Closed whedon closed 3 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @soodoku, @sbenthall it looks like you're currently assigned to review this paper :tada:.
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@soodoku Sorry for the delay on starting the review. Now the review has started, and you can see the checklist on this issue.
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1177/0022343317691330 is OK
- 10.1177/0022343316682065 is OK
- 10.1177/0022343316682064 is OK
MISSING DOIs
- 10.1126/science.aal4483 may be a valid DOI for title: Predicting armed conflict: Time to adjust our expectations?
- 10.1088/1748-9326/11/5/054002 may be a valid DOI for title: Forecasting civil conflict along the shared socioeconomic pathways
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @soodoku, please update us on how your review is going.
:wave: @sbenthall, please update us on how your review is going.
HI @soodoku and @sbenthall, in the meantime, the model evolved to version 0.0.6 (https://github.com/JannisHoch/copro/releases/tag/v0.0.6). All changes made in the process of this review will be committed to the branch 'joss-review' (https://github.com/JannisHoch/copro/tree/joss_review).
i am done w/ my review.
I apologize for the delay in my review. There have been some personal issues on my end that have needed extra attention. I'm proceeding with my review now.
I think this is terribly exciting and I am eager to see it published in the best form possible. To that end:
I have not yet completed reviewing the code--these are first impressions of the document and paper only. But I think these improvements to the writeup and documentation are important for the publication.
When I get to the sh run.sh
part of the instructions in the README, I get the following error:
https://gist.github.com/sbenthall/83de0ce8675283c01d3f3fa973dc6f38
Hi @sbenthall, Absolutely no problem!
From your comments I assume you were not looking at the most recent version of the model. For instance, in the joss-review branch (https://github.com/JannisHoch/copro/tree/joss_review), there is no file run.sh anymore. It is renamed to 'run_notebooks.sh' for running the jupyter notebooks, and 'runscript*.sh' for executing the command line scripts.
If your problems still occur after installing the latest copro version, please let me know. thanks :)
in f9326d36bcbf20e93a54e6ea5733f1ae515f4477 I have added notes that the model was developed and tested with anaconda/miniconda.
regarding your question of other state-of-the-art software: to my knowledge, there is no freely available software model with such an extensive documentation out there. of course there is model code as supplement to a publication, and publications covering similar approaches (see the references in the joss manuscript), but not in a 'structured' way like done for CoPro.
I also have added a bit more technical detail to the JOSS manuscript. based on the review of @soodoku, the model goal and purpose were made clearer in the README and in the documentation.
Hello. Apologies for the further delay. I've had to take some family leave but am now back to work. I'll look at the branch you've referenced; sorry to miss it the first time.
I am being held up by some local Python environment issues. (The rasterio
dependency is not installing properly.) I'm pretty sure this is just a problem on my end! I'll try to repair my environment setup and get back to you.
@sbenthall, first of all, good to hear you're back!
Could you maybe attach a screenshot or so for me to look into it?
And I assume you were using the yml file to create the environment?
This is the stack trace. https://gist.github.com/sbenthall/5edad4e128fea79a99c2486ab6333bfe Googling for it makes it look like a local python issue. I'll keep kicking at it.
Hmm.
So what's strange here is that conda install rasterio==1.1.0
works fine, but then I get an error when it installs again via pip install -e .
.
I wonder if the conda version is conflicting with the pip version somehow (the pip version is invoked in the setup.py
file.)
Commenting out the rasterio
dependency in setup.py
and rerunning the pip
installation gets me this error:
https://gist.github.com/sbenthall/6a7f135970232dad08eb65ecebfd97cf
I do notice that rasterio
installation instructions look like they require a number of other GDAL related packages, which in the rasterio
installation instructions are listed as separate steps.
https://rasterio.readthedocs.io/en/latest/
I wonder if you could confirm that your instructions for CoPro, as written, work on a fresh system that does not have these GDAL packages installed. It is quite likely that these are being handled correctly by Anaconda and there's some issue going on locally, but if you could test on another machine that would be additional confirmation that it's a local issue and not a problem with the installation instructions.
Hmmm, this all sounds pretty odd to me.
I have never seen any of the error messages before when installing copro - neither the one when running pip install -e .
(as it seems that rasterio is correctly installed from cache and the error occurs bit later somehow), nor the one with altered setup.py
file (which is a permission error after all if I get it right?).
Also, I was able to install copro (branch joss_review) on a pretty 'fresh' Linux environment.
So yes, it may be that it's a local issue. I have two ideas:
environment.yml
file, put the rasterio dependency in the pip section instead the conda-forge section and see if this solves the suspected conflict between conda/pip?Or, as another possible fix, specify a more recent rasterio version? current one is 1.1.8. maybe there are some flaws in version 1.1.0 for some specific circumstances.
Good news. I've got the install working. Sorry about that.
Now I'm trying to test the library. Tiny snag: downloading the demo data and putting it in the right place so that the .cfg files can find it requires a little trial and error for me at the moment.
Certainly not a dealbreaker but some scripting around that would be nice.
I'll continue my review over the weekend -- it should be done by Monday. Thanks for your patience on this--I know it's been a long wait.
great to hear - i am curious, what exactly was the problem?
so the 'download_example_data.sh' does not what it's supposed to do? guess i'll here that from you soon. but to not slow down the review process, i could also send you the example data via mail?
looking forward to the remaining review!
so the 'download_example_data.sh' does not what it's supposed to do?
oh! I didn't see this. It is not mentioned in the README --- it just says the data is on Zenodo. So I fetched it by hand...
https://copro.readthedocs.io/en/latest/examples/nb02_XY_data.ipynb.html 4.2.2.2. "Assing" -> "Assign"
I see your example notebooks use %matplotlib inline
. I believe more recent versions of Jupyter have made this unnecessary.
As you direct users to use your Jupyter notebook examples, it would be helpful if you referred them to instructions for setting up their Jupyter notebooks to be able to use the conda environment as a kernel. e.g.
nb01 cell [5] I'm getting the following error:
conflict_gdf, extent_gdf, selected_polygons_gdf, global_df = selection.select(config, out_dir, root_dir)
https://gist.github.com/sbenthall/24da689b34fef8fc2ef9e16b99027215
nb02 cell 3 I'm getting the following error:
conflict_gdf = gpd.read_file('conflicts.shp') selected_polygons_gdf = gpd.read_file('polygons.shp')
https://gist.github.com/sbenthall/d8a722add82fa013d3779e39953773fe
....
I see now that these shapefiles are created by n01 in normal operation, and that the run_notebooks.sh
script cleans these out. But I'm not deep enough in to know why nb01 is failing when ran manually.
....
I know it's hard to get the tooling around this perfectly but I think with a little more documentation the initial user experience would be more idiot-proof.
hi @sbenthall ,
thanks for your comments. Regarding the first three, I will change them asap.
Regarding the last, few commetns from my side.
rtree
installed. I checked the environment.yml
file and it is indeed missing there. but thus far i was under the impression that this was installed along rasterio
- maybe your initial installation issues can explain this error. either way, i will add rtree
to the yml-file.I have added rtree
and ipykernel
to the environment.yml
file, so hope that a) writing the files in nb01 works now, and b) adding the copro-environmen to your jupyter kernel is possible.
Also, I have fixed the typo, added info about the download_example_data.sh
file in README.md
, and placed contextual info on the execution of the notebooks there as well.
Ok, just tried the .sh
scripts version of working README.
I ran sh run_script_reference.sh
no problem.
Then with sh run_script_projections.sh
I got this error:
https://gist.github.com/sbenthall/11fdd17af6f690c13933383e504eac50
hi @sbenthall, I am again stligthly puzzled about the errror you get. If I run the scripts in the 'joss_review' branch (which is the one under review I guess?), I don't get any issues at all. Also, I get different console output than you.
sure you use the right branch?
dear @sbenthall , hope you are doing well. I am just curious how the review process is going on your side. Not wanna be pushy as I know that this work is voluntary and Covid-19 is not doing any good either... Since I want to use the code in a manuscript, I'd very much appreciate it if there could be a citable version of the code until then. Thanks! Looking forward to any new bugs you find. Jannis
I apologize again for the delay. We had a baby in December. I'm double checking this today
I'm using the joss_review
branch and am getting the same error.
What is your output for that script?
that's great news, congrats!
i am bit puzzled by your error message, or more precisely by the console output you get.
it does not look like anything i get when using the joss_review
branch with the cfg-files as is plus the downloaded example data.
it seems like you getting debug output, but not the one i get using the joss_review
branch.
that is what makes me assume that there is something odd about your model exeuction, but cannot pinpoint what it is.
did you alter any of the files by any chance? maybe good if you could send me the cfg-files you use if the error persists?
I'll try a fresh install
It works! Thanks for your patience. This passes review and we'll proceed to the next stage.
@whedon check references
@whedon generate pdf
@sbenthall so what was the magic trick? anything i can add to the package to make the installation bullet-proof?
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1177/0022343317691330 is OK
- 10.1177/0022343316682065 is OK
- 10.1177/0022343316682064 is OK
MISSING DOIs
- 10.1126/science.aal4483 may be a valid DOI for title: Predicting armed conflict: Time to adjust our expectations?
- 10.1088/1748-9326/11/5/054002 may be a valid DOI for title: Forecasting civil conflict along the shared socioeconomic pathways
INVALID DOIs
- None
It was likely just human error initially. Don't worry about it.
Next steps:
This is the final editing stage.
am i supposed to push any changes to the joss_review
branch or how does this work?
If you have edits to the paper, then yes, that's right.
When it's absolutely finalized, you tag it.
Yeah, those DOI's Whedon pointed out should be added to the joss .bib file
Submitting author: @JannisHoch (Jannis Hoch) Repository: https://github.com/JannisHoch/copro Version: v0.0.5 Editor: @sbenthall Reviewer: @soodoku, @sbenthall Archive: 10.5281/zenodo.4548904
: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.
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Review checklist for @soodoku
Conflict of interest
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Software paper
Review checklist for @sbenthall
Conflict of interest
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General checks
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Documentation
Software paper