| Name | cdm-reader-mapper JSON |
| Version |
1.0.2
JSON |
| download |
| home_page | None |
| Summary | Common Data Model reader and mapper toolbox |
| upload_time | 2024-11-13 10:40:18 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | None |
| keywords |
cdm_reader_mapper
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
==================================================================
Common Data Model reader and mapper: ``cdm_reader_mapper`` toolbox
==================================================================
+----------------------------+----------------------------------------------------------------+
| Versions | |pypi| |versions| |
+----------------------------+----------------------------------------------------------------+
| Documentation and Support | |docs| |
+----------------------------+----------------------------------------------------------------+
| Open Source | |license| |zenodo| |
+----------------------------+----------------------------------------------------------------+
| | |fair-software| |ossf| |
+----------------------------+----------------------------------------------------------------+
| Coding Standards | |black| |ruff| |pre-commit| |
+----------------------------+----------------------------------------------------------------+
| | |security| |fossa| |codefactor| |
+----------------------------+----------------------------------------------------------------+
| Development Status | |status| |build| |coveralls| |
+----------------------------+----------------------------------------------------------------+
| Funding | |c3s| |
+----------------------------+----------------------------------------------------------------+
| | |noc| |ukmcas| |
+----------------------------+----------------------------------------------------------------+
The ``cdm_reader_mapper`` toolbox is a python_ tool designed for both:
* to read data files compliant with a user specified `data model`_
* map observed variables and its associated metadata from a `data model`_ or models combination to the `C3S CDS Common Data Model`_ (CDM) format
It was developed to read the IMMA_ (International Maritime Meteorological Archive) data format, but it has been enhanced to account for meteorological data formats in the case of:
* Data that is stored in a human-readable manner: “ASCII” format.
* Data is stored in a Network Common Data Format: "NetCDF" format.
* Data that is organized in single line reports
* Reports that have a coherent internal structure and can be modelised.
* Reports that have a fixed width or field delimited types
* Reports that can be organized in sections, in which case each section can be of different types (fixed width of delimited)
Installation
------------
You can install the package directly from pip:
.. code-block:: console
pip install cdm_reader_mapper
If you want to contribute, we recommend cloning the repository and installing the package in development mode, e.g.
.. code-block:: console
git clone https://github.com/glamod/cdm_reader_mapper
cd cdm_reader_mapper
pip install -e .
This will install the package but you can still edit it and you don't need the package in your :code:`PYTHONPATH`
Documentation
-------------
The official documentation is at https://cdm-reader-mapper.readthedocs.io/
How to make the most of cdm_reader_mapper:
* `How to read an IMMA file`_
* `How to build your own data model schema`_
* `How to map to the Common Data Model (CDM)`_
Logging
-------
By default, :code:`cdm_reader_mapper` outputs logging information to :code:`stdout`. To tell :code:`cdm_reader_mapper` to output logs to a file, set the :code:`CDM_LOG_FILE` environment variable **before** loading :code:`cdm_reader_mapper`.
.. code-block:: python
import os
os.environ["CDM_LOG_FILE"] = "log_file.log"
import cdm_reader_mapper as cdm
This will set the file :code:`log_file.log` as the output for all logging information from :code:`cdm_reader_mapper`, including the initial logging on loading of the package.
Run a test
----------
Read imma data with the `cdm_reader_mapper.mdf_reader.read()` function and copy the data attributes:
.. code-block:: python
from cdm_reader_mapper.mdf_reader import read
from cdm_reader_mapper.data import test_data
data = test_data.test_icoads_r300_d701.get("source")
imma_data = read(
filepath, imodel="icoads_r300_d701", sections=["core", "c1", "c98"]
)
data_raw = imma_data.data.copy()
Map this data to a CDM build for the same deck (in this case deck 704: US Marine Metereological Journal collection of data):
.. code-block:: python
from cdm_reader_mapper.cdm_mapper import map_model
name_of_model = "icoads_r300_d704"
cdm_dict = map_model(
data_raw,
imodel=name_of_model,
log_level="DEBUG",
)
For more details on how to use the ``cdm_reader_mapper`` toolbox see the following `jupyter example notebooks`_.
Contributing to cdm_reader_mapper
---------------------------------
If you're interested in participating in the development of `cdm_reader_mapper` by suggesting new features, new indices or report bugs, please leave us a message on the `issue tracker`_.
If you would like to contribute code or documentation (which is greatly appreciated!), check out the `Contributing Guidelines`_ before you begin!
How to cite this library
------------------------
If you wish to cite `glamod-marine-processing` in a research publication, we kindly ask that you refer to Zenodo: https://zenodo.org/records/14056188.
License
-------
This is free software: you can redistribute it and/or modify it under the terms of the `Apache License 2.0`_. A copy of this license is provided in the code repository (`LICENSE`_).
Credits
-------
``cdm_reader_mapper`` development is funded through Copernicus Climate Change Service (C3S_).
Furthermore, acknowledgments go to National Oceanography Centre (NOC_) and UK Marine and Climate Advisory Service (UKMCAS_).
This package was created with Cookiecutter_ and the `audreyfeldroy/cookiecutter-pypackage`_ project template.
.. hyperlinks
.. _Apache License 2.0: https://opensource.org/license/apache-2-0/
.. _audreyfeldroy/cookiecutter-pypackage: https://github.com/audreyfeldroy/cookiecutter-pypackage/
.. _C3S: https://climate.copernicus.eu/
.. _C3S CDS Common Data Model: https://git.noc.ac.uk/brecinosrivas/cdm-mapper/-/blob/master/docs/cdm_latest.pdf
.. _Contributing Guidelines: https://github.com/glamod/cdm_reader_mapper/blob/main/CONTRIBUTING.rst
.. _Cookiecutter: https://github.com/cookiecutter/cookiecutter/
.. _data model: https://cds.climate.copernicus.eu/toolbox/doc/how-to/15_how_to_understand_the_common_data_model/15_how_to_understand_the_common_data_model.html
.. _How to build your own data model schema: https://cdm-reader-mapper.readthedocs.io/en/latest/example_notebooks/CLIWOC_datamodel.html
.. _How to map to the Common Data Model (CDM): https://cdm-reader-mapper.readthedocs.io/en/latest/example_notebooks/CDM_mapper_example_deck704.html
.. _How to read an IMMA file: https://cdm-reader-mapper.readthedocs.io/en/latest/example_notebooks/mdf_reader_test_overview.html
.. _IMMA: https://icoads.noaa.gov/e-doc/imma/R3.0-imma1.pdf
.. _jupyter example notebooks: https://github.com/glamod/cdm_reader_mapper/tree/main/docs/example_notebooks
.. _LICENSE: https://github.com/glamod/cdm_reader_mapper/blob/main/LICENSE
.. _NOC: https://noc.ac.uk/
.. _python: https://www.python.org
.. _Issue #11038: https://github.com/dask/dask/issues/11038
.. _issue tracker: https://github.com/glamod/cdm_reader_mapper/issues
.. _PR #11035: https://github.com/dask/dask/pull/11035
.. _UKMCAS: https://www.metoffice.gov.uk/services/data/met-office-marine-data-service
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"description": "==================================================================\nCommon Data Model reader and mapper: ``cdm_reader_mapper`` toolbox\n==================================================================\n\n+----------------------------+----------------------------------------------------------------+\n| Versions | |pypi| |versions| |\n+----------------------------+----------------------------------------------------------------+\n| Documentation and Support | |docs| |\n+----------------------------+----------------------------------------------------------------+\n| Open Source | |license| |zenodo| |\n+----------------------------+----------------------------------------------------------------+\n| | |fair-software| |ossf| |\n+----------------------------+----------------------------------------------------------------+\n| Coding Standards | |black| |ruff| |pre-commit| |\n+----------------------------+----------------------------------------------------------------+\n| | |security| |fossa| |codefactor| |\n+----------------------------+----------------------------------------------------------------+\n| Development Status | |status| |build| |coveralls| |\n+----------------------------+----------------------------------------------------------------+\n| Funding | |c3s| |\n+----------------------------+----------------------------------------------------------------+\n| | |noc| |ukmcas| |\n+----------------------------+----------------------------------------------------------------+\n\nThe ``cdm_reader_mapper`` toolbox is a python_ tool designed for both:\n\n* to read data files compliant with a user specified `data model`_\n* map observed variables and its associated metadata from a `data model`_ or models combination to the `C3S CDS Common Data Model`_ (CDM) format\n\nIt was developed to read the IMMA_ (International Maritime Meteorological Archive) data format, but it has been enhanced to account for meteorological data formats in the case of:\n\n* Data that is stored in a human-readable manner: \u201cASCII\u201d format.\n* Data is stored in a Network Common Data Format: \"NetCDF\" format.\n* Data that is organized in single line reports\n* Reports that have a coherent internal structure and can be modelised.\n* Reports that have a fixed width or field delimited types\n* Reports that can be organized in sections, in which case each section can be of different types (fixed width of delimited)\n\n\nInstallation\n------------\n\nYou can install the package directly from pip:\n\n.. code-block:: console\n\n pip install cdm_reader_mapper\n\nIf you want to contribute, we recommend cloning the repository and installing the package in development mode, e.g.\n\n.. code-block:: console\n\n git clone https://github.com/glamod/cdm_reader_mapper\n cd cdm_reader_mapper\n pip install -e .\n\nThis will install the package but you can still edit it and you don't need the package in your :code:`PYTHONPATH`\n\nDocumentation\n-------------\n\nThe official documentation is at https://cdm-reader-mapper.readthedocs.io/\n\nHow to make the most of cdm_reader_mapper:\n\n* `How to read an IMMA file`_\n* `How to build your own data model schema`_\n* `How to map to the Common Data Model (CDM)`_\n\nLogging\n-------\n\nBy default, :code:`cdm_reader_mapper` outputs logging information to :code:`stdout`. To tell :code:`cdm_reader_mapper` to output logs to a file, set the :code:`CDM_LOG_FILE` environment variable **before** loading :code:`cdm_reader_mapper`.\n\n.. code-block:: python\n\n import os\n\n os.environ[\"CDM_LOG_FILE\"] = \"log_file.log\"\n\n import cdm_reader_mapper as cdm\n\nThis will set the file :code:`log_file.log` as the output for all logging information from :code:`cdm_reader_mapper`, including the initial logging on loading of the package.\n\n\nRun a test\n----------\n\nRead imma data with the `cdm_reader_mapper.mdf_reader.read()` function and copy the data attributes:\n\n.. code-block:: python\n\n from cdm_reader_mapper.mdf_reader import read\n from cdm_reader_mapper.data import test_data\n\n data = test_data.test_icoads_r300_d701.get(\"source\")\n\n imma_data = read(\n filepath, imodel=\"icoads_r300_d701\", sections=[\"core\", \"c1\", \"c98\"]\n )\n\n data_raw = imma_data.data.copy()\n\n\nMap this data to a CDM build for the same deck (in this case deck 704: US Marine Metereological Journal collection of data):\n\n.. code-block:: python\n\n from cdm_reader_mapper.cdm_mapper import map_model\n\n name_of_model = \"icoads_r300_d704\"\n\n cdm_dict = map_model(\n data_raw,\n imodel=name_of_model,\n log_level=\"DEBUG\",\n )\n\n\nFor more details on how to use the ``cdm_reader_mapper`` toolbox see the following `jupyter example notebooks`_.\n\nContributing to cdm_reader_mapper\n---------------------------------\n\nIf you're interested in participating in the development of `cdm_reader_mapper` by suggesting new features, new indices or report bugs, please leave us a message on the `issue tracker`_.\n\nIf you would like to contribute code or documentation (which is greatly appreciated!), check out the `Contributing Guidelines`_ before you begin!\n\nHow to cite this library\n------------------------\n\nIf you wish to cite `glamod-marine-processing` in a research publication, we kindly ask that you refer to Zenodo: https://zenodo.org/records/14056188.\n\nLicense\n-------\n\nThis is free software: you can redistribute it and/or modify it under the terms of the `Apache License 2.0`_. A copy of this license is provided in the code repository (`LICENSE`_).\n\nCredits\n-------\n\n``cdm_reader_mapper`` development is funded through Copernicus Climate Change Service (C3S_).\n\nFurthermore, acknowledgments go to National Oceanography Centre (NOC_) and UK Marine and Climate Advisory Service (UKMCAS_).\n\nThis package was created with Cookiecutter_ and the `audreyfeldroy/cookiecutter-pypackage`_ project template.\n\n.. hyperlinks\n\n.. _Apache License 2.0: https://opensource.org/license/apache-2-0/\n\n.. _audreyfeldroy/cookiecutter-pypackage: https://github.com/audreyfeldroy/cookiecutter-pypackage/\n\n.. _C3S: https://climate.copernicus.eu/\n\n.. _C3S CDS Common Data Model: https://git.noc.ac.uk/brecinosrivas/cdm-mapper/-/blob/master/docs/cdm_latest.pdf\n\n.. _Contributing Guidelines: https://github.com/glamod/cdm_reader_mapper/blob/main/CONTRIBUTING.rst\n\n.. _Cookiecutter: https://github.com/cookiecutter/cookiecutter/\n\n.. _data model: https://cds.climate.copernicus.eu/toolbox/doc/how-to/15_how_to_understand_the_common_data_model/15_how_to_understand_the_common_data_model.html\n\n.. _How to build your own data model schema: https://cdm-reader-mapper.readthedocs.io/en/latest/example_notebooks/CLIWOC_datamodel.html\n\n.. _How to map to the Common Data Model (CDM): https://cdm-reader-mapper.readthedocs.io/en/latest/example_notebooks/CDM_mapper_example_deck704.html\n\n.. _How to read an IMMA file: https://cdm-reader-mapper.readthedocs.io/en/latest/example_notebooks/mdf_reader_test_overview.html\n\n.. _IMMA: https://icoads.noaa.gov/e-doc/imma/R3.0-imma1.pdf\n\n.. _jupyter example notebooks: https://github.com/glamod/cdm_reader_mapper/tree/main/docs/example_notebooks\n\n.. _LICENSE: https://github.com/glamod/cdm_reader_mapper/blob/main/LICENSE\n\n.. _NOC: https://noc.ac.uk/\n\n.. _python: https://www.python.org\n\n.. _Issue #11038: https://github.com/dask/dask/issues/11038\n\n.. _issue tracker: 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