Merge pull request #799 from kr-2003/eliminate_astropy_logging

Eliminated the usage of astropy logging

docs/changes/799.removal.rst

@@ -0,0 +1 @@
+Eliminated the usage of astropy logging

docs/conf.py

@@ -34,16 +34,14 @@
 try:
     from sphinx_astropy.conf.v1 import *  # noqa
 except ImportError:
-    print(
-        'ERROR: the documentation requires the sphinx-astropy package to be installed'
-    )
+    print("ERROR: the documentation requires the sphinx-astropy package to be installed")
     sys.exit(1)
 
 # Get configuration information from setup.cfg
 conf = ConfigParser()
 
-conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')])
-setup_cfg = dict(conf.items('metadata'))
+conf.read([os.path.join(os.path.dirname(__file__), "..", "setup.cfg")])
+setup_cfg = dict(conf.items("metadata"))
 
 # -- General configuration ----------------------------------------------------
 
@@ -59,10 +57,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns += ['_templates',
-                     'notebooks/README.rst',
-                     'notebooks/Debug',
-                     'changes']
+exclude_patterns += ["_templates", "notebooks/README.rst", "notebooks/Debug", "changes"]
 
 # This is added to the end of RST files - a good place to put substitutions to
 # be used globally.
@@ -72,20 +67,19 @@
 # -- Project information ------------------------------------------------------
 
 # This does not *have* to match the package name, but typically does
-project = setup_cfg['name']
-author = setup_cfg['author']
-copyright = '{0}, {1}'.format(datetime.datetime.now().year,
-                              setup_cfg['author'])
+project = setup_cfg["name"]
+author = setup_cfg["author"]
+copyright = "{0}, {1}".format(datetime.datetime.now().year, setup_cfg["author"])
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-import_module(setup_cfg['name'])
-package = sys.modules[setup_cfg['name']]
+import_module(setup_cfg["name"])
+package = sys.modules[setup_cfg["name"]]
 
 # The short X.Y version.
-version = package.__version__.split('-', 1)[0]
+version = package.__version__.split("-", 1)[0]
 # The full version, including alpha/beta/rc tags.
 release = package.__version__
 
@@ -110,15 +104,17 @@
 html_css_files = ["css/custom.css"]
 
 html_theme_options = {
-    'logotext1': 'Sting',  # white,  semi-bold
-    'logotext2': 'ray',  # orange, light
-    'logotext3': ':docs'  # white,  light
+    "logotext1": "Sting",  # white,  semi-bold
+    "logotext2": "ray",  # orange, light
+    "logotext3": ":docs",  # white,  light
 }
 
 extensions += [
-    'matplotlib.sphinxext.plot_directive', 'sphinx.ext.autodoc',
-    'sphinx.ext.napoleon', 'nbsphinx', 
-    'IPython.sphinxext.ipython_console_highlighting'
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "nbsphinx",
+    "IPython.sphinxext.ipython_console_highlighting",
 ]
 
 # Custom sidebar templates, maps document names to template names.
@@ -139,47 +135,43 @@
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = '{0} v{1}'.format(project, release)
+html_title = "{0} v{1}".format(project, release)
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = project + 'doc'
+htmlhelp_basename = project + "doc"
 
 # -- Options for LaTeX output -------------------------------------------------
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [('index', project + '.tex', project + u' Documentation',
-                    author, 'manual')]
+latex_documents = [("index", project + ".tex", project + " Documentation", author, "manual")]
 
 # -- Options for manual page output -------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [('index', project.lower(), project + u' Documentation', [author],
-              1)]
+man_pages = [("index", project.lower(), project + " Documentation", [author], 1)]
 
 # Trust the links from doi.org, even if they might have Client errors or other minor issues
 linkcheck_ignore = [r"https://doi.org/"]
 
 # -- Options for the edit_on_github extension ---------------------------------
 
-if setup_cfg.get('edit_on_github').lower() == 'true':
+if setup_cfg.get("edit_on_github").lower() == "true":
+    extensions += ["sphinx_astropy.ext.edit_on_github"]
 
-    extensions += ['sphinx_astropy.ext.edit_on_github']
-
-    edit_on_github_project = setup_cfg['github_project']
+    edit_on_github_project = setup_cfg["github_project"]
     edit_on_github_branch = "master"
 
     edit_on_github_source_root = ""
     edit_on_github_doc_root = "docs"
 
 # -- Resolving issue number to links in changelog -----------------------------
-github_issues_url = 'https://github.com/{0}/issues/'.format(
-    setup_cfg['github_project'])
+github_issues_url = "https://github.com/{0}/issues/".format(setup_cfg["github_project"])
 
 # -- Configuration for nbsphinx -----------------------------------------------
 # disable notebook execution
-nbsphinx_execute = 'never'
+nbsphinx_execute = "never"
 
 # -- Generate DOI listing from Zenodo -----------------------------------------
 import json
@@ -207,18 +199,14 @@ def zenodo_url(self):
 
     @property
     def github_url(self):
-        return (
-            f"https://github.com/StingraySoftware/stingray/releases/tag/{self.version}"
-        )
+        return f"https://github.com/StingraySoftware/stingray/releases/tag/{self.version}"
 
     @property
     def bibtex_url(self):
         return self.zenodo_url + "/export/hx"
 
 
-params = urllib.parse.urlencode(
-    {"q": f'conceptdoi: "{CONCEPT_DOI}"', "all_versions": 1}
-)
+params = urllib.parse.urlencode({"q": f'conceptdoi: "{CONCEPT_DOI}"', "all_versions": 1})
 try:
     with urllib.request.urlopen(ZENODO_API_ENDPOINT + "?" + params) as url:
         data = json.loads(url.read().decode("utf-8"))

setup.py

@@ -33,7 +33,7 @@
   http://docs.astropy.org/en/latest/development/testguide.html#running-tests
 """
 
-if 'test' in sys.argv:
+if "test" in sys.argv:
     print(TEST_HELP)
     sys.exit(1)
 
@@ -58,7 +58,7 @@
   http://docs.astropy.org/en/latest/install.html#builddocs
 """
 
-if 'build_docs' in sys.argv or 'build_sphinx' in sys.argv:
+if "build_docs" in sys.argv or "build_sphinx" in sys.argv:
     print(DOCS_HELP)
     sys.exit(1)
 
@@ -75,6 +75,7 @@
 
 setup(
     use_scm_version={
-        'write_to': os.path.join('stingray', 'version.py'),
-        'write_to_template': VERSION_TEMPLATE
-    })
+        "write_to": os.path.join("stingray", "version.py"),
+        "write_to_template": VERSION_TEMPLATE,
+    }
+)

stingray/__init__.py

@@ -25,3 +25,4 @@
     from stingray.bispectrum import *
     from stingray.varenergyspectrum import *
     from stingray.lombscargle import *
+    from stingray.loggingconfig import *

stingray/base.py

@@ -13,6 +13,7 @@
 from astropy.table import Table
 from astropy.time import Time, TimeDelta
 from astropy.units import Quantity
+from stingray.loggingconfig import setup_logger
 
 from .io import _can_save_longdouble, _can_serialize_meta
 from .utils import (
@@ -58,6 +59,8 @@
     "StingrayTimeseries",
 ]
 
+logger = setup_logger()
+
 
 def convert_table_attrs_to_lowercase(table: Table) -> Table:
     """Convert the column names of an Astropy Table to lowercase."""
@@ -1971,7 +1974,7 @@ def _get_all_array_attrs(objs):
                 all_meta_attrs.remove(attr)
 
         for attr in ignore_meta:
-            logging.info(f"The {attr} attribute will be removed from the output ")
+            logger.info(f"The {attr} attribute will be removed from the output ")
             if attr in all_meta_attrs:
                 all_meta_attrs.remove(attr)
 
@@ -2242,7 +2245,7 @@ def fill_bad_time_intervals(
 
         btis = get_btis(self.gti, self.time[0], self.time[-1])
         if len(btis) == 0:
-            logging.info("No bad time intervals to fill")
+            logger.info("No bad time intervals to fill")
             return copy.deepcopy(self)
         filtered_times = self.time[self.mask]
 
@@ -2255,7 +2258,7 @@ def fill_bad_time_intervals(
             even_sampling = False
             if self.dt > 0 and np.isclose(mean_data_separation, self.dt, rtol=0.01):
                 even_sampling = True
-            logging.info(f"Data are {'not' if not even_sampling else ''} evenly sampled")
+            logger.info(f"Data are {'not' if not even_sampling else ''} evenly sampled")
 
         if even_sampling:
             est_samples_in_gap = int(max_length / self.dt)
@@ -2272,7 +2275,7 @@ def fill_bad_time_intervals(
             length = bti[1] - bti[0]
             if length > max_length:
                 continue
-            logging.info(f"Filling bad time interval {bti} ({length:.4f} s)")
+            logger.info(f"Filling bad time interval {bti} ({length:.4f} s)")
             epsilon = 1e-5 * length
             added_gtis.append([bti[0] - epsilon, bti[1] + epsilon])
             filt_low_t, filt_low_idx = find_nearest(filtered_times, bti[0])
@@ -2307,7 +2310,7 @@ def fill_bad_time_intervals(
                     new_attrs[attr].append(np.zeros(nevents) + np.nan)
             total_filled_time += length
 
-        logging.info(f"A total of {total_filled_time} s of data were simulated")
+        logger.info(f"A total of {total_filled_time} s of data were simulated")
 
         new_gtis = join_gtis(self.gti, added_gtis)
         new_times = np.concatenate(new_times)
@@ -2497,7 +2500,7 @@ def estimate_segment_size(self, min_counts=None, min_samples=None, even_sampling
                 and np.isclose(mean_data_separation, self.dt, rtol=0.01)
             ):
                 even_sampling = True
-            logging.info(f"Data are {'not' if not even_sampling else ''} evenly sampled")
+            logger.info(f"Data are {'not' if not even_sampling else ''} evenly sampled")
 
         if min_counts is None:
             if even_sampling and hasattr(self, "counts"):

stingray/deadtime/fad.py

@@ -5,10 +5,10 @@
 
 from scipy.ndimage import gaussian_filter1d
 from scipy.interpolate import UnivariateSpline
-from astropy import log
 from astropy.table import Table
 
 from stingray.lightcurve import Lightcurve
+from stingray.loggingconfig import setup_logger
 from ..crossspectrum import AveragedCrossspectrum, get_flux_generator
 from ..powerspectrum import AveragedPowerspectrum
 from ..fourier import normalize_periodograms, fft, fftfreq, positive_fft_bins
@@ -18,6 +18,8 @@
 
 __all__ = ["calculate_FAD_correction", "get_periodograms_from_FAD_results", "FAD"]
 
+logger = setup_logger()
+
 
 def FAD(
     data1,
@@ -249,7 +251,7 @@ def FAD(
     )
 
     if verbose and is_compliant:
-        log.info(verbose_string)
+        logger.info(verbose_string)
     elif not is_compliant:
         warnings.warn(verbose_string)
 

stingray/deadtime/model.py

@@ -1,12 +1,14 @@
 from stingray.utils import njit, prange
+from stingray.loggingconfig import setup_logger
 import numpy as np
 import matplotlib.pyplot as plt
-from astropy import log
 from scipy.special import factorial
 
 
 __FACTORIALS = factorial(np.arange(160))
 
+logger = setup_logger()
+
 
 def r_in(td, r_0):
     """Calculate incident countrate given dead time and detected countrate."""
@@ -188,7 +190,7 @@ def pds_model_zhang(N, rate, td, tb, limit_k=60):
     tau = 1 / rate
     r0 = r_det(td, rate)
     # Nph = N / tau
-    log.info("Calculating PDS model (update)")
+    logger.info("Calculating PDS model (update)")
     P = _inner_loop_pds_zhang(N, tau, r0, td, tb, limit_k=limit_k)
 
     maxf = 0.5 / tb

stingray/events.py

@@ -10,6 +10,7 @@
 import numpy as np
 
 from stingray.utils import _int_sum_non_zero
+from stingray.loggingconfig import setup_logger
 
 from .base import StingrayTimeseries
 from .filters import get_deadtime_mask
@@ -21,6 +22,8 @@
 
 __all__ = ["EventList"]
 
+logger = setup_logger()
+
 
 @njit
 def _from_lc_numba(times, counts, empty_times):
@@ -309,7 +312,7 @@ def to_binned_timeseries(self, dt, array_attrs=None):
 
         for attr in array_attrs:
             if getattr(self, attr, None) is not None:
-                logging.info(f"Creating the {attr} array")
+                logger.info(f"Creating the {attr} array")
 
                 attr_dict[attr] = histogram(
                     self.time, bins=nbins, weights=getattr(self, attr), range=ranges

stingray/filters.py

@@ -4,13 +4,14 @@
 
 import numpy as np
 import numpy.random as ra
-from astropy import log
-from astropy.logger import AstropyUserWarning
 
 from .utils import njit
+from .loggingconfig import setup_logger
 
 __all__ = ["Window1D", "Optimal1D"]
 
+logger = setup_logger()
+
 
 class Window1D(object):
     """
@@ -259,7 +260,7 @@ def get_deadtime_mask(
     deadtime_values = deadtime_values[saved_mask]
     final_len = tot_ev_list_filt.size
     if verbose:
-        log.info(
+        logger.info(
             "filter_for_deadtime: "
             "{0}/{1} events rejected".format(initial_len - final_len, initial_len)
         )