Closed editorialbot closed 9 months ago
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OK DOIs
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- 10.1088/0067-0049/192/1/9 is OK
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK
MISSING DOIs
- None
INVALID DOIs
- None
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@rvg296 I believe the command is:
@editorialbot generate my checklist
@rvg296 I believe the command is:
@editorialbot generate my checklist
Yes I have corrected it
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK
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@editorialbot generate pdf
@rvg296 @AnnikaStein Please use this version here for review: I have included reference to performance data repository.
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hi @AnnikaStein @rvg296 thanks for getting started here - please let me know if you have any questions or concerns.
hi @AnnikaStein @rvg296 friendly reminder about this review π please let me know if you have any questions or concerns, or if you need to set this down.
Hi @kellyrowland dont have any questions at this moment. In the process of review currently stage by stage.
Same for me, I also donβt have any questions at the moment, but just recently came back from a vacation. Continuing reviewing this + next week.
Great, thank you both!
@akashdhruv May be a minor edit, but in line 54 of the paper should'nt the Scikit method be named as skimage.measure
instead of skimage_measure
for measuring the bubble shape and size??
@akashdhruv May be a minor edit, but in line 54 of the paper should'nt the Scikit method be named as
skimage.measure
instead ofskimage_measure
for measuring the bubble shape and size??
I will address this.
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@akashdhruv May be a minor edit, but in line 54 of the paper should'nt the Scikit method be named as
skimage.measure
instead ofskimage_measure
for measuring the bubble shape and size??I will address this.
Done!
@kellyrowland @rvg296 @AnnikaStein
I transferred the repository to: https://github.com/Box-Tools/BoxKit to meet licensing requirements from Argonne National Laboratory. It should not change anything.
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@akashdhruv Tried installing this in a virtual environment created with Conda with Py310. I get this installation error. (py310) C:\Users\MENDR>pip install BoxKit --user
Collecting BoxKit
Downloading BoxKit-2023.6.7.tar.gz (852 kB)
---------------------------------------- 852.5/852.5 kB 1.9 MB/s eta 0:00:00
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
Γ python setup.py egg_info did not run successfully.
β exit code: 1
β°β> [10 lines of output]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\setup.py", line 14, in <module>
import bin.cmd as bin_cmd # pylint: disable=wrong-import-position
File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cmd.py", line 13, in <module>
from cbox import cbox_build # pylint: disable=wrong-import-position
File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cbox.py", line 21, in <module>
if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
Γ Encountered error while generating package metadata.
β°β> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
(py310) C:\Users\MENDR>pip install BoxKit
Collecting BoxKit
Using cached BoxKit-2023.6.7.tar.gz (852 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
Γ python setup.py egg_info did not run successfully.
β exit code: 1
β°β> [10 lines of output]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\setup.py", line 14, in <module>
import bin.cmd as bin_cmd # pylint: disable=wrong-import-position
File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cmd.py", line 13, in <module>
from cbox import cbox_build # pylint: disable=wrong-import-position
File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cbox.py", line 21, in <module>
if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
Γ Encountered error while generating package metadata.
β°β> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Are there any specific dependencies that needs to be installed prior to this?
@akashdhruv Tried installing this in a virtual environment created with Conda with Py310. I get this installation error. (py310) C:\Users\MENDR>pip install BoxKit --user
Collecting BoxKit Downloading BoxKit-2023.6.7.tar.gz (852 kB) ---------------------------------------- 852.5/852.5 kB 1.9 MB/s eta 0:00:00 Preparing metadata (setup.py) ... error error: subprocess-exited-with-error Γ python setup.py egg_info did not run successfully. β exit code: 1 β°β> [10 lines of output] Traceback (most recent call last): File "<string>", line 2, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\setup.py", line 14, in <module> import bin.cmd as bin_cmd # pylint: disable=wrong-import-position File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cmd.py", line 13, in <module> from cbox import cbox_build # pylint: disable=wrong-import-position File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cbox.py", line 21, in <module> if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost") TypeError: unsupported operand type(s) for +: 'NoneType' and 'str' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed Γ Encountered error while generating package metadata. β°β> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details. (py310) C:\Users\MENDR>pip install BoxKit Collecting BoxKit Using cached BoxKit-2023.6.7.tar.gz (852 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error Γ python setup.py egg_info did not run successfully. β exit code: 1 β°β> [10 lines of output] Traceback (most recent call last): File "<string>", line 2, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\setup.py", line 14, in <module> import bin.cmd as bin_cmd # pylint: disable=wrong-import-position File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cmd.py", line 13, in <module> from cbox import cbox_build # pylint: disable=wrong-import-position File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cbox.py", line 21, in <module> if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost") TypeError: unsupported operand type(s) for +: 'NoneType' and 'str' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed Γ Encountered error while generating package metadata. β°β> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details.
I think this maybe originating from the command os.getenv("PWD")
being executed on a Windows Operating System. $PWD
only exists on Linux/Unix based Operating Systems. I will write a fix for this.
Thank you for reporting this bug.
Can you try pip install boxkit==2023.9
Yes, I have tried. Here's what I get and I believe its related to pathname
`Collecting boxkit==2023.9
Downloading BoxKit-2023.9.0.tar.gz (1.4 MB)
---------------------------------------- 1.4/1.4 MB 3.2 MB/s eta 0:00:00
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
Γ python setup.py egg_info did not run successfully.
β exit code: 1
β°β> [10 lines of output]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-zydhqfqy\boxkit_9dbb73bbaeb0445ca87594bacf0d2c0f\setup.py", line 49, in <module>
packages=find_packages(where="./"),
File "C:\Users\MENDR\AppData\Local\ESRI\conda\envs\py310\lib\site-packages\setuptools\discovery.py", line 127, in find
convert_path(str(where)),
File "C:\Users\MENDR\AppData\Local\ESRI\conda\envs\py310\lib\site-packages\setuptools\_distutils\util.py", line 141, in convert_path
raise ValueError("path '%s' cannot end with '/'" % pathname)
ValueError: path './' cannot end with '/'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
Γ Encountered error while generating package metadata.
β°β> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.`
It looks like I will have to fix the source code to be able to work with either windows or linux machines. I originally intended BoxKit to be used on HPC clusters which are largely linux based.
I have setup a minimal test to replicate your windows test problem: https://github.com/Box-Tools/BoxKit/actions/runs/6343640315
@rvg296 It has been fixed. See: https://github.com/Box-Tools/BoxKit/actions/runs/6344172628/job/17233705158?pr=144
Can you try, pip install boxkit==2023.9.1 --user
and also, git+ssh://git@github.com/akashdhruv/BoxKit.git@main --user
@akashdhruv That worked, thanks for fixing that.
Perfect. Thank you for reporting the bug.
Please update this link (https://akashdhruv.github.io/BoxKit/) in BoxKit docs wherever related.
Please update this link (https://akashdhruv.github.io/BoxKit/) in BoxKit docs wherever related.
Its already up to date on the repository page: https://github.com/Box-Tools/BoxKit
I was referring to these, under contribution and usage.
I was referring to these, under contribution and usage.
Done.
@akashdhruv , In the paper, you have mentioned the performance is improved ~5x for measuring the bubble shape and size for Flash-X boiling simulations. Could you please locate that in the box-kit performance repo. Is that in the Jupyter notebook?
Submitting author: !--author-handle-->@akashdhruv<!--end-author-handle-- (Akash Dhruv) Repository: https://github.com/akashdhruv/BoxKit Branch with paper.md (empty if default branch): development Version: 2023.12 Editor: !--editor-->@kellyrowland<!--end-editor-- Reviewers: @rvg296, @Abinashbunty Archive: 10.5281/zenodo.10257565
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