Joss-reviews: [PRE REVIEW]: PyAutoLens: Open-Source Strong Gravitational Lensing

[whedon]

Submitting author: @Jammy2211 (James Nightingale)
Repository: https://github.com/Jammy2211/PyAutoLens
Version: 1.7.8
Editor: @xuanxu
Reviewers: @aureliocarnero, @zonca
Managing EiC: Arfon Smith

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Thanks for submitting your paper to JOSS @Jammy2211. Currently, there isn't an JOSS editor assigned to your paper.

@Jammy2211 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

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[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=1.02 s (349.6 files/s, 62193.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         239           8079           7478          22710
JSON                            29              0              0           8527
Jupyter Notebook                30              0           4896           6425
TeX                              3             25              0           1075
reStructuredText                25            729            875            936
INI                             21            120              0            853
Markdown                         4             52              0            264
DOS Batch                        1              8              1             26
Bourne Shell                     1             14              1             25
make                             1              4              7              9
YAML                             1              4              2              8
-------------------------------------------------------------------------------
SUM:                           355           9035          13260          40858
-------------------------------------------------------------------------------


Statistical information for the repository '4ffdf1ee10792ce326b99c55' was
gathered on 2020/10/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
James Nightingale               75          9641           8457            0.10
Jammy2211                     9590       5397504        4320697           51.57
Nan Li                           9           279              0            0.00
Richard                       1045         46333          40057            0.46
Richard Hayes                40235       4060350        3995003           42.75
amyetherington                  19         22046          15834            0.20
ashkelly                         2            23             54            0.00
jammy2211                     1197        453824         475011            4.93

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
Jammy2211                 37411            0.7          6.3                9.02
Richard Hayes               813            0.0         12.0                3.81
amyetherington               77            0.3         17.5               20.78

[whedon]

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

OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4365/aaee8c is OK
- 10.21105/joss.00024 is OK
- 10.1093/mnras/staa278 is OK
- 10.1086/670067 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1051/0004-6361/201322971 is OK
- 10.3390/jimaging4030051 is OK
- 10.5281/zenodo.3936959 is OK
- 10.21105/joss.00433 is OK
- 10.1016/j.physletb.2019.134871 is OK
- 10.1088/0004-637X/757/1/82 is OK
- 10.1088/0004-637X/811/1/20 is OK
- 10.1111/j.1365-2966.2011.19726.x is OK
- 10.1093/mnras/stu305 is OK
- 10.1093/mnras/sty021 is OK
- 10.1088/0004-637X/703/1/L51 is OK
- 10.1093/mnras/stu1316 is OK
- 10.1093/mnras/stu413 is OK
- 10.1093/mnras/stv1455 is OK
- 10.1093/mnras/sty1264 is OK
- 10.1093/mnras/stz2220 is OK
- 10.1088/0004-637X/800/2/94 is OK
- 10.1093/mnras/stx483 is OK
- 10.1088/0004-637X/690/1/670 is OK
- 10.1111/j.1365-2966.2008.14005.x is OK
- 10.1093/mnras/stu943 is OK
- 10.1088/0004-637X/800/1/18 is OK
- 10.1126/science.1185759 is OK
- 10.1093/mnras/stu1395 is OK
- 10.1093/mnras/staa2740 is OK
- 10.1016/j.dark.2018.11.002 is OK
- 10.3847/0004-637X/826/2/112 is OK

MISSING DOIs

- 10.1109/mcse.2011.37 may be a valid DOI for title: The NumPy Array: A Structure for Efficient Numerical Computation

INVALID DOIs

- https://doi.org/10.1038/s41592-019-0686-2 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

[arfon]

:wave: @Jammy2211 - is this submission associated with a paper in a AAS publication?

[Jammy2211]

It is not.

[arfon]

@whedon invite @xuanxu as editor

:wave: @xuanxu - could you edit this submission for us?

[whedon]

@xuanxu has been invited to edit this submission.

[xuanxu]

@whedon assign me as editor

[whedon]

OK, the editor is @xuanxu

[xuanxu]

@Jammy2211 A quick comment before I look for reviewers: I got some errors cloning the repo, because the .git directory is big (~260Mb), so I had to install the LFS extension for git to be able to work with it. I'd recommend adding a note in the _Cloning/forking_ section of the Installation guide, and/or trying to reduce the size of the repo objects in the git history if possible.

[Jammy2211]

Thanks. I literally added the LFS stuff last night, having not used it before. Sounds like it is cumbersome so I will remove it entirely and switch the files to some sort of a URL download or separate GIt repo :).

[Jammy2211]

We're also aware of an issue where the imports in the transdimensional and slam runners in the autolens_workspace will give import errors, which require setting your PYTHONPATH to fix.

We did a big refactor before submitting (probably not the best idea...) changing how we handle paths / configs / output and are still having a few teething issues, but the goal is to make it so users don't have to set environment variables to run every!

EDIT: I have pushed a restructured autolens_workspace that fixes some of the imports, I will address the remaining issues (HowToLens chapter 3) tonight alongside the LFS :).

[xuanxu]

@HeloiseS / @aureliocarnero: would you be willing to review this paper? I think your knowledge of Astrophysics and Python makes both of you a great fit for this submission.

[aureliocarnero]

Dear @xuanxu I'm willing to review it, so count on me.
Thank you!
Aurelio

[xuanxu]

@zonca would you be willing to review this paper? I think your knowledge of Cosmology and Python makes you a great fit for this submission.

[zonca]

yes, I can

[xuanxu]

@whedon add aureliocarnero as reviewer

[whedon]

OK, aureliocarnero is now a reviewer

[xuanxu]

@whedon add @zonca as reviewer

[whedon]

OK, @zonca is now a reviewer

[xuanxu]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2825.

[xuanxu]

@aureliocarnero, @zonca thank you both. Please head over to #2825 where the review will take place.