[REVIEW]: Frackit: a framework for stochastic fracture network generation and analysis

whedon commented 4 years ago

Submitting author: @dglaeser (Dennis Gläser) Repository: https://git.iws.uni-stuttgart.de/tools/frackit Version: v1.2 Editor: @diehlpk Reviewers: @ilyasst, @ctdegroot Archive: 10.5281/zenodo.4315059

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Reviewers and authors:

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) by leaving comments 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

@ilyasst, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @ilyasst

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@dglaeser) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

diehlpk commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

diehlpk commented 3 years ago

@whedon remove @johntfoster as reviewer

whedon commented 3 years ago

OK, @johntfoster is no longer a reviewer

ctdegroot commented 3 years ago

@ctdegroot Could you please tell me your timeline for this review?

I’ve started my review but the invitation link gave me a page not found error so I still can’t modify the checklist. Can you send the invite once more and see if I can get it to work?

diehlpk commented 3 years ago

@whedon re-invite @ctdegroot as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@ctdegroot please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

diehlpk commented 3 years ago

@ctdegroot Please click on the link above.

diehlpk commented 3 years ago

@ctdegroot Are you able to edit the checkboxes?

dglaeser commented 3 years ago

@whedon check repository

whedon commented 3 years ago

Failed to discover a Statement of need section in paper

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.30 s (923.3 files/s, 106847.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                   143           2685           7165           9898
C++                             58           1095            760           5114
Markdown                         8            445              0           1861
Python                          11            329            411            963
CMake                           53             95            105            641
TeX                              1             33              0            273
GLSL                             2              7              3             56
-------------------------------------------------------------------------------
SUM:                           276           4689           8444          18806
-------------------------------------------------------------------------------

Statistical information for the repository 'f6518d3f2bcc969b4e8a1a00' was
gathered on 2020/11/09.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Dennis.Glaeser                 641         41719          13299          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Dennis.Glaeser            28420           68.1          4.2               28.99

dglaeser commented 3 years ago

We implemented several new features, especially in Python, and I wanted to use this service to get a new overview. I hope that's ok!

diehlpk commented 3 years ago

@ctdegroot How is your review going? When do you expect to finish it?

diehlpk commented 3 years ago

We implemented several new features, especially in Python, and I wanted to use this service to get a new overview. I hope that's ok!

That is ok, but note that you should address Failed to discover a Statement of need section in paper

and add a dedicated section to the new paper.

dglaeser commented 3 years ago

That is ok, but note that you should address Failed to discover a Statement of need section in paper

Yes, I saw that also and will adress it. I suppose I should wait for the review before editing the paper, or at least don't merge the edits to master? I would also like to add a few sentences on the new features, if possible? I just wasn't sure what the guidelines are here during a review, I though I'd wait for the revision phase. Thanks a lot for your help!

diehlpk commented 3 years ago

That is ok, but note that you should address Failed to discover a Statement of need section in paper

Yes, I saw that also and will adress it. I suppose I should wait for the review before editing the paper, or at least don't merge the edits to master? I would also like to add a few sentences on the new features, if possible? I just wasn't sure what the guidelines are here during a review, I though I'd wait for the revision phase. Thanks a lot for your help!

Yes, please update the paper, so the second reviewer can look at the new paper. Could you highlight the new changes here?

dglaeser commented 3 years ago

Sure, no problem. Once I have edited the paper I will post here the changes I have made to it. Thank you!

diehlpk commented 3 years ago

@ctdegroot Can you edit the checkboxes?

dglaeser commented 3 years ago

@diehlpk, I've updated the paper in the repository.

Regarding the new capabilities in the code, I only changed the wording a bit, to emphasize that all functionality is acessible from Python, while in the old version it said much of the functionality is accessible. In the section on random geometry sampling I added that there is also a sampler for general polygons available now, and I changed the code snippets in that section, as the usage as described in the previous version is actually deprecated now.

What involved some more changes was the rearrangement of the Summary in favor of a Statement of Need section, which was previously missing. I didn't know it was a requirement to have that as a section, I just thought the text should make that clear somehow. In that context I added more references and some text regarding existing software packages and the differences to this one.

dglaeser commented 3 years ago

@whedon check paper

whedon commented 3 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

dglaeser commented 3 years ago

@whedon check references

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18419/opus-289 is OK
- 10.1016/j.cageo.2015.04.012 is OK
- 10.1016/j.jhydrol.2015.08.065 is OK
- 10.5194/hess-23-19-2019 is OK
- 10.1016/j.cageo.2017.02.002 is OK
- 10.1016/j.advwatres.2011.03.007 is OK
- 10.1016/j.camwa.2020.02.012 is OK
- 10.1016/j.advwatres.2017.10.031 is OK
- 10.1007/s13137-019-0116-8 is OK
- 10.1007/s10596-020-10002-5 is OK
- 10.1002/nme.2579 is OK
- 10.1002/nme.6238 is OK
- 10.1016/j.advwatres.2017.10.036 is OK
- 10.1016/j.petrol.2019.106350 is OK
- 10.1016/j.jcp.2014.12.047 is OK
- 10.1016/j.jcp.2017.07.041 is OK
- 10.1007/s13137-019-0117-7 is OK
- 10.1016/j.cageo.2019.06.014 is OK
- 10.1007/s10596-018-9778-9 is OK
- 10.1016/j.jcp.2017.12.003 is OK
- 10.1007/s12665-014-3211-z is OK
- 10.1016/j.fuel.2011.08.037 is OK
- 10.1016/j.applthermaleng.2011.01.038 is OK
- 10.1016/j.rser.2014.04.068 is OK
- 10.1016/j.compgeo.2016.12.024 is OK
- 10.1016/j.cageo.2015.08.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ctdegroot commented 3 years ago

@ctdegroot Are you able to edit the checkboxes?

Yes, I can!

dglaeser commented 3 years ago

@whedon check repository

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.97 s (291.9 files/s, 33594.7 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C/C++ Header                    143           2686           7165           9893
C++                              58           1095            767           5115
Markdown                          9            458              0           1971
Python                           11            329            411            963
CMake                            53            113            125            672
TeX                               1             35              0            297
YAML                              1             17              9             97
Bourne Shell                      2             11             19             73
GLSL                              2              7              3             56
Bourne Again Shell                2             14              9             46
--------------------------------------------------------------------------------
SUM:                            282           4765           8508          19183
--------------------------------------------------------------------------------

Statistical information for the repository '4319c37808cd50d8ef65f97b' was
gathered on 2020/11/16.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Dennis.Glaeser                 644         35761           7337          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Dennis.Glaeser            28424           79.5          4.4               29.01

diehlpk commented 3 years ago

@ctdegroot Are you able to edit the checkboxes?

Yes, I can!

@ctdegroot Can you estimate when you intend to finish the review?

ctdegroot commented 3 years ago

@ctdegroot Are you able to edit the checkboxes?

Yes, I can!

@ctdegroot Can you estimate when you intend to finish the review?

Aiming for this week. Sorry for the delays.

diehlpk commented 3 years ago

@ctdegroot How is your review going?

ctdegroot commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ctdegroot commented 3 years ago

@ctdegroot How is your review going?

Almost done.

@dglaeser In the readme you have the following for building example applications:

make build_example_applications

However, I do not find this. I have build_example_tests. Is this what you mean?

dglaeser commented 3 years ago

@ctdegroot, thanks a lot for the hint! I recently changed the examples to appear in the test pipeline. I will change this to build_example_tests now!

ctdegroot commented 3 years ago

@ctdegroot, thanks a lot for the hint! I recently changed the examples to appear in the test pipeline. I will change this to build_example_tests now!

Great, that concludes my review!

diehlpk commented 3 years ago

@ilyasst and @ctdegroot Thanks for your review.

@dglaeser, Please do following steps;

[x] Generate a new release with the all the changes you made during the review
[x] Post the release number here
[ ] Generate a DOI on Zenodo or Figshare. Not that the title and the authors have to match the ones in the paper.
[ ] Post the DOI here

dglaeser commented 3 years ago

Great, thanks a lot to everybody! I'll work on the TODOs throughout this week and let you know once I am done. Thanks again!

dglaeser commented 3 years ago

@diehlpk, I can't edit the checkboxes in your command, but a new tag v1.2 is available now.

diehlpk commented 3 years ago

@whedon help

whedon commented 3 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

diehlpk commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

diehlpk commented 3 years ago

@whedon set v1.2 as version

whedon commented 3 years ago

OK. v1.2 is the version.

diehlpk commented 3 years ago

@dglaeser Ok, I clicked the boxes for you. Once you added the DOI, I can recommend the paper for acceptance and the EIC will do the final check.

dglaeser commented 3 years ago

@diehlpk, I got the DOI now:

10.5281/zenodo.4315059

Thanks a lot!

dglaeser commented 3 years ago

Maybe rather: https://doi.org/10.5281/zenodo.4315059

diehlpk commented 3 years ago

@whedon generate pdf

diehlpk commented 3 years ago

@dglaeser The title of the DOI is Frackit 1.2, however, the paper's title is Frackit: a framework for stochastic fracture network generation and analysis can you please update the title on Zenodo?

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

openjournals / joss-reviews