docs: replaced api ref

Author: pabloitu

docs/reference/api_reference.rst

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+API Reference
+=============
+
+This contains a reference document to the floatCSEP API.
+
+
+Commands
+--------
+
+The commands and entry-points with which to call `floatcsep` from the terminal
+are:
+
+.. :currentmodule:: floatcsep.commands.main
+
+.. automodule:: floatcsep.commands.main
+
+.. autosummary::
+   :toctree: generated
+
+    run
+    plot
+    reproduce
+
+
+Experiment
+----------
+
+.. :currentmodule:: floatcsep.experiment
+
+.. automodule:: floatcsep.experiment
+
+
+The experiment is defined using the :class:`Experiment` class.
+
+.. autosummary::
+   :toctree: generated
+
+    Experiment
+    Experiment.set_models
+    Experiment.get_model
+    Experiment.stage_models
+    Experiment.set_tests
+    Experiment.catalog
+    Experiment.set_test_cat
+    Experiment.set_tasks
+    Experiment.run
+    Experiment.read_results
+    Experiment.plot_results
+    Experiment.plot_catalog
+    Experiment.plot_forecasts
+    Experiment.generate_report
+    Experiment.to_dict
+    Experiment.to_yml
+    Experiment.from_yml
+
+
+Models
+------
+
+.. :currentmodule:: floatcsep.model
+
+.. automodule:: floatcsep.model
+
+A model is defined using the :class:`Model` class.
+
+.. autosummary::
+   :toctree: generated
+
+    Model
+    Model.get_source
+    Model.stage
+    Model.init_db
+    Model.rm_db
+    Model.get_forecast
+    Model.create_forecast
+    Model.forecast_from_func
+    Model.forecast_from_file
+    Model.to_dict
+    Model.from_dict
+
+
+Evaluations
+-----------
+
+.. :currentmodule:: floatcsep.evaluation
+
+.. automodule:: floatcsep.evaluation
+
+A test is defined using the :class:`Evaluation` class.
+
+.. autosummary::
+   :toctree: generated
+
+    Evaluation
+    Evaluation.type
+    Evaluation.get_catalog
+    Evaluation.prepare_args
+    Evaluation.compute
+    Evaluation.write_result
+    Evaluation.to_dict
+    Evaluation.from_dict
+
+
+Accessors
+---------
+
+.. :currentmodule:: floatcsep.utils.accessors
+
+.. automodule:: floatcsep.utils.accessors
+
+.. autosummary::
+   :toctree: generated
+
+    from_zenodo
+    from_git
+    download_file
+    check_hash
+
+
+Helper Functions
+----------------
+
+.. :currentmodule:: floatcsep.utils.helpers
+
+.. automodule:: floatcsep.utils.helpers
+
+.. autosummary::
+   :toctree: generated
+
+    parse_csep_func
+    parse_timedelta_string
+    read_time_config
+    read_region_config
+    timewindows_ti
+    timewindows_td
+    timewindow2str
+    plot_sequential_likelihood
+    magnitude_vs_time
+    sequential_likelihood
+    sequential_information_gain
+    vector_poisson_t_w_test
+
+
+Readers
+-------
+
+.. :currentmodule:: floatcsep.utils.readers
+
+.. automodule:: floatcsep.utils.readers
+
+.. autosummary::
+   :toctree: generated
+
+    ForecastParsers.dat
+    ForecastParsers.xml
+    ForecastParsers.quadtree
+    ForecastParsers.csv
+    ForecastParsers.hdf5
+    HDF5Serializer.grid2hdf5
+    serialize
+
+
+Environments
+------------
+
+.. :currentmodule:: floatcsep.infrastructure.environments
+
+.. automodule:: floatcsep.infrastructure.environments
+
+.. autosummary::
+   :toctree: generated
+
+    CondaManager
+    CondaManager.create_environment
+    CondaManager.env_exists
+    CondaManager.install_dependencies
+    CondaManager.run_command
+
+    VenvManager
+    CondaManager.create_environment
+    CondaManager.env_exists
+    CondaManager.install_dependencies
+    CondaManager.run_command
+
+
+Registries
+----------
+
+.. :currentmodule:: floatcsep.infrastructure.registries
+
+.. automodule:: floatcsep.infrastructure.registries
+
+.. autosummary::
+   :toctree: generated
+
+    FileRegistry
+    FileRegistry.abs
+    FileRegistry.absdir
+    FileRegistry.rel
+    FileRegistry.rel_dir
+    FileRegistry.file_exists
+
+    ForecastRegistry
+    ForecastRegistry.get
+    ForecastRegistry.get_forecast
+    ForecastRegistry.dir
+    ForecastRegistry.fmt
+    ForecastRegistry.as_dict
+    ForecastRegistry.forecast_exist
+    ForecastRegistry.build_tree
+    ForecastRegistry.log_tree
+
+    ExperimentRegistry
+    ExperimentRegistry.add_forecast_registry
+    ExperimentRegistry.get_forecast_registry
+    ExperimentRegistry.log_forecast_trees
+    ExperimentRegistry.get
+    ExperimentRegistry.get_result
+    ExperimentRegistry.get_test_catalog
+    ExperimentRegistry.get_figure
+    ExperimentRegistry.result_exist
+    ExperimentRegistry.as_dict
+    ExperimentRegistry.build_tree
+    ExperimentRegistry.log_results_tree
+
+
+Repositories
+------------
+
+.. :currentmodule:: floatcsep.infrastructure.repositories
+
+.. automodule:: floatcsep.infrastructure.repositories
+
+.. autosummary::
+   :toctree: generated
+
+   ForecastRepository
+   ForecastRepository.factory
+
+   CatalogForecastRepository
+   CatalogForecastRepository.load_forecast
+   CatalogForecastRepository._load_single_forecast
+
+   GriddedForecastRepository.load_forecast
+   GriddedForecastRepository._get_or_load_forecast
+   GriddedForecastRepository._load_single_forecast
+
+   ResultsRepository
+   ResultsRepository._load_result
+   ResultsRepository.load_results
+   ResultsRepository.write_result
+
+   CatalogRepository
+   CatalogRepository.set_main_catalog
+   CatalogRepository.catalog
+   CatalogRepository.get_test_cat
+   CatalogRepository.set_test_cat
+   CatalogRepository.set_input_cat
+
+
+Engine
+------
+
+.. :currentmodule:: floatcsep.infrastructure.engine
+
+.. automodule:: floatcsep.infrastructure.engine
+
+.. autosummary::
+   :toctree: generated
+
+    Task
+    Task.sign_match
+    Task.run
+    Task.check_exist
+
+    TaskGraph
+    TaskGraph.ntasks
+    TaskGraph.add
+    TaskGraph.add_dependency
+    TaskGraph.run
+    TaskGraph.check_exist