remove_dagmc_tags

A python package and command line tool for removing DAGMC tags such as graveyard and vacuum

https://github.com/svalinn/remove_dagmc_tags

Science Score: 44.0%

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Scientific vocabulary similarity
Low similarity (14.2%) to scientific vocabulary

Keywords from Contributors

neutrons photon openmc dagmc serpent mcnp fispact spectrum containerised flux

Last synced: 7 months ago · JSON representation ·

Repository

A python package and command line tool for removing DAGMC tags such as graveyard and vacuum

Basic Info

Host: GitHub
Owner: svalinn
License: mit
Language: Python
Default Branch: main
Size: 6.52 MB

Statistics

Stars: 2
Watchers: 11
Forks: 1
Open Issues: 2
Releases: 4

Created about 5 years ago · Last pushed almost 3 years ago

Metadata Files

Readme License Citation

README.md

This is a minimal Python package that provides both command line and API interfaces for removing multiple tags from a DAGMC h5m file.

This is useful for preparing the h5m file for visulisation where it is desirable to remove reflecting surfaces, vacuum materials and the graveyard(s) region from the geometry before viewing the vtk file.

Command line usage

Perhaps the most common use of this program is to remove a DAGMC graveyard. bash remove-dagmc-tags -i dagmc.h5m -o dagmc_no_graveyard.h5m -t mat:graveyard

the -i or --input argument specifies the input h5m file
the -o or --output argument specifies the output h5m or vtk filename
the -t or --tags argument specifies the tags to remove.
the -v or --verbose argument enables (true) or disables (false) the printing of additional details

Multiple tags can also be removed and vtk files can be generated. This example removes three tags from the dagmc.h5m file and saves the result as a vtk file.

bash remove-dagmc-tags -i dagmc.h5m -o output.vtk -t mat:graveyard mat:vacuum reflective

Python API usage

Removing a single tag called mat:graveyard from the dagmc.h5m file.

```python from removedagmctags import remove_tags

remove_tags( input='dagmc.h5m', output='output.h5m', tags='mat:graveyard' ) ```

Removing two tags called mat:graveyard and reflective from the dagmc.h5m file and saving the result as a vtk file and h5m file.

```python from removedagmctags import remove_tags

remove_tags( input='dagmc.h5m', output=['output.vtk', 'output.h5m'], tags=['reflective', 'mat:graveyard'] ) ```

Installation

The recommended method of installing is via conda install as this is able to install all the dependencies including PyMoab. bash conda install -c conda-forge remove_dagmc_tags

However the package is available via the PyPi package manager. In this case you will have to seperatly install PyMoab.

bash pip install remove_dagmc_tags

Some Python dependencies (such as Numpy) are installed during the pip install remove_dagmc_tags process, however PyMoab needs to be installed seperatly to make full use of this package.

One method of installing pymoab is to install MOAB via Conda which includes PyMoab.

bash conda install -c conda-forge moab

Another method of installing pymoab is to compile MOAB with pymoab enabled.

bash mkdir MOAB cd MOAB ; \ mkdir build ; \ git clone --single-branch --branch develop https://bitbucket.org/fathomteam/moab.git cd build cmake ../moab -DENABLE_HDF5=ON \ -DENABLE_NETCDF=ON \ -DENABLE_FORTRAN=OFF \ -DENABLE_BLASLAPACK=OFF \ -DBUILD_SHARED_LIBS=OFF \ -DCMAKE_INSTALL_PREFIX=/MOAB make -j"$compile_cores" make -j"$compile_cores" install cmake ../moab -DENABLE_HDF5=ON \ -DENABLE_PYMOAB=ON \ -DENABLE_FORTRAN=OFF \ -DBUILD_SHARED_LIBS=ON \ -DENABLE_BLASLAPACK=OFF \ -DCMAKE_INSTALL_PREFIX=/MOAB make -j"$compile_cores" make -j"$compile_cores" install cd pymoab bash install.sh python setup.py install

Achknowledgments

The package is largely inspired by the DAGMC-viz(https://github.com/svalinn/DAGMC-viz) repository.

Owner

Name: Svalinn
Login: svalinn
Kind: organization
Email: dagmc@office365.wisc.edu

Website: http://svalinn.github.com
Repositories: 31
Profile: https://github.com/svalinn

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Shimwell"
  given-names: "Jonathan"
  orcid: "https://orcid.org/0000-0001-6909-0946"
title: "A python package and command line tool for removing DAGMC tags such as graveyard and vacuum "
version: 0.0.5
date-released: 2021-4-30
url: "https://github.com/svalinn/remove_dagmc_tags"

GitHub Events

Total

Last Year

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 45
Total Committers: 6
Avg Commits per committer: 7.5
Development Distribution Score (DDS): 0.222

Past Year

Commits: 2
Committers: 2
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Jonathan Shimwell	j**l@u**k	35
Jonathan Shimwell	d**l@g**m	4
autopep8	a**8@u**m	3
Jonathan Shimwell	m**l@j**m	1
Patrick Shriwise	p**e@g**m	1
shimwell	s**l@u**m	1

Committer Domains (Top 20 + Academic)

jshimwell.com: 1 ukaea.uk: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 4
Total pull requests: 14
Average time to close issues: about 1 month
Average time to close pull requests: 14 days
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 1.25
Average comments per pull request: 0.57
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

shimwell (4)

Pull Request Authors

shimwell (13)
pshriwise (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 314 last-month

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 5
Total maintainers: 1

pypi.org: remove-dagmc-tags

A tool for selectively removing tags such as the graveyard from DAGMC h5m files.

Homepage: https://github.com/svalinn/remove_dagmc_tags
Documentation: https://remove-dagmc-tags.readthedocs.io/
License: mit
Latest release: 0.0.5
published almost 5 years ago

Versions: 4
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 314 Last month

Rankings

Dependent packages count: 4.7%

Average: 20.0%

Dependent repos count: 21.6%

Forks count: 22.6%

Downloads: 23.4%

Stargazers count: 27.8%

Maintainers (1)

shimwell

Last synced: 8 months ago

conda-forge.org: remove_dagmc_tags

This is a minimal Python package that provides both command line and API interfaces for removing multiple tags from a DAGMC h5m file. This is useful for preparing the h5m file for visulisation where it is desirable to remove reflecting surfaces, vacuum materials and the graveyard(s) region from the geometry before viewing the vtk file.

Homepage: https://github.com/svalinn/remove_dagmc_tags
License: MIT
Latest release: 0.0.5
published almost 5 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 39.3%

Dependent packages count: 51.6%

Average: 55.1%

Stargazers count: 63.6%

Forks count: 66.0%

Last synced: 8 months ago

Dependencies

setup.py pypi

numpy *

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actions/setup-python v2 composite

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continuumio/miniconda3 4.9.2 build