repo: Restructured floatcsep repo layout. Registries, repos, task handlers, environments and loggers are now part of infrastructure submodule. Report and Plot_handlers (old postprocess) now placed onto postprocess submodule. accessors, readers, and helpers (old utils.pt) now places onto utils submodule. modified tests and docs accordingly

Author: pabloitu

docs/intro/concepts.rst

@@ -12,7 +12,7 @@ The CSEP experiments consist in the prospective evaluation of probabilistic eart
 A Floating Testing Experiment encapsulates each experiment into its own runnable environment, taking advantage of version control (i.e. ``git``), open-data repositories (e.g. `Zenodo <https://zenodo.org>`_) and Infrastructure as Code (e.g. `Docker <https://docker.com>`_) technologies, making it reproducible, re-usable and shareable during the time scale of the
 evaluations.
 
-``feCSEP`` goals
+``floatCSEP`` goals
 ----------------
 
 This is an application to deploy reproducible and prospective experiments of earthquake forecasting, namely a Floating Eperiment, that can operate independent of a particular testing server. With this application, researchers, institutions and users can

docs/reference/api_reference.rst

@@ -10,9 +10,9 @@ Commands
 The commands and entry-points with which to call `floatcsep` from the terminal
 are:
 
-.. :currentmodule:: floatcsep.cmd.main
+.. :currentmodule:: floatcsep.commands.main
 
-.. automodule:: floatcsep.cmd.main
+.. automodule:: floatcsep.commands.main
 
 .. autosummary::
    :toctree: generated
@@ -104,46 +104,25 @@ A test is defined using the :class:`Evaluation` class.
 Accessors
 ---------
 
-.. :currentmodule:: floatcsep.accessors
+.. :currentmodule:: floatcsep.utils.accessors
 
-.. automodule:: floatcsep.accessors
+.. automodule:: floatcsep.utils.accessors
 
 .. autosummary::
    :toctree: generated
 
     from_zenodo
     from_git
+    download_file
+    check_hash
 
 
-Environments
-------------
+Helper Functions
+----------------
 
-.. :currentmodule:: floatcsep.environments
+.. :currentmodule:: floatcsep.utils.helpers
 
-.. automodule:: floatcsep.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
-
-
-Utilities
----------
-
-.. :currentmodule:: floatcsep.utils
-
-.. automodule:: floatcsep.utils
+.. automodule:: floatcsep.utils.helpers
 
 .. autosummary::
    :toctree: generated
@@ -154,9 +133,6 @@ Utilities
     read_region_config
     timewindows_ti
     timewindows_td
-    Task
-    Task.run
-    Task.check_exist
     timewindow2str
     plot_sequential_likelihood
     magnitude_vs_time
@@ -168,9 +144,9 @@ Utilities
 Readers
 -------
 
-.. :currentmodule:: floatcsep.readers
+.. :currentmodule:: floatcsep.utils.readers
 
-.. automodule:: floatcsep.readers
+.. automodule:: floatcsep.utils.readers
 
 .. autosummary::
    :toctree: generated
@@ -184,3 +160,122 @@ Readers
     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

examples/case_h/custom_report.py

@@ -1,5 +1,5 @@
-from floatcsep.report import MarkdownReport
-from floatcsep.utils import timewindow2str
+from floatcsep.postprocess.reporting import MarkdownReport
+from floatcsep.utils.helpers import timewindow2str
 
 
 def main(experiment):

floatcsep/__init__.py

@@ -1,9 +1,8 @@
-from floatcsep import logger
-from floatcsep import registry
-from floatcsep import accessors
 from floatcsep import evaluation
 from floatcsep import experiment
 from floatcsep import model
-from floatcsep import readers
+from floatcsep.infrastructure import engine, environments, registries, repositories, logger
+from floatcsep.utils import readers, accessors, helpers
+from floatcsep.postprocess import reporting, plot_handler
 
 __version__ = "0.1.4"

floatcsep/commands/__init__.py

@@ -3,9 +3,14 @@
 
 from floatcsep import __version__
 from floatcsep.experiment import Experiment, ExperimentComparison
-from floatcsep.logger import setup_logger, set_console_log_level
-from floatcsep.postprocess import plot_results, plot_forecasts, plot_catalogs, plot_custom
-from floatcsep.report import generate_report, reproducibility_report
+from floatcsep.infrastructure.logger import setup_logger, set_console_log_level
+from floatcsep.postprocess.plot_handler import (
+    plot_results,
+    plot_forecasts,
+    plot_catalogs,
+    plot_custom,
+)
+from floatcsep.postprocess.reporting import generate_report, reproducibility_report
 
 setup_logger()
 log = logging.getLogger("floatLogger")

floatcsep/cmd/main.py renamed to floatcsep/commands/main.py

@@ -7,8 +7,8 @@
 from matplotlib import pyplot
 
 from floatcsep.model import Model
-from floatcsep.registry import ExperimentRegistry
-from floatcsep.utils import parse_csep_func
+from floatcsep.infrastructure.registries import ExperimentRegistry
+from floatcsep.utils.helpers import parse_csep_func
 
 
 class Evaluation:

floatcsep/evaluation.py

@@ -13,20 +13,18 @@
 
 
 from floatcsep.evaluation import Evaluation
-from floatcsep.logger import add_fhandler
+from floatcsep.infrastructure.logger import add_fhandler
 from floatcsep.model import Model, TimeDependentModel
-from floatcsep.registry import ExperimentRegistry
-from floatcsep.repository import ResultsRepository, CatalogRepository
-from floatcsep.utils import (
+from floatcsep.infrastructure.registries import ExperimentRegistry
+from floatcsep.infrastructure.repositories import ResultsRepository, CatalogRepository
+from floatcsep.utils.helpers import (
     NoAliasLoader,
     read_time_cfg,
     read_region_cfg,
-    Task,
-    TaskGraph,
     timewindow2str,
     parse_nested_dicts,
 )
-
+from floatcsep.infrastructure.engine import Task, TaskGraph
 
 log = logging.getLogger("floatLogger")
 
@@ -150,7 +148,7 @@ def __init__(
         self.model_config = models if isinstance(models, str) else None
         self.test_config = tests if isinstance(tests, str) else None
 
-        logger = kwargs.get("logging", True)
+        logger = kwargs.get("logging", False)
         if logger:
             filename = "experiment.log" if logger is True else logger
             self.registry.logger = os.path.join(workdir, rundir, filename)