V0.8.0 candidate

.coveragerc

@@ -5,7 +5,6 @@ omit =
     tests/*
     docs/*
     examples/*
-    csep/utils/plots.py
     csep/utils/constants.py
     csep/utils/datasets.py
     csep/utils/documents.py

.github/workflows/build-sphinx-no-deploy.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: mamba-org/setup-micromamba@v1
         with:
           generate-run-shell: true
-          environment-file: requirements.yml
+          environment-file: environment.yml
           create-args: >-
             python=3.10
             pillow

.github/workflows/build-sphinx.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: mamba-org/setup-micromamba@v1
         with:
           generate-run-shell: true
-          environment-file: requirements.yml
+          environment-file: environment.yml
           create-args: >-
             python=3.9
             pillow

.github/workflows/build-test.yml

@@ -27,7 +27,7 @@ jobs:
       - uses: mamba-org/setup-micromamba@v1
         with:
           generate-run-shell: true
-          environment-file: requirements.yml
+          environment-file: environment.yml
           create-args: >-
             python=${{ matrix.python-version }}
 

.github/workflows/publish-pypi.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: mamba-org/setup-micromamba@v1
         with:
           generate-run-shell: true
-          environment-file: requirements.yml
+          environment-file: environment.yml
           create-args: >-
             python=3.10
 
@@ -28,13 +28,13 @@ jobs:
           conda info -a
           conda list
 
-      - name: Create sdist
+      - name: Create sdist and wheel
         run: |
-          python setup.py check
-          python setup.py sdist
+          python -m pip install --upgrade pip build
+          python -m build
 
       - name: Publish Package
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.pypi_upload_token }}

MANIFEST.in

@@ -2,7 +2,7 @@ include README.md
 include CONTRIBUTING.md
 include CODE_OF_CONDUCT.md
 include Dockerfile
-include LICENSE.txt
+include LICENSE
 include CHANGELOG.md
 include CREDITS.md
 include codemeta.json
@@ -23,8 +23,5 @@ global-exclude .git*
 global-exclude *.pyc
 global-exclude *.html
 global-exclude *.so
-global-exclude *.xls
-global-exclude *.xlsm
-global-exclude *.xlsx
 global-exclude *~
 global-exclude .DS_Store

README.md

@@ -89,4 +89,4 @@ Development of pyCSEP is a group effort. A list of developers that have contribu
 are listed in the [credits](CREDITS.md) file in this repository.
 
 # License:
-The pyCSEP software is distributed under the BSD 3-Clause open-source license. Please see the [license](LICENSE.txt) file for more information.
+The pyCSEP software is distributed under the BSD 3-Clause open-source license. Please see the [license](LICENSE) file for more information.

csep/__init__.py

@@ -2,8 +2,6 @@
 import os
 import time
 
-from csep._version import __version__
-
 from csep.core import forecasts
 from csep.core import catalogs
 from csep.core import poisson_evaluations
@@ -37,6 +35,13 @@
     utc_now_epoch
 )
 
+from importlib.metadata import version as _pkg_version, PackageNotFoundError
+
+try:
+    __version__ = _pkg_version("pycsep")
+except PackageNotFoundError:
+    __version__ = "0+unknown"
+
 # this defines what is imported on a `from csep import *`
 __all__ = [
     'load_json',
@@ -80,8 +85,8 @@ def load_stochastic_event_sets(filename, type='csv', format='native',
         (generator): :class:`~csep.core.catalogs.AbstractBaseCatalog`
 
     """
-    if type not in ('ucerf3', 'csv'):
-        raise ValueError("type must be one of the following: (ucerf3)")
+    if type not in ('ucerf3', 'csv', 'csep'):
+        raise ValueError("type must be one of the following: (ucerf3, csv, csep)")
 
     # use mapping to dispatch to correct function
     # in general, stochastic event sets are loaded with classmethods and single catalogs use the
@@ -105,7 +110,7 @@ def load_stochastic_event_sets(filename, type='csv', format='native',
         elif format == 'csep':
             yield catalog.get_csep_format()
         else:
-            raise ValueError('format must be either "native" or "csep!')
+            raise ValueError('format must be either "native" or "csep!"')
 
 
 def load_catalog(filename, type='csep-csv', format='native', loader=None,
@@ -333,7 +338,7 @@ def query_gns(start_time, end_time,  min_magnitude=2.950,
         verbose (bool): print catalog summary statistics
 
     Returns:
-        :class:`csep.core.catalogs.CSEPCatalog
+        :class:`csep.core.catalogs.CSEPCatalog`
     """
 
     # Timezone should be in UTC
@@ -366,7 +371,7 @@ def query_gcmt(start_time, end_time, min_magnitude=5.0,
                max_depth=None,
                catalog_id=None,
                min_latitude=None, max_latitude=None,
-               min_longitude=None, max_longitude=None):
+               min_longitude=None, max_longitude=None, verbose=True):
 
     eventlist = readers._query_gcmt(start_time=start_time,
                                      end_time=end_time,
@@ -381,6 +386,17 @@ def query_gcmt(start_time, end_time, min_magnitude=5.0,
                                    name='gCMT',
                                    catalog_id=catalog_id,
                                    date_accessed=utc_now_datetime())
+
+    if verbose:
+        print("Downloaded catalog from GCMT with following parameters")
+        print("Start Date: {}\nEnd Date: {}".format(str(catalog.start_time),
+                                                    str(catalog.end_time)))
+        print("Min Latitude: {} and Max Latitude: {}".format(catalog.min_latitude,
+                                                             catalog.max_latitude))
+        print("Min Longitude: {} and Max Longitude: {}".format(catalog.min_longitude,
+                                                               catalog.max_longitude))
+        print("Min Magnitude: {}".format(catalog.min_magnitude))
+        print(f"Found {catalog.event_count} events in the gns catalog.")
     return catalog
 
 

csep/core/binomial_evaluations.py

@@ -65,7 +65,7 @@ def negative_binomial_number_test(gridded_forecast, observed_catalog, variance):
     delta1, delta2 = _nbd_number_test_ndarray(fore_cnt, obs_cnt, variance, epsilon=epsilon)
 
     # store results
-    result.test_distribution = ('negative_binomial', fore_cnt)
+    result.test_distribution = ('negative_binomial', fore_cnt, variance)
     result.name = 'NBD N-Test'
     result.observed_statistic = obs_cnt
     result.quantile = (delta1, delta2)
@@ -126,7 +126,7 @@ def _simulate_catalog(sim_cells, sampling_weights, sim_fore, random_numbers=None
 
 
 def _binary_likelihood_test(forecast_data, observed_data, num_simulations=1000, random_numbers=None, 
-                              seed=None, use_observed_counts=True, verbose=True, normalize_likelihood=False):
+                              seed=None, use_observed_counts=True, verbose=False, normalize_likelihood=False):
     """  Computes binary conditional-likelihood test from CSEP using an efficient simulation based approach.
 
     Args:

csep/core/brier_evaluations.py

@@ -71,7 +71,7 @@ def _simulate_catalog(sim_cells, sampling_weights, random_numbers=None):
 
 
 def _brier_score_test(forecast_data, observed_data, num_simulations=1000,
-                      random_numbers=None, seed=None, verbose=True):
+                      random_numbers=None, seed=None, verbose=False):
     """  Computes the Brier consistency test conditional on the total observed
     number of events
 

csep/core/catalog_evaluations.py

@@ -23,7 +23,7 @@
     from csep.core.forecasts import CatalogForecast
 
 
-def number_test(forecast, observed_catalog, verbose=True):
+def number_test(forecast, observed_catalog, verbose=False):
     """ Performs the number test on a catalog-based forecast.
 
     The number test builds an empirical distribution of the event counts for each data. By default, this
@@ -62,7 +62,7 @@ def number_test(forecast, observed_catalog, verbose=True):
     return result
 
 
-def spatial_test(forecast, observed_catalog, verbose=True):
+def spatial_test(forecast, observed_catalog, verbose=False):
     """ Performs spatial test for catalog-based forecasts.
 
 
@@ -136,7 +136,7 @@ def spatial_test(forecast, observed_catalog, verbose=True):
         delta_1, delta_2 = get_quantiles(test_distribution_spatial_1d, obs_lh_norm)
 
     result = CatalogSpatialTestResult(test_distribution=test_distribution_spatial_1d,
-                                      name='S-Test',
+                                      name='Catalog S-Test',
                                       observed_statistic=obs_lh_norm,
                                       quantile=(delta_1, delta_2),
                                       status=message,
@@ -148,7 +148,7 @@ def spatial_test(forecast, observed_catalog, verbose=True):
     return result
 
 
-def magnitude_test(forecast, observed_catalog, verbose=True):
+def magnitude_test(forecast, observed_catalog, verbose=False):
     """ Performs magnitude test for catalog-based forecasts """
     test_distribution = []
 
@@ -160,7 +160,7 @@ def magnitude_test(forecast, observed_catalog, verbose=True):
         print("Cannot perform magnitude test when observed event count is zero.")
         # prepare result
         result = CatalogMagnitudeTestResult(test_distribution=test_distribution,
-                                            name='M-Test',
+                                            name='Catalog M-Test',
                                             observed_statistic=None,
                                             quantile=(None, None),
                                             status='not-valid',
@@ -212,7 +212,7 @@ def magnitude_test(forecast, observed_catalog, verbose=True):
 
     # prepare result
     result = CatalogMagnitudeTestResult(test_distribution=test_distribution,
-                              name='M-Test',
+                              name='Catalog M-Test',
                               observed_statistic=obs_d_statistic,
                               quantile=(delta_1, delta_2),
                               status='normal',
@@ -224,7 +224,7 @@ def magnitude_test(forecast, observed_catalog, verbose=True):
     return result
 
 
-def pseudolikelihood_test(forecast, observed_catalog, verbose=True):
+def pseudolikelihood_test(forecast, observed_catalog, verbose=False):
     """ Performs the spatial pseudolikelihood test for catalog forecasts.
 
     Performs the spatial pseudolikelihood test as described by Savran et al., 2020. The tests uses a pseudolikelihood
@@ -307,7 +307,7 @@ def pseudolikelihood_test(forecast, observed_catalog, verbose=True):
     # prepare evaluation result
     result = CatalogPseudolikelihoodTestResult(
         test_distribution=test_distribution_1d,
-        name='PL-Test',
+        name='Catalog PL-Test',
         observed_statistic=obs_plh,
         quantile=(delta_1, delta_2),
         status=message,

csep/core/catalogs.py

@@ -23,7 +23,7 @@
 from csep.utils.log import LoggingMixin
 from csep.utils.readers import csep_ascii
 from csep.utils.file import get_file_extension
-from csep.utils.plots import plot_catalog
+from csep.plots import plot_catalog, plot_magnitude_versus_time
 
 
 class AbstractBaseCatalog(LoggingMixin):
@@ -733,7 +733,8 @@ def magnitude_counts(self, mag_bins=None, tol=None, retbins=False):
             else:
                 return out
         idx = bin1d_vec(self.get_magnitudes(), mag_bins, tol=tol, right_continuous=True)
-        numpy.add.at(out, idx, 1)
+        valid = idx >= 0
+        numpy.add.at(out, idx[valid], 1)
         if retbins:
             return (mag_bins, out)
         else:
@@ -840,48 +841,59 @@ def b_positive(self):
         """ Implements the b-positive indicator from Nicholas van der Elst """
         pass
 
-    def plot(self, ax=None, show=False, extent=None, set_global=False, plot_args=None):
-        """ Plot catalog according to plate-carree projection
+    def plot(self, ax=None, show=False, extent=None, set_global=False, **kwargs):
+        """ Plots the catalog epicenters.
+
+        See :func:`csep.utils.plots.plot_catalog` for a description of keyword arguments.
 
         Args:
-            ax (`matplotlib.pyplot.axes`): Previous axes onto which catalog can be drawn
-            show (bool): if true, show the figure. this call is blocking.
+            ax (matplotlib.pyplot.axes): Previous axes onto which catalog can be drawn
+            show (bool): If True, shows the figure.
             extent (list): Force an extent [lon_min, lon_max, lat_min, lat_max]
-            plot_args (optional/dict): dictionary containing plotting arguments for making figures
+            set_global (bool): Whether to plot using a global projection
+            **kwargs (dict): Keyword arguments passed to
+                :func:`csep.utils.plots.plot_catalog`
 
         Returns:
             axes: matplotlib.Axes.axes
         """
 
         # no mutable function arguments
-        plot_args_default = {
-             'basemap': 'ESRI_terrain',
-             'markersize': 2,
-             'markercolor': 'red',
-             'alpha': 0.3,
-             'mag_scale': 7,
-             'legend': True,
-             'grid_labels': True,
-             'legend_loc': 3,
-             'figsize': (8, 8),
-             'title': self.name,
-             'mag_ticks': False
+        plot_args = {
+             'basemap': kwargs.pop('basemap', 'ESRI_terrain') if ax is None else None
         }
 
         # Plot the region border (if it exists) by default
         try:
             # This will throw error if catalog does not have region
             _ = self.region.num_nodes
-            plot_args_default['region_border'] = True
+            plot_args['region_border'] = True
         except AttributeError:
             pass
 
-        plot_args = plot_args or {}
-        plot_args_default.update(plot_args)
+        plot_args.update(kwargs.get('plot_args', {}))
+        plot_args.update(kwargs)
 
         # this call requires internet connection and basemap
-        ax = plot_catalog(self, ax=ax,show=show, extent=extent,
-                          set_global=set_global, plot_args=plot_args_default)
+        ax = plot_catalog(self, ax=ax, show=show, extent=extent,
+                          set_global=set_global, **plot_args)
+        return ax
+
+    def plot_magnitude_versus_time(self, ax=None, show=False, **kwargs):
+        """ Plot the magnitude-time series of a catalog. See
+        https://docs.cseptesting.org/reference/generated/csep.utils.plots.plot_magnitude_versus_time.html for
+        a description of keyword arguments.
+
+        Args:
+            ax (`matplotlib.pyplot.axes`): Previous axes onto which catalog can be drawn
+            show (bool): if true, show the figure. this call is blocking.
+
+        Returns:
+            axes: matplotlib.Axes.axes
+        """
+
+        ax = plot_magnitude_versus_time(self, ax=ax, show=show, **kwargs)
+
         return ax