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[REVIEW]: pyMARS: automatically reducing chemical kinetic models in Python #1543

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whedon opened this issue Jul 2, 2019 · 56 comments

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@whedon
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commented Jul 2, 2019

Submitting author: @kyleniemeyer (Kyle E Niemeyer)
Repository: https://github.com/Niemeyer-Research-Group/pyMARS
Version: v1.1.0
Editor: @katyhuff
Reviewer: @fcontino, @jcsutherland
Archive: 10.5281/zenodo.3401549

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/18b77352fe7eb7c3c638eb3f12d6f11a"><img src="http://joss.theoj.org/papers/18b77352fe7eb7c3c638eb3f12d6f11a/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/18b77352fe7eb7c3c638eb3f12d6f11a/status.svg)](http://joss.theoj.org/papers/18b77352fe7eb7c3c638eb3f12d6f11a)

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

@fcontino, @jcsutherland please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Please try and complete your review in the next two weeks

Review checklist for @fcontino

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: v1.1.0
  • Authorship: Has the submitting author (@kyleniemeyer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jcsutherland

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: v1.1.0
  • Authorship: Has the submitting author (@kyleniemeyer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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commented Jul 2, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fcontino it looks like you're currently assigned to review this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands
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commented Jul 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 2, 2019

@kyleniemeyer

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commented Jul 8, 2019

Hi @katyhuff, I just noticed that @jcsutherland doesn't have a checklist and isn't listed as a reviewer above—I think that's because you had used the @whedon assign ... as reviewer rather than add for @fcontino. I think it's possible to add him manually at this point, not sure about adding via whedon.

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commented Jul 9, 2019

Good catch. Fixing now.

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commented Jul 9, 2019

@jcsutherland & @fcontino please see the issue description for guidance regarding the review process and for checklists associated with each of your reviews. Thank you!

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commented Jul 15, 2019

@katyhuff I don't seem to have access to check any boxes for the review. When I follow the invitation URL you supplied above, I see the following:

Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.

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commented Jul 15, 2019

👋 @arfon - can you check/resend the invitation?

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commented Jul 15, 2019

@arfon @danielskatz @katyhuff I just added @jcsutherland as a collaborator in the joss-reviews repo, which (I believe) is what whedon does when adding a reviewer at the pre-review stage.

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commented Jul 15, 2019

jcsutherland Review Comments

Critical issues to be resolved prior to acceptance

  • Unit tests should be implemented. See issue 26. It appears that this is in progress, but the documentation doesn't indicate how to run tests.
  • The documentation should clearly specify units expected in the input file. See issue 56
  • Raise errors if a species from the inputs isn't found in the Cantera file. See issue 58
  • pyMARS presently has a few critical bugs that should be corrected prior to acceptance:
    • CH4 is assumed to be present in the mechanism. See issue 59
    • Specifying Cantera groups causes exceptions. See issue 60

Other issues to consider

  • Consider required consolidating inputs to the input file. See issue 57. This isn't a showstopper for me, just something for the developers to consider since I think that it would improve user workflow.
  • Consider making a stead-state solve the default behavior. See issue 61. I don't think that this is a major issue - more food for thought.
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commented Jul 15, 2019

Hi @jcsutherland, thanks so much for all your feedback! We will start to address these items, but quickly, pyMARS does actually already have an automated testing suite, based on pytest.

If you have pytest installed, navigating to the repo and running pytest should automatically find and run all the tests, contained in the pymars/tests directory.

However, I do see that this isn't described in the documentation, so we will add that.

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commented Jul 23, 2019

I'm good with acceptance at this point.

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commented Jul 23, 2019

Thanks @jcsutherland ! I appreciate your thorough review.

@fcontino: Thank you again for volunteering to review. I know you initially expressed some scheduling challenges. Will you be able to address this review sometime soon? I hope you'll let us know what deadline will work for you.

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commented Jul 23, 2019

Thanks @jcsutherland!

FYI @fcontino, we released v1.1.0a0 based on the changes made in response to @jcsutherland's comments, if you grabbed an earlier version.

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commented Aug 5, 2019

Hi @katyhuff @fcontino just checking in on this.

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commented Aug 5, 2019

I'll send an email -- he may not be getting notifications.

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commented Aug 7, 2019

Sorry everyone, I didn't receive the notifications. I'll check this quickly.

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commented Aug 7, 2019

I have installed pyMARS successfully on my Mac.

I am proceeding with some tests.

My first concern is that after installing, pymars --help does not give me the same as stated here. It gives me the following:

`pymars -help
usage: pymars [-h] -m MODEL [-e ERROR] [--method {DRG,DRGEP,PFA}]
[--targets TARGETS [TARGETS ...]] [--conditions CONDITIONS]
[--retained_species [RETAINED_SPECIES [RETAINED_SPECIES ...]]]
[--sensitivity_analysis] [--sensitivity_type {initial,greedy}]
[--upper_threshold UPPER_THRESHOLD] [--path PATH]
[--num_threads [NUM_THREADS]] [--convert] [--thermo THERMO]
[--transport TRANSPORT]

pyMARS: Reduce chemical kinetic models.

optional arguments:
-h, --help show this help message and exit
-m MODEL, --model MODEL
input model filename (e.g., "mech.cti").
-e ERROR, --error ERROR
Maximum error percentage for the reduced model.
--method {DRG,DRGEP,PFA}
skeletal reduction method to use.
--targets TARGETS [TARGETS ...]
List of target species (e.g., "CH4 O2").
--conditions CONDITIONS
File with list of autoignition initial conditions.
--retained_species [RETAINED_SPECIES [RETAINED_SPECIES ...]]
List of non-target species to always retain (e.g., "N2
Ar")
--sensitivity_analysis
Run sensitivity analysis after completing another
method.
--sensitivity_type {initial,greedy}
Sensitivity analysis algorithm to be used
--upper_threshold UPPER_THRESHOLD
Upper threshold value used to determine species for
sensitivity analysis.
--path PATH Path to directory for writing files.
--num_threads [NUM_THREADS]
Number of CPU cores to use for running simulations in
parallel. If no number, then use available number of
cores minus 1.
--convert Convert files between Cantera and Chemkin formats
(.cti <=> .inp)
--thermo THERMO thermodynamic data filename (only necessary for
Chemkin files).
--transport TRANSPORT
transport data filename (only necessary for Chemkin
files).
`

And I'm getting the following error. Not sure if it relates to my configuration.

pymars --input example_input_file.yaml usage: pymars [-h] -m MODEL [-e ERROR] [--method {DRG,DRGEP,PFA}] [--targets TARGETS [TARGETS ...]] [--conditions CONDITIONS] [--retained_species [RETAINED_SPECIES [RETAINED_SPECIES ...]]] [--sensitivity_analysis] [--sensitivity_type {initial,greedy}] [--upper_threshold UPPER_THRESHOLD] [--path PATH] [--num_threads [NUM_THREADS]] [--convert] [--thermo THERMO] [--transport TRANSPORT] pymars: error: the following arguments are required: -m/--model

I have tried to specify the same

@kyleniemeyer

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commented Aug 7, 2019

Hi @fcontino, it looks like the version you installed is not the latest version (v1.1.0a8). That command-line interface was used before we made some changes in response to @jcsutherland's feedback.

If you installed using conda, could you try installing the latest version with conda install -c niemeyer-research-group pymars=1.1.0a8?

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commented Sep 3, 2019

Sorry for the huge delay. I'm still having issues. Can you help me?

conda install -c niemeyer-research-group pymars=1.1.0a8
Collecting package metadata (repodata.json): done
Solving environment: failed
Initial quick solve with frozen env failed.  Unfreezing env and trying again.
Solving environment: failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:


Package entrypoints conflicts for:
_ipyw_jlab_nb_ext_conf -> jupyterlab -> jupyterlab_server[version='>=0.2.0,<0.3.0'] -> notebook[version='>=4.2.0'] -> nbconvert -> entrypoints[version='>=0.2.2']
jupyterlab -> jupyterlab_server[version='>=0.2.0,<0.3.0'] -> notebook[version='>=4.2.0'] -> nbconvert -> entrypoints[version='>=0.2.2']
spyder -> nbconvert -> entrypoints[version='>=0.2.2']
entrypoints
nbconvert -> entrypoints[version='>=0.2.2']
jupyter -> notebook -> nbconvert -> entrypoints[version='>=0.2.2']
anaconda==5.2.0=py36_3 -> jupyterlab==0.32.1=py36_0 -> notebook[version='>=4.2.0'] -> nbconvert -> entrypoints[version='>=0.2.2']
nltk -> twython -> requests-oauthlib[version='>=0.4.0'] -> oauthlib[version='>=0.6.2'] -> pyjwt[version='>=1.0.0'] -> pep8-naming -> flake8-polyfill[version='>=1.0.2,>=1.0.2,<2'] -> flake8 -> entrypoints[version='>=0.3.0,<0.4.0']
widgetsnbextension -> notebook[version='>=4.4.1'] -> nbconvert -> entrypoints[version='>=0.2.2']
notebook -> nbconvert -> entrypoints[version='>=0.2.2']
jupyterlab_launcher -> notebook -> nbconvert -> entrypoints[version='>=0.2.2']
Package pyyaml conflicts for:
anaconda-navigator -> anaconda-project[version='>=0.4'] -> anaconda-client -> pyyaml[version='>=3.12']
anaconda-client -> pyyaml[version='>=3.12']
odo -> dask[version='>=0.11.1'] -> bokeh[version='>=0.13.0'] -> pyyaml[version='>=3.10']
conda-verify -> pyyaml
pyyaml
dask -> bokeh[version='>=0.13.0'] -> pyyaml[version='>=3.10']
bokeh -> pyyaml[version='>=3.10']
distributed -> pyyaml
conda-build -> conda-verify -> pyyaml
anaconda==5.2.0=py36_3 -> blaze==0.11.3=py36h02e7a37_0 -> odo[version='>=0.5.0'] -> dask[version='>=0.11.1'] -> bokeh -> pyyaml[version='>=3.10']
anaconda-project -> anaconda-client -> pyyaml[version='>=3.12']
scikit-image -> dask[version='>=0.5'] -> bokeh[version='>=0.13.0'] -> pyyaml[version='>=3.10']
blaze -> odo[version='>=0.5.0'] -> dask[version='>=0.11.1'] -> bokeh[version='>=0.13.0'] -> pyyaml[version='>=3.10']
pymars=1.1.0a8 -> pyyaml[version='>=4.2b1']
Package mkl-service conflicts for:
mkl-service
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commented Sep 3, 2019

OK. So the problems were coming from my machine. I tried on another machine and it works perfectly. Sorry again and excellent job!!

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commented Sep 3, 2019

@whedon check references

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commented Sep 3, 2019

Attempting to check references...
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commented Sep 3, 2019


OK DOIs

- 10.1016/j.pecs.2008.10.002 is OK
- 10.1016/j.combustflame.2010.12.010 is OK
- 10.1016/j.combustflame.2009.12.022 is OK
- 10.1016/j.combustflame.2010.03.006 is OK
- 10.1021/ef5022126 is OK
- 10.1016/j.combustflame.2014.05.001 is OK
- 10.1016/j.combustflame.2007.11.013 is OK
- 10.1016/j.combustflame.2005.02.015 is OK
- 10.1016/j.proci.2006.07.182 is OK
- 10.1016/j.proci.2006.08.025 is OK
- 10.1016/j.combustflame.2006.04.017 is OK
- 10.1016/j.proci.2004.08.145 is OK
- 10.1016/j.combustflame.2007.10.020 is OK
- 10.1007/bf01386390 is OK
- 10.1007/bf01166355 is OK
- 10.1146/annurev.pc.34.100183.002223 is OK
- 10.1016/s0097-8485(00)00077-2 is OK
- 10.5281/zenodo.1174508 is OK
- 10.1109/mcse.2011.37 is OK
- 10.2172/481621 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Sep 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 6, 2019

@kyleniemeyer

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commented Sep 6, 2019

@whedon generate pdf

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commented Sep 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 6, 2019

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commented Sep 6, 2019

@whedon generate pdf

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commented Sep 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 6, 2019

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commented Sep 6, 2019

@whedon generate pdf

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commented Sep 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 6, 2019

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commented Sep 6, 2019

@katyhuff ok, sorry for the spam—I resolved that pytables reference by just changing it to "2002-2019", which is still accurate.

I released v1.1.0, and the DOI is 10.5281/zenodo.3401549.

Thanks everyone!

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commented Sep 7, 2019

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commented Sep 7, 2019

@whedon set v1.1.0 as version

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commented Sep 7, 2019

OK. v1.1.0 is the version.

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commented Sep 7, 2019

@whedon set 10.5281/zenodo.3401549 as archive

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commented Sep 7, 2019

OK. 10.5281/zenodo.3401549 is the archive.

@katyhuff katyhuff added the accepted label Sep 7, 2019

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commented Sep 7, 2019

Congratulations @kyleniemeyer, and thanks again @jcsutherland and @fcontino for your reviews!

@openjournals/jose-eics I think this is ready for acceptance!

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commented Sep 8, 2019

@whedon accept

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commented Sep 8, 2019

Attempting dry run of processing paper acceptance...
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commented Sep 8, 2019

Check final proof 👉 openjournals/joss-papers#952

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#952, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented Sep 8, 2019

@whedon accept deposit=true

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commented Sep 8, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Sep 8, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Sep 8, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#953
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01543
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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commented Sep 8, 2019

@fcontino, @jcsutherland - many thanks for your reviews here and to @katyhuff for editing this submission

@kyleniemeyer - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Sep 8, 2019

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commented Sep 8, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01543/status.svg)](https://doi.org/10.21105/joss.01543)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01543">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01543/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01543/status.svg
   :target: https://doi.org/10.21105/joss.01543

This is how it will look in your documentation:

DOI

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