Some code cleanup- and added the ability to concatenate smartmooring

[pieterbartsmit]

• added a requirements.txt for installation
• removed the weird local scope importing I used to do and replaced with global imports
• introduced standard "import numpy as np"
• allow for smartmooring parsing (very rudimentary)
• allow for parsing of files if no sys files are available (use latest defaults to try and parse).

[tcj]

@pieterbartsmit thanks for all the useful changes and cleanup!

I am noticing one problem, which I can dig into more later. While testing with data from SPOT-0552:

Traceback (most recent call last):
  File "/Users/tcj/src/spotter-sd-parser/sd_file_parser.py", line 1699, in <module>
    main(**arguments)
  File "/Users/tcj/src/spotter-sd-parser/sd_file_parser.py", line 553, in main
    if spectra.spectral_data_is_available:
AttributeError: 'str' object has no attribute 'spectral_data_is_available'

[randallpittman]

@tcj - It looks like that should be spectrum.spectral_data_is_available instead of spectra.spectral_data_is_available in line 553.

diff --git a/sd_file_parser.py b/sd_file_parser.py
index 1d29dec..04e13ad 100755
--- a/sd_file_parser.py
+++ b/sd_file_parser.py
@@ -550,7 +550,7 @@ def main( path = None , outpath=None, outputFileType='CSV',
         # Generate bulk parameter file
         if bulkParameters:
             spectrum = Spectrum(path=outpath,outpath=outpath)
-            if spectra.spectral_data_is_available:
+            if spectrum.spectral_data_is_available:
                 spectrum.generate_text_file()
     #Versions
     #

[randallpittman]

@pieterbartsmit
Since the PR needs updating, how about also sorting the imports a la PEP8?

import fnmatch
import gzip
import os
import sys
import time

import numpy as np
import pandas as pd
from scipy import io, signal