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Observation and Modeling","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# Open Methane Prior emissions estimate\n\nMethod to calculate a gridded, prior emissions estimate for methane across Australia.\n\nThis repository is matched with downloadable input data so that it will run out of the box.\n\n## Initialise\n\nCopy the `.env.example` file to `.env` and customise the paths as you need.\n\nIn order to download the GFAS emissions data, credentials for the Copernicus\nAtmospheric Data Store (ADS) API are required. Instructions for registering for\nthe ADS API and setting up the credentials are provided at \n[ADS Docs](https://ads.atmosphere.copernicus.eu/how-to-api).\n\nStep-by-step:\n- Register for an [ECMWF](https://www.ecmwf.int/) account\n- While logged in to ECMWF, register your account with [ADS](https://ads.atmosphere.copernicus.eu/)\n- Accept the ADS terms and conditions\n- Accept the License to use Copernicus products, by visiting the Download tab of the dataset you wish to use and scrolling to the Terms of use section: https://ads.atmosphere.copernicus.eu/datasets/cams-global-fire-emissions-gfas?tab=download\n\nNote: the ADS API is different from the CDS (Climate Data Store) API\neven though they are both parts of the Copernicus program\nand share the same credentials file.\n\n\n### Requirements\n\nBefore installation, you will need to make sure that [poetry](https://python-poetry.org/docs/) version 1 is installed.\n\nStep-by-step:\n- Install pipx \n```bash\npython -m pip install --user pipx\n```\n\n- Install poetry and downgrading your poetry version to version v1.\n```bash\npipx install poetry~=1.0 --force\n```\n\n\n### Installation\n\nThe Open Methane prior can be installed from source into a virtual environment with:\n\n```bash\nmake virtual-environment\n```\n\nThe `Makefile` contains the set of commands to create the virtual environment.\nYou can read the instructions out and run the commands by hand if you wish.\n\n### Input Data\n\nInput data will be downloaded on-demand by the layers that use it while running\nomPrior.py. To inspect where data is fetched from, look for instances of\n`DataSource` defined in each layer.\n\nThe downloaded files will be stored in the path specified in `INPUTS` env var\n(`data/inputs` by default).\n\n### Domain Info\n\nThe domain of interest for the prior is defined using an input domain netCDF\nfile. The format of the input domain is based on the CMAQ domain file format,\nbut updated to follow (CF Conventions)[https://cfconventions.org/cf-conventions/cf-conventions.html].\n\nNote that the input domain uses a staggered grid, so `x`, `y` coordinates, as\nwell as `lat`, `lon` coordinates, represent the center point of each grid cell.\nThe edges of each grid cell are made available in `x_bounds` and `y_bounds`\nbased on the CF Conventions \"bounds\" methodology.\n\nThis domain input file should contain the following:\n\n* Coordinates:\n  * `x`\n  * `y`\n* Variables \n  * `lat`\n  * `lon`\n  * `x_bounds`\n  * `y_bounds`\n  * `land_mask` - binary land/sea mask\n  * `lambert_conformal` - projection details\n  * `cell_name` - unique name for each grid cell based on grid.x.y format\n  * (Optionally) `inventory_mask` - binary mask denoting the area covered by\n    the inventory figures present in the input files\n* Attributes\n  * `DX`/`XCELL` - size of each grid cell in grid projection coordinates\n  * `DY`/`YCELL` - size of each grid cell in grid projection coordinates\n  * `domain_name` - the name of the domain of interest\n  * `domain_version` - a version string for the domain, typically `v1`, `v2`, etc\n  * `domain_slug` - a short, URL-safe name for the grid, often the same as `domain_name`\n\nAs part of the [Open Methane](https://openmethane.org/) project,\nwe have provided a domain file for a 10km grid over Australia.\n\nThis file will be downloaded with the other layer inputs (see [Source data](#source-data))\nusing the default configuration values.\n\nA new domain can be created using one of the provided scripts:\n- `scripts/create_prior_domain.py`\n  - create a domain from WRF and MCIP files\n- `scripts/create_subset_domain.py`\n  - create a domain by subsetting an existing Open Methane domain\n\nOr you can use these scripts as the basis for creating your domain from other\nsources.\n\n### Clean outputs\n\nThese two commands are set up so that not all generated files have to be deleted manually\nDelete all files in the `intermediates` and `outputs` directory with\n\n```\nmake clean\n```\n\nOr delete all files in `intermediates`, `outputs`, and `inputs` directory with\n\n```\nmake clean-all\n```\n\n## Run\n\n### All sectors\n\nTo calculate emissions for all sectors, run `omPrior.py` with a start and end date:\n\n```shell\npoetry run python scripts/omPrior.py --start-date 2022-07-01 --end-date 2022-07-01\n```\n\nThis takes a while to process (~10 minutes) with the vast majority of that time\nspent on the sectors which re-project large input datasets.\n\n### Specific sectors\n\nTo run a single sector or a subset of sectors, use the `--sectors` argument:\n\n```shell\npoetry run python scripts/omPrior.py --start-date 2022-07-01 --end-date 2022-07-01 \\\n  --sectors livestock,termite,fire\n```\n\nSectors must be separated by commas, without spaces, using the value from the\ndesired PriorSector `name` attribute.\n\n### Console output\n\nThe detail of console output can be controlled by setting the `LOG_LEVEL` env\nvariable. By default, this is set to `INFO`, but more or less can be achieved\nby setting other log levels:\n\n```shell\n# verbose debug output\nLOG_LEVEL=DEBUG poetry run python scripts/omPrior.py --start-date 2022-07-01 --end-date 2022-07-01\n\n# only warnings and errors\nLOG_LEVEL=WARNING poetry run python scripts/omPrior.py --start-date 2022-07-01 --end-date 2022-07-01\n```\n\nLog output can also be written to a file while still logging to the console\nwith the `LOG_FILE` env variable.\n\n```shell\nLOG_FILE=/var/log/prior.log poetry run python scripts/omPrior.py --start-date 2022-07-01 --end-date 2022-07-01\n```\n\n\n## Outputs\n\nOutputs can be found in the `data/outputs` folder. The emissions layers will be written as variables to a copy of the\ninput domain file, with an `ch4_sector_` prefix for the methane layer variable names. The sum of all layers will be stored in\nthe `ch4_total` layer.\n\nThe name of the layered output file will be `om-prior-output.nc`.\n\nThe `data/processed` folder will contain any re-projected raster data, and any files downloaded or generated in the\nprocess.\n\nOutputs can be plotted using the ncl file `plot_emis.ncl`. \n\n```console \nncl plot_emis.ncl\n```\n\n## Source data\n\nFor details about all data sources used by the prior, see [Data sources](./docs/data-sources.md).\n\n## Data directories\n\n* `data/inputs` \n  This folder should contain all the required input files. Any missing input data\n  will be fetched automatically while running the prior (see\n  [Input Data](#input-data) for more detail).\n* `data/intermediates` This folder contains any intermediate files generated\n  through the process. Everything within this folder should be ignored.\n* `data/outputs` Outputs files will be saved here.\n\n\n## Run in a Docker container\n\nTo carry out the steps described above in a Docker container, first build the Docker image with\n\n```\nmake build\n```\n\nThen run the commands to with the project path mounted as a volume:\n\n```\ndocker run --rm -v \u003c/your/path/to/openmethane-prior\u003e:/opt/project openmethane-prior python scripts/omPrior.py --start-date 2022-12-07\n```\n\nReplace the python files according to the commands in the Makefile for the other steps.\n\nNote: the CDS API credentials will also need to be provided via .env file to run\nvia docker.\n\n## For developers\n\nThe ruff-fixes target runs a series of ruff commands to format the code, check and fix linting\nissues, and then format the code again to ensure that all formatting and fixes are applied.\n\n```\nmake ruff-fixes\n```\n\nThe test target will run all the tests\n\n```\nmake test\n```\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["climate-change","climate-data"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/191748","html_url":"https://ost.ecosyste.ms/projects/191748"}