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Observation and Modeling","monthly_downloads":419,"total_dependent_repos":1,"total_dependent_packages":0,"readme":"![OpenGHG logo](https://github.com/openghg/logo/raw/main/OpenGHG_Logo_Landscape.png)\n\n## OpenGHG - a cloud platform for greenhouse gas data analysis and collaboration\n\n[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) ![OpenGHG tests](https://github.com/openghg/openghg/workflows/OpenGHG%20tests/badge.svg?branch=master)\n\nOpenGHG is a project based on the prototype [HUGS platform](https://github.com/hugs-cloud/hugs) which aims to be a platform for collaboration and analysis\nof greenhouse gas (GHG) data.\n\nThe platform will be built on open-source technologies and will allow researchers to collaborate on large datasets by harnessing the\npower and scalability of the cloud.\n\nFor more information please see [our documentation](https://docs.openghg.org/).\n\n## Install locally\n\nTo run OpenGHG locally you'll need Python 3.8 or later on Linux or MacOS, we don't currently support Windows.\n\nYou can install OpenGHG using `pip` or `conda`, though `conda` allows the complete functionality to be accessed at once.\n\n## Using `pip`\n\nTo use `pip`, first create a virtual environment\n\n```bash\npython -m venv openghg_env\n```\n\nThen activate the environment\n\n```bash\nsource openghg_env/bin/activate\n```\n\nIt'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.\n\n```bash\npip install --upgrade pip wheel setuptools\n```\n\nThen we can install OpenGHG itself\n\n```bash\npip install openghg\n```\n\nEach time you use OpenGHG please make sure to activate the environment using the `source` step above.\n\n\n\u003e **_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.\n\n## Using `conda`\n\nTo get OpenGHG installed using `conda` we'll first create a new environment\n\n```bash\nconda create --name openghg_env\n```\n\nThen activate the environment\n\n```bash\nconda activate openghg_env\n```\n\nThen install OpenGHG and its dependencies from our [conda channel](https://anaconda.org/openghg/openghg)\nand conda-forge.\n\n```bash\nconda install --channel conda-forge --channel openghg openghg\n```\n\nNote: the `xesmf` library is already incorporated into the conda install from vx.x onwards and so does not need to be installed separately.\n\n## Create the configuration file\n\nOpenGHG 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\ncreate this file in one of two ways\n\n### Command line\n\nUsing the `openghg` command line tool\n\n```\nopenghg --quickstart\n\nOpenGHG configuration\n---------------------\n\nEnter path for object store (default /home/gareth/openghg_store):\nINFO:openghg.util:Creating config at /home/gareth/.config/openghg/openghg.conf\n\nINFO:openghg.util:Configuration written to /home/gareth/.config/openghg/openghg.conf\n```\n\n### Python\n\nUsing the `create_config` function from the `openghg.util` submodule.\n\n```\nfrom openghg.util import create_config\n\ncreate_config()\n\nOpenGHG configuration\n---------------------\n\nEnter path for object store (default /home/gareth/openghg_store):\nINFO:openghg.util:Creating config at /home/gareth/.config/openghg/openghg.conf\n\nINFO:openghg.util:Configuration written to /home/gareth/.config/openghg/openghg.conf\n```\n\nYou 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`.\n\n## Additional functionality\n\nSome 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](https://xesmf.readthedocs.io/en/latest/). This Python library is built upon underlying FORTRAN and C libraries (ESMF) which cannot be installed directly within a Python virtual environment.\n\nTo use this functionality these libraries must be installed separately. One suggestion for how to do this is as follows.\n\nIf still within the created virtual environment, exit this using\n```bash\ndeactivate\n```\n\nWe 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`\n```bash\nconda create --name openghg_add esmf -c conda-forge\n```\n\nThen activate the Python virtual environment in the same way as above:\n```bash\nsource openghg_env/bin/activate\n```\n\nRun 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`):\n```bash\nESMFVERSION='v'$(conda list -n openghg_add esmf | tail -n1 | awk '{print $2}')\n$ export ESMFMKFILE=\"$(conda env list | grep openghg_add | awk '{print $2}')/lib/esmf.mk\"\n$ pip install \"git+https://github.com/esmf-org/esmf.git@${ESMFVERSION}#subdirectory=src/addon/ESMPy/\"\n```\n\n**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](https://github.com/esmf-org/esmf/pull/49) is merged.\n\nNow the dependencies have all been installed, the `xesmf` library can be installed within the virtual environment\n\n```bash\npip install xesmf\n```\n\n## Developers\n\nIf 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.\n\n### Clone\n\n```bash\ngit clone https://github.com/openghg/openghg.git\n```\n\n### Install dependencies\n\nWe recommend you create a virtual environment first\n\n```bash\npython -m venv openghg_env\n```\n\nThen activate the environment\n\n```bash\nsource openghg_env/bin/activate\n```\n\nThen install the dependencies\n\n```bash\ncd openghg\npip install --upgrade pip wheel setuptools\npip install -r requirements.txt -r requirements-dev.txt\n```\n\nNext you can install OpenGHG in editable mode using the `-e` flag. This installs the package from\nthe local path and means any changes you make to the code will be immediately available when\nusing the package.\n\n```bash\npip install -e .\n```\n\nOpenGHG should now be installed in your virtual environment.\n\nSee above for additional steps to install the `xesmf` library as required.\n\n### Run the tests\n\nTo run the tests\n\n```bash\npytest -v tests/\n```\n\n\u003e **_NOTE:_**  Some of the tests require the [udunits2](https://www.unidata.ucar.edu/software/udunits/) library to be installed.\n\nThe `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\n\n```bash\nsudo apt-get install libudunits2-0\n```\n\n#### Running CF Checker tests\n\nYou can then run the `cfchecks` marked tests using\n\n```bash\npytest -v --run-cfchecks tests/\n```\n\n#### Running ICOS tests\n\nSome 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`.\n\n```bash\npytest -v --run-icos tests/\n```\n\nIf all the tests pass then you're good to go. If they don't please [open an issue](https://github.com/openghg/openghg/issues/new) and let us\nknow some details about your setup.\n\n## Documentation\n\nFor further documentation and tutorials please visit [our documentation](https://docs.openghg.org/).\n\n## Community\n\nIf you'd like further help or would like to talk to one of the developers of this project, please join\nour Gitter at gitter.im/openghg/lobby.\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["greenhouse-gas-emissions","greenhouse-gases","greenhouse-monitoring"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/20232","html_url":"https://ost.ecosyste.ms/projects/20232"}