[pkgsrc/trunk]: pkgsrc/geography/py-obspy Update to 1.0.1

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/geography/py-obspy Update to 1.0.1
From: wen <wen%pkgsrc.org@localhost>
Date: Wed, 15 Jan 2020 05:39:46 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/51cf5f2e5c34
branches:  trunk
changeset: 349810:51cf5f2e5c34
user:      wen <wen%pkgsrc.org@localhost>
date:      Sat Jul 16 04:11:55 2016 +0000

description:
Update to 1.0.1
Update DEPENDS

Upstream changes:
1.0.1: (doi: 10.5281/zenodo.48254)
 - General:
   * Some methods might have unnecessarily upcasted float32 arrays to float64.
     Now methods for which it makes sense and which don't lose accuracy don't
     upcast float32 arrays. Integers are still upcasted. Trace.resample() will
     also no longer return the original dtype which might have resulted in a
     large loss of accuracy but it now always returns float64 arrays.
     (see #1302)
 - obspy.core:
   * Trace.normalize() does no longer divide by zero in case an all-zeros
     data trace is being used. (see #1343)
   * Inventory.select() and consorts now behave as expected even with empty
     child elements. (see #1126, #1348)
   * Code formatting is no longer checked for clean release versions. Thus
     updates to the linters no longer break the tests for releases.
     (see #1312)
   * remove_response(..., pre_file=None, plot=True) works again. (see #1320)
 - obspy.clients.arclink:
   * Restored ArcLink encryption support. (see #1352, #1347)
 - obspy.clients.fdsn:
   * Local URLs are now recognized as valid URLs. (see #1309)
   * Some bug fixes for the mass downloader. (see #1293, #1304)
   * The NOA node has been added to the list of known nodes.
     (see 2347a25714bc3e16068031f4b6138fafd627d34e)
 - obspy.io.sac:
   * More automatic merging of SAC and ObsPy headers. The new `obspy.io.sac`
     modules thus behaves more like the old one and more in line with
     expectations of users. (see #1285)
   * No more out of bounds errors when assigning coordinates. (see #1300)
   * The evdp header can be set again. (see #1345)
   * Correctly propagating sampling rate changes to the SAC headers.
     (see #1317)
   * Always set nvhdr, leven, lovrok, iftype to ensure valid SAC files.
     (see #1204)
 - obspy.io.xseed:
   * The Parser.get_paz() method now works with multiple blockette 53s.
     (see #1281)
 - obspy.taup
   * Fixed wrong azimuth direction for paths > 180 degrees distance (see #1289)
   * Azimuth is appended to arrivals as well (see #1289)
   * Fixed issue with taup cache function on Python 2.7. (see #1308)

1.0.0:
 - General:
   * Requirements have been increased to reflect latest distributions:
     * Removed support for Python 2.6.
     * Added support for Python 3.5.
     * matplotlib >= 1.1.0 is now required.
     * numpy >= 1.6.1 is now required
     * scipy >= 0.9.0 is now required
   * Reorganized the submodule structure. We provide a deprecation path so the
     old imports will continue to work for one ObsPy version.
   * Consistent naming scheme across the code base. This results in some
     functions having different names. Most things that worked with ObsPy 0.10
     will continue to work with this version, but starting with the next
     version they will fail. Pay attention to the deprecation warnings.
   * Support for additional waveform data formats:
     - Read support for the ASCII format for waveforms from the K-NET and
       KiK-net strong-motion seismograph networks.
   * Support for additional event data formats:
     - CMTSOLUTION files used by many waveform solvers.
     - ESRI shapefile write support, useful in GIS applications (see #1066)
     - Google Earth KML output.
   * Support for additional station data format:
     - The FDSN web service station text format can now be read.
     - Read support for the NIED's moment tensor TEXT format (see #1125)
     - Google Earth KML output.
     - Read support for SeisComP3 inventory files.
 - obspy.core:
   * New method for generating sliding windows from Stream/Trace windows.
     (see #860)
   * Stream/Trace.slice() now has the optional `nearest_sample` argument from
     Stream/Trace.trim().
   * Trace.remove_response() now has `plot` option to show/output a plot of all
     individual steps of instrument response removal in frequency domain
     (see #1116).
   * New method Stream/Trace.remove_sensitivity() to remove instrument
     sensitivity
   * Fix incorrect parsing of some non-ISO8601 date/time strings. (see #1215)
   * Added plotting method to Event (customizable subplots from a selection
     of map, beachball and farfield radiation plots, see #1192)
 - obspy.clients.fdsn:
   * Replace FDSN webservice shortcut `NERIES` with `EMSC` and deprecate the
     `NERIES` shortcut, will be removed in a future release (see #1146).
   * Now requests gzipped data for the XML files. Much smaller files!
   * The station service can now also be used to download files in the text
     format. This has limited information but is much faster.
   * New mass downloader to assist in downloading data across a large number
     of FDSN web services.
   * Catch invalid URLs when initialising Client and avoid confusing error
     messages (see #1162)
 - obspy.clients.filesystem.sds:
   * New client to read data from local SDS directory structure (see #1135).
   * Command line script `obspy-sds-report` to generate html page with
     information on latency, data availability percentage and number of gaps
     for a local SDS archive (see #1202)
 - obspy.clients.neries:
   * Removed the dedicated client. Data can still be accessed by using the FDSN
     client.
 - obspy.clients.syngine:
   * New client for the IRIS Syngine service to retrieve custom synthetic
     seismograms.
 - obspy.imaging:
   * Experimental support for Cartopy when plotting maps. Use the `method`
     argument to functions that plot maps to select between Basemap or Cartopy.
   * New default colormap for all plots. A backport of the new viridis colormap
     from matplotlib is available for those using older matplotlib releases.
   * Added plotting routines for farfield radiation patterns of moment tensors
 - obspy.io.kml:
   * New module for Google KML output of Inventory and Catalog objects
     (e.g. for use in Google Earth)
 - obspy.io.mseed:
   * Upgrade to libmseed 2.16
 - obspy.io.seiscomp.sc3ml:
   * New module reading SeisComP3 inventory files to ObsPy inventory objects
     (see #1182).
 - obspy.io.shapefile:
   * New module for ESRI shapefile write support (see #1066)
 - obspy.io.stationtxt:
   * New module reading the FDSN station files.
 - obspy.signal:
   * Switch to second-order sections for filters; backported from SciPy 0.16.0
     (see #1028)
   * New Lanczos interpolation/resampling (see #1101)
   * Higher order detrending methods (see #1173)
   * PPSD (see #931, #1108, #1130, #1187):
     - Algorithm for PSD computation was improved, especially affecting results
       at long periods (for detailed discussion see #931 and #1108).
     - Keywords `paz` and `parser` were removed in favor of new keyword
       `metadata`. PPSD now accepts `metadata` in a much wider range
       of formats:
          * Inventory objects (e.g. from StationXML or from FDSN webservice)
          * obspy.io.xseed Parser objects (e.g. from dataless SEED file)
          * filename of a RESP file
          * dictionary with poles and zeros information (like in
            prior versions)
       Most old codes should still work, issuing a deprecation warning, but
       old code that specifies *both* `paz` and `parser` keywords will raise
       an exception.
     - Whenever possible (i.e. when using for `metadata` an Inventory,
       a Parser or a RESP file), response calculation now takes into account
       the full response (all stages) as opposed to only using the poles and
       zeros response stage (as was done in previous versions when using a
       Parser object). When using a poles and zeros dictionary response
       calculation is unchanged (as no information on other stages is
       available, of course).
     - PPSD now stores the psd for each time segment that gets processed,
       instead of only storing the stacked histogram. That way, differing
       custom stacks with various selection criteria (e.g. time of day, by
       weekday, etc.) can now be made from the same processed data
       (see #1130).
     - New save/load mechanism using numpy .npz binary format that circumvents
       some problems with the old pickle mechanism:
       `PPSD.save_npz()` and `PPSD.load_npz()` (and `PPSD.add_npz()` to add
       data from additional npz files)
     - Change default colormap to new obspy default sequential colormap
       (matplotlibs new viridis colormap). The old PQLX colormap is provided by
       `obspy.imaging.cm.pqlx` and can be used with
       `PPSD.plot(..., cmap=...)`.
     - new option `PPSD.plot(..., cumulative=True)` for a cumulative plot of
       the histogram, i.e. a non-exceedence percentage visualization, similar
       to the `percentile` option.
     - x axis in `PPSD.plot()` can be switched to frequency in Hz with
       `PPSD.plot(..., xaxis_frequency=True)` (see #1130)
     - changes to special handling of rotational: now handled by kwarg
       `special_handling="ringlaser"` (kwarg `is_rotational_data` is
       deprecated, see #916)
     - special handling option for hydrophone data (no differentiation, see
       #916)
     - bin width on frequency axis can now be controlled using
       `PPSD(..., frequency_bin_width_octaves=...)` (in fractions of octaves,
       default is the old fixed setting of 1/8 octaves as in PQLX)
 - obspy.taup
   * Added support for nd file format for input velocity models. Allows for
     named discontinuities at arbitrary depths allowing for less Earth like
     models (see #1147).
   * Added three methods (`get_travel_times_geo()`, `get_pierce_points_geo()`
     and `get_ray_paths_geo()`) to `TauPyModel` to handle station and
     event location data as latitude and longitude, instead of the source to
     station distance in degrees. In addition `get_ray_paths_geo()` and
     `get_pierce_points_geo()` decorate the returned pierce points and ray
     paths with the latitude and longitude of each point. Some functionality
     needs the `geographiclib` module to be installed. (See #1164.)
   * ObsPy now ships with a bunch of new velocity models in addition to the
     existing ones: `prem`, `sp6`, `1066a,b`, `herrin` (See #1196).
   * Add support for buried receivers (see #1103.)
   * Port more accurate calculation of ray parameter from Java. The effect is
     stronger for longer phases, but also corrects issues with shorter body and
     surface waves (see #986.)
   * Fix incorrect branch splitting which also caused issues for extremely
     shallow phases (see #1057.)
   * Proper cache for model splits resulting in much faster calculations if
     the source depth is repeatedly the same (see #1248).

0.10.3:
  - obspy.core:
    * Fix reading of multiple catalog files using globs (see #1065).
    * Fixed a bug when using
      `Trace.remove_response(..., water_level=None)`.
      With that setting that is supposed to not use any water level
      stabilization in the inversion of the instrument response
      spectrum actually the instrument response was never inverted and
      thus instead of a deconvolution a convolution was performed
      (see #1104).
    * Fixing floating point precision/rounding issue with UTCDateTime when
      initializing with floating point seconds, i.e. with microseconds,
      that could lead to microseconds being off by 1 microsecond
      (see #1096)
    * Correct gap/overlap time returned by Stream.get_gaps() and printed
      by Stream.print_gaps() which was incorrect by one time the sampling
      interval (see #1151)
    * Stream.get_gaps(): return overlaps specified in units of samples
      as negative integers (see #1151)
  - obspy.fdsn:
    * More detailed error messages on failing requests (see #1079)
    * Follows redirects for POST requests (see #1143)
  - obspy.imaging:
    * fix some bugs in `obspy-scan` (see #1138)
  - obspy.mseed:
    * Blockette 100 is now only written for Traces that need it. Previously
      it was written or not for all Traces, depending on whether the last
      Trace needed it or not. (see #1069)
    * Fixed a bug that prevented microsecond accuracy for times before 1970
      (see #1102).
    * Updated to libmseed 2.17.
  - obspy.signal:
    * Bug fixed within rotate.rotate2zne(). Additionally it can now also
      perform the inverse rotation (see #1061).
    * Bug fixed in triggering. When using option `max_len_delete` and a trigger
      occurred right before the end of data, one trigger was potentially lost
      (see #1145 for details).
  - obspy.station:
    * Plotting responses across multiple channels is more robust now in
      presence of some strange channels (e.g. with zero sampling rate,
      happens e.g. for state of health channels, see #1115)
    * ObsPy no longer assumes that the StationXML namespace is the default
      namespace (see #1060).
    * Checking if a file is a StationXML file is less rigorous (and much
      faster) now (not checking strict validity against xsd schema but
      only looking for a FDSNStationXML root element, see #1114).
      This means that `read_inventory()` without explicitly specified
      format will correctly detect more files as StationXML that have very
      slight breaches of the schema but still can be interpreted as
      StationXML.
    * fix saving `xcorrPickCorrection()` results to an image file (see #1154)
  - obspy.taup:
    * Calculating arrival times for surface waves now works (see #1055)
    * Calculating arrivals for underside reflections now works (see #1089)
  - obspy.y:
    * correct misspelled name of a Y specific header field (see #1127)
  - obspy.zmap
    * Add support for time values with sub-second precision (see #1093)

diffstat:

 geography/py-obspy/Makefile |     8 +-
 geography/py-obspy/PLIST    |  2489 ++++++++++++++++++++++++------------------
 geography/py-obspy/distinfo |    10 +-
 3 files changed, 1416 insertions(+), 1091 deletions(-)

diffs (truncated from 2808 to 300 lines):

diff -r e3ce835f2ab2 -r 51cf5f2e5c34 geography/py-obspy/Makefile
--- a/geography/py-obspy/Makefile       Sat Jul 16 04:02:13 2016 +0000
+++ b/geography/py-obspy/Makefile       Sat Jul 16 04:11:55 2016 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.4 2016/07/09 13:03:49 wiz Exp $
+# $NetBSD: Makefile,v 1.5 2016/07/16 04:11:55 wen Exp $
 
-DISTNAME=      obspy-0.10.2
+DISTNAME=      obspy-1.0.1
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    geography python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=o/obspy/}
@@ -14,6 +14,10 @@
 DEPENDS+=      ${PYPKGPREFIX}-scipy>=0.12.0:../../math/py-scipy
 DEPENDS+=      ${PYPKGPREFIX}-suds>=0.4:../../net/py-suds
 DEPENDS+=      ${PYPKGPREFIX}-lxml>=3.2.3:../../textproc/py-lxml
+DEPENDS+=      ${PYPKGPREFIX}-future>=0.12.4:../../devel/py-future
+DEPENDS+=      ${PYPKGPREFIX}-requests>=0:../../devel/py-requests
+DEPENDS+=      ${PYPKGPREFIX}-decorator>=0:../../devel/py-decorator
+DEPENDS+=      ${PYPKGPREFIX}-sqlalchemy>=0:../../databases/py-sqlalchemy
 
 USE_LANGUAGES= c fortran
 USE_TOOLS+=    bash:run
diff -r e3ce835f2ab2 -r 51cf5f2e5c34 geography/py-obspy/PLIST
--- a/geography/py-obspy/PLIST  Sat Jul 16 04:02:13 2016 +0000
+++ b/geography/py-obspy/PLIST  Sat Jul 16 04:11:55 2016 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2015/05/30 03:27:52 wen Exp $
+@comment $NetBSD: PLIST,v 1.2 2016/07/16 04:11:55 wen Exp $
 bin/obspy-dataless2resp
 bin/obspy-dataless2xseed
 bin/obspy-flinn-engdahl
@@ -10,6 +10,7 @@
 bin/obspy-reftek-rescue
 bin/obspy-runtests
 bin/obspy-scan
+bin/obspy-sds-report
 bin/obspy-xseed2dataless
 ${PYSITELIB}/${EGG_FILE}/PKG-INFO
 ${PYSITELIB}/${EGG_FILE}/SOURCES.txt
@@ -17,6 +18,7 @@
 ${PYSITELIB}/${EGG_FILE}/entry_points.txt
 ${PYSITELIB}/${EGG_FILE}/namespace_packages.txt
 ${PYSITELIB}/${EGG_FILE}/not-zip-safe
+${PYSITELIB}/${EGG_FILE}/pbr.json
 ${PYSITELIB}/${EGG_FILE}/requires.txt
 ${PYSITELIB}/${EGG_FILE}/top_level.txt
 ${PYSITELIB}/obspy/CONTRIBUTORS.txt
@@ -25,143 +27,331 @@
 ${PYSITELIB}/obspy/__init__.py
 ${PYSITELIB}/obspy/__init__.pyc
 ${PYSITELIB}/obspy/__init__.pyo
-${PYSITELIB}/obspy/ah/README.txt
-${PYSITELIB}/obspy/ah/__init__.py
-${PYSITELIB}/obspy/ah/__init__.pyc
-${PYSITELIB}/obspy/ah/__init__.pyo
-${PYSITELIB}/obspy/ah/core.py
-${PYSITELIB}/obspy/ah/core.pyc
-${PYSITELIB}/obspy/ah/core.pyo
-${PYSITELIB}/obspy/ah/tests/__init__.py
-${PYSITELIB}/obspy/ah/tests/__init__.pyc
-${PYSITELIB}/obspy/ah/tests/__init__.pyo
-${PYSITELIB}/obspy/ah/tests/data/TSG/BRV.TSG.DS.lE21.asc
-${PYSITELIB}/obspy/ah/tests/data/TSG/BRV.TSG.DS.lE21.resp
-${PYSITELIB}/obspy/ah/tests/data/TSG/BRV.TSG.KSM.sE12.asc
-${PYSITELIB}/obspy/ah/tests/data/TSG/BRV.TSG.KSM.sE12.resp
-${PYSITELIB}/obspy/ah/tests/data/TSG/Readme_TSG_response.txt
-${PYSITELIB}/obspy/ah/tests/data/ah1.c
-${PYSITELIB}/obspy/ah/tests/data/ah1.f
-${PYSITELIB}/obspy/ah/tests/data/ah1.t
-${PYSITELIB}/obspy/ah/tests/data/ah2.c
-${PYSITELIB}/obspy/ah/tests/data/ah2.f
-${PYSITELIB}/obspy/ah/tests/data/ah2.f-e
-${PYSITELIB}/obspy/ah/tests/data/ah2.t
-${PYSITELIB}/obspy/ah/tests/data/hrv.lh.zne
-${PYSITELIB}/obspy/ah/tests/test_core.py
-${PYSITELIB}/obspy/ah/tests/test_core.pyc
-${PYSITELIB}/obspy/ah/tests/test_core.pyo
-${PYSITELIB}/obspy/arclink/README.txt
-${PYSITELIB}/obspy/arclink/__init__.py
-${PYSITELIB}/obspy/arclink/__init__.pyc
-${PYSITELIB}/obspy/arclink/__init__.pyo
-${PYSITELIB}/obspy/arclink/client.py
-${PYSITELIB}/obspy/arclink/client.pyc
-${PYSITELIB}/obspy/arclink/client.pyo
-${PYSITELIB}/obspy/arclink/decrypt.py
-${PYSITELIB}/obspy/arclink/decrypt.pyc
-${PYSITELIB}/obspy/arclink/decrypt.pyo
-${PYSITELIB}/obspy/arclink/tests/__init__.py
-${PYSITELIB}/obspy/arclink/tests/__init__.pyc
-${PYSITELIB}/obspy/arclink/tests/__init__.pyo
-${PYSITELIB}/obspy/arclink/tests/test_client.py
-${PYSITELIB}/obspy/arclink/tests/test_client.pyc
-${PYSITELIB}/obspy/arclink/tests/test_client.pyo
-${PYSITELIB}/obspy/arclink/tests/test_decrypt.py
-${PYSITELIB}/obspy/arclink/tests/test_decrypt.pyc
-${PYSITELIB}/obspy/arclink/tests/test_decrypt.pyo
-${PYSITELIB}/obspy/cnv/README.txt
-${PYSITELIB}/obspy/cnv/__init__.py
-${PYSITELIB}/obspy/cnv/__init__.pyc
-${PYSITELIB}/obspy/cnv/__init__.pyo
-${PYSITELIB}/obspy/cnv/core.py
-${PYSITELIB}/obspy/cnv/core.pyc
-${PYSITELIB}/obspy/cnv/core.pyo
-${PYSITELIB}/obspy/cnv/tests/__init__.py
-${PYSITELIB}/obspy/cnv/tests/__init__.pyc
-${PYSITELIB}/obspy/cnv/tests/__init__.pyo
-${PYSITELIB}/obspy/cnv/tests/data/obspyck_20141020150701.cnv
-${PYSITELIB}/obspy/cnv/tests/data/obspyck_20141020150701.xml
-${PYSITELIB}/obspy/cnv/tests/test_core.py
-${PYSITELIB}/obspy/cnv/tests/test_core.pyc
-${PYSITELIB}/obspy/cnv/tests/test_core.pyo
+${PYSITELIB}/obspy/clients/__init__.py
+${PYSITELIB}/obspy/clients/__init__.pyc
+${PYSITELIB}/obspy/clients/__init__.pyo
+${PYSITELIB}/obspy/clients/arclink/README.txt
+${PYSITELIB}/obspy/clients/arclink/__init__.py
+${PYSITELIB}/obspy/clients/arclink/__init__.pyc
+${PYSITELIB}/obspy/clients/arclink/__init__.pyo
+${PYSITELIB}/obspy/clients/arclink/client.py
+${PYSITELIB}/obspy/clients/arclink/client.pyc
+${PYSITELIB}/obspy/clients/arclink/client.pyo
+${PYSITELIB}/obspy/clients/arclink/decrypt.py
+${PYSITELIB}/obspy/clients/arclink/decrypt.pyc
+${PYSITELIB}/obspy/clients/arclink/decrypt.pyo
+${PYSITELIB}/obspy/clients/arclink/tests/__init__.py
+${PYSITELIB}/obspy/clients/arclink/tests/__init__.pyc
+${PYSITELIB}/obspy/clients/arclink/tests/__init__.pyo
+${PYSITELIB}/obspy/clients/arclink/tests/test_client.py
+${PYSITELIB}/obspy/clients/arclink/tests/test_client.pyc
+${PYSITELIB}/obspy/clients/arclink/tests/test_client.pyo
+${PYSITELIB}/obspy/clients/arclink/tests/test_decrypt.py
+${PYSITELIB}/obspy/clients/arclink/tests/test_decrypt.pyc
+${PYSITELIB}/obspy/clients/arclink/tests/test_decrypt.pyo
+${PYSITELIB}/obspy/clients/base.py
+${PYSITELIB}/obspy/clients/base.pyc
+${PYSITELIB}/obspy/clients/base.pyo
+${PYSITELIB}/obspy/clients/earthworm/README.txt
+${PYSITELIB}/obspy/clients/earthworm/__init__.py
+${PYSITELIB}/obspy/clients/earthworm/__init__.pyc
+${PYSITELIB}/obspy/clients/earthworm/__init__.pyo
+${PYSITELIB}/obspy/clients/earthworm/client.py
+${PYSITELIB}/obspy/clients/earthworm/client.pyc
+${PYSITELIB}/obspy/clients/earthworm/client.pyo
+${PYSITELIB}/obspy/clients/earthworm/tests/__init__.py
+${PYSITELIB}/obspy/clients/earthworm/tests/__init__.pyc
+${PYSITELIB}/obspy/clients/earthworm/tests/__init__.pyo
+${PYSITELIB}/obspy/clients/earthworm/tests/test_client.py
+${PYSITELIB}/obspy/clients/earthworm/tests/test_client.pyc
+${PYSITELIB}/obspy/clients/earthworm/tests/test_client.pyo
+${PYSITELIB}/obspy/clients/earthworm/waveserver.py
+${PYSITELIB}/obspy/clients/earthworm/waveserver.pyc
+${PYSITELIB}/obspy/clients/earthworm/waveserver.pyo
+${PYSITELIB}/obspy/clients/fdsn/README.txt
+${PYSITELIB}/obspy/clients/fdsn/__init__.py
+${PYSITELIB}/obspy/clients/fdsn/__init__.pyc
+${PYSITELIB}/obspy/clients/fdsn/__init__.pyo
+${PYSITELIB}/obspy/clients/fdsn/client.py
+${PYSITELIB}/obspy/clients/fdsn/client.pyc
+${PYSITELIB}/obspy/clients/fdsn/client.pyo
+${PYSITELIB}/obspy/clients/fdsn/header.py
+${PYSITELIB}/obspy/clients/fdsn/header.pyc
+${PYSITELIB}/obspy/clients/fdsn/header.pyo
+${PYSITELIB}/obspy/clients/fdsn/mass_downloader/__init__.py
+${PYSITELIB}/obspy/clients/fdsn/mass_downloader/__init__.pyc
+${PYSITELIB}/obspy/clients/fdsn/mass_downloader/__init__.pyo
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