author-handle-->@villaa<!--end-author-handle-- (Anthony Villano) Repository: https://github.com/villano-lab/nrCascadeSim Branch with paper.md (empty if default branch): Version: v1.4.0 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @matthewfeickert, @altavir Archive: 10.5281/zenodo.6056681
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