diff --git a/.gitlab/issue_templates/Bug.md b/.gitlab/issue_templates/Bug.md
index 0a15ec0656cefe121904788a5a38d2ed0f1d1100..285e734ad76c35038605836594267dc2add34717 100644
--- a/.gitlab/issue_templates/Bug.md
+++ b/.gitlab/issue_templates/Bug.md
@@ -1,4 +1,4 @@
-* rt2ms version:
+* refscrub version:
* Python version:
* Operating System:
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index c54a658cc305f592ed8f54561e0a1b084f051b92..3f3c1fa5ce376afedaff562eda6794ec635cf85d 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -32,7 +32,7 @@ wanted" is open to whoever wants to implement it.
Implement Features
~~~~~~~~~~~~~~~~~~
-Look through the GitHub issues for features. Anything tagged with "enhancement"
+Look through the GitLab issues for features. Anything tagged with "enhancement"
and "help wanted" is open to whoever wants to implement it.
Write Documentation
@@ -88,10 +88,10 @@ Ready to contribute? Here's how to set up `refscrub` for local development.
Pull Request Guidelines
-----------------------
-Before you submit a pull request, check that it meets these guidelines:
+Before you submit a merge request, check that it meets these guidelines:
-1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
+1. The merge request should include tests.
+2. If the merge request adds functionality, the docs should be updated. Put
your new functionality into a function with a docstring, and add the
feature to the list in README.rst.
3. The pull request should work for Python 2.7
diff --git a/HISTORY.rst b/HISTORY.rst
index 26bb6d4f2aaf90ea538b3a7e8dbea9841d357c89..158c12cd5c93c27ecc13f0c418b34d0242f8c3a0 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,7 +2,17 @@
History
=======
-2011.046 (2018-06-05)
+2011.046 (2018-06-07)
------------------
* First release on new build system.
+
+2018.180 (2018-06-29)
+------------------
+
+* 2nd release on new build system.
+
+2018.204 (2018-07-23)
+------------------
+
+* Minor fixes of global variables
diff --git a/LICENSE b/LICENSE
index e67492509cb2a711807a2c15156eefe18e83b111..197ea95ed00b37a266e0429338fa35b723a39c0f 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,7 +1,7 @@
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
- Remove select packets from RT130 data.
+ Remove select packets from RT130 data
Copyright (C) 2018 IRIS PASSCAL
This program is free software: you can redistribute it and/or modify
diff --git a/README.rst b/README.rst
index a9817e2dd06360c6de70d91063a434979b45f026..198b6c62481dfb99f4c334e547613502f350a459 100644
--- a/README.rst
+++ b/README.rst
@@ -3,7 +3,7 @@ refscrub
========
-Remove select packets from RT130 data.
+Remove select packets from RT130 data
* Free software: GNU General Public License v3 (GPLv3)
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..69ed63fa4709740e1860cb60ea4dc51f0b2a7182
--- /dev/null
+++ b/conda.recipe/meta.yaml
@@ -0,0 +1,24 @@
+package:
+ name: refscrub
+ version: 2011.046
+
+source:
+ path: ..
+
+build:
+ # If the installation is complex, or different between Unix and Windows, use
+ # separate bld.bat and build.sh files instead of this key. Add the line
+ # "skip: True # [py<35]" (for example) to limit to Python 3.5 and newer, or
+ # "skip: True # [not win]" to limit to Windows.
+ script: python setup.py install --single-version-externally-managed --record=record.txt
+
+requirements:
+ build:
+ - python
+ - setuptools
+ run:
+ - python
+
+about:
+ home: https://git.passcal.nmt.edu/passoft/refscrub
+ summary: Remove select packets from RT130 data
diff --git a/docs/installation.rst b/docs/installation.rst
index 8a4b8fef8517f1888e3728105fcc45c6d77f7e32..799288229a993862a97839ecf8eb5d6fcc9e5783 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -4,25 +4,6 @@
Installation
============
-
-Stable release
---------------
-
-To install refscrub, run this command in your terminal:
-
-.. code-block:: console
-
- $ pip install refscrub
-
-This is the preferred method to install refscrub, as it will always install the most recent stable release.
-
-If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-you through the process.
-
-.. _pip: https://pip.pypa.io
-.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
-
-
From sources
------------
diff --git a/refscrub/__init__.py b/refscrub/__init__.py
index 96b57e94ac3f41f297b81a7cd7a8b5922074918d..384ebd4b593cd0e4342bbd51910853f15ed33099 100644
--- a/refscrub/__init__.py
+++ b/refscrub/__init__.py
@@ -4,4 +4,4 @@
__author__ = """IRIS PASSCAL"""
__email__ = 'software-support@passcal.nmt.edu'
-__version__ = '2011.046'
+__version__ = '2018.204'
diff --git a/refscrub/refscrub b/refscrub/refscrub
deleted file mode 100755
index 7605a99d4b56058b37bd869eec25f4792e0e46af..0000000000000000000000000000000000000000
--- a/refscrub/refscrub
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-
-EXEC='neo'
-ARGS=$@
-
-if [ ! -z "${PASSCAL}" ]
-then
- PYTHON=${PASSCAL}/other/bin/picpython
- export PYTHON
- set PYTHONPATH ${PASSCAL}/lib/python/${EXEC}
- export PYTHONPATH
-else
- echo "PASSCAL environment not set! Can not continue."
- exit 1
-fi
-
-if [ ! -e "$PYTHON" ]
-then
- echo "$PYTHON not found! PyPASSCAL is required. Make sure picpython is in your path variable"
- exit
-fi
-
-
-${PYTHON} ${PASSCAL}/lib/python/${EXEC}/refscrub.py $ARGS
diff --git a/refscrub/refscrub.py b/refscrub/refscrub.py
index 2305927657e9964f9c61821dca1fa705a4a6a675..ba46a854e99619a3b1d8b775a5d1c246e65425b1 100755
--- a/refscrub/refscrub.py
+++ b/refscrub/refscrub.py
@@ -3,12 +3,16 @@
Lloyd Carothers
February 2011
Rewrite of original refscrub
+
+Derick Hess
+July 2018
+Minor fixes for new build system
'''
from __future__ import with_statement
USAGE = 'usage: %prog [options] infile1 [ infile2 ... infileN]'
#USAGE = '''Scans (default) or extracts good reftek packets from a REFTEK file or CF card.'''
-PROG_VERSION = '2011.046'
+PROG_VERSION = '2018.204'
VERBOSE = False
EXTRACT = False
SUMMARY_FILE = 'scrubsum.txt'
@@ -21,6 +25,8 @@ import struct
class SN():
def __init__(self, SN):
+ global EXTRACT
+ global PREFIX
self.SN = SN
self.count = 0
self.dates = list()
@@ -37,8 +43,8 @@ class SN():
def __str__(self):
self.dates = list(set(self.dates))
self.dates.sort()
- start = "%0.2d:%0.3d:%0.2d" % (self.dates[0])
- end = "%0.2d:%0.3d:%0.2d" % (self.dates[-1])
+ start = "%0.2d:%0.3d:%0.2d" % (self.dates[0])
+ end = "%0.2d:%0.3d:%0.2d" % (self.dates[-1])
return "%7s: %s -- %s : %12d\n" % (self.SN , start , end, self.count )
class SNseen(dict):
@@ -53,7 +59,7 @@ class SNseen(dict):
for sn in self.values():
s += str(sn)
return s
-
+
##class SNseen(dict):
## def __init__(self):
@@ -73,11 +79,11 @@ class SNseen(dict):
## for sn in self.keys():
## dates = self[sn]
## dates.sort()
-## start = "%0.2d:%0.3d:%0.2d" % (dates[0])
-## end = "%0.2d:%0.3d:%0.2d" % (dates[-1])
+## start = "%0.2d:%0.3d:%0.2d" % (dates[0])
+## end = "%0.2d:%0.3d:%0.2d" % (dates[-1])
## s += "%7s: %s -- %s\n" % (sn , start , end )
## return s
-
+
class RTPacket:
RTstruct = struct.Struct('2c1B1B2B6B2B2B')
#packetHdrFmt = '2c1B1B2B6B2B2B'
@@ -107,6 +113,8 @@ class RTPacket:
Returns True if a valid reftek packet (headers parse well and are valid)
Also populates the objects attributes SN, time, etc.
'''
+
+ global VERBOSE
try:
tup = RTPacket.RTstruct.unpack(self.data[:16])
#tup = unpack( self.packetHdrFmt, self.data[:16])
@@ -142,10 +150,12 @@ class RTPacket:
RTPacket.seen.look(self.sn, self.year, self.day, self.hour)
RTPacket.goodpkts +=1
return True
-
+
def readfile(infile):
ticker = 1
#speedup local vars
+ global VERBOSE
+ global EXTRACT
tell = infile.tell
read = infile.read
seek = infile.seek
@@ -183,12 +193,14 @@ def readfile(infile):
print tabs + "NOT VALID"
print tabs + ">>>>>>>>"
seek(-1023, 1)
-
+
print summary()
#commented out as when run with many files as input like a cf dir the closed fh's need to be written to and isn't smart enough to be opened
#RTPacket.seen.close_fhs()
-
+
def summary():
+ global infile
+ global FILESIZE
OFFSTRING = "%6s: %12d\n"
s = OFFSTRING % ( "OFFSET", infile.tell())
s += OFFSTRING % ( "OF", FILESIZE)
@@ -196,39 +208,49 @@ def summary():
s+= "IOErrors: %d\n" % (RTPacket.IOErrorCount)
s += str(RTPacket.seen) + '\n'
return s
-
-if __name__ == '__main__':
+def main():
+ global VERBOSE
+ global EXTRACT
+ global PREFIX
+ global infile
+ global FILESIZE
from optparse import OptionParser
- parser = OptionParser(USAGE, version = "%prog " + PROG_VERSION)
+ parser = OptionParser(USAGE, version="%prog " + PROG_VERSION)
parser.description = "infile can be a REFTEK file or a raw disk (/dev/disk1) of a CF card."
- parser.add_option('-v', '--verbose', dest="VERBOSE", action = 'store_true', default=False,
- help = "Prints info about each packet, good or bad. This will increase runtime.")
- parser.add_option('-e', '--extract', dest='EXTRACT', action = 'store_true', default=False,
- help = 'Writes good packets to files named infile.SNXX.scrub.ref OR PREFIX.SNXX.scrub.ref, if given, for each Serial Number found. If output file exists it will append. Be careful not to duplicate data by running more than once on the same file in the same dir.' )
- parser.add_option('-p', '--prefix', dest='PREFIX',
- help = 'Prefix of output filename. Defaults to inputfilename' )
- parser.add_option('-s', '--savesum', dest = 'SUMMARY', action = 'store_true', default = False,
- help = 'Appends summary to %s' % SUMMARY_FILE)
+ parser.add_option('-v', '--verbose', dest="VERBOSE", action='store_true', default=False,
+ help="Prints info about each packet, good or bad. This will increase runtime.")
+ parser.add_option('-e', '--extract', dest='EXTRACT', action='store_true', default=False,
+ help='Writes good packets to files named infile.SNXX.scrub.ref OR PREFIX.SNXX.scrub.ref, if given, for each Serial Number found. If output file exists it will append. Be careful not to duplicate data by running more than once on the same file in the same dir.')
+ parser.add_option('-p', '--prefix', dest='PREFIX',
+ help='Prefix of output filename. Defaults to inputfilename')
+ parser.add_option('-s', '--savesum', dest='SUMMARY', action='store_true', default=False,
+ help='Appends summary to %s' % SUMMARY_FILE)
options, args = parser.parse_args()
VERBOSE = options.VERBOSE
- EXTRACT = options.EXTRACT
+ EXTRACT = options.EXTRACT
PREFIX = options.PREFIX
if options.SUMMARY:
- summaryfh = open (SUMMARY_FILE, 'a')
+ summaryfh = open(SUMMARY_FILE, 'a')
for infilename in args:
- print "Processing: %s" % infilename
+ print
+ "Processing: %s" % infilename
if not PREFIX:
PREFIX = basename(infilename)
- print "Using prefix %s" % PREFIX
+ print
+ "Using prefix %s" % PREFIX
FILESIZE = getsize(infilename)
with open(infilename) as infile:
- #with open( infile.name + 'scrub.ref')) as outfile:
- #import profile
- #profile.run('readfile(infile)')
- readfile(infile)
+ # with open( infile.name + 'scrub.ref')) as outfile:
+ # import profile
+ # profile.run('readfile(infile)')
+ readfile(infile)
if options.SUMMARY:
- summaryfh.write(infilename + ', ' + PREFIX + '\n' )
+ summaryfh.write(infilename + ', ' + PREFIX + '\n')
summaryfh.write(summary())
-
- print "----------------------------------------"
\ No newline at end of file
+
+ print
+ "----------------------------------------"
+
+if __name__ == '__main__':
+ main()
diff --git a/setup.cfg b/setup.cfg
index 76c2845d324d4195d5d2942e63d7a796764921e6..01be8885ce5ae39815a7295d2e34698c2975ddc9 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 2011.046
+current_version = 2018.180
commit = True
tag = True
diff --git a/setup.py b/setup.py
index 9e1746b8d8633ccedeb535eb10830516b81d2ac8..194d54d9d5340156de7ab0a92601105d5cdb61a3 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@ setup(
'Natural Language :: English',
'Programming Language :: Python :: 2.7',
],
- description="Remove select packets from RT130 data.",
+ description="Remove select packets from RT130 data",
entry_points={
'console_scripts': [
'refscrub=refscrub.refscrub:main',
@@ -51,6 +51,6 @@ setup(
packages=find_packages(include=['refscrub']),
test_suite='tests',
url='https://git.passcal.nmt.edu/passoft/refscrub',
- version='2011.046',
+ version='2018.204',
zip_safe=False,
)