openghg
A platform for greenhouse gas (GHG) data analysis and collaboration.
Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
7 of 15 committers (46.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.8%) to scientific vocabulary
Keywords
Repository
A platform for greenhouse gas (GHG) data analysis and collaboration.
Basic Info
- Host: GitHub
- Owner: openghg
- License: apache-2.0
- Language: Python
- Default Branch: devel
- Homepage: https://www.openghg.org
- Size: 272 MB
Statistics
- Stars: 40
- Watchers: 3
- Forks: 9
- Open Issues: 222
- Releases: 0
Topics
Metadata Files
README.md
OpenGHG - a cloud platform for greenhouse gas data analysis and collaboration
OpenGHG is a project based on the prototype HUGS platform which aims to be a platform for collaboration and analysis of greenhouse gas (GHG) data.
The platform will be built on open-source technologies and will allow researchers to collaborate on large datasets by harnessing the power and scalability of the cloud.
For more information please see our documentation.
Install locally
To run OpenGHG locally you'll need Python 3.8 or later on Linux or MacOS, we don't currently support Windows.
You can install OpenGHG using pip or conda, though conda allows the complete functionality to be accessed at once.
Using pip
To use pip, first create a virtual environment
bash
python -m venv openghg_env
Then activate the environment
bash
source openghg_env/bin/activate
It's best to make sure you have the most up to date versions of the packages that pip will use behind the scenes when installing OpenGHG.
bash
pip install --upgrade pip wheel setuptools
Then we can install OpenGHG itself
bash
pip install openghg
Each time you use OpenGHG please make sure to activate the environment using the source step above.
NOTE: Some functionality is not completely accessible when OpenGHG is installed with
pip. This only affects some map regridding functionality. See the Additional Functionality section below for more information.
Using conda
To get OpenGHG installed using conda we'll first create a new environment
bash
conda create --name openghg_env
Then activate the environment
bash
conda activate openghg_env
Then install OpenGHG and its dependencies from our conda channel and conda-forge.
bash
conda install --channel conda-forge --channel openghg openghg
Note: the xesmf library is already incorporated into the conda install from vx.x onwards and so does not need to be installed separately.
Create the configuration file
OpenGHG stores object store and user data in a configuration file in the user's home directory at ~/.config/openghg/openghg.conf. As this sets the path of the object store, the user must
create this file in one of two ways
Command line
Using the openghg command line tool
``` openghg --quickstart
OpenGHG configuration
Enter path for object store (default /home/gareth/openghg_store): INFO:openghg.util:Creating config at /home/gareth/.config/openghg/openghg.conf
INFO:openghg.util:Configuration written to /home/gareth/.config/openghg/openghg.conf ```
Python
Using the create_config function from the openghg.util submodule.
``` from openghg.util import create_config
create_config()
OpenGHG configuration
Enter path for object store (default /home/gareth/openghg_store): INFO:openghg.util:Creating config at /home/gareth/.config/openghg/openghg.conf
INFO:openghg.util:Configuration written to /home/gareth/.config/openghg/openghg.conf ```
You will be prompted to enter the path to the object store, leaving the prompt empty tells OpenGHG to use the default path in the user's home directory at ~/openghg_store.
Additional functionality
Some optional functionality is available within OpenGHG to allow for multi-dimensional regridding of map data (openghg.tranform sub-module). This makes use of the xesmf package. This Python library is built upon underlying FORTRAN and C libraries (ESMF) which cannot be installed directly within a Python virtual environment.
To use this functionality these libraries must be installed separately. One suggestion for how to do this is as follows.
If still within the created virtual environment, exit this using
bash
deactivate
We will need to create a conda environment to contain just the additional C and FORTRAN libraries necessary for the xesmf module (and dependencies) to run. This can be done by installing the esmf package using conda
bash
conda create --name openghg_add esmf -c conda-forge
Then activate the Python virtual environment in the same way as above:
bash
source openghg_env/bin/activate
Run the following lines to link the Python virtual environment to the installed dependencies, doing so by installing the esmpy Python wrapper (a dependency of xesmf):
bash
ESMFVERSION='v'$(conda list -n openghg_add esmf | tail -n1 | awk '{print $2}')
$ export ESMFMKFILE="$(conda env list | grep openghg_add | awk '{print $2}')/lib/esmf.mk"
$ pip install "git+https://github.com/esmf-org/esmf.git@${ESMFVERSION}#subdirectory=src/addon/ESMPy/"
Note: The pip install command above for esmf module may produce an AttributeError. At present (19/07/2022) an error of this type is expected and may not mean the xesmf module cannot be installed. This error will be fixed if PR #49 is merged.
Now the dependencies have all been installed, the xesmf library can be installed within the virtual environment
bash
pip install xesmf
Developers
If you'd like to contribute to OpenGHG please see the contributing section of our documentation. If you'd like to take a look at the source and run the tests follow the steps below.
Clone
bash
git clone https://github.com/openghg/openghg.git
Install dependencies
We recommend you create a virtual environment first
bash
python -m venv openghg_env
Then activate the environment
bash
source openghg_env/bin/activate
Then install the dependencies
bash
cd openghg
pip install --upgrade pip wheel setuptools
pip install -r requirements.txt -r requirements-dev.txt
Next you can install OpenGHG in editable mode using the -e flag. This installs the package from
the local path and means any changes you make to the code will be immediately available when
using the package.
bash
pip install -e .
OpenGHG should now be installed in your virtual environment.
See above for additional steps to install the xesmf library as required.
Run the tests
To run the tests
bash
pytest -v tests/
NOTE: Some of the tests require the udunits2 library to be installed.
The udunits package is not pip installable so we've added a separate flag to specifically run these tests. If you're on Debian / Ubuntu you can do
bash
sudo apt-get install libudunits2-0
Running CF Checker tests
You can then run the cfchecks marked tests using
bash
pytest -v --run-cfchecks tests/
Running ICOS tests
Some of our tests retrieve data from the ICOS Carbon Portal and so to avoid load on the ICOS severs these should not be run frequently. They should only be run when working on this functionality or before a release. These tests are marked icos with pytest.mark.
bash
pytest -v --run-icos tests/
If all the tests pass then you're good to go. If they don't please open an issue and let us know some details about your setup.
Documentation
For further documentation and tutorials please visit our documentation.
Community
If you'd like further help or would like to talk to one of the developers of this project, please join our Gitter at gitter.im/openghg/lobby.
Owner
- Name: OpenGHG
- Login: openghg
- Kind: organization
- Email: contact@openghg.org
- Website: https://www.openghg.org
- Repositories: 7
- Profile: https://github.com/openghg
GitHub Events
Total
- Create event: 121
- Issues event: 202
- Watch event: 9
- Delete event: 85
- Issue comment event: 248
- Push event: 719
- Gollum event: 106
- Pull request event: 233
- Pull request review event: 513
- Pull request review comment event: 373
- Fork event: 5
Last Year
- Create event: 121
- Issues event: 202
- Watch event: 9
- Delete event: 85
- Issue comment event: 248
- Push event: 719
- Gollum event: 106
- Pull request event: 233
- Pull request review event: 513
- Pull request review comment event: 373
- Fork event: 5
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gareth Jones | o****g@g****m | 2,123 |
| Rachel Tunnicliffe | r****3@b****k | 1,012 |
| SutarPrasad | v****5@b****k | 809 |
| Brendan Murphy | b****y@b****k | 569 |
| Ben | q****0@b****k | 55 |
| Alexandre Danjou | a****o@g****m | 49 |
| joe-pitt | j****t@b****k | 23 |
| Matt Rigby | m****y@b****k | 20 |
| Christopher Woods | c****s@g****m | 17 |
| Elena Fillola | e****8@b****k | 17 |
| EricSaboya | e****4@g****m | 11 |
| zh21490 | z****0@b****v | 11 |
| Helene De Longueville | q****4@b****e | 5 |
| ro21302 | r****2@b****v | 2 |
| Noah Brelage | b****e@e****t | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 768
- Total pull requests: 889
- Average time to close issues: 4 months
- Average time to close pull requests: 21 days
- Total issue authors: 21
- Total pull request authors: 16
- Average comments per issue: 1.39
- Average comments per pull request: 0.98
- Merged pull requests: 684
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 143
- Pull requests: 302
- Average time to close issues: 18 days
- Average time to close pull requests: 8 days
- Issue authors: 10
- Pull request authors: 8
- Average comments per issue: 0.57
- Average comments per pull request: 0.41
- Merged pull requests: 207
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- gareth-j (363)
- rt17603 (200)
- brendan-m-murphy (77)
- SutarPrasad (44)
- joe-pitt (25)
- EricSaboya (10)
- alexdanjou (8)
- elenafillo (8)
- mrghg (7)
- aliceramsden (5)
- ag12733 (5)
- hdelongueville (3)
- qq23840 (3)
- hanchawn (3)
- jess-randell (1)
Pull Request Authors
- gareth-j (263)
- rt17603 (220)
- SutarPrasad (185)
- brendan-m-murphy (138)
- alexdanjou (28)
- joe-pitt (13)
- elenafillo (11)
- mrghg (10)
- EricSaboya (9)
- qq23840 (4)
- pearson01 (2)
- Brelage (2)
- aliceramsden (1)
- achhayapathak (1)
- hdelongueville (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 473 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 26
- Total maintainers: 1
pypi.org: openghg
OpenGHG: A platform for greenhouse gas data analysis
- Documentation: https://www.openghg.org
- License: apache-2.0
-
Latest release: 1.0.0
published almost 4 years ago