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Merge pull request #203 from tobac-project/RC_v1.4.0
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| [run] | ||
| source=tobac | ||
| omit = tobac/tests/* | ||
| omit = | ||
| tobac/tests/* | ||
| setup.py |
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| __pycache__ | ||
| .vscode | ||
| htmlcov | ||
| .coverage | ||
| .coverage | ||
| build | ||
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| version: 2 | ||
| formats: all | ||
| python: | ||
| version: 3 | ||
| install: | ||
| - requirements: doc/requirements.txt | ||
| system_packages: true |
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| { | ||
| "title": "tobac - Tracking and Object-based Analysis of Clouds", | ||
| "description": "tobac is a Python package to identify, track and analyze clouds in different types of gridded datasets, such as 3D model output from cloud-resolving model simulations or 2D data from satellite retrievals.", | ||
| "creators": [ | ||
| { | ||
| "name": "tobac Community" | ||
| }, | ||
| { | ||
| "name": "Heikenfeld, Max", | ||
| "affiliation": "University of Oxford", | ||
| "orcid": "0000-0001-8124-8048" | ||
| }, | ||
| { | ||
| "name": "Marinescu, Peter J.", | ||
| "affiliation": "Colorado State University", | ||
| "orcid": "0000-0002-5842-969X" | ||
| }, | ||
| { | ||
| "name": "Freeman, Sean W.", | ||
| "affiliation": "Colorado State University", | ||
| "orcid": "0000-0002-7398-1597" | ||
| }, | ||
| { | ||
| "name": "Kukulies, Julia", | ||
| "affiliation": "University of Gothenburg (Sweden)", | ||
| "orcid": "0000-0001-6084-0069" | ||
| }, | ||
| { | ||
| "name": "Jones, William K.", | ||
| "affiliation": "University of Oxford", | ||
| "orcid": "0000-0001-9786-3723" | ||
| }, | ||
| { | ||
| "name": "Senf, Fabian", | ||
| "affiliation": "Leibniz Institute for Tropospheric Research, Leipzig (Germany)", | ||
| "orcid": "0000-0003-1685-2657" | ||
| }, | ||
| { | ||
| "name": "Bruning, Eric", | ||
| "affiliation": "Texas Tech University", | ||
| "orcid": "0000-0003-1959-442X" | ||
| }, | ||
| { | ||
| "name": "Brunner, Kelcy", | ||
| "affiliation": "Texas Tech University", | ||
| "orcid": "0000-0003-3938-0963" | ||
| }, | ||
| { | ||
| "name": "Collis, Scott M.", | ||
| "affiliation": "Argonne National Laboratory", | ||
| "orcid": "0000-0002-2303-687X" | ||
| }, | ||
| { | ||
| "name": "Pfeifer, Nils", | ||
| "affiliation": "Leibniz Institute for Tropospheric Research, Leipzig (Germany)", | ||
| "orcid": "0000-0002-5350-1445" | ||
| }, | ||
| { | ||
| "name": "Raut, Bhupendra A.", | ||
| "affiliation": "Northwestern-Argonne Institute of Science and Engineering, Argonne National Laboratory", | ||
| "orcid": "0000-0001-5598-1393" | ||
| }, | ||
| { | ||
| "name": "Stier, Philip", | ||
| "affiliation": "University of Oxford", | ||
| "orcid": "0000-0002-1191-0128" | ||
| }, | ||
| { | ||
| "name": "van den Heever, Sue C.", | ||
| "affiliation": "Colorado State University", | ||
| "orcid": "0000-0001-9843-3864" | ||
| }, | ||
| { | ||
| "name": "Zhang, Xin", | ||
| "affiliation": "Nanjing University of Information Science & Technology (China)", | ||
| "orcid": "0000-0002-1756-6620" | ||
| } | ||
| ], | ||
| "license": "BSD-3-Clause", | ||
| "keywords": [ | ||
| "cloud tracking" | ||
| ], | ||
| "access_right": "open", | ||
| "upload_type": "software" | ||
| } |
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| # Codecov.io settings | ||
|
|
||
| coverage: | ||
| status: | ||
| project: | ||
| default: | ||
| # basic settings | ||
| # auto target means look at deltas from previous | ||
| target: auto | ||
| # Threshold we can drop coverage before failing CI | ||
| threshold: 1% | ||
| base: auto | ||
| flags: | ||
| - unit | ||
| paths: | ||
| - "tobac" | ||
|
|
||
| # what folders and files to ignore | ||
| ignore: | ||
| - "tobac/tests/.*" | ||
| - "setup.py" | ||
|
|
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| /* from https://github.com/readthedocs/sphinx_rtd_theme/issues/117#issuecomment-41506687 */ | ||
| /* with augmentations from https://github.com/readthedocs/sphinx_rtd_theme/issues/117#issuecomment-153083280 */ | ||
| /* override table width restrictions */ | ||
| @media screen and (min-width: 767px) { | ||
|
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| .wy-table-responsive table td { | ||
| /* !important prevents the common CSS stylesheets from | ||
| overriding this as on RTD they are loaded after this stylesheet */ | ||
| white-space: normal !important; | ||
| } | ||
|
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| .wy-table-responsive { | ||
| max-width: 100%; | ||
| overflow: visible !important; | ||
|
|
||
| } | ||
|
|
||
| } |
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| .. | ||
| Documentation of analysis functions | ||
| TODO: include descriptions of the analysis functions and examples | ||
| Analysis | ||
| ======= | ||
| tobac provides several analysis functions that allow for the calculation of important quantities based on the tracking results. This includes the calculation of important properties of the tracked objects such as cloud lifetimes, cloud areas/volumes, but also allows for a convenient calculation of statistics for arbitratry fields of the same shape as as the input data used for the tracking analysis. | ||
|
|
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| ========= | ||
| tobac provides several analysis functions that allow for the calculation of important quantities based on the tracking results. This includes the calculation of properties such as feature lifetimes and feature areas/volumes, but also allows for a convenient calculation of statistics for arbitrary fields of the same shape as as the input data used for the tracking analysis. | ||
|
|
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| Handling Large Datasets | ||
| ------------------------------------- | ||
|
|
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| Often, one desires to use *tobac* to identify and track features in large datasets ("big data"). This documentation strives to suggest various methods for doing so efficiently. Current versions of *tobac* do not allow for out-of-memory computation, meaning that these strategies may need to be employed for both computational and memory reasons. | ||
|
|
||
| .. _Split Feature Detection: | ||
| ======================= | ||
| Split Feature Detection | ||
| ======================= | ||
| Current versions of threshold feature detection (see :doc:`feature_detection_overview`) are time independent, meaning that one can parallelize feature detection across all times (although not across space). *tobac* provides the :py:meth:`tobac.utils.combine_tobac_feats` function to combine a list of dataframes produced by a parallelization method (such as :code:`jug` or :code:`multiprocessing.pool`) into a single combined dataframe suitable to perform tracking with. | ||
|
|
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| '''This file is used to configure the Sphinx build of our documentation. | ||
| The documentation on setting this up is here: https://www.sphinx-doc.org/en/master/usage/configuration.html | ||
| ''' | ||
|
|
||
| # This is the standard readthedocs theme. | ||
| import sphinx_rtd_theme | ||
| import sys, os | ||
|
|
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| sys.path.insert(0, os.path.abspath('extensions')) | ||
|
|
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| # What Sphinx extensions do we need | ||
| extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo', | ||
| 'sphinx.ext.coverage', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', | ||
| 'sphinx_rtd_theme','sphinx.ext.napoleon', 'nbsphinx'] | ||
|
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| html_theme = "sphinx_rtd_theme" | ||
|
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| html_static_path = ['_static'] | ||
|
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| project = u'tobac' | ||
|
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| master_doc = 'index' | ||
|
|
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| # allow dropdowns | ||
| collapse_navigation = False | ||
|
|
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| # Include our custom CSS (currently for special table config) | ||
| def setup(app): | ||
| app.add_css_file("theme_overrides.css") | ||
|
|
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| # This should include all modules used in tobac. These are dummy imports, | ||
| # but should include both required and optional dependencies. | ||
| autodoc_mock_imports = ['numpy', 'scipy', 'scikit-image', 'pandas', 'pytables', 'matplotlib', 'iris', | ||
| 'cf-units', 'xarray', 'cartopy', 'trackpy', 'numba'] | ||
|
|
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| sys.path.insert(0, os.path.abspath("../")) | ||
|
|
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| # Napoleon settings for configuring the Napoleon extension | ||
| # See documentation here: | ||
| # https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html | ||
| napoleon_google_docstring = True | ||
| napoleon_numpy_docstring = True | ||
| napoleon_include_init_with_doc = False | ||
| napoleon_include_private_with_doc = False | ||
| napoleon_include_special_with_doc = True | ||
| napoleon_use_admonition_for_examples = False | ||
| napoleon_use_admonition_for_notes = False | ||
| napoleon_use_admonition_for_references = False | ||
| napoleon_use_ivar = False | ||
| napoleon_use_param = True | ||
| napoleon_use_rtype = True | ||
| napoleon_preprocess_types = False | ||
| napoleon_type_aliases = None | ||
| napoleon_attr_annotations = True |
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