Comments (34)
editorialbot
commented on July 20, 2024
Hello human, 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:
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editorialbot
commented on July 20, 2024
Checking the BibTeX entries failed with the following error:
No paper file path
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editorialbot
commented on July 20, 2024
Software report:
github.com/AlDanial/cloc v 1.88 T=0.10 s (575.6 files/s, 89380.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 56 1115 1290 6530
Markdown 1 38 0 124
JSON 2 3 0 62
-------------------------------------------------------------------------------
SUM: 59 1156 1290 6716
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
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editorialbot
commented on July 20, 2024
Failed to discover a Statement of need section in paper
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editorialbot
commented on July 20, 2024
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kyleniemeyer
commented on July 20, 2024
Hi @temmy222, it does not appear that you included a paper with your submission. Is it located on a different branch?
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temmy222
commented on July 20, 2024
Hi @kyleniemeyer. Yes the paper is in the branch master_refactor. Should I move it to the main branch. Thank you.
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kyleniemeyer
commented on July 20, 2024
@editorialbot set master_refactor as branch
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editorialbot
commented on July 20, 2024
Done! branch is now master_refactor
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kyleniemeyer
commented on July 20, 2024
@editorialbot generate pdf
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editorialbot
commented on July 20, 2024
👉📄 Download article proof 📄 View article proof on GitHub 📄 👈
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kyleniemeyer
commented on July 20, 2024
@temmy222 no problem, just needed to specify the branch.
We do not have an editor available for this topic area right now, so I'm going to put your submission on our waitlist until someone opens up. In the meantime, we welcome reviewer suggestions from our list (or elsewhere)—for any you mention, please leave off the @ so they are not actually notified.
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kyleniemeyer
commented on July 20, 2024
@editorialbot invite @matthewfeickert as editor
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editorialbot
commented on July 20, 2024
Invitation to edit this submission sent!
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matthewfeickert
commented on July 20, 2024
@editorialbot assign me as editor
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editorialbot
commented on July 20, 2024
Assigned! @matthewfeickert is now the editor
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matthewfeickert
commented on July 20, 2024
@editorialbot commands
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editorialbot
commented on July 20, 2024
Hello @matthewfeickert, here are the things you can ask me to do:
# List all available commands
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matthewfeickert
commented on July 20, 2024
@editorialbot check references
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editorialbot
commented on July 20, 2024
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.cageo.2012.04.008 is OK
- 10.1016/j.cageo.2016.06.014 is OK
- 10.21105/joss.02412 is OK
- 10.1111/j.1745-6584.2008.00462.x is OK
MISSING DOIs
- None
INVALID DOIs
- None
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matthewfeickert
commented on July 20, 2024
@editorialbot check repository
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editorialbot
commented on July 20, 2024
Software report:
github.com/AlDanial/cloc v 1.88 T=0.12 s (534.8 files/s, 82534.7 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 56 1115 1290 6530
Markdown 2 118 0 381
JSON 2 3 0 62
TeX 1 0 0 46
YAML 1 1 4 18
-------------------------------------------------------------------------------
SUM: 62 1237 1294 7037
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
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editorialbot
commented on July 20, 2024
Wordcount for paper.md is 1976
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matthewfeickert
commented on July 20, 2024
As
gitinspector failed to run statistical information for the repository
Here's the same/similar check using cloc:
$ cd /tmp && git clone --quiet https://github.com/temmy222/PyTOUGHREACT && cd PyTOUGHREACT && printf "commit: $(git rev-parse HEAD)\n\n" && cloc --git .
commit: 32d8324a35f65783dab04b099cdc1765ac215d64
65 text files.
64 unique files.
22 files ignored.
github.com/AlDanial/cloc v 1.90 T=0.05 s (1219.9 files/s, 189435.0 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 56 1115 1290 6530
Markdown 1 38 0 124
JSON 2 3 0 62
-------------------------------------------------------------------------------
SUM: 59 1156 1290 6716
-------------------------------------------------------------------------------from joss-reviews.
matthewfeickert
commented on July 20, 2024
👋 @temmy222 I'll be serving as the editor for your review. I'm going to begin the process of finding reviewers, so please be patient while we work on this. 👍 As Kyle already mentioned, if you have suggestions for reviewers we would be open to hearing them, though for any you mention, please leave off the @ so they are not actually notified.
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matthewfeickert
commented on July 20, 2024
@temmy222 I'm now noticing that this is a resubmission from Issue #4260 (which is fine). However, as was noted in #4260 (comment) and the submission requirements we require an OSI-approved open source license for the software before we can review it. At the moment the LICENSE file in the repository is an empty file and although the README mentions it is licensed under MIT there is no actual license file. You did "add license file to every file" in temmy222/PyTOUGHREACT#1, which is fine, but please make sure that you also include the proper LICENSE file to avoid ambiguity as not all files in the repository contain this LICENSE header.
Additionally, while I see that you've factored out the PyTOUGH files that were discussed in #4260 (comment) and now vendor them in the setup.py (which is fine) in temmy222/PyTOUGHREACT@75ebdae if we look at the files that you're currently distributing on PyPI the files in question are still in the latest release
$ docker run --rm -ti python:3.10 /bin/bash
root@1f7645166e38:/# python -m venv venv && . venv/bin/activate
(venv) root@1f7645166e38:/# python -m pip --quiet install --upgrade pip setuptools wheel
(venv) root@1f7645166e38:/# cd /tmp/
(venv) root@1f7645166e38:/tmp# python -m pip download pytoughreact
Collecting pytoughreact
Downloading pytoughreact-0.0.2-py3-none-any.whl (232 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 232.2/232.2 kB 7.2 MB/s eta 0:00:00
Collecting numpy
Downloading numpy-1.24.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 18.7 MB/s eta 0:00:00
Saved ./pytoughreact-0.0.2-py3-none-any.whl
Saved ./numpy-1.24.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Successfully downloaded pytoughreact numpy
(venv) root@1f7645166e38:/tmp# python -m zipfile --list pytoughreact-0.0.2-py3-none-any.whl
File Name Modified Size
pytoughreact/__init__.py 2022-02-15 23:57:40 872
pytoughreact/ChemicalCompositions/__init__.py 2021-01-22 14:35:58 0
pytoughreact/ChemicalCompositions/mineral.py 2022-01-24 00:52:26 4890
pytoughreact/ChemicalCompositions/primaryspecies.py 2022-01-24 00:57:22 1341
pytoughreact/ChemicalCompositions/zone.py 2021-01-22 14:35:58 496
pytoughreact/Domain/__init__.py 2020-10-19 17:21:00 0
pytoughreact/Domain/domain.py 2020-10-19 17:21:00 1176
pytoughreact/Grid/__init__.py 2020-10-19 17:21:00 0
pytoughreact/Grid/grid.py 2020-10-23 16:49:48 1846
pytoughreact/pytough/IAPWS97.py 2020-10-19 17:21:00 19951
pytoughreact/pytough/__init__.py 2020-10-19 17:21:00 0
pytoughreact/pytough/customError.py 2022-01-24 04:52:12 451
pytoughreact/pytough/fixed_format_file.py 2022-02-15 23:57:40 26651
pytoughreact/pytough/geometry.py 2020-10-19 17:21:00 14241
pytoughreact/pytough/mulgrids.py 2022-02-15 23:57:40 205138
pytoughreact/pytough/t2bio.py 2022-02-15 23:57:40 140147
pytoughreact/pytough/t2bioresults.py 2022-02-15 23:57:40 11271
pytoughreact/pytough/t2chemical.py 2022-02-15 23:57:40 39424
pytoughreact/pytough/t2components.py 2022-01-11 06:38:34 9436
pytoughreact/pytough/t2data.py 2022-02-15 23:57:40 125608
pytoughreact/pytough/t2grids.py 2022-02-15 23:57:40 63064
pytoughreact/pytough/t2incons.py 2022-02-15 23:57:40 13877
pytoughreact/pytough/t2listing.py 2022-02-15 23:57:40 88053
pytoughreact/pytough/t2process.py 2022-01-12 00:28:22 3830
pytoughreact/pytough/t2react.py 2022-02-15 23:57:40 128850
pytoughreact/pytough/t2reactgrids.py 2022-02-15 23:57:40 64208
pytoughreact/pytough/t2reactresult.py 2022-02-15 23:57:40 6469
pytoughreact/pytough/t2result.py 2022-02-15 23:57:40 1610
pytoughreact/pytough/t2solute.py 2022-02-15 23:57:40 37148
pytoughreact/pytough/t2thermo.py 2020-10-19 17:21:00 15240
pytoughreact/pytough/t2utilities.py 2022-02-15 18:04:58 11497
tests/__init__.py 2021-01-22 14:35:58 0
tests/run_tests.py 2022-02-15 23:57:40 21702
pytoughreact-0.0.2.dist-info/METADATA 2022-02-16 05:28:16 757
pytoughreact-0.0.2.dist-info/WHEEL 2022-02-16 05:28:16 92
pytoughreact-0.0.2.dist-info/top_level.txt 2022-02-16 05:28:16 13
pytoughreact-0.0.2.dist-info/RECORD 2022-02-16 05:28:16 3287
(venv) root@1f7645166e38:/tmp# mv pytoughreact-0.0.2-py3-none-any.whl pytoughreact-0.0.2-py3-none-any.zip
(venv) root@1f7645166e38:/tmp# unzip pytoughreact-0.0.2-py3-none-any.zip
Archive: pytoughreact-0.0.2-py3-none-any.zip
inflating: pytoughreact/__init__.py
inflating: pytoughreact/ChemicalCompositions/__init__.py
inflating: pytoughreact/ChemicalCompositions/mineral.py
inflating: pytoughreact/ChemicalCompositions/primaryspecies.py
inflating: pytoughreact/ChemicalCompositions/zone.py
inflating: pytoughreact/Domain/__init__.py
inflating: pytoughreact/Domain/domain.py
inflating: pytoughreact/Grid/__init__.py
inflating: pytoughreact/Grid/grid.py
inflating: pytoughreact/pytough/IAPWS97.py
inflating: pytoughreact/pytough/__init__.py
inflating: pytoughreact/pytough/customError.py
inflating: pytoughreact/pytough/fixed_format_file.py
inflating: pytoughreact/pytough/geometry.py
inflating: pytoughreact/pytough/mulgrids.py
inflating: pytoughreact/pytough/t2bio.py
inflating: pytoughreact/pytough/t2bioresults.py
inflating: pytoughreact/pytough/t2chemical.py
inflating: pytoughreact/pytough/t2components.py
inflating: pytoughreact/pytough/t2data.py
inflating: pytoughreact/pytough/t2grids.py
inflating: pytoughreact/pytough/t2incons.py
inflating: pytoughreact/pytough/t2listing.py
inflating: pytoughreact/pytough/t2process.py
inflating: pytoughreact/pytough/t2react.py
inflating: pytoughreact/pytough/t2reactgrids.py
inflating: pytoughreact/pytough/t2reactresult.py
inflating: pytoughreact/pytough/t2result.py
inflating: pytoughreact/pytough/t2solute.py
inflating: pytoughreact/pytough/t2thermo.py
inflating: pytoughreact/pytough/t2utilities.py
inflating: tests/__init__.py
inflating: tests/run_tests.py
inflating: pytoughreact-0.0.2.dist-info/METADATA
inflating: pytoughreact-0.0.2.dist-info/WHEEL
inflating: pytoughreact-0.0.2.dist-info/top_level.txt
inflating: pytoughreact-0.0.2.dist-info/RECORD
(venv) root@1f7645166e38:/tmp# head pytoughreact/pytough/t2
t2bio.py t2chemical.py t2data.py t2incons.py t2process.py t2reactgrids.py t2result.py t2thermo.py
t2bioresults.py t2components.py t2grids.py t2listing.py t2react.py t2reactresult.py t2solute.py t2utilities.py
(venv) root@1f7645166e38:/tmp# head pytoughreact/pytough/t2react.py
"""Class for TOUGH2 data.
Copyright 2011 University of Auckland.
This file is part of PyTOUGH.
PyTOUGH is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
PyTOUGH is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
(venv) root@1f7645166e38:/tmp# and the distribution is a broken install due to undefined dependencies
(venv) root@1f7645166e38:/tmp# cd
(venv) root@1f7645166e38:~# python -m pip install pytoughreact
Collecting pytoughreact
Using cached pytoughreact-0.0.2-py3-none-any.whl (232 kB)
Collecting numpy
Using cached numpy-1.24.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
Installing collected packages: numpy, pytoughreact
Successfully installed numpy-1.24.2 pytoughreact-0.0.2
(venv) root@1f7645166e38:~# python -c 'import pytoughreact'
Please check for errors
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/venv/lib/python3.10/site-packages/pytoughreact/__init__.py", line 9, in <module>
from pytoughreact.pytough.t2result import t2result
File "/venv/lib/python3.10/site-packages/pytoughreact/pytough/t2result.py", line 3, in <module>
from pytoughreact.pytough.t2bioresults import Tough3
File "/venv/lib/python3.10/site-packages/pytoughreact/pytough/t2bioresults.py", line 8, in <module>
from pytoughreact.pytough.t2utilities import t2utilities
File "/venv/lib/python3.10/site-packages/pytoughreact/pytough/t2utilities.py", line 7, in <module>
import matplotlib.pyplot as plt
ModuleNotFoundError: No module named 'matplotlib'
(venv) root@1f7645166e38:~# I will still move forward with looking for reviewers for now, but please make sure that you address all of the above in the immediate future before the review starts.
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matthewfeickert
commented on July 20, 2024
@temmy222 In #4260 (comment) @jgostick gave you multiple examples of problems that would keep reviewers from being able to accept your submission. However, by looking at the repo almost none of them have been implemented (e.g. no docs, no automated tests, my previous points).
I am similarly going to suggest that you retract your submission, address these points, read carefully the Submitting a paper to JOSS docs and, as was mentioned in #4260 (comment), the Review criteria docs, and submit again in the future.
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matthewfeickert
commented on July 20, 2024
@editorialbot ping track-eic
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editorialbot
commented on July 20, 2024
🛎️❗Hey @openjournals/pe-eics, this submission requires your attention.
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temmy222
commented on July 20, 2024
@matthewfeickert Thank you for your feedback. Does the information on the README.md not serve as docs? Also I have some tests in the repo. These do not serve also? I am working on your previous points
Please advise
Thank you
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matthewfeickert
commented on July 20, 2024
Does the information on the README.md not serve as docs? Also I have some tests in the repo. These do not serve also?
No. Please see the links that I provided that explain with examples what the required critiera are, as well as the examples provided in #4260 (comment) for more information.
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kyleniemeyer
commented on July 20, 2024
Hello @temmy222, as @matthewfeickert pointed out, it appears that your resubmission has not fully addressed the issues that were raised for your original submission. Since these issues are things that reviewers will point out that need to be addressed, and are in the JOSS review criteria, I am going to reject this resubmission.
Please review all of the comments and direction that we have provided. We will still consider future resubmissions, but you need to significantly address all of these issues first.
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kyleniemeyer
commented on July 20, 2024
@editorialbot reject
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editorialbot
commented on July 20, 2024
Paper rejected.
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