[PRE REVIEW]: NetworkSedimentTransporter: A Landlab submodule for bed material transport through river networks

[whedon]

Submitting author: @pfeiffea (Allison Pfeiffer)
Repository: https://github.com/landlab/landlab
Version: 2.1
Editor: @kthyng
Reviewers: @zsylvester, @ebgoldstein
Managing EiC: Kristen Thyng

⚠️ JOSS reduced service mode ⚠️

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.

Author instructions

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

The author's suggestion for the handling editor is @kthyng.

@pfeiffea 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:

@whedon commands

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

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:

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- 10.5194/esurf-5-21-2017 is OK
- 10.5194/esurf-2020-12 is OK
- 10.1016/j.geomorph.2018.08.031 is OK
- 10.1002/esp.4195 is OK
- 10.1002/2014WR016862 is OK
- 10.1002/2016JF003965 is OK
- 10.1002/esp.4635 is OK
- 10.1080/00221686.2006.9521683 is OK
- 10.1080/00221686.2006.9521684 is OK
- 10.1002/rra.1012 is OK
- 10.1061/(ASCE)0733-9429(2003)129:2(120) is OK
- 10.1029/2006WR005330 is OK
- 10.1029/97WR02387 is OK
- 10.1002/2015JF003491 is OK
- 10.1029/2006WR005172 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=9.18 s (84.5 files/s, 18771.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         454          19043          41823          57758
Markdown                        10            358              0           8396
reStructuredText               199           3396           4068           6862
Jupyter Notebook                47              0          16925           4475
Cython                          34           1064           1140           3858
HTML                             2             28              7            736
TeX                              4             60              0            660
CSS                              1            114             14            526
SVG                              8              1              1            427
DOS Batch                        2             31              1            246
YAML                             9             23              3            199
make                             2             21              6             71
Bourne Shell                     2             16             13             46
XML                              2              0              0              4
-------------------------------------------------------------------------------
SUM:                           776          24155          64001          84264
-------------------------------------------------------------------------------


Statistical information for the repository '2199' was gathered on 2020/05/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
(no author)                      1          2534              0            0.29
Allison Pfeiffer                 1          3088             43            0.36
Amanda Manaster                  2             2              4            0.00
Charlie Shobe                    1           207             55            0.03
Dan Hobley                     110          7815           3428            1.30
David Litwin                     9           140             55            0.02
DavidLitwin                      6           836            189            0.12
Eric Hutton                     21         36910          43668            9.30
Giuseppecipolla95               10          1059            650            0.20
Glader011235                    10           590             58            0.07
Greg Tucker                    443         23064          14808            4.37
Jenny Knuth                     25          2020            978            0.35
Jordan                           1            74              0            0.01
Jordan Adams                   145         11574           8402            2.30
Katy                             1             3              2            0.00
Katy Barnhart                  303         24808          17404            4.87
Nathan Lyons                     7          4451           1332            0.67
NathanLyons                      1            47              5            0.01
Nicole M Gasparini               1            16              5            0.00
Rachel Glade                     2            71             11            0.01
Ronda Strauch                    3           439              4            0.05
RondaStrauch                    43          1469           1005            0.29
Sai Nudurupati                  12           582             55            0.07
Sai Siddhartha Nudur             1            11              8            0.00
SiccarPoint                    687        121464          47087           19.45
alangston                        1          1327              0            0.15
barnhark                         2           182              0            0.02
cmshobe                         66          3213           1121            0.50
danhobley                      127         17100           7696            2.86
gregtucker                     109          7939           2623            1.22
gtucker                         79          6643           1740            0.97
huttone                        289         22411          13022            4.09
jadams15                        72          4064           3439            0.87
jordan                          19          4621           3264            0.91
kbarnhart                      649         55900          43882           11.51
margauxmouchene                 37          4252           1973            0.72
mcflugen                      2183        128494         103894           26.81
nathanlyons                     15           712            254            0.11
nicgaspar                       71          5103           2798            0.91
saisiddu                       215         18818          17767            4.22

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
Allison Pfeiffer           3083           99.8          0.1                8.37
Amanda Manaster               1           50.0         31.0                0.00
Charlie Shobe                73           35.3         10.3                6.85
Dan Hobley                11227          143.7         43.8               11.02
David Litwin                 90           64.3          2.0               13.33
DavidLitwin                 551           65.9          6.7               10.89
Eric Hutton               22828           61.8          4.4                4.81
Giuseppecipolla95           249           23.5         25.0               26.51
Greg Tucker                6115           26.5         37.0               15.85
Jenny Knuth                 504           25.0         50.2                3.97
Jordan Adams                147            1.3         40.6                8.16
Katy Barnhart             24590           99.1         19.4                5.35
Nathan Lyons               3429           77.0          5.9                7.76
NathanLyons                  70          148.9         34.6               10.00
Nicole M Gasparini          195         1218.8         66.1                4.10
Rachel Glade                222          312.7         36.4               18.47
RondaStrauch                205           14.0         40.2               16.59
Sai Nudurupati               17            2.9         72.1                5.88
alangston                  1206           90.9          8.1               17.41
barnhark                     16            8.8         75.3               37.50
cmshobe                     537           16.7         27.1               18.99
danhobley                   260            1.5         76.5               16.15
gregtucker                  706            8.9         59.7               10.48
gtucker                     271            4.1         78.3               18.08
huttone                    3343           14.9         80.4                9.72
jadams15                   1222           30.1         52.3                9.49
margauxmouchene            1224           28.8         22.2               16.18
mcflugen                  34234           26.6         33.6                5.40
nicgaspar                   305            6.0         47.5               18.69
saisiddu                   1674            8.9         48.4               13.20

[kthyng]

@kbarnhart, @openjournals/dev - Do you know the typical setup for reviewing a landlab module? I would like the statistics above to show the number of lines for just this submission (https://github.com/landlab/landlab/tree/master/landlab/components/network_sediment_transporter). Somehow it did find the correct paper — those move to be elsewhere when they aren't being reviewed.

[kbarnhart]

@kthyng I can provide some info. I first note that I am an author on this submission.

Most Landlab component submissions to JOSS (all, I think) have three parts: component source code, tests, and example notebooks. Each live in a separate location in the Landlab repository. In the case of this specific contribution the content is located at:

• component source: landlab/components/network_sediment_transporter and landlab/plot/network_sediment_transporter
• tests: tests/components/network_sediment_transporter
• example notebooks: notebooks/tutorials/network_sediment_transporter

Perhaps run cloc on this set of folders?

re finding the right paper: yes, there is only one paper.md, the prior submissions were renamed to address this issue.

The only thing that is really different about the review process for a landlab component (as compared with a typical submission in which the entire repository is the focus of review)... the reviewers need to be reminded that the scope of the review is not the entire repo. Obviously there are some whole-package things that get reviewed (install instructions, docs, contributing, etc).

Let me know if there are aspects of your question that I haven't addressed.

[arfon]

@kthyng will you be handling this submission as editor?

[kthyng]

Sorry for my delay, all. yes, I will handle this and will be able to address it in the next few days.

[kthyng]

@whedon assign @kthyng as editor

[whedon]

OK, the editor is @kthyng

[kthyng]

@openjournals/dev Might it be possible in the future to run @whedon check repository on a subset of a repository, sort of like generating a pdf from a branch of a repo? Just an idea.

[kthyng]

@kbarnhart Thanks so much for the info.

[kthyng]

For reference, I am going to paste in the cloc output I ran on my laptop since the information above is not accurate for this specific project:

(base) tatoosh:~ kthyng$ cloc Downloads/landlab-master/landlab/components/network_sediment_transporter
       3 text files.
       3 unique files.                              
       0 files ignored.

github.com/AlDanial/cloc v 1.84  T=0.03 s (117.3 files/s, 47959.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2            229            426            545
Markdown                         1             10              0             17
-------------------------------------------------------------------------------
SUM:                             3            239            426            562
-------------------------------------------------------------------------------
(base) tatoosh:~ kthyng$ cloc Downloads/landlab-master/landlab/plot/network_sediment_transporter
       3 text files.
       3 unique files.                              
       0 files ignored.

github.com/AlDanial/cloc v 1.84  T=0.01 s (200.1 files/s, 39156.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           3             99            187            301
-------------------------------------------------------------------------------
SUM:                             3             99            187            301
-------------------------------------------------------------------------------
(base) tatoosh:~ kthyng$ cloc Downloads/landlab-master/tests/components/network_sediment_transporter
       8 text files.
       8 unique files.                              
       1 file ignored.

github.com/AlDanial/cloc v 1.84  T=0.02 s (348.9 files/s, 34540.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            173             20            599
-------------------------------------------------------------------------------
SUM:                             8            173             20            599
-------------------------------------------------------------------------------
(base) tatoosh:~ kthyng$ cloc Downloads/landlab-master/notebooks/tutorials/network_sediment_transporter
       4 text files.
       4 unique files.                              
       0 files ignored.

github.com/AlDanial/cloc v 1.84  T=0.03 s (159.7 files/s, 78338.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                 4              0           1298            664
-------------------------------------------------------------------------------
SUM:                             4              0           1298            664
-------------------------------------------------------------------------------

[kthyng]

@pfeiffea I just read your personal description on github and it made me happy.

Sorry for my delay, getting work done right now is slow going. Could you look at this list and give a handful of suggestions for reviewers? Please don't @ them so that they aren't specifically mentioned, just give their github handle, like kthyng for me. https://bit.ly/joss-reviewers

[pfeiffea]

Glad the description brought a smile @kthyng -- those feel extra needed right now. No worries on delay.

Potential reviewers:
amandersillinois
ebgoldstein
anowacki
alangston
zsylvester

[kthyng]

@pfeiffea I should say you are welcome to suggest other reviewers too. I'll check them out tomorrow.

[arfon]

@openjournals/dev Might it be possible in the future to run @whedon check repository on a subset of a repository, sort of like generating a pdf from a branch of a repo? Just an idea.

Good idea. I've added this as a possible enhancement in openjournals/whedon-api#101

[kthyng]

Hi @zsylvester and @ebgoldstein! Are you willing and interested in reviewing this submission to the Journal for Open Source Software? The reviews are all done openly through GitHub and given the present world circumstances, I'd hope for reviews within about 6 weeks. You can learn more about the review process here: https://joss.readthedocs.io/en/latest/review_criteria.html

[zsylvester]

Hi @kthyng - I will need to learn a bit about the JOSS review process, but yes, I am interested.

[ebgoldstein]

Hi @kthyng, I can review.

[kthyng]

Hi @zsylvester and @ebgoldstein: awesome! I will start the review issue and close this one — the rest of the action should take place in the review issue. Please reach out if you have questions on the process. The JOSS docs have information, and it can also help to look through old submissions to see how things work. Thanks!!

[kthyng]

@whedon assign @zsylvester as reviewer

[whedon]

OK, @zsylvester is now a reviewer

[kthyng]

@whedon add @ebgoldstein as reviewer

[whedon]

OK, @ebgoldstein is now a reviewer

[kthyng]

@whedon start review

[whedon]

OK, I've started the review over in #2341.