./geography/py-obspy, Python framework for seismological observatories

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Branch: CURRENT, Version: 1.1.0nb1, Package name: py27-obspy-1.1.0nb1, Maintainer: pkgsrc-users

ObsPy is an open-source project dedicated to provide a Python framework for
processing seismological data.

Required to run:
[graphics/py-matplotlib] [lang/g95] [shells/bash] [devel/py-setuptools] [databases/py-sqlalchemy] [textproc/py-lxml] [math/py-scipy] [math/py-numpy] [lang/python27] [devel/py-decorator] [devel/py-requests] [devel/py-future]

Required to build:

Master sites:

SHA1: 511e816d1fb40409c790aa1eb412a7c2687b2fbe
RMD160: cfc1c65b2bd956990baea2316d8221da82efbecd
Filesize: 23308.891 KB

Version history: (Expand)

CVS history: (Expand)

   2018-01-30 11:24:17 by Adam Ciarcinski | Files touched by this commit (1)
Log message:
Now DEPENDS on py-matplotlib rather than buildlinking
   2017-12-28 15:03:29 by David A. Holland | Files touched by this commit (2) | Package updated
Log message:
Restore plist vars, clobbered by last update.
   2017-11-13 08:49:46 by Wen Heping | Files touched by this commit (3) | Package updated
Log message:
Update to 1.1.0

Upstream changes:
1.1.0: (doi: 10.5281/zenodo.165135)
 - General:
   * Read support for Guralp Compressed Format (GCF) waveform data,
     obspy.io.gcf (see #1449)
   * Read support for Reftek 130 (rt130) waveform data,
     obspy.io.reftek (see #1433)
   * Add Nordic format (s-file) read/write (see #1517)
   * Read and write support for events in the SCARDEC catlogue format
     (see #1391).
   * Read support for IASPEI ISF ISM 1.0 Bulletin event data,
     (see #1946)
   * Write support for AH (Ad Hoc version 1) format (see #1754)
   * Client to access the Nominal Response Library (NRL) (see #1185).
   * `obspy.read_inventory()` can now read dataless SEED and RESP files
     (see #1185).
   * change version number scheme for scenarios when no official version number
     can be determined (see #1889 and #1916)
   * Support for the IRIS Federator and EIDAWS FDSNWS web routing services
     (see #1779 and #1919).
 - obspy.core:
   * UTCDateTime is now based on nanoseconds (long) instead of a unix
     timestamp in microseconds (float) - resulting in higher precision and
     support for years 1-9999 (see #1325)
   * Ensure that Trace.data is always C-contiguous in memory (see #1732)
   * Event/ResourceIdentifier is now object aware, meaning even if two
     objects share a resource_id the distinct objects will be returned with
     the get_referred_object method provided both are still in scope. If one
     of the objects gets garbage collected, however, a warning will be issued
     and the behavior will be the same as before (see #1644).
   * Better error message when attempting to write invalid QuakeML resource
     ids (see #1699).
   * Stream/Trace.write() can now autodetect file format from file extension
     (see #1321).
   * New convenience property `.matplotlib_date` for `UTCDateTime` objects to
     get matplotlib datetime float representation (which can be used in
     time-based matplotlib axes, e.g. by Stream.plot(); see #1339).
   * Trace.times() has new options `type` and `reftime` to support fetching an
     array of sampletimes in various different timing varieties \ 
     the old default, float relative to trace starttime or `reftime` in
     seconds; "utcdatetime": absolute times as UTCDateTime objects;
     "timestamp": array of float POSIX timestamps, compare
     `UTCDateTime.timestamp`; "matplotlib": array of float matplotlib \ 
     useful for plotting on matplotlib time axes; see #1307)
   * A trace's stats.network/station/location/channel can now also be set in
     one line using a SEED ID string (e.g. `trace.id = "GR.FUR..HHZ"`,
     see #1439).
   * Instrument correction for response list stages originating from inventory
     objects (see #1514).
   * `Stream.rotate(...)` can now also be used to rotate unaligned channels to
     Z-N-E, given an Inventory (see #1310)
   * Non finite floats (NaN, inf, -inf) can now no longer be set for all
     event objects (see #1597).
   * Instrument responses can now also be calculated for a given list of
     frequencies (see #1598).
   * Order of extra tags for event type classes serialized to QuakeML can now
     be controlled by using an OrderedDict (see #1617)
   * Bode plots can now optionally plot the phase in degrees (see #1763).
   * `Stream.select()` now also works on the component level if channels only
     have one letter (see #1847).
   * Now strips all invalid characters from the temporary filenames used for
     downloading data using the `read_X()` methods (see #1958).
 - obspy.clients.earthworm:
   * Much faster trace unpacking (see #1762).
 - obspy.clients.fdsn:
   * empty SEED codes (e.g. ``network=''``) will now be properly sent to the
     server as options and not omitted, which led to wildcard matching (for
     details see #1578)
   * The mass downloader now has `exclude_networks` and `exclude_stations`
     arguments to not download certain pieces of data. (see #1305)
   * The mass downloader can now download stations that are part of a given
     inventory object.
   * The mass downloader now also works with restricted data. (See #1350)
   * No data (HTTP 204) responses now raise `FDSNNoDataException` rather than
     the more general `FDSNException`.
   * Fixing cross implementation of bulk waveform and station requests (see
   * Adding mappings for the TEXNET (see #1852) and the ICGC (see #1902)
   * Support for the non-standard EIDA token authentication (see #1928).
 - obspy.imaging:
   * The functionality behind the `obspy-scan` command line script has been
     refactored into a `Scanner` class so that it can be reused in custom
     workflows. (see #1444)
 - obspy.imaging.cm:
   * new colormap: viridis_white. This is a modification of viridis that
     goes to white instead of yellow but remains perceptually uniform. It
     is especially useful for printing when an image should merge with the
     white background.
 - obspy.imaging.waveform:
   * Support for filling the wiggles when plotting sections (horizontal and
     vertical, see #1445).
 - obspy.io.arclink:
    * Read support for Arclink Inventory XML (see #1539)
    * default for `route` parameter in metadata requests is changed to `False`
      (see #1756)
 - obspy.io.ascii:
    * Custom formatting of sample values when writing SLIST and TSPAIR.
 - obspy.io.datamark:
    * Renamed without deprectation to obspy.io.win to match its original name.
      Datamark is a datalogger, saving the WIN format.
 - obspy.io.gse2:
    * Read support for GSE2.0 bulletin (see #1528)
 - obspy.io.nlloc:
    * Also parse author information and COMMENT line (see #1484)
    * Fix reading hypocenter files created by NonLinLoc versions of the 6.0.x
      beta branch (see #1760 and #1783)
 - obspy.io.quakeml:
    * Read and write support for nested custom tags (see #1463)
    * Fix some minor bugs that could lead to empty stub elements, e.g. like
      empty MomentTensor when reading and later writing again a QuakeML file
      with a FocalMechanism but no MomentTensor, potentially resulting in
      QuakeML files that breach the QuakeML schema (see #1896)
 - obspy.io.seiscomp:
    * Read and write support for SC3ML event (see #1638 and #1848)
    * Fix bug where files with arbitrary publicIDs and files with missing
      depth, latitude, longitude, or elevation tags could not be read
      (see #1817)
 - obspy.io.stationtxt:
    * Write support for stationtxt format (see #1466)
 - obspy.io.stationxml:
    * Read and write support for custom tags (see #1024)
    * No longer add the (unused) time zone field to StationXML datetimes to
      follow the example of big data centers. (see #1572)
    * Level of detail can be specified during inventory write (see #1830)
      using the level keyword (one of: network, station, channel, response).
    * Skip empty and incomplete channels during reading (see #1839, #1840).
 - obspy.io.segy:
    * Fixing an issue when comparing two still packed SEG-Y trace headers
      (see #1735).
    * Iterative reading of large SEG-Y and SU files with
      `obspy.io.segy.segy.iread_segy` and `obspy.io.segy.segy.iread_su`.
      (see #1400).
    * Write correct revision number (see #1737).
    * Textual headers will now always contain the file revision number and the
      end header mark if nothing else exists at these positions (see #1738).
    * The SEG-Y format detection now also checks the format version number
      (see #1781).
    * Enable reading SEG-Y files that have day of year 0 in trace header
      (see #1722).
    * Write textual file headers also if given as a text string
      (see #1811, #1813).
 - obspy.io.css:
   * Read support for NNSA KB Core format waveform data. (see #1332)
 - obspy.io.mseed:
   * New generic get_flags() utility function able to retrieve statistics
     about all fixed header flags and the timing quality. This makes the
     get_timing_and_data_quality() function obsolete which is thus
     deprecated and will be removed with the next release. The get_flags()
     function is also much faster. (see #1141)
   * Always hook up the libmseed logging to its Python counterpart to avoid
     some rare segfaults. (see #1658)
   * Update to libmseed v2.19.5 (see #1703, #1780, #1939).
   * Correctly read MiniSEED files with a data offset of 48 bytes (see #1540).
   * InternalMSEEDReadingError now called InternalMSEEDError and
     InternalMSEEDReadingWarning now called InternalMSEEDWarning as both
     can now also be raised in non-reading contexts (see #1658).
   * Should no-longer segfault with arbitrarily truncated files (see #1728).
   * Will now raise an exception when attempting to directly read mini-SEED
     files larger than 2048 MiB (#1746).
   * `.stats.mseed` attributes are no longer per-file but per-trace where
     applicable (see #1782).
   * `get_record_information()` - Don't fail if the word order is invalid.
 - obspy.io.nlloc:
   * Set preferred origin of event (see #1570)
 - obspy.io.nordic:
   * Add Nordic format (s-file) read/write (see #1517)
 - obspy.io.win:
   * see obspy.io.datamark.
 - obspy.io.xseed:
   * Added azimuth and dip to the get_coordinates() function. (see #1315)
   * Fixing some issues with the get_resp() output on Python 3 (see #1748).
   * Can now also parse RESP files (see #1185).
   * Can transform responses in the Parser object to ObsPy Inventory objects
     (see #1185).
 - obspy.scripts:
   * obspy-scan command line script now also plots and prints overlaps
     alongside gaps (see #1366)
   * obspy-plot now has option to disable min/max plot (see #1583)
 - obspy.signal:
   * fixed a bug in calibration.rel_calib_stack (resulting amplitude response
     had wrong scaling if using non-default "overlap_fraction", see #1821)
   * fixed a bug in coincidence_trigger() with event templates. when a template
     with mismatching SEED ID was encountered all following (potentially valid)
     templates were skipped as well (see #1850)
   * New obspy.signal.quality_control module to compute quality metrics from
     MiniSEED files. (see #1141)
   * New correlate function for calculating the cross-correlation function
     (new implementation based on Scipy).
     To calculate the shift of the maximum of the cross correlation use
     xcorr_max. The old xcorr function is deprecated but currently still
     exists (see #1585).
   * New obspy.signal.regression module to compute linear regressions, with or
     without weights, with or without allowing for an intercept. (see #1716,
   * add new plotting capabilities to PPSD (temporal variations per frequency
     and spectrogram-like plot) and also make underlying processed PSDs
     available via `PPSD.psd_values` property (see #1327)
   * Fixed bug in `rotate2zne()` for non-orthogonal configurations
     (see #1913, #1927).
   * Fixed build warnings in evalresp, partially backported from evalresp
     4.0.6 (see #1939).
 - obspy.taup:
   * Add obspy.taup.taup_geo.calc_dist_azi, a function to return the distance,
     azimuth and backazimuth for a source - receiver pair. (see #1538)
   * Fixing calculations through very small regional models. (see #1761)
   * Updated ray path plot method, added travel time plot method, and wrapper
     functions for both ray path and travel time plotting. (see #1501, #1877)
   2017-03-04 12:05:35 by Wen Heping | Files touched by this commit (3) | Package updated
Log message:
Update to 1.0.3

Upstream changes:
1.0.3: (doi: 10.5281/zenodo.165134)
 - obspy.core:
   * properly pass through kwargs specified for Trace.plot() down to the
     low-level plotting routines (e.g. events were not shown properly in
     dayplot of a trace, see #1566)
   * properly pass through kwargs from Stream.detrend() to Trace.detrend()
     (see #1607)
   * Correctly splitting masked arrays in Trace objects for a couple of corner
     cases (see #1650, #1653).
 - obspy.core.event.source:
   * Fix `farfield` if input `points` is a 2D array. (see #1499, #1553)
 - obspy.clients.earthworm:
   * Better end of stream detection. (see #1605)
   * More efficient unpacking of server response. (see #1680)
 - obspy.clients.neic:
   * Better end of stream detection. (see #1563)
 - obspy.clients.seedlink:
   * Better end of stream detection. (see #1605)
 - obspy.clients.seishub:
   * Fix wrong kwargs `first_pick` and `last_pick` in
     `Client.event.get_list()`. (see #1661)
 - obspy.io.mseed:
   * ObsPy can now also read (Mini)SEED files with noise records. (see #1495)
   * ObsPy can now read records with a data-offset of zero. (see #1509, #1525)
   * ObsPy can now read MiniSEED files with micro-second wrap arounds.
     (see #1531)
   * ObsPy can now read MiniSEED files with no blockette 1000. (see #1544)
   * ObsPy now always writes Blockette 100 if sampling rate accuracy is
     otherwise lost. (see #1550)
   * obspy.io.mseed.util.set_flags_in_fixed_header() now works with Python 3
     and also for files with Blockette 100 (see #1648).
 - obspy.io.quakeml:
   * write StationMagnitude.residual even when it is zero (see #1625)
   * read & write Event.region
 - obspy.io.sac:
   * `SACTrace.lpspol` and `lcalda` are `True` and `False` by default, when
      created via `SACTrace.from_obspy_trace` with a `Trace` that has no SAC
      inheritance. (see #1507)
   * Reference time not written to SAC file when made from scratch
     (see #1575)
 - obspy.io.sh:
   * Fix writing of long headers for python3
   * Whitespace in header fields is not ignored anymore (see #1552)
 - obspy.io.stationxml:
   * Datetime fields are written with microseconds to StationXML if
     microseconds are present. (see #1511)
 - obspy.io.zmap:
   * Use first origin/magnitude when writing to zmap if no origin/magnitude is
     set as preferred. (see #1569)
   * Parse origin time seconds as a float to avoid losing accuracy (see #1573)
 - obspy.signal:
   * PPSD: fix warning message on Python 3 that gets shown when waveforms and
     metadata mismatch (see #1506)
 - obspy.taup:
   * Allow for more than 10 phases with identical names (can happen for certain
     custom models, see #1593).
   2016-09-07 15:36:35 by Richard PALO | Files touched by this commit (1)
Log message:
Apparently python3 insists that print arguments are inside parens
should fix PLIST issues on py34 & py35
   2016-09-05 18:09:11 by Richard PALO | Files touched by this commit (1)
Log message:
PYTHONBIN doesn't exist during the first phase of the build.
   2016-08-20 20:56:56 by Richard PALO | Files touched by this commit (2) | Package updated
Log message:
remove obsoleted dependency on py-suds permitting the package to build
under py3 necessiting a bump of PKGREVISION for changed dependencies.

Update PLIST processing to use egg.mk and add support to other platforms
than NetBSD x86_64.

At the request of wen@, MAINTAINER is now set to pkgsrc-users@
(thanks to wiz@ for early feedback too)
   2016-08-07 12:36:44 by Wen Heping | Files touched by this commit (3) | Package updated
Log message:
Update to 1.0.2

Upstream changes:
1.0.2: (doi: 10.5281/zenodo.49636)
 - obspy.core:
   * Added workaround for numpy issue where many FFTs of various lengths fill
     a cache that never gets cleared, effectively creating a memory leak
     (see #1424).
   * Trace.filter and Stream.filter don't work on masked arrays anymore because
     it produced unpredictable results due to the un-initialized data-chunk.
     The uninitialized masked gap is now also initialized to np.nan in case
     of floating point data which and a consistent fill value in case of
     integer data. (see #1363)
 - obspy.clients.fdsn:
   * Fixing issue with location codes potentially resulting in unwanted data
     to be requested. (see #1422)
   * Included low-gain seismometers in default channel filters in
     mass-downloader, also included non-oriented channels by default
     (see #1373).
 - obspy.db:
   * Fixed a bug in obspy-indexer command line script (see #1369,
     command line script was not working, probably since 0.10.0)
 - obspy.imaging:
   * Fixed a bug that leads to pressure/tension color blending when plotting
     semi-transparent DC beachball patches (i.e. with "alpha" not \ 
equal to 1,
     see #1464)
   * Fixed a bug when plotting non-DC beachball patches without fill colors
     (i.e. with "nofill=True", see #1464)
   * Fix arbitrary units in waveform section plot's offset axis, making it
     possible to add customizations to the plot afterwards (see #1382, see
 - obspy.io.ascii:
   * Fixed a bug that lead to wrong header information in output files when
     writing non-integer sampling rate data to SLIST or TSPAIR formats
     (see #1447)
- obspy.io.cmtsolution:
   * Make sure newer CMTSOLUTION files can also be read (see #1479).
 - obspy.io.gse2:
   * Fixed a bug that could lead to network code not present in GSE2 output
     (see #1448)
 - obspy.io.mseed:
   * Fixed a bug in obspy-mseed-recordanalyzer (see #1386)
 - obspy.io.nlloc:
   * Use geographic coordinates from the NonLinLoc Hypocenter-Phase file if
     no custom coordinate converter is provided. (see #1390)
   * Fix reading NonLinLoc Hypocenter-Phase files with more than one
     hypocenter in it. (see #1480)
   * Fix reading NonLinLoc Hypocenter-Phase files with unicode characters in
     them. (see #1483)
 - obspy.io.quakeml:
   * Fixed issue with improperly raised warnings when the same file is read
     twice. (#1376)
   * Fix writing empty network/station/channel codes in WaveformStreamID
     objects to QuakeML. (see #1483)
 - obspy.io.sac:
   * Try to set SAC distances (dist, az, baz, gcarc) on read, if \ 
"lcalda" is
     true.  If "dist" header is found, distances aren't calculated.
   * SACTrace class returns header values as native Python types instead of
     NumPy types.
   * SACTrace.iqual is no longer accepts enumerated string values, but
     arbitrary integer values. (see #1472)
   * SACTrace.read now replaces non-ASCII and null-termination characters in
     string headers with whitespace unless the "debug_strings=True" flag is
     used. (see #1432)
 - obspy.io.stationxml:
   * Always set the number attribute for poles and zeros. (see #1481)
 - obspy.signal:
   * PPSD.plot(): fix plotting of percentiles, mode and mean and setting
     period limits when using "xaxis_frequency=True" (see #1406, #1416)
   * Work around a bug in SciPy that results in wrong results for bandpass
     filter when using Nyquist frequency (or higher) as high corner of the
     passband (see #1451)
 - obspy.taup:
   * Fixing path for Pn. (see #1392)