Update for Julia 0.7

jpjones76 · Aug 11, 2018 · 230e375 · 230e375
1 parent 7f1c667
commit 230e375
Show file tree

Hide file tree

Showing 127 changed files with 15,925 additions and 2,797 deletions.
diff --git a/README.md b/README.md
@@ -4,7 +4,27 @@ A minimalist, platform-agnostic package for working with univariate geophysical
 # Documentation
 http://seisio.readthedocs.org
 
+# KNOWN ISSUES (2018-08-10)
+* Rarely, `SeedLink!` may cause a Julia session to hang when a connection fails to initialize.
+* Required packages LightXML and Blosc both generate "Deprecated syntax" warnings.
+
 # CHANGELOG
+## 2018-08-10
+* Updated for Julia 0.7. Testing for 1.0.
+  + Please report all warnings produced.
+* `wseis` has changed:
+  + New syntax: `wseis(filename, objects)`
+  + Keywords are no longer accepted.
+* `SeisHdr` has changed:
+  + The field `:mag` (magnitude) is now Tuple(Float32, String) to allow freeform magnitude scale designations. (was: Tuple(Float32, Char, Char))
+* `batch_read` has been removed.
+* Switched to HTTP.jl due to Requests.jl being abandoned by its creators.
+  + In web requests, keyword `to=` (timeout) must now be an Integer. (was: Real)
+* SeisIO objects can no longer be saved in single-object files.
+* Notable bug fixes:
+  + Issues with `wseis` and `SeisHdr` objects should be corrected.
+  + Improved partial string matches for channel names and IDs.
+
 ## 2017-08-07
 * Improved `note!` functionality and logging of basic processing operations.
 * New function: `clear_notes!` can delete notes for a given channel number or string ID.
@@ -25,22 +45,10 @@ http://seisio.readthedocs.org
   + `t_win`, `w_time`: Convert between SeisIO time representations and time windows
   + `demean!`, `unscale!`: Basic processing operations
 
-## 2017-07-16
-* `readmseed` rewritten; performance improvements should be very noticeable.
-  + Many bugfixes.
-  + SeisIO now uses a small (~500k) memory-resident structure for SEED packets.
-  + SEED defaults can be changed with `seeddef`.
-* `findid` no longer relies on the ever-redoubtable combination of `findfirst` and String arrays.
-* Faster initialization of empty SeisData structs with `SeisData()`.
-
 ## 2017-07-04
 * Updated for Julia v0.6.0. Compatibility with earlier versions is not guaranteed. Please report any deprecation warnings!
 
-## Known Issues (2017-07-24)
-* batch_read is no longer useful. Julia 0.6.0 slowed batch_read execution time by roughly a factor of 4; it currently offers only ~10-20% speedup over standard file read methods.
-* Rarely, SeedLink! can cause a Julia session to hang by failing to initialize a connection.
-
-# Current Functionality
+# CURRENT FUNCTIONALITY
 SeisIO presently includes three web clients, readers for several data formats, and writers for SAC and a native SeisIO format. Utility functions allow synchronization, seamless data merging, and padding time gaps.
 
 ## Web clients
@@ -58,10 +66,10 @@ SeisIO presently includes three web clients, readers for several data formats, a
 * Win32
 * UW
 
-# Acknowledgements
+# ACKNOWLEGEMENTS
 miniSEED routines are based on rdmseed.m for Matlab by Francois Beauducel, Institut de Physique du Globe de Paris (France). Many thanks to Robert Casey and Chad Trabant (IRIS, USA) for discussions of IRIS web services, and Douglas Neuhauser (UC Berkeley Seismological Laboratory, USA) for discussions of the SAC data format.
 
-# References
+# REFERENCES
 1. IRIS (2010), SEED Reference Manual: SEED Format Version 2.4, May 2010, IFDSN/IRIS/USGS, http://www.iris.edu
 2. Trabant C. (2010), libmseed: the Mini-SEED library, IRIS DMC.
 3. Steim J.M. (1994), 'Steim' Compression, Quanterra Inc.
diff --git a/REQUIRE b/REQUIRE
@@ -1,6 +1,8 @@
-julia 0.5
+julia 0.7
+Dates
 DSP
-Requests
+HTTP
 Distributions
 Blosc
 LightXML
+Compat
diff --git a/docs/_build/doctrees/src/Appendices/examples.doctree b/docs/_build/doctrees/src/Appendices/examples.doctree
diff --git a/docs/_build/doctrees/src/Appendices/function_list.doctree b/docs/_build/doctrees/src/Appendices/function_list.doctree
diff --git a/docs/_build/doctrees/src/Appendices/seisdata_fileformat.doctree b/docs/_build/doctrees/src/Appendices/seisdata_fileformat.doctree
diff --git a/docs/_build/doctrees/src/Appendices/web_syntax.doctree b/docs/_build/doctrees/src/Appendices/web_syntax.doctree
diff --git a/docs/_build/doctrees/src/Formats/fileformats.doctree b/docs/_build/doctrees/src/Formats/fileformats.doctree
diff --git a/docs/_build/doctrees/src/Web/webclients.doctree b/docs/_build/doctrees/src/Web/webclients.doctree
diff --git a/docs/_build/doctrees/src/examples.doctree b/docs/_build/doctrees/src/examples.doctree
diff --git a/docs/_build/doctrees/src/fileformats.doctree b/docs/_build/doctrees/src/fileformats.doctree
diff --git a/...es/src/Appendices/seisdata_fields.doctree → ...uild/doctrees/src/seisdata_fields.doctree b/...es/src/Appendices/seisdata_fields.doctree → ...uild/doctrees/src/seisdata_fields.doctree
diff --git a/docs/_build/doctrees/src/seisdata_fileformat.doctree b/docs/_build/doctrees/src/seisdata_fileformat.doctree
diff --git a/docs/_build/doctrees/src/utils.doctree b/docs/_build/doctrees/src/utils.doctree
diff --git a/docs/_build/doctrees/src/webclients.doctree b/docs/_build/doctrees/src/webclients.doctree
diff --git a/docs/_build/html/_sources/index.txt b/docs/_build/html/_sources/index.txt
@@ -0,0 +1,23 @@
+.. SeisIO documentation master file, created by
+   sphinx-quickstart on Sun May 22 18:44:14 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+######
+SeisIO
+######
+SeisIO is a collection of utilities for reading and downloading geophysical timeseries data.
+
+********
+Contents
+********
+.. toctree::
+   :maxdepth: 3
+
+   src/intro.rst
+   src/webclients.rst
+   src/fileformats.rst
+   src/seisdata.rst
+   src/seisdata_fields.rst
+   src/seisdata_fileformat.rst
+   src/utils.rst
diff --git a/docs/_build/html/_sources/src/Appendices/examples.rst.txt b/docs/_build/html/_sources/src/Appendices/examples.rst.txt
@@ -130,13 +130,13 @@ SeedLink
 
   S = SeisData()
   SeedLink!(S, sta, mode="TIME", r=10.0, s=d0, t=d1)
-  println(STDOUT, "...first link initialized...")
+  println(stdout, "...first link initialized...")
 
   # Seedlink with a config file
   config_file = "seedlink.conf"
   SeedLink!(S, config_file, r=10.0, mode="TIME", s=d0, t=d1)
-  println(STDOUT, "...second link initialized...")
+  println(stdout, "...second link initialized...")
 
   # Seedlink with a config string
   SeedLink!(S, "CC.VALT..???, UW.ELK..EHZ", mode="TIME", r=10.0, s=d0, t=d1)
-  println(STDOUT, "...third link initialized...")
+  println(stdout, "...third link initialized...")
diff --git a/docs/_build/html/_sources/src/Appendices/function_list.rst.txt b/docs/_build/html/_sources/src/Appendices/function_list.rst.txt
@@ -63,7 +63,7 @@ Read files matching ``fstr`` into memory using parallel read and shared arrays.
 
 .. function:: chanspec()
 
-Type ``?chanspec`` to print detailed channel specification syntax to STDOUT.
+Type ``?chanspec`` to print detailed channel specification syntax to stdout.
 
 .. function:: t = d2u(DT::DateTime)
 
@@ -184,11 +184,11 @@ Read SeisIO data from ``fname`` into an array of SeisIO-compatible structures.
 
 .. function:: sachdr(fname)
 
-Print headers from SAC file ``fname`` to STDOUT.
+Print headers from SAC file ``fname`` to stdout.
 
 .. function:: segyhdr(fname)
 
-Print headers from SEG Y file ``fname`` to STDOUT. Specify ``passcal=true`` for PASSCAL SEG Y.
+Print headers from SEG Y file ``fname`` to stdout. Specify ``passcal=true`` for PASSCAL SEG Y.
 
 .. function:: T = sort(S, rev=false)
 

diff --git a/docs/_build/html/_sources/src/Formats/fileformats.rst.txt b/docs/_build/html/_sources/src/Formats/fileformats.rst.txt
diff --git a/docs/_build/html/_sources/src/Web/webclients.rst.txt b/docs/_build/html/_sources/src/Web/webclients.rst.txt
diff --git a/docs/_build/html/_sources/src/examples.txt b/docs/_build/html/_sources/src/examples.txt
@@ -0,0 +1,34 @@
+:mod:`Examples`
+====================
+
+SeedLink
+--------------------------
+Download a minute of real-time data from stations GPW (Glacier Peak, WA, USA) and MBW (Mt. Baker, WA, USA) to a SeisData object named seis:
+
+::
+
+  sta = ["GPW UW"; "MBW UW"]
+  seis = SeedLink(sta, t=60.0)
+
+FDSN
+------------------------
+Downloads roughly 10 minutes of data from 4 stations at Mt. St. Helens (WA, USA), delete the low-gain channels, plot, and save to the current directory:
+
+::
+
+  S = FDSNget(net="CC,UW", sta="SEP,SHW,HSR,VALT", cha="*", t=600)
+  S -= "SHW    ELZUW"
+  S -= "HSR    ELZUW"
+  plotseis(S)
+  writesac(S)
+
+
+IRISget
+--------------------------
+Request 10 minutes of continuous data recorded during the May 2016 earthquake swarm at Mt. Hood, OR, USA:
+
+::
+
+  STA = ["UW.HOOD.BHZ"; "UW.HOOD.BHN"; "UW.HOOD.BHE"; "CC.TIMB.EHZ"; "CC.TIMB.EHN"; "CC.TIMB.EHE"]
+  TS = "2016-05-16T14:50:00"; TE = 600
+  S = IRISget(STA, s=TS, t=TE)