Joss-reviews: [REVIEW]: fibergen: An introductory tool for FFT-based material homogenization
Submitting author: @fospald (Felix Ospald)
Repository: https://github.com/fospald/fibergen
Version: v1.0
Editor: @jedbrown
Reviewer: @tisaac, @ctdegroot
Archive: 10.5281/zenodo.2556861
Status
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Markdown: [](http://joss.theoj.org/papers/add4f02dcedfaae8f81da200000d64ee)
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Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@tisaac & @ctdegroot, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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✨ Please try and complete your review in the next two weeks ✨
Review checklist for @tisaac
Conflict of interest
- [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.
Code of Conduct
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the repository url?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Version: v1.0
- [x] Authorship: Has the submitting author (@fospald) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Functionality
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
Documentation
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
- [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
Software paper
- [x] Authors: Does the
paper.mdfile include a list of authors with their affiliations? - [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
Review checklist for @ctdegroot
Conflict of interest
- [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.
Code of Conduct
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the repository url?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Version: v1.0
- [x] Authorship: Has the submitting author (@fospald) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Functionality
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
Documentation
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
- [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
Software paper
- [x] Authors: Does the
paper.mdfile include a list of authors with their affiliations? - [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
whedon
All 130 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tisaac, it looks like you're currently assigned as the reviewer for this paper :tada:.
:star: Important :star:
If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿
To fix this do the following two things:
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@whedon commands
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1027 with the following error:
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1027 (Errno::ENOENT)
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/bin/whedon:32:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/bin/whedon:98:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 18 Oct 2018
@whedon generate pdf
jedbrown
on 18 Oct 2018
Attempting PDF compilation. Reticulating splines etc...
@arfon Do you know why this review issue was created with the repository linked to https://fospald.github.io/fibergen/ instead of the repository from the pre-review issue #986? (I edited it before asking whedon to regenerate.)
@tisaac @ctdegroot Welcome! The comments from whedon above outline the review process. I'll be watching this thread if you have any questions. Thanks!
jedbrown
on 18 Oct 2018
@jedbrown, is a github release version necessary (submission has no tagged releases)? I think it _should_ have a release, but as I understand it, the reviewed version will get a zenodo doi or similar which is what is actually important to identifying what was reviewed.
tisaac
on 18 Oct 2018
@tisaac A tag should be made after the review (which may include new commits to the software), as part of archiving (using Zenodo or similar). It isn't necessary at this stage.
jedbrown
on 18 Oct 2018
I'm checking off "Does the full list of paper authors seem appropriate and complete?", but the second commit (fospald/fibergen@c6a91c98e) appears to be an import an existing project, so I'm relying on the honesty of the submitting author.
tisaac
on 18 Oct 2018
I'm the original author of every line of the code and all demos, etc.
I did not use github right from the beginning for the project. I'm adding the project because research and publications are done.
fospald
on 19 Oct 2018
Hi, what to do next?
fospald
on 8 Nov 2018
@ctdegroot How is your review going?
jedbrown
on 8 Nov 2018
@jedbrown Working on the review. Hope to finish next week.
@fospald I am supposed to check "Does the release version given match the GitHub release (2018.1)?", but the GitHub repo shows no releases tagged. Can you clarify this for me?
ctdegroot
on 9 Nov 2018
@fospald I read the review above and can see that the release issue has already been discussed.
ctdegroot
on 9 Nov 2018
_Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)._ I don't see any examples of how to use the code. If there are some, can you please tell me where they are and please put something in the README about these.
_Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support_ I don't see any guidelines for how third parties can contribute to the software. Can you add something to the README?
ctdegroot
on 9 Nov 2018
@fospald Where are the test cases located? To what extent do they cover the code?
ctdegroot
on 9 Nov 2018
I cannot find any documentation of the code API. It seems that all of the core code is stuffed into the 27,000 line fibergen.cpp. How would one go about understanding the code and potentially working with it, without the GUI? Maybe try Doxygen to at least give a basic bit of documentation?
ctdegroot
on 10 Nov 2018
@fospald I am supposed to check "Does the release version given match the GitHub release (2018.1)?", but the GitHub repo shows no releases tagged. Can you clarify this for me?
I will make only minor changes to the project and keep everything compatible. I don't want to maintain several branches. There will be no future releases with big changes.
fospald
on 12 Nov 2018
_Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)._ I don't see any examples of how to use the code. If there are some, can you please tell me where they are and please put something in the README about these.
You run the GUI and then you can select one of the demos (located in the demo directory).
See here
The editor gives help about the available settings in the project file.
See here
_Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support_ I don't see any guidelines for how third parties can contribute to the software. Can you add something to the README?
Ok. I added a "Contributing" section in the README.
fospald
on 12 Nov 2018
@fospald Where are the test cases located? To what extent do they cover the code?
@ctdegroot The test cases are located in fibergen.cpp at line 23113 to 24194.
The tests cover core math operations, functions to compute geometric intersections, material laws (derivatives), solver operators for various methods.
fospald
on 12 Nov 2018
I cannot find any documentation of the code API. It seems that all of the core code is stuffed into the 27,000 line fibergen.cpp. How would one go about understanding the code and potentially working with it, without the GUI? Maybe try Doxygen to at least give a basic bit of documentation?
@ctdegroot End users should use the GUI and should not do any coding.
But I understand the issue. I will try my best add some documentation with Doxygen and reply when I'm done. Also I know that the single file concept is not ideal. Limited time for the project...
fospald
on 12 Nov 2018
@ctdegroot I added a Doxygen documentation. You have to
git pull
cd doc/doxygen
make (or just doxygen)
firefox html/index.html
(also added this to the README.md)
fospald
on 13 Nov 2018
@fospald Where are the test cases located? To what extent do they cover the code?
@ctdegroot The test cases are located in fibergen.cpp at line 23113 to 24194.
The tests cover core math operations, functions to compute geometric intersections, material laws (derivatives), solver operators for various methods.
@fospald Can you pull the test cases out of this file? It would be a lot easier for users to learn the code from the test cases if they are easier to find.
ctdegroot
on 15 Nov 2018
@ctdegroot I added a Doxygen documentation. You have to
git pull
cd doc/doxygen
make (or just doxygen)
firefox html/index.html
(also added this to the README.md)
Ok, this helps. I don't think the code structure is ideal by any means. It would be much better to create different header files and source files for different purposes. It's acceptable for the review though. I won't insist on this.
ctdegroot
on 15 Nov 2018
@fospald I am getting an error "Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)", but OpenMP is not listed as a dependency.
ctdegroot
on 15 Nov 2018
@fospald I am getting an error "Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)", but OpenMP is not listed as a dependency.
@ctdegroot fixed that
fospald
on 15 Nov 2018
@fospald Can you pull the test cases out of this file? It would be a lot easier for users to learn the code from the test cases if they are easier to find.
@ctdegroot Yes I can, but the test cases are pretty low level and the user should use only XML or Python for doing something. I don't think the test cases are helpful for anybody, except maybe developers.
I will try to also generate a documentation for the Python interface and a short tutorial/help for the GUI and XML files. Ok?
fospald
on 15 Nov 2018
Yes I can, but the test cases are pretty low level and the user should use only XML or Python for doing something. I don't think the test cases are helpful for anybody, except maybe developers.
@fospald Ok. This review is a bit strange for me because normally the code is made accessible to developers as well as users. I suppose that is fine if the scope is made clear.
@jedbrown Can you help clarify the position of JOSS on GUI-only type software contributions? There's not much available here to understand the code, but the GUI is well documented.
ctdegroot
on 19 Nov 2018
I can solicit more specific input from the editorial board, but the policy states (among other points):
- The software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler)
- The software should be feature complete (no half-baked solutions) and designed for maintainable extension (not one-off modifications). Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable.
It doesn't really matter whether the interface is a GUI, a library, or something else, but it does matter that the software provide a good platform for research.
jedbrown
on 20 Nov 2018
@jedbrown This package does seem to provide a platform for research. I was a bit unsure what to do because the code can’t really be understood without a lot of effort.
I’ll finish my review once the installation issues I’m having are solved.
ctdegroot
on 20 Nov 2018
It's fair to use your judgment about what a researcher would need and, for example, to ask for improved code documentation or pointers for researchers who wish to extend the package.
jedbrown
on 20 Nov 2018
I’ll finish my review once the installation issues I’m having are solved.
@ctdegroot can I help you with the installation issues?
fospald
on 20 Nov 2018
@fospald I submitted an issue on the repository; let's discuss there. I have OpenMP installed, but CMake isn't finding it. I'm not that familiar with CMake, so if the error message gives you any clues, please let me know.
ctdegroot
on 20 Nov 2018
@ctdegroot I added a tutorial and Python interface docstring to the documentation/source code.
fospald
on 20 Nov 2018
@ctdegroot Do you need help with boost.python? Can you file an issue for that?
fospald
on 22 Nov 2018
@ctdegroot Also have a look at
https://github.com/fospald/fibergen#troubleshooting
regarding boost-python. I will try, If I can somehow automate this better.
fospald
on 22 Nov 2018
Created an issue about boost-python:
fospald/fibergen#6
ctdegroot
on 23 Nov 2018
Having an issue now about ITK:
fospald/fibergen#7
ctdegroot
on 25 Nov 2018
@ctdegroot ITK is optional. There must be another error message if it does not compile.
fospald
on 26 Nov 2018
@jedbrown @ctdegroot How to continue here?
fospald
on 30 Nov 2018
@fospald The ITK issue is solved but there is another package that needs to be installed on my system and my package manager doesn’t include it. I’ll have to install manually. I haven’t really had a chance to work on it this week (end of teaching semester) but I will get back to it as soon as I can.
ctdegroot
on 30 Nov 2018
@ctdegroot I can also just say that MacOS is not supported yet, if it is too time consuming.
fospald
on 30 Nov 2018
@fospald I’ll try on Linux so that I can finish my review sooner
ctdegroot
on 30 Nov 2018
@ctdegroot I really appreciate that you test this on MacOS. You are the first. It would be really beneficial for other users as well. But it is your decision.
fospald
on 30 Nov 2018
@fospald I can definitely help work out the issues on MacOS, since I bet this will be beneficial for your users. I'll do Linux as well so that I can at least verify everything works there first.
ctdegroot
on 30 Nov 2018
@fospald Seems like I have fixed all of the remaining cmake dependency issues. The last one was to install boost-numeric-bindings. I am now having the following error:
fatal error: 'boost/gil/extension/io/png_dynamic_io.hpp' file not found
Any idea where this comes from?
Also, I should note that I had to set the following in the file CMakeLists.txt:
set (CMAKE_CXX_STANDARD 11)
Otherwise there were fatal errors due to templates not having a space between the angled brackets, i.e. (">>" vs "> >"). Seems the clang compiler is picky about this.
ctdegroot
on 6 Dec 2018
@fospald I also noted that there were errors because my host name had periods in it, so I added the following to CMakeLists.txt:
STRING(REPLACE "." "_" HOST_NAME ${HOST_NAME})
fatal error: 'boost/gil/extension/io/png_dynamic_io.hpp' file not foundAny idea where this comes from?
@ctdegroot Looks like boost gill is missing an extension. Do you have libpng and zlib installend? Maybe there is some boost-gil-png-dev extension package? I will try to avoid inclusion of this header.
Do you have the "gil/extension/io/png_io.hpp" header?
fospald
on 7 Dec 2018
@ctdegroot Looks like since Boost 1.68, Boost.GIL is a separate module.
https://github.com/boostorg
Not sure if this solves the issue, but then you maybe have to install this module separately with your installer. I'll update the CMake file.
fospald
on 7 Dec 2018
@fospald Ok thanks for the updates. I do have libpng and zlib installed. I will look into installing Boost.GIL separately and hopefully that solves it.
ctdegroot
on 7 Dec 2018
@fospald I've just installed the headers for boost.gil but as you can see from the repo that you linked, the png_dynamic_io.hpp and png_io.hpp headers are not present in that version.
ctdegroot
on 7 Dec 2018
@ctdegroot In boost 1.68 they changed the GIL headers completely. I tried to fix this now.
If there is still an error let me know. It is probably line 7054 of fibergen.cpp. You can temporarily disable this line in this case until I have a fix.
fospald
on 10 Dec 2018
Testing on Linux with boost-1.68 and python-3.7, I need the following (i.e., suggest eliminating the switch unless it's needed for some reason).
diff --git i/CMakeLists.txt w/CMakeLists.txt
index 665655d..bad9ce8 100644
--- i/CMakeLists.txt
+++ w/CMakeLists.txt
@@ -116,7 +116,7 @@ SET(Boost_USE_STATIC_RUNTIME OFF)
IF(APPLE)
SET(Boost_Python python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR})
ELSE()
- SET(Boost_Python python-py${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR})
+ SET(Boost_Python python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR})
ENDIF()
# TODO: Boost >= 1.68: also add gil component?
FIND_PACKAGE(Boost REQUIRED COMPONENTS system program_options thread ${Boost_Python} iostreams filesystem)
My build still fails (gcc-8.2.1).
/bin/c++ -DFFTWF_ENABLED -DFG_PYTHON_HEADER_NAME=\"/home/jed/joss/fibergen/build/joule/PythonModuleHeader_joule.h\" -DHOST_NAME=joule -DLIB_BUILD -DOPENMP_ENABLED -I/usr/include/python3.7m -
I/usr/lib/python3.7/site-packages/numpy/core/include -O3 -march=native -DNDBUG -Wall -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-local-typedefs -Wno-long-long -fopenmp -O3 -DNDEBUG
-std=gnu++11 -o CMakeFiles/fibergen_joule.dir/src/fibergen.cpp.o -c /home/jed/joss/fibergen/src/fibergen.cpp
/home/jed/joss/fibergen/src/fibergen.cpp: In member function ‘void FiberGenerator<T, DIM>::writeDistanceMap(const string&, const boost::numeric::ublas::c_vector<T, DIM>&, const boost::numeric
::ublas::c_vector<T, DIM>&, const boost::numeric::ublas::c_vector<T, DIM>&, std::size_t, std::size_t, T, T, T, bool, int) const’:
/home/jed/joss/fibergen/src/fibergen.cpp:7054:49: error: no matching function for call to ‘write_view(const string&, const const_view_t)’
gil::write_view(filename, gil::const_view(img));
^
In file included from /usr/include/boost/gil/extension/io/png/write.hpp:29,
from /usr/include/boost/gil/extension/io/png.hpp:23,
from /home/jed/joss/fibergen/src/fibergen.cpp:150:
/usr/include/boost/gil/io/write_view.hpp:40:6: note: candidate: ‘template<class Writer, class View> void boost::gil::write_view(Writer&, const View&, typename boost::enable_if<typename boost$
:mpl::and_<typename boost::gil::detail::is_writer<Writer>::type, typename boost::gil::is_format_tag<typename Reader::format_tag_t>::type, typename boost::gil::is_write_supported<typename boo$
t::gil::get_pixel_type<View>::type, typename Writer::format_tag_t>::type>::type>::type*)’
void write_view( Writer& writer
^~~~~~~~~~
/usr/include/boost/gil/io/write_view.hpp:40:6: note: template argument deduction/substitution failed:
/usr/include/boost/gil/io/write_view.hpp: In substitution of ‘template<class Writer, class View> void boost::gil::write_view(Writer&, const View&, typename boost::enable_if<typename boost::m$
l::and_<typename boost::gil::detail::is_writer<Writer>::type, typename boost::gil::is_format_tag<typename Reader::format_tag_t>::type, typename boost::gil::is_write_supported<typename boost:$
gil::get_pixel_type<View>::type, typename Writer::format_tag_t>::type>::type>::type*) [with Writer = const std::__cxx11::basic_string<char>; View = boost::gil::image_view<boost::gil::memory_$
ased_2d_locator<boost::gil::memory_based_step_iterator<const boost::gil::pixel<unsigned char, boost::gil::layout<boost::mpl::vector1<boost::gil::gray_color_t> > >*> > >]’:
/home/jed/joss/fibergen/src/fibergen.cpp:7054:49: required from here
(several screens of template-related errors follow). Commenting that line allows the build to complete (5 minutes to build that one source file).
jedbrown
on 29 Dec 2018
@fospald Sorry for the delay since your latest update. The code does compile with line 7054 commented out.
ctdegroot
on 29 Dec 2018
@fospald When I run fibergen-gui, I get the following error:
Traceback (most recent call last):
File "/Users/ctdegroot/GitRepos/fibregen/bin/../gui/main.py", line 4, in <module>
import fibergen_gui as fg_gui
File "/Users/ctdegroot/GitRepos/fibregen/lib/fibergen_gui.py", line 7, in <module>
import fibergen
File "/Users/ctdegroot/GitRepos/fibregen/lib/fibergen.py", line 12, in <module>
fibergen = __import__(libname)
ModuleNotFoundError: No module named 'fibergen_Christopher_DeGroots_Macbook_Pro'
The contents of lib includes the shared object file fibergen_Christopher_DeGroots_Macbook_Pro_local.so. Seems to be a naming issue here.
ctdegroot
on 29 Dec 2018
@ctdegroot @jedbrown I think I fixed the build and naming issues mentioned above. Can you please retry?
fospald
on 7 Jan 2019
@fospald I get the following:
/Users/ctdegroot/GitRepos/fibregen/bin/fibergen-gui: line 13: 11684 Segmentation fault: 11 $PYTHON "${FIBERGEN_DIR}/../gui/main.py" "$@"
I should mention that Mac doesn't have ldd so I replaced with otool -L which should be equivalent.
ctdegroot
on 8 Jan 2019
@ctdegroot can you run:
fibergen demo/elasticity/hashin/project.xml
python3 -c "import fibergen; fg = fibergen.FG(); fg.run()"
without error?
fospald
on 9 Jan 2019
@fospald First command results in:
dyld: Library not loaded: @rpath/libpython3.7m.dylib
Referenced from: /Users/ctdegroot/GitRepos/fibregen/bin/fibergen_cdg_mac01_eng_uwo_ca
Reason: image not found
/Users/ctdegroot/GitRepos/fibregen/bin/fibergen: line 6: 18485 Abort trap: 6 "${FIBERGEN_DIR}/fibergen_${HOST}" "$@"
Second command results in:
Segmentation fault: 11
Let me know if you want to keep trying on Mac. I can finish the review on Linux if you want.
ctdegroot
on 10 Jan 2019
@ctdegroot This seems to be an installation/search path issue for libpython3.
https://github.com/pre-commit/pre-commit/issues/618
You can finish the review on Linux if you want.
fospald
on 11 Jan 2019
@ctdegroot there is only one item left in the checklist. Does it work on Linux?
fospald
on 18 Jan 2019
@fospald Still not getting through the install on Linux. First there was a problem with naming of the boost.python library. Had to make the following change in CMakeLists.txt
# Try to find boost python
-SET(Boost_Python python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR})
+SET(Boost_Python python${PYTHON_VERSION_MAJOR})
I now have an error:
Could not find the following Boost libraries:
boost_iostreams
Still trying to figure that one out.
ctdegroot
on 18 Jan 2019
@ctdegroot Can you locate libboost_iostreams?
Which distribution and boost version are you using?
It might be possible that they simply removed the library and only the headers are required.
You can try to remove iostreams in the CMakeListst.txt
fospald
on 18 Jan 2019
@fospald I am using boost version 1.60.0. I could find the library file in my installation. I've tried removing iostreams from the CMakeLists.txt file, however the build fails. It seems like this library is required. Looks like iostreams doesn't build unless libbz2 is installed first.
I have now managed to get it build but cannot import QtWebKitWidgets. I guess this is some component of PyQt5 that I don't have. Is there any way to automate the install of all these dependencies? Very tedious to install everything manually.
ctdegroot
on 18 Jan 2019
I got everything to compile now, but the GUI crashes immediately. I've created an issue fospald/fibergen#8.
ctdegroot
on 18 Jan 2019
@ctdegroot I updated the code. Can you try running with
fibergen-gui --disable-browser
This will disable all QTWebKit components. Then you have to open the demo files manually.
fospald
on 29 Jan 2019
@fospald @jedbrown The software is working with the browser disabled. As such I was able to complete my review, and everything seems to be working fine. I would suggest that the installation procedure (mainly handling of dependencies) could be streamlined; however I give that as a future goal and won't let that hold up this review any further. I would suggest placing a note in the installation instructions that Mac is not fully supported, since we could not get this working.
ctdegroot
on 29 Jan 2019
@ctdegroot Thank you for testing. I updated the README with some more installation notes.
fospald
on 30 Jan 2019
@ctdegroot @jedbrown Now I also added a fallback browser, when using "fibergen-gui --disable-browser", which at least provides the same functionality as the QtWebEngine browser but is a bit ugly.
fospald
on 1 Feb 2019
@whedon check references
jedbrown
on 4 Feb 2019
Attempting to check references...
```Reference check summary:
OK DOIs
- http://doi.org/10.1016/j.jnnfm.2010.12.010 is OK
- http://doi.org/10.1007/s00466-014-1071-8 is OK
- http://doi.org/10.1016/j.cma.2015.06.003 is OK
- http://doi.org/10.1007/s00466-015-1227-1 is OK
- http://doi.org/10.1002/nme.5008 is OK
- http://doi.org/10.1002/pamm.201410320 is OK
- http://doi.org/10.1016/j.crme.2014.12.005 is OK
MISSING DOIs
- https://doi.org/10.1016/j.cma.2015.06.003 may be missing for title: FFT-based homogenization using composite voxels
- https://doi.org/10.7712/100016.1944.5977 may be missing for title: Hyperelastic laminates, composite voxels and FFT-based homogenization at finite strains
- https://doi.org/10.1002/nme.5371 may be missing for title: Optimal Experimental Design for Linear Elastic Model Parameter Identification of Injection Molded Short Fiber-Reinforced Plastics
- https://doi.org/10.1016/s1387-1609(99)80001-2 may be missing for title: A fast numerical method for computing the linear and nonlinear mechanical properties of composites
INVALID DOIs
- None
```
whedon
on 4 Feb 2019
@fospald Can you fix the citations that use inline style to use appropriate syntax the method of @bibkey versus the method of [@bibkey]? See https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citation_syntax
Looks good to me otherwise.
jedbrown
on 4 Feb 2019
@whedon generate pdf
fospald
on 4 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
fospald
on 4 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon check references
fospald
on 4 Feb 2019
Attempting to check references...
```Reference check summary:
OK DOIs
- http://doi.org/10.1016/j.jnnfm.2010.12.010 is OK
- http://doi.org/10.1007/s00466-014-1071-8 is OK
- http://doi.org/10.1016/j.cma.2015.06.003 is OK
- http://doi.org/10.1007/s00466-015-1227-1 is OK
- http://doi.org/10.1002/nme.5008 is OK
- http://doi.org/10.1002/pamm.201410320 is OK
- http://doi.org/https://doi.org/10.1016/j.cma.2016.06.021 is OK
- http://doi.org/10.1002/nme.5371 is OK
- http://doi.org/10.1016/j.crme.2014.12.005 is OK
MISSING DOIs
- https://doi.org/10.1016/s1387-1609(99)80001-2 may be missing for title: A fast numerical method for computing the linear and nonlinear mechanical properties of composites
INVALID DOIs
- None
```
whedon
on 4 Feb 2019
PDF failed to compile for issue #1027 with the following error:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 17 0 17 0 0 31 0 --:--:-- --:--:-- --:--:-- 31
100 17 0 17 0 0 31 0 --:--:-- --:--:-- --:--:-- 31
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
pandoc: 10.21105.joss.01027.pdf: openBinaryFile: does not exist (No such file or directory)
Looks like we failed to compile the PDF
whedon
on 4 Feb 2019
@whedon generate pdf
fospald
on 4 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
@jedbrown I updated the citations (DOIs and titles) but there were no inline citations.
fospald
on 4 Feb 2019
original method by [@MoulinecSuquet1994] should be original method by @MoulinecSuquet1994 (it will place the parentheses differently). There are several other citations like this.
If it's a part of the sentence, then it's "inline". The alternative would be to write so the citations are parenthetical, as in `original method [@MoulinecSuquet1994] and more recent ... on rotated [@Willot2015] and staggered [@SchneiderOspaldKabel2015] grids."
jedbrown
on 4 Feb 2019
@whedon generate pdf
fospald
on 4 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
fospald
on 4 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
@jedbrown Understood. I updated the citations.
fospald
on 4 Feb 2019
@fospald Thanks! Go ahead and tag a release (please use an annotated tag), then archive on Zenodo or similar, and report the DOI back in this thread.
jedbrown
on 4 Feb 2019
@jedbrown The DOI is: 10.5281/zenodo.2556861
for the v1.0 release.
https://doi.org/10.5281/zenodo.2556861
Not sure, why it is not found (takes time to register?)
fospald
on 4 Feb 2019
@fospald Can you please use an annotated tag?
jedbrown
on 4 Feb 2019
No need to let that hold up acceptance. You can upgrade to an annotated tag on GitHub at your leisure, if you so desire. (It makes git describe work and offers better provenance.)
jedbrown
on 5 Feb 2019
@whedon set v1.0 as version
jedbrown
on 5 Feb 2019
OK. v1.0 is the version.
whedon
on 5 Feb 2019
@whedon set 10.5281/zenodo.2556861 as archive
jedbrown
on 5 Feb 2019
OK. 10.5281/zenodo.2556861 is the archive.
whedon
on 5 Feb 2019
@openjournals/joss-eics Over to you. Thanks, @tisaac and @ctdegroot for reviewing.
jedbrown
on 5 Feb 2019
@jedbrown I annotated the tag.
fospald
on 5 Feb 2019
If you want an annotated tag on the server, you'd have to delete it and re-push, something like
git push origin :refs/tags/v1.0
git push --tags origin
@jedbrown Now it should be fine.
fospald
on 5 Feb 2019
@whedon generate pdf
kyleniemeyer
on 6 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon check references
kyleniemeyer
on 6 Feb 2019
Attempting to check references...
```Reference check summary:
OK DOIs
- http://doi.org/10.1016/j.jnnfm.2010.12.010 is OK
- http://doi.org/10.1007/s00466-014-1071-8 is OK
- http://doi.org/10.1016/j.cma.2015.06.003 is OK
- http://doi.org/10.1007/s00466-015-1227-1 is OK
- http://doi.org/10.1002/nme.5008 is OK
- http://doi.org/10.1002/pamm.201410320 is OK
- http://doi.org/https://doi.org/10.1016/j.cma.2016.06.021 is OK
- http://doi.org/10.1002/nme.5371 is OK
- http://doi.org/10.1016/j.crme.2014.12.005 is OK
MISSING DOIs
- https://doi.org/10.1016/s1387-1609(99)80001-2 may be missing for title: A fast numerical method for computing the linear and nonlinear mechanical properties of composites
INVALID DOIs
- None
```
whedon
on 6 Feb 2019
It looks like that missing DOI is a fluke, so we can ignore that and proceed.
kyleniemeyer
on 6 Feb 2019
@whedon accept
kyleniemeyer
on 6 Feb 2019
Attempting dry run of processing paper acceptance...
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/476
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/476, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true
whedon
on 6 Feb 2019
```Reference check summary:
OK DOIs
- http://doi.org/10.1016/j.jnnfm.2010.12.010 is OK
- http://doi.org/10.1007/s00466-014-1071-8 is OK
- http://doi.org/10.1016/j.cma.2015.06.003 is OK
- http://doi.org/10.1007/s00466-015-1227-1 is OK
- http://doi.org/10.1002/nme.5008 is OK
- http://doi.org/10.1002/pamm.201410320 is OK
- http://doi.org/https://doi.org/10.1016/j.cma.2016.06.021 is OK
- http://doi.org/10.1002/nme.5371 is OK
- http://doi.org/10.1016/j.crme.2014.12.005 is OK
MISSING DOIs
- https://doi.org/10.1016/s1387-1609(99)80001-2 may be missing for title: A fast numerical method for computing the linear and nonlinear mechanical properties of composites
INVALID DOIs
- None
```
whedon
on 6 Feb 2019
@whedon accept deposit=true
kyleniemeyer
on 6 Feb 2019
Doing it live! Attempting automated processing of paper acceptance...
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
- Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/477
- Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01027
- If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘
Any issues? notify your editorial technical team...
whedon
on 6 Feb 2019
@fospald congrats, your article is now published in JOSS! Thanks for submitting a solid article and piece of software.
@tisaac & @ctdegroot thank you for reviewing this submission, and thanks to @jedbrown for editing it.
kyleniemeyer
on 6 Feb 2019
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[](https://doi.org/10.21105/joss.01027)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01027">
<img src="http://joss.theoj.org/papers/10.21105/joss.01027/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01027/status.svg
:target: https://doi.org/10.21105/joss.01027
This is how it will look in your documentation:
We need your help!
Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
- Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
- Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=
whedon
on 6 Feb 2019
@kyleniemeyer @jedbrown Looking at some published papers (including mine)
http://joss.theoj.org/papers/10.21105/joss.01027
http://joss.theoj.org/papers/10.21105/joss.01168
it seems in the section "Cite as:" (on the left) the first name is missing.
"Ospald, (2019)."
Can this be fixed?
fospald
on 6 Feb 2019
@fospald I believe that is the intended formatting, but it's unusual that the accepted papers list shows a URL https://fospald.github.io/fibergen/ instead of the usual fospald / fibergen. http://joss.theoj.org/papers/accepted
jedbrown
on 6 Feb 2019
@jedbrown How to change the URL?
fospald
on 6 Feb 2019
I don't know; might be a question for @arfon.
jedbrown
on 6 Feb 2019
@jedbrown How to change the URL?
I can fix this.
arfon
on 6 Feb 2019
OK, fixed.
arfon
on 6 Feb 2019
Thanks!
jedbrown
on 6 Feb 2019
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