search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
725 stars 38 forks source link

[REVIEW]: Halotools: A New Release Adding Intrinsic Alignments to Halo Based Methods #7421

Open editorialbot opened 2 weeks ago

editorialbot commented 2 weeks ago

Submitting author: !--author-handle-->@nvanalfen<!--end-author-handle-- (Nicholas Van Alfen) Repository: https://github.com/nvanalfen/halotools Branch with paper.md (empty if default branch): paper Version: v0.9 Editor: !--editor-->@ivastar<!--end-editor-- Reviewers: @matroxel, @cmlamman, @fjcastander Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e3768941d02ae5749fd764e77c8d9852"><img src="https://joss.theoj.org/papers/e3768941d02ae5749fd764e77c8d9852/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e3768941d02ae5749fd764e77c8d9852/status.svg)](https://joss.theoj.org/papers/e3768941d02ae5749fd764e77c8d9852)

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

@matroxel & @cmlamman, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @cmlamman

editorialbot commented 2 weeks ago

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

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 2 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.33232/001c.118783 is OK
- 10.1088/0004-637X/762/2/109 is OK
- 10.1093/mnras/stv2036 is OK
- 10.3847/1538-4365/ab1658 is OK
- 10.1088/0004-637X/763/1/18 is OK
- 10.1086/305262 is OK
- 10.1093/mnras/stw439 is OK
- 10.1093/mnras/stw248 is OK
- 10.1093/mnras/stt1403 is OK
- 10.1111/j.1365-2966.2011.18858.x is OK
- 10.1086/313015 is OK
- 10.1111/j.1365-2966.2005.09655.x is OK
- 10.1086/521074 is OK
- 10.1086/670067 is OK
- 10.3847/1538-3881/aa859f is OK
- 10.1093/mnras/staa3802 is OK
- 10.3847/1538-4357/ab042c is OK
- 10.2307/2333824 is OK
- 10.1093/mnras/stt1618 is OK
- 10.1088/1475-7516/2011/05/010 is OK
- 10.1103/PhysRevD.100.103506 is OK
- 10.1088/1367-2630/9/12/444 is OK
- 10.1103/PhysRevD.70.063526 is OK
- 10.1111/j.1365-2966.2009.15956.x is OK
- 10.1111/j.1365-2966.2005.09946.x is OK
- 10.1093/mnras/stac2083 is OK
- 10.1051/0004-6361:20066170 is OK
- 10.1051/0004-6361/202141938 is OK
- 10.3847/1538-4357/ab042c is OK
- 10.1086/341065 is OK
- 10.1088/1475-7516/2012/05/030 is OK
- 10.1093/mnras/stad2013 is OK
- 10.1103/PhysRevD.106.123510 is OK
- 10.1093/mnras/stab3222 is OK
- 10.1016/j.jmva.2012.08.010 is OK
- 10.1093/mnras/staa3388 is OK
- 10.1093/mnras/stx2956 is OK
- 10.48550/arXiv.2210.10068 is OK
- 10.1093/mnras/stx3349 is OK
- 10.1093/mnras/sty495 is OK
- 10.1093/mnras/stab1170 is OK
- 10.1093/mnras/stad473 is OK
- 10.1093/mnras/stac042 is OK
- 10.1093/mnras/stab3355 is OK
- 10.1093/mnras/stab1623 is OK
- 10.1093/mnras/stz2458 is OK
- 10.1093/mnras/sts006 is OK
- 10.1093/mnras/stw840 is OK
- 10.1093/mnras/staa623 is OK
- 10.1093/mnras/stz3442 is OK
- 10.1093/mnras/sty1089 is OK
- 10.1086/304888 is OK
- 10.1046/j.1365-8711.2003.06254.x is OK
- 10.1086/376517 is OK
- 10.1093/mnras/stw1705 is OK
- 10.1093/mnras/stx1828 is OK
- 10.1086/172900 is OK
- 10.3847/1538-4357/aafe11 is OK
- 10.1093/mnras/stx3040 is OK
- 10.1093/mnras/stx3112 is OK
- 10.1093/mnras/sty618 is OK
- 10.1093/mnras/stx3304 is OK
- 10.1093/mnras/sty2206 is OK
- 10.1093/mnras/stac1858 is OK
- 10.1093/mnras/stab748 is OK
- 10.1111/j.1365-2966.2006.10705.x is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1088/1475-7516/2015/08/015 is OK
- 10.1093/mnras/stv2615 is OK
- 10.1088/0004-637X/740/2/102 is OK
- 10.1093/mnras/stz3114 is OK
- 10.2172/1420403 is OK
- 10.1103/PhysRevD.105.023515 is OK
- 10.1088/1475-7516/2013/12/029 is OK
- 10.1103/PhysRevD.108.123518 is OK
- 10.1103/PhysRevD.105.023520 is OK
- 10.1051/0004-6361/202039063 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The Wide Field Infrared Survey Telescope: 100 Hubb...
- No DOI given, and none found for title: Towards Physical Understanding of Galaxy-Halo Alig...
- No DOI given, and none found for title: halotools: A New Release Adding Intrinsic Alignmen...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 2 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.64 s (1024.5 files/s, 189108.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         442          17632          25320          44591
reStructuredText               116           3796           2220           6163
Cython                          54           1948           2157           5598
TeX                              1            112              0           1258
Jupyter Notebook                29              0           8786            966
YAML                             6             28             22            179
DOS Batch                        1             21              1            148
Markdown                         5             79              0            114
make                             1             22              5            107
TOML                             1             10              8             74
INI                              1             12              0             72
CSS                              1              1              0              4
-------------------------------------------------------------------------------
SUM:                           658          23661          38519          59274
-------------------------------------------------------------------------------

Commit count by author:

  3904  Andrew Hearin
   444  Duncan Campbell
    72  Erik Tollerud
    47  Brigitta Sipocz
    47  Christopher Bradshaw
    46  Nick Van Alfen
    42  Thomas Robitaille
    14  Michael Droettboom
    13  Andrew Zentner
    10  Erik M. Bray
     9  Johannes Lange
     7  Yu Feng
     6  EiffL
     6  P. L. Lim
     6  Sean McLaughlin
     6  johannesulf
     5  Benedikt Diemer
     5  Yao-Yuan Mao
     5  sean
     4  Kyle Barbary
     4  Larry Bradley
     4  Matthew Craig
     4  Surhud More
     3  Christoph Deil
     3  Haojie Xu
     3  Manodeep Sinha
     2  Alan Pearl
     2  Clément Robert
     2  Johannes U. Lange
     2  Kevin Tan
     2  Matt Craig
     2  Nick Hand
     2  Wolfgang Kerzendorf
     1  Benjamin Alan Weaver
     1  Matthew R Becker
     1  Nels Beckman
     1  Pey Lian Lim
     1  Pey Lian Lim (Github)
     1  Shulei Cao
     1  Syrtis Major
     1  Tom McClintock
     1  alexieleauthaud
     1  dependabot[bot]
     1  hamogu
     1  kilianbreathnach
     1  larrybradley
     1  mclaughlin6464
editorialbot commented 2 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1211

✅ The paper includes a Statement of need section

editorialbot commented 2 weeks ago

License info:

🔴 Failed to discover a valid open source license

editorialbot commented 2 weeks ago

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

ivastar commented 2 weeks ago

@matroxel, @cmlamman welcome to the review issue! We are looking for a review in 3-4 weeks. It would be great if we can aim for the end of November. For instructions on generating the review checklist, see the top of this issue.

This review is for contributions to halotools made by @nvanalfen. We are not reviewing the full library because that is already published, but just these specific contributions. I'm pasting here Nick's note from the pre-review issue:

"The short version is that all commits made by me @.***) are part of the review. It's hard to pin down a single piece, as Andrew was making changes and bug fixes to the official version while I was working on this and we had to iterate a little in the end to merge things. Here's https://github.com/nvanalfen/halotools/commit/18e9b59812a4ae1a24bf0bffe1f00452f0acec58 the link to the latest commit I made on the material for this paper/work (commit 18e9b59). And this https://github.com/nvanalfen/halotools/commit/17422b87703fbfc3577ba6e0d48ed01cd7b3e361 is the commit right before my first contribution (commit 17422b8). If that comparison is sufficient (the version before I committed anything vs the version upon my last commit), here https://github.com/nvanalfen/halotools/compare/17422b8..18e9b59 is the link to that git diff."

If you have any questions, don't hesitate to tag me here or send me an email.

ivastar commented 2 weeks ago

@editorialbot add @fjcastander as reviewer

editorialbot commented 2 weeks ago

@fjcastander added to the reviewers list!

ivastar commented 2 weeks ago

License info:

🔴 Failed to discover a valid open source license

@@nvanalfen, I see that the license is basically a BSD 3-clause, but done in a non-standard way. Do you think it would be possible to refactor it to a standard BSD 3-clause? Also tagging @aphearin.

aphearin commented 2 weeks ago

Happy to refactor @ivastar - any templates I should look at?

ivastar commented 2 weeks ago

Happy to refactor @ivastar - any templates I should look at?

https://github.com/astropy/halotools/pull/1105 should do it. And then @nvanalfen can pull to his fork to bring the changes over.

nvanalfen commented 1 week ago

@ivastar I have synced my fork to include these changes. Thank you both of you!

cmlamman commented 1 day ago

Review checklist for @cmlamman

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

cmlamman commented 15 hours ago

@nvanalfen I'm having a problem with reproducing the IA tutorials: https://github.com/nvanalfen/halotools/issues/9#issue-2680924483