[REVIEW]: Metatheory.jl: Fast and Elegant Algebraic Computation in Julia with Extensible Equality Saturation

whedon commented 3 years ago

Submitting author: @ 0x0f0f0f (Alessandro Cheli) Repository: https://github.com/0x0f0f0f/Metatheory.jl Version: v0.3.2 Editor: @dpsanders Reviewers: @mwillsey, @jpfairbanks, @philzook58 Archive: 10.5281/zenodo.4646136

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@mwillsey & @jpfairbanks & @philzook58, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @mwillsey

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 (@ 0x0f0f0f) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

Review checklist for @jpfairbanks

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 (@ 0x0f0f0f) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

Review checklist for @philzook58

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 (@ 0x0f0f0f) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

philzook58 commented 3 years ago

Duplication fixed! Looks Good!

0x0f0f0f commented 3 years ago

LGTM! Thanks!

dpsanders commented 3 years ago

@0x0f0f0f: Please add DOIs for all the references.

dpsanders commented 3 years ago

@0x0f0f0f: Please add an explanation for the meaning of Figure 1. What do the arrows and dashed boxes represent? I suggest you also lightly shade or colour what is new in each subsequent part of the figure.

0x0f0f0f commented 3 years ago

@dpsanders some references are github repos and do not have DOIs. Do I have to remove them from .bib file and move the links to the paper body?

0x0f0f0f 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

- 10.1145/3434304 is OK
- 10.1137/141000671 is OK
- 10.1145/2813885.2737959 is OK
- 10.1145/2737924.2737959 is OK
- 10.1145/322186.322198 is OK

MISSING DOIs

- None

INVALID DOIs

- None

0x0f0f0f commented 3 years ago

@whedon generate pdf

0x0f0f0f commented 3 years ago

@dpsanders added explanation and coloring to the figure

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:

0x0f0f0f commented 3 years ago

@whedon generate pdf

0x0f0f0f 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

- 10.1145/3434304 is OK
- 10.1137/141000671 is OK
- 10.1145/3428275 is OK
- 10.1145/3276483 is OK
- 10.1145/2813885.2737959 is OK
- 10.1145/2737924.2737959 is OK
- 10.1145/322186.322198 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

dpsanders 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:

dpsanders commented 3 years ago

Could you please make a new tagged release and archive it, e.g. at zenodo.org. Then please report the version number and archive DOI here. Thanks!

0x0f0f0f commented 3 years ago

10.5281/zenodo.4646136

v0.3.2

dpsanders commented 3 years ago

@whedon set v0.3.2 as version

whedon commented 3 years ago

OK. v0.3.2 is the version.

dpsanders commented 3 years ago

@whedon set 10.5281/zenodo.4646136 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4646136 is the archive.

dpsanders commented 3 years ago

@whedon accept

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

dpsanders 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

dpsanders commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1145/3434304 is OK
- 10.1137/141000671 is OK
- 10.1145/3428275 is OK
- 10.1145/3276483 is OK
- 10.1145/2813885.2737959 is OK
- 10.1145/2737924.2737959 is OK
- 10.1145/322186.322198 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2164

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2164, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

0x0f0f0f commented 3 years ago

Thanks everybody!

kthyng commented 3 years ago

@0x0f0f0f Please change the metadata in your Zenodo archive so the author and title exactly match your JOSS paper.

kthyng commented 3 years ago

@0x0f0f0f Starting to read your paper. I don't see a reason to put your position in your author list ("undergraduate student"). Do you have a special reason to include it? If not I suggest removing it. Also is there is a reason you have an additional label as "independent researcher"? If you are attending University of Pisa, you could just list that, though you should expand the information to include at least the country.

0x0f0f0f 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:

0x0f0f0f commented 3 years ago

@kthyng Thanks! I should have fixed everything.

kthyng commented 3 years ago

@0x0f0f0f The author list for this submission on Zenodo should just be you since you are the author for JOSS. Can you update that?

kthyng commented 3 years ago

@0x0f0f0f I wasn't able to finish reading your paper earlier, sorry. But I've looked through it now and just a few more comments:

Please differentiate between references that are cited inline, in which case you should remove the [] from the reference, and references that are parenthetical (usually at the end of the sentence) which should keep the [] around the reference. You can get more info here.
At least a couple references in the reference list look like they should have "Julia" capitalized (i think it is supposed to be capitalized?). You can preserve capitalization from the .bib file by placing {} around those words.

0x0f0f0f 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:

0x0f0f0f 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:

0x0f0f0f commented 3 years ago

@kthyng Thanks again for the formatting suggestions. LGTM now

dpsanders commented 3 years ago

You're still missing a capital J in the last reference.

0x0f0f0f 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:

0x0f0f0f commented 3 years ago

Fixed

kthyng commented 3 years ago

ok everything looks good!

kthyng commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

Doing it live! Attempting automated processing of paper acceptance...

openjournals / joss-reviews