gwsumm 2.2.4__tar.gz → 2.2.6__tar.gz

{gwsumm-2.2.4 → gwsumm-2.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwsumm
-Version: 2.2.4
+Version: 2.2.6
 Summary: A python toolbox used by the LIGO Scientific Collaboration for detector characterisation
 Author-email: Alex Urban <alex.urban@ligo.org>, Duncan Macleod <duncan.macleod@ligo.org>
 Maintainer-email: Evan Goetz <evan.goetz@ligo.org>
@@ -28,7 +28,7 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: astropy>=3.0.0
 Requires-Dist: gwdatafind>=1.1.1
-Requires-Dist: gwdetchar>=2.2.4
+Requires-Dist: gwdetchar>=2.2.6
 Requires-Dist: gwpy>=2.0.0
 Requires-Dist: gwtrigfind
 Requires-Dist: lalsuite

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.2.4'
-__version_tuple__ = version_tuple = (2, 2, 4)
+__version__ = version = '2.2.6'
+__version_tuple__ = version_tuple = (2, 2, 6)

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm/archive.py

@@ -302,18 +302,48 @@ def read_data_archive(sourcefile, rm_source_on_fail=True):
 
 def find_daily_archives(start, end, ifo, tag, basedir=os.curdir):
     """Find the daily archives spanning the given GPS [start, end) interval
+
+    Parameters
+    ----------
+    start : `float`, `~datetime.datetime`, `~astropy.time.Time`, `str`
+        start time of the archive file to find, any object that can be
+        converted into a `LIGOTimeGPS`, `~astropy.time.Time`, or
+        `~datetime.datetime` is acceptable
+    end : `float`, `~datetime.datetime`, `~astropy.time.Time`, `str`
+        end time of the archive file to find, any object that can be
+        converted into a `LIGOTimeGPS`, `~astropy.time.Time`, or
+        `~datetime.datetime` is acceptable
+    ifo : `str`
+        interferometer string, ex. 'H1'
+    tag : `str`
+        tag string for the archive file
+    basedir : `path-like`, optional
+        base path to archive files, default: '.'
+
+    Returns
+    -------
+    archives : `list`
+        list of matching archive files
+
+    Notes
+    -----
+    This will only search the day directories with the format `YYYYMMDD`
     """
     archives = []
+
+    # Convert start and end to properly formatted datetime objects
     s = from_gps(to_gps(start))
     e = from_gps(to_gps(end))
+
+    # append to the archives list as long as the iterating start time is
+    # earlier than the end time
     while s < e:
         daybase = mode.get_base(s, mode=mode.Mode.day)
         ds = to_gps(s)
         s += datetime.timedelta(days=1)
         de = to_gps(s)
         archivedir = os.path.join(basedir, daybase, 'archive')
-        arch = os.path.join(archivedir, '%s-%s-%d-%d.h5'
-                            % (ifo, tag, ds, de-ds))
+        arch = os.path.join(archivedir, f'{ifo}-{tag}-{ds}-{de-ds}.h5')
         if os.path.isfile(arch):
             archives.append(arch)
     return archives
@@ -323,6 +353,27 @@ def find_daily_archives(start, end, ifo, tag, basedir=os.curdir):
 
 def _write_object(data, *args, **kwargs):
     """Internal method to write something to HDF5 with error handling
+
+    Parameters
+    ----------
+    data : gwpy object
+        TimeSeries or FrequencySeries
+    args :
+        passed to underlying write method
+    kwargs :
+        passed to underlying write method
+
+    Warns
+    -----
+    TypeError
+    ValueError
+    RuntimeError
+        If the name already exists in the HDF5 file
+
+    Raises
+    ------
+    RuntimeError
+        Any error other than the object name already exists in the HDF5 file
     """
     try:
         return data.write(*args, **kwargs)
@@ -337,6 +388,16 @@ def _write_object(data, *args, **kwargs):
 
 def segments_to_array(segmentlist):
     """Convert a `SegmentList` to a 2-dimensional `numpy.ndarray`
+
+    Parameters
+    ----------
+    segmentlist : `~gwpy.segments.SegmentList`
+        input segment list to convert
+
+    Returns
+    -------
+    out : `float` `numpy.ndarray`
+        output segment list as a numpy array
     """
     out = ndarray((len(segmentlist), 2), dtype=float)
     for i, seg in enumerate(segmentlist):
@@ -346,6 +407,16 @@ def segments_to_array(segmentlist):
 
 def segments_from_array(array):
     """Convert a 2-dimensional `numpy.ndarray` to a `SegmentList`
+
+    Parameters
+    ----------
+    array : `float` `numpy.ndarray`
+        input numpy array to convert into a segment list
+
+    Returns
+    -------
+    out : `~gwpy.segments.SegmentList`
+        output segment list
     """
     out = SegmentList()
     for row in array:

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm/channels.py

@@ -43,6 +43,18 @@ re_channel = re.compile(r'[A-Z]\d:[a-zA-Z0-9]+'  # core channel section L1:TEST
 # -- channel creation ---------------------------------------------------------
 
 def _match(channel):
+    """Find a matching channel in global memory variable
+
+    Parameters
+    ----------
+    channel : `str`, `~gwpy.detector.Channel`
+        name of a channel
+
+    Returns
+    -------
+    found : `Channel`
+        matching channel from global memory or an empty list
+    """
     channel = Channel(channel)
     name = str(channel)
     type_ = channel.type
@@ -69,22 +81,45 @@ def _find_parent(channel):
     This is either the raw channel from which a trend was generated, or the
     real channel for a mathematically-manipulated channel.
 
+    Parameters
+    ----------
+    channel : `~gwpy.detector.Channel`
+        trend channel or mathematically-manipulated channel
+
+    Returns
+    -------
+    parent_channel : `~gwpy.detector.Channel`
+        the raw channel from the trend or real channel from manipulated channel
+
     Raises
     ------
     ValueError
         if the parent cannot be parsed
     """
+    # If the channel is a trend, then get the part of the name before the dot
     if channel.trend:
         parent = str(channel).rsplit('.')[0]
     else:
         parent, = re_channel.findall(str(channel))
+    # If the parent and input channel are the same, then no parent is found
     if parent == str(channel):
-        raise ValueError("Cannot find parent for '{0!s}'".format(channel))
-    return get_channel(parent)
+        raise ValueError(f"Cannot find parent for '{str(channel)}'")
+    parent_channel = get_channel(parent)
+    return parent_channel
 
 
 def _update_dependent(channel):
     """Update a trend channel from its parent
+
+    TODO: what does this mean?
+
+    Parameters
+    ----------
+    channel : `~gwpy.detector.Channel`
+
+    Returns
+    -------
+    channel : `~gwpy.detector.Channel`
     """
     try:
         source = _find_parent(channel)
@@ -126,6 +161,22 @@ def _with_update_dependent(func):
 
 def _new(channel, find_parent=True):
     """Create a new `~gwpy.detector.Channel` in the globalv cache.
+
+    Parameters
+    ----------
+    channel : `str`, `~gwpy.detector.Channel`
+        channel string or object to create in the global memory
+    find_parent : `bool`, optional, default: `True`
+        query for raw version of trend channel (trends not in CIS)
+
+    Returns
+    -------
+    Channel : `~gwpy.detector.Channel`
+        newly created channel
+
+    Raises
+    ------
+    RuntimeError
     """
     # convert to Channel
     if isinstance(channel, Channel):
@@ -229,7 +280,19 @@ def get_channel(channel, find_parent=True, timeout=5):
 
 
 def get_channels(channels, **kwargs):
-    """Find (or create) multiple channels.
+    """Find (or create) multiple channels calling get_channel()
+
+    Parameters
+    ----------
+    channels : `list`
+        list of channels as `str` or `~gwpy.detector.Channel` objects
+    **kwargs
+        keyword arguments applied to each channel in the list
+
+    Returns
+    -------
+    ChannelList : `~gwpy.detector.ChannelList`
+        a list of channels
 
     See Also
     --------
@@ -252,6 +315,11 @@ def update_missing_channel_params(channel, **kwargs):
         channel to update
     **kwargs
         `(key, value)` pairs to set
+
+    Returns
+    -------
+    target : `~gwpy.detector.Channel`
+        the channel after updating parameters
     """
     target = get_channel(str(channel))
     if isinstance(channel, Channel):
@@ -292,6 +360,16 @@ def update_channel_params():
 def split(channelstring):
     """Split a comma-separated list of channels that may, or may not
     contain NDS2 channel types as well
+
+    Parameters
+    ----------
+    channelstring : `str`
+        comma-separated string of channels
+
+    Returns
+    -------
+    out : `list`
+        list of strings for each channel
     """
     out = []
     channelstring = re_quote.sub('', channelstring)
@@ -331,9 +409,13 @@ def split(channelstring):
 def split_combination(channelstring):
     """Split a math-combination of channels
 
+    Parameters
+    ----------
+    channelstring : `str`
+
     Returns
     -------
-    channels : `~gwpy.detector.ChannelList`
+    ChannelList : `~gwpy.detector.ChannelList`
     """
     return get_channels(re_channel.findall(str(channelstring)),
                         find_parent=False)

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm/data/coherence.py

@@ -29,7 +29,8 @@ import numpy
 
 from astropy import units
 
-from gwpy.segments import (DataQualityFlag, SegmentList, Segment)
+from gwpy.segments import (DataQualityFlag, SegmentList,
+                           Segment, SegmentListDict)
 from gwpy.frequencyseries import FrequencySeries
 from gwpy.spectrogram import SpectrogramList
 
@@ -131,8 +132,41 @@ def _get_coherence_spectrogram(channel_pair, segments, config=None,
         sampling = None
 
     # initialize component lists if they don't exist yet
+    # store compnents in a backup variable
+    coherence_bkp = {}
     for ck in ckeys:
         globalv.COHERENCE_COMPONENTS.setdefault(ck, SpectrogramList())
+        coherence_bkp[ck] = globalv.COHERENCE_COMPONENTS.get(
+            ck, SpectrogramList())
+
+    # When coherence components contain different segments,
+    # computing coherence for new segments can result in a
+    # ValueError traceback due to incompatible shapes.
+    # To prevent this issue, we collect segments from all components,
+    # clear them from the global variable, and then restore from the
+    # coherence_bkp only the data that the segments available in
+    # coherence all components.
+
+    # get the segment spans from all components
+    spans = SegmentListDict()
+    for ck in ckeys:
+        spans[ck] = SegmentList(
+            [spec.span for spec in globalv.COHERENCE_COMPONENTS[ck]])
+    # keep only the intersection of the segments
+    spans = spans.intersection(list(ckeys))
+
+    # clean the components in the global variable
+    globalv.COHERENCE_COMPONENTS.update(
+        {ck: SpectrogramList() for ck in ckeys})
+
+    # restore the data for segments available in all components
+    for seg in spans:
+        for ck in ckeys:
+            spec = _get_from_list(coherence_bkp[ck], seg)
+            add_coherence_component_spectrogram(spec, key=ck)
+
+    # explicitly delete the backup variable to decrease RAM consuption
+    del coherence_bkp
 
     # get data if query=True or if there are new segments
     query &= abs(new) != 0

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm/data/range.py

@@ -122,16 +122,20 @@ def get_range_spectrogram(channel, segments, config=None, cache=None,
 
     # return correct data, according to state segment
     out = SpectrogramList()
-    for specgram in globalv.SPECTROGRAMS[key]:
-        for seg in segments:
-            if abs(seg) < specgram.dt.value:
-                continue
-            if specgram.span.intersects(seg):
-                common = specgram.span & type(seg)(seg[0],
-                                                   seg[1] + specgram.dt.value)
-                s = specgram.crop(*common)
-                if s.shape[0]:
-                    out.append(s)
+    try:
+        for specgram in globalv.SPECTROGRAMS[key]:
+            for seg in segments:
+                if abs(seg) < specgram.dt.value:
+                    continue
+                if specgram.span.intersects(seg):
+                    common = specgram.span & type(seg)(
+                        seg[0], seg[1] + specgram.dt.value)
+                    s = specgram.crop(*common)
+                    if s.shape[0]:
+                        out.append(s)
+    except KeyError:
+        # in case the key does not exist return empty SpectrogramList
+        return out
     return out.coalesce()
 
 

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm/html/bootstrap.py

@@ -162,7 +162,7 @@ def state_switcher(states, default=0):
         page.a(str(state), class_='dropdown-item state', title=str(state),
                id_='state_%s' % re_cchar.sub('_', str(state)).lower(),
                onclick='jQuery(this).load_state(\'%s\');' % href)
-    page.div.close()  # dropdown-menu dropdown-menu-right
+    page.div.close()  # dropdown-menu dropdown-menu-end
     page.li.close()  # nav-item dropdown state-switch
     page.ul.close()  # nav navbar-nav
     return page

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm/html/static.py

@@ -34,7 +34,7 @@ CSS = OrderedDict((
                      'font-awesome/6.5.1/css/fontawesome.min.css'),
     ('font-awesome-solid', 'https://cdnjs.cloudflare.com/ajax/libs/'
                            'font-awesome/6.5.1/css/solid.min.css'),
-    ('gwbootstrap', 'https://cdn.jsdelivr.net/npm/gwbootstrap@1.3.4/'
+    ('gwbootstrap', 'https://cdn.jsdelivr.net/npm/gwbootstrap@1.3.6/'
                     'lib/gwbootstrap.min.css'),
 ))
 
@@ -51,7 +51,7 @@ JS = OrderedDict((
     ('datepicker', 'https://cdnjs.cloudflare.com/ajax/libs/'
                    'bootstrap-datepicker/1.9.0/js/'
                    'bootstrap-datepicker.min.js'),
-    ('gwbootstrap', 'https://cdn.jsdelivr.net/npm/gwbootstrap@1.3.4/'
+    ('gwbootstrap', 'https://cdn.jsdelivr.net/npm/gwbootstrap@1.3.6/'
                     'lib/gwbootstrap-extra.min.js'),
 ))
 

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwsumm
-Version: 2.2.4
+Version: 2.2.6
 Summary: A python toolbox used by the LIGO Scientific Collaboration for detector characterisation
 Author-email: Alex Urban <alex.urban@ligo.org>, Duncan Macleod <duncan.macleod@ligo.org>
 Maintainer-email: Evan Goetz <evan.goetz@ligo.org>
@@ -28,7 +28,7 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: astropy>=3.0.0
 Requires-Dist: gwdatafind>=1.1.1
-Requires-Dist: gwdetchar>=2.2.4
+Requires-Dist: gwdetchar>=2.2.6
 Requires-Dist: gwpy>=2.0.0
 Requires-Dist: gwtrigfind
 Requires-Dist: lalsuite

{gwsumm-2.2.4 → gwsumm-2.2.6}/gwsumm.egg-info/requires.txt

@@ -1,6 +1,6 @@
 astropy>=3.0.0
 gwdatafind>=1.1.1
-gwdetchar>=2.2.4
+gwdetchar>=2.2.6
 gwpy>=2.0.0
 gwtrigfind
 lalsuite

{gwsumm-2.2.4 → gwsumm-2.2.6}/pyproject.toml

@@ -39,7 +39,7 @@ classifiers = [
 dependencies = [
   "astropy >=3.0.0",
   "gwdatafind >=1.1.1",
-  "gwdetchar >=2.2.4",
+  "gwdetchar >=2.2.6",
   "gwpy >=2.0.0",
   "gwtrigfind",
   "lalsuite",