https://github.com/boutproject/xbout
Collects BOUT++ data from parallelized simulations into xarray.
Science Score: 46.0%
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Repository
Collects BOUT++ data from parallelized simulations into xarray.
Basic Info
- Host: GitHub
- Owner: boutproject
- License: apache-2.0
- Language: Python
- Default Branch: master
- Homepage: https://xbout.readthedocs.io/en/latest/
- Size: 5.94 MB
Statistics
- Stars: 22
- Watchers: 15
- Forks: 12
- Open Issues: 56
- Releases: 15
Metadata Files
README.md
xBOUT
Documentation: https://xbout.readthedocs.io
Examples: https://github.com/boutproject/xBOUT-examples
xBOUT provides an interface for collecting the output data from a BOUT++ simulation into an xarray dataset in an efficient and scalable way, as well as accessor methods for common BOUT++ analysis and plotting tasks.
Currently only in alpha (until 1.0 released) so please report any bugs, and feel free to raise issues asking questions or making suggestions.
Installation
With pip:
bash
pip install --user xbout
With conda:
bash
conda install -c conda-forge xbout
You can test your installation of xBOUT by running pytest --pyargs xbout.
xBOUT requires other python packages, which will be installed when you run one of the above install commands if they are not already installed on your system.
Loading your data
The function open_boutdataset() uses xarray & dask to collect BOUT++
data spread across multiple NetCDF files into one contiguous xarray
dataset.
The data from a BOUT++ run can be loaded with just
python
bd = open_boutdataset('./run_dir*/BOUT.dmp.*.nc', inputfilepath='./BOUT.inp')
open_boutdataset() returns an instance of an xarray.Dataset which
contains BOUT-specific information in the attrs, so represents a
general structure for storing all of the output of a simulation,
including data, input options and (soon) grid data.
BoutDataset Accessor Methods
xBOUT defines a set of
accessor
methods on the loaded Datasets and DataArrays, which are called by
ds.bout.method().
This is where BOUT-specific data manipulation, analysis and plotting functionality is stored, for example
python
ds['n'].bout.animate2D(animate_over='t', x='x', y='z')
or
python
ds.bout.create_restarts(savepath='.', nxpe=4, nype=4)
Extending xBOUT for your BOUT module
The accessor classes BoutDatasetAccessor and BoutDataArrayAccessor
are intended to be subclassed for specific BOUT++ modules. The subclass
accessor will then inherit all the .bout accessor methods, but you
will also be able to override these and define your own methods within
your new accessor.
For example to add an extra method specific to the STORM BOUT++
module:
```python from xarray import registerdatasetaccessor from xbout.boutdataset import BoutDatasetAccessor
@registerdatasetaccessor('storm') class StormAccessor(BoutAccessor): def init(self, dsobject): super().init(dsobject)
def special_method(self):
print("Do something only STORM users would want to do")
ds.storm.special_method()
Out [1]: Do something only STORM users would want to do
```
There is included an example of a
StormDataset which contains all the data from a
STORM simulation, as well as
extra calculated quantities which are specific to the STORM module.
Contributing
Feel free to raise issues about anything, or submit pull requests, though I would encourage you to submit an issue before writing a pull request. For a general guide on how to contribute to an open-source python project see xarray's guide for contributors.
The existing code was written using Test-Driven Development, and I would
like to continue this, so please include pytest tests with any pull
requests.
If you write a new accessor, then this should really live with the code for your BOUT module, but it could potentially be added as an example to this repository too.
Developers
Clone the repository with:
bash
git clone git@github.com:boutproject/xBOUT.git
The recommended way to work with xBOUT from the git repo is to do an editable
install with pip. Run this command from the xBOUT/ directory:
bash
pip install --user -e .
which will also install all the required dependencies. Dependencies can also be
installed using pip
bash
pip install --user -r requirements.txt
or conda
conda install --file requirements.txt
It is possible to use xBOUT by adding the xBOUT/ directory to your
$PYTHONPATH.
Test by running pytest in the xBOUT/ directory.
Development plan
Things which definitely need to be included (see the 1.0 milestone):
- [x] More tests, both with
and against the original
boutdata.collect() - [ ] Speed test against old collect
Things which would be nice and I plan to do:
- [ ] Infer concatenation order from global indexes (see issue)
- [ ] Real-space coordinates
- [ ] Variable names and units (following CF conventions)
- [ ] Unit-aware arrays
- [ ] Variable normalisations
Things which might require a fair amount of effort by another developer but could be very powerful:
- [x] Using real-space coordinates to create tokamak-shaped plots
- [ ] Support for staggered grids using xgcm
- [ ] Support for encoding topology using xgcm
- [ ] API for applying BoutCore operations (hopefully using
xr.apply_ufunc)
GitHub Events
Total
- Fork event: 1
- Create event: 13
- Commit comment event: 4
- Release event: 2
- Issues event: 6
- Watch event: 1
- Delete event: 8
- Member event: 2
- Issue comment event: 39
- Push event: 32
- Pull request review comment event: 1
- Pull request review event: 8
- Pull request event: 14
Last Year
- Fork event: 1
- Create event: 13
- Commit comment event: 4
- Release event: 2
- Issues event: 6
- Watch event: 1
- Delete event: 8
- Member event: 2
- Issue comment event: 39
- Push event: 32
- Pull request review comment event: 1
- Pull request review event: 8
- Pull request event: 14
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| John Omotani | j****i@u****k | 732 |
| Thomas Nicholas | t****0@y****k | 185 |
| Rhys Doyle | r****5@m****e | 35 |
| Peter Hill | z****e@g****m | 32 |
| David Bold | d****e@i****e | 20 |
| Rhys Doyle | 4****5@u****m | 10 |
| David Bold | d****r@u****m | 5 |
| Mike Kryjak | m****k@g****m | 5 |
| David Schwörer | s****2@m****e | 4 |
| Tom Nicholas | 3****s@u****m | 4 |
| gregordecristoforo | g****o@g****m | 3 |
| Vandoo | q****a@u****k | 2 |
| David | d****h@f****g | 2 |
| Ben Dudson | b****2@y****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 36
- Total pull requests: 96
- Average time to close issues: 4 months
- Average time to close pull requests: about 1 month
- Total issue authors: 11
- Total pull request authors: 9
- Average comments per issue: 2.36
- Average comments per pull request: 2.38
- Merged pull requests: 80
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 13
- Average time to close issues: 5 months
- Average time to close pull requests: about 2 months
- Issue authors: 3
- Pull request authors: 5
- Average comments per issue: 0.25
- Average comments per pull request: 3.77
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dschwoerer (10)
- johnomotani (8)
- ZedThree (5)
- TomNicholas (3)
- mrhardman (2)
- bendudson (2)
- mikekryjak (1)
- jonycastagna (1)
- EdmundBenedict (1)
- frenzymadness (1)
- QuLogic (1)
Pull Request Authors
- johnomotani (56)
- dschwoerer (21)
- bendudson (5)
- mikekryjak (5)
- mrhardman (4)
- ZedThree (4)
- pnorbert (2)
- gregordecristoforo (1)
- Vandoo (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 453 last-month
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 4
(may contain duplicates) - Total versions: 23
- Total maintainers: 2
pypi.org: xbout
Collect data from BOUT++ runs in python using xarray
- Documentation: https://xbout.readthedocs.io/en/latest/
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We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright 2020 The contributors to the xBOUT project. xBOUT provides an interface for collecting the output data from a BOUT++ simulation into an xarray dataset in an efficient and scalable way, as well as accessor methods for common BOUT++ analysis and plotting tasks. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at https://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
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Latest release: 0.3.8
published 8 months ago
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conda-forge.org: xbout
- Homepage: https://xbout.readthedocs.io/en/latest/
- License: Apache-2.0
-
Latest release: 0.3.3
published over 3 years ago