Software review

[xuanxu]

Submitting Author: JJ (@xuanxu)
Repository: https://github.com/xuanxu/intergalactic
Version submitted: 1.3

Editor: TBD
Reviewers: Alice, Kate
Archive: TBD
Version accepted: TBD

---

Description

This software is a Q-Matrices generator.

Based on explicit values for solar abundances, z and IMF, it calculates matrices Q(i,j) of masses of 
elements i ejected to the galactic medium as element j, for a complete range of stellar masses, 
accounting for supernovas of types Ia and II. 
You can read more about the Matrices Q formalism in Ferrini et al. 1992.

Intergalactic computes the contribution matrix of 15 elements:

H  D  He3  He4  C  C13  N  O  n.r.  Ne  Mg  Si  S  Ca  Fe

Scope

• Please indicate which category or categories this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • scientific software wrappers
  • field and lab reproducibility tools
  • geospatial data
  • text analysis

Technical checks

Confirm each of the following by checking the box.
This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation.
• has a test suite.
• has continuous integration.

Code of conduct

• I agree to abide by our Code of Conduct during the review process and in maintaining my package should it be accepted.

Review checklist for @xuanxu

Conflict of interest

• I confirm that I have no COIs with reviewing this work or that any perceived COIs have been waived by an editor for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the code of conduct.

General checks

• Repository: Is the source code for this software available at the repo url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@xuanxu) made major contributions to the software?
• Substantial scholarly effort: Does this submission meet the scope eligibility?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• 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

Review checklist for @gemgon

Conflict of interest

• I confirm that I have no COIs with reviewing this work or that any perceived COIs have been waived by an editor for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the code of conduct.

General checks

• Repository: Is the source code for this software available at the repo url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@xuanxu) made major contributions to the software?
• Substantial scholarly effort: Does this submission meet the scope eligibility?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• 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

[botsci]

Welcome xuanxu, thanks for opening this issue 🎉

Thanks for sending your software to aliadalabs/sunnydale

[xuanxu]

@botsci help

[botsci]

Hello @xuanxu, here are the things you can ask me to do:

# List all available commands
@botsci help

# Assign a user as the reviewer N of this submission (where N=1,2...)
@botsci assign @username as reviewer 2

# Remove the user assigned as reviewer N of this submission (where N=1,2...)
@botsci remove reviewer 2

# Assign a user as the editor of this submission
@botsci assign @username as editor

# Remove the editor assigned to this submission
@botsci remove editor

# Send an invitation to a user to collaborate in the review
@botsci invite @username

# Add a user to this issue's assignees list
@botsci add assignee: @username

# Remove a user from this issue's assignees list
@botsci remove assignee: @username

# Set a value for version
@botsci set v1.0.0 as version

# Set a value for archive
@botsci set 10.21105/joss.12345 as archive

# Label issue with: reviewed, recommend publication, pending publication. Remove labels: ongoing, pending review
@botsci review successful

# Label issue with: recommend rejection
@botsci review failed

# Label the issue with: [rejected] and close it.
@botsci reject

# Reports on the quality of the code
@botsci analyze code

# Random facts about cats
@botsci tell me something about cats

# Add review checklist for a user
@botsci add checklist for @username

# Remove the checklist for a user
@botsci remove checklist for @username

[xuanxu]

@botsci remove checklist for @gemgon

[botsci]

There is not a checklist for @gemgon

[xuanxu]

@botsci add checklist for @gemgon

[botsci]

Checklist added for @gemgon

[xuanxu]

@botsci add checklist for @xuanxu

[botsci]

Checklist added for @xuanxu

[xuanxu]

@botsci remove checklist for @gemgon

[botsci]

There is not a checklist for @gemgon

[xuanxu]

@botsci remove checklist for @gemgon

[botsci]

Checklist for @gemgon removed

[xuanxu]

@botsci add checklist for @gemgon

[botsci]

Checklist added for @gemgon

[xuanxu]

@botsci help

[botsci]

Hello @xuanxu, here are the things you can ask me to do:

# List all available commands
@botsci help

# Assign a user as the reviewer N of this submission (where N=1,2...)
@botsci assign @username as reviewer 2

# Remove the user assigned as reviewer N of this submission (where N=1,2...)
@botsci remove reviewer 2

# Assign a user as the editor of this submission
@botsci assign @username as editor

# Remove the editor assigned to this submission
@botsci remove editor

# Send an invitation to a user to collaborate in the review
@botsci invite @username

# Add a user to this issue's assignees list
@botsci add assignee: @username

# Remove a user from this issue's assignees list
@botsci remove assignee: @username

# Set a value for version
@botsci set v1.0.0 as version

# Set a value for archive
@botsci set 10.21105/joss.12345 as archive

# Label issue with: reviewed, recommend publication, pending publication. Remove labels: ongoing, pending review
@botsci review successful

# Label issue with: recommend rejection
@botsci review failed

# Label the issue with: [rejected] and close it.
@botsci reject

# Reports on the quality of the code
@botsci analyze code

# Random facts about cats
@botsci tell me something about cats

# Add review checklist for a user
@botsci add checklist for @username

# Remove the checklist for a user
@botsci remove checklist for @username

[xuanxu]

@botsci help

[botsci]

Hello @xuanxu, here are the things you can ask me to do:

# List all available commands
@botsci help

# Assign a user as the reviewer N of this submission (where N=1,2...)
@botsci assign @username as reviewer 2

# Remove the user assigned as reviewer N of this submission (where N=1,2...)
@botsci remove reviewer 2

# Assign a user as the editor of this submission
@botsci assign @username as editor

# Remove the editor assigned to this submission
@botsci remove editor

# Send an invitation to a user to collaborate in the review
@botsci invite @username

# Add a user to this issue's assignees list
@botsci add assignee: @username

# Remove a user from this issue's assignees list
@botsci remove assignee: @username

# Check the references of the paper for missing DOIs
# Optionally, it can be run on a non-default branch 
@botsci check references
@botsci check references from custom-branch-name

# Set a value for version
@botsci set v1.0.0 as version

# Set a value for archive
@botsci set 10.21105/joss.12345 as archive

# Label issue with: reviewed, recommend publication, pending publication. Remove labels: ongoing, pending review
@botsci review successful

# Label issue with: recommend rejection
@botsci review failed

# Label the issue with: [rejected] and close it.
@botsci reject

# Reports on the quality of the code
@botsci analyze code

# Random facts about cats
@botsci tell me something about cats

# Add review checklist for a user
@botsci add checklist for @username

# Remove the checklist for a user
@botsci remove checklist for @username

[xuanxu]

@botsci add juanjo to reviewers

[botsci]

I can't find the reviewers list

[xuanxu]

@botsci add juanjo from reviewers

[botsci]

That command is confusing. Did you mean to ADD TO reviewers or to REMOVE FROM reviewers?

[xuanxu]

@botsci add juanjo to reviewers

[botsci]

juanjo added to the reviewers list!

[xuanxu]

@botsci remove juanjo from reviewers

[xuanxu]

@botsci remove laura from reviewers

[botsci]

laura is not in the reviewers list

[xuanxu]

@botsci remove juanjo from reviewers

[botsci]

juanjo removed from the reviewers list!

[xuanxu]

@botsci add John to reviewers

[botsci]

John added to the reviewers list!

[xuanxu]

@botsci add Kate to reviewers

[botsci]

Kate added to the reviewers list!

[xuanxu]

@botsci add Alice to reviewers

[botsci]

Alice added to the reviewers list!

[xuanxu]

@botsci remove Kate from reviewers

[botsci]

Kate removed from the reviewers list!

[xuanxu]

thanks @botsci

[botsci]

You are welcome

[xuanxu]

@botsci check repository

[botsci]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (391.6 files/s, 37195.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          22            619            304           1592
reStructuredText                 8            172             40            361
Markdown                         2             37              0             95
YAML                             2             12             42             31
make                             1              4              6              9
-------------------------------------------------------------------------------
SUM:                            35            844            392           2088
-------------------------------------------------------------------------------


Statistical information for the repository 'a78ccc90f72ffa12721304ce' was
gathered on 2020/11/20.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Juanjo Bazán                    8           547             33            7.24
Juanjo Bazán                   352          5267           2167           92.76

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
Juanjo Bazán               3374           64.1         15.9                5.63

[botsci]

Failed to discover a Statement of need section in paper

[xuanxu]

@botsci add Kate to reviewers

[botsci]

Kate added to the reviewers list!

[xuanxu]

@botsci remove John from reviewers

[botsci]

John removed from the reviewers list!

[xuanxu]

@botsci code of conduct

[botsci]

Our CoC: https://github.com/openjournals/joss/blob/master/CODE_OF_CONDUCT.md

[botsci]

It's adapted from the Contributor Covenant: http://contributor-covenant.org

[botsci]

Reports of abusive or harassing behavior may be reported to [email protected]

[xuanxu]

@botsci list editors

[botsci]

Here is the list of current topic editors:

Astronomy

- astroeditor_33
- astro_editor_2

Social science

- sociology_editor_1
- sociology_editor_2

Genomics

- @xuanxu
- genomics_editor_7

Machine Learning

- Alice
- Bob

Thanks for asking, xuanxu.

[xuanxu]

@botsci help

[botsci]

Hello @xuanxu, here are the things you can ask me to do:

# List all available commands
@botsci help

# Assign a user as the reviewer N of this submission (where N=1,2...)
@botsci assign @username as reviewer 2

# Remove the user assigned as reviewer N of this submission (where N=1,2...)
@botsci remove reviewer 2

# Add to this issue's reviewers list
@botsci add @username to reviewers

# Remove from this issue's reviewers list
@botsci remove @username from reviewers

# Assign a user as the editor of this submission
@botsci assign @username as editor

# Remove the editor assigned to this submission
@botsci remove editor

# Send an invitation to a user to collaborate in the review
@botsci invite @username

# Add a user to this issue's assignees list
@botsci add assignee: @username

# Remove a user from this issue's assignees list
@botsci remove assignee: @username

# Check the references of the paper for missing DOIs
# Optionally, it can be run on a non-default branch 
@botsci check references
@botsci check references from custom-branch-name

# Perform checks on the repository
# Optionally, it can be run on a non-default branch 
@botsci check repository
@botsci check repository from custom-branch-name

# Set a value for version
@botsci set v1.0.0 as version

# Set a value for archive
@botsci set 10.21105/joss.12345 as archive

# Label issue with: reviewed, recommend publication, pending publication. Remove labels: ongoing, pending review
@botsci review successful

# Label issue with: recommend rejection
@botsci review failed

# Close the issue
@botsci reject

# Reports on the quality of the code
@botsci analyze code

# Random facts about cats
@botsci tell me something about cats

# Add review checklist for a user
@botsci add checklist for @username

# Remove the checklist for a user
@botsci remove checklist for @username

[xuanxu]

@botsci help

[botsci]

Hello @xuanxu, here are the things you can ask me to do:

# List all available commands
@botsci help

# Replies to code of conduct
@botsci code of conduct

# Replies to list editors
@botsci list editors

# Assign a user as the reviewer N of this submission (where N=1,2...)
@botsci assign @username as reviewer 2

# Remove the user assigned as reviewer N of this submission (where N=1,2...)
@botsci remove reviewer 2

# Add to this issue's reviewers list
@botsci add @username to reviewers

# Remove from this issue's reviewers list
@botsci remove @username from reviewers

# Assign a user as the editor of this submission
@botsci assign @username as editor

# Remove the editor assigned to this submission
@botsci remove editor

# Send an invitation to a user to collaborate in the review
@botsci invite @username

# Add a user to this issue's assignees list
@botsci add assignee: @username

# Remove a user from this issue's assignees list
@botsci remove assignee: @username

# Check the references of the paper for missing DOIs
# Optionally, it can be run on a non-default branch 
@botsci check references
@botsci check references from custom-branch-name

# Perform checks on the repository
# Optionally, it can be run on a non-default branch 
@botsci check repository
@botsci check repository from custom-branch-name

# Set a value for version
@botsci set v1.0.0 as version

# Set a value for archive
@botsci set 10.21105/joss.12345 as archive

# Label issue with: reviewed, recommend publication, pending publication. Remove labels: ongoing, pending review
@botsci review successful

# Label issue with: recommend rejection
@botsci review failed

# Close the issue
@botsci reject

# Reports on the quality of the code
@botsci analyze code

# Random facts about cats
@botsci tell me something about cats

# Add review checklist for a user
@botsci add checklist for @username

# Remove the checklist for a user
@botsci remove checklist for @username