commit for JOSS talk

MANIFEST.in

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+include README.md
+include LICENSE
+include MANIFEST.in
+recursive-include dfistpy/ *
+recursive-include dfitspy/docs/ *
+

README.md

@@ -1 +1,3 @@
-# dfitspy_RSECon24
+# dfitspy_RSECon24
+
+

dfitspy/__info__.py

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+__version__ = '20.7.0'
+__place__ = 'ESO Paranal observatory'
+__credits__ = "Romain Thomas"
+__license__ = "GNU GPL v3"
+__maintainer__ = "Romain Thomas"
+__email__ = "the.spartan.proj@gmail.com"
+__status__ = "released"
+__website__ = "https://astrom-tom.github.io/dfitspy/build/html/index.html"

dfitspy/__init__.py

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+__all__ = ["get_files", "get_keys", "test", "read_fitsfile", "dfitsort", \
+        "keywords_in_file", "get_all_values", "dfitsort_view", "keywords_view","version"]
+
+
+from dfitspy.get_files_and_keys import get_files, get_keys
+from dfitspy.readfits import read_fitsfile, get_all_keyword, keywords_in_file, dfitsort
+from dfitspy.display import dfitsort_view, keywords_view
+from dfitspy.tests import test
+from dfitspy.__info__ import __version__ as version

dfitspy/__main__.py

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+#!/usr/bin/./python
+# -*- coding: utf-8 -*-
+
+'''
+---dfitspy---
+
+dfitspy is a program aimed at reproducing the dfits program in python.
+the functions can be used inside another program or it can also be called
+as an executable
+
+usage: dfitspy -f FILE.fits -k OBJECT
+
+@place: ESO - La Silla - Paranal Observatory
+@author(s): Romain Thomas
+@year(s):  ex 2018
+@First version: 19.9-0
+@Current version: 19.9-0
+@Telescope(s): ALL
+@Instrument(s): ALL
+@Valid for SciOpsPy: v0.1-b
+@Documentation url:
+@Last SciOps review [date + name]: 18-09-2018 - Romain Thomas
+@Usage: dfitspy FILE.fits HEADER_KEY_WORD, diftspy --help for more options
+@Licence: GPL
+@Testable: Yes
+@Test data place (if any required): inside the package
+'''
+
+
+###Python standard library
+import sys
+import os
+from subprocess import call
+import datetime
+import socket
+import time
+
+
+###local imports
+from . import __info__ as info
+from . import cli
+from . import display as dp
+from . import readfits
+from . import get_files_and_keys as get
+from . import tests
+
+def main():
+    '''
+    This is the main function of the program.
+    '''
+    ###first we load the command line interface
+    args = cli.command_line(sys.argv[1:])
+
+    ###here we check if at least one argument was given:
+    if not args.docs and args.file is None and args.grep is None and \
+            args.key is None and not args.list and not args.test:
+        print('\033[1m[DFITSPY Error]> no argument passed ...exit\033[0;0m')
+        sys.exit()
+
+    if args.docs is True:
+        ##check if there is any internet connection
+        try:
+            socket.setdefaulttimeout(3)
+            socket.socket(socket.AF_INET, socket.SOCK_STREAM).connect(("8.8.8.8", 53))
+            url = info.__website__
+        ##if not we use the local documentation distributed along the software
+        except:
+            print('No internet connection detected, open local documentation')
+            dir_path = os.path.dirname(os.path.realpath(__file__))
+            url = os.path.join(dir_path, 'docs/build/html/index.html')
+
+        for i in ['firefox', 'falkon', 'open', 'chromium', 'google-chrome']:
+            ##we check if the command exist in the system
+            exist = call(['which', i])
+            if exist == 0:
+                if i == 'firefox':
+                    call([i, '--no-remote', url])
+                    sys.exit()
+                ##if it does then we use it to load the documentation
+                else:
+                    call([i, url])
+                    ##and we stop the loop
+                    sys.exit()
+                break
+
+    if args.test:
+        tests.test()
+        ###exit code
+        sys.exit()
+
+    ###get all the files
+    list_files = get.get_files(args.file)
+
+    if list_files == []:
+        print('\n\033[1m[DFITSPY Error]>Invalid file name or no fits file found \033[0;0m')
+        sys.exit()
+
+    if args.list:
+        ###get all keywords
+        all_keywords = readfits.get_all_keyword(list_files[0], int(args.HDU))
+        ###display them
+        print('\n\033[1m[DFITSPY INFO]>keywords in %s \033[0;0m'%\
+                os.path.basename(list_files[0]))
+        dp.keywords_view(all_keywords)
+        sys.exit()
+
+    ##display number of files
+    print('\n\033[1m[DFITSPY INFO]> Current directory: %s \033[0;0m'%os.getcwd())
+    print('\033[1m[DFITSPY INFO]> %s fits files will be considered \033[0;0m'%len(list_files))
+    print('\033[1m[DFITSPY INFO]> We look in HDU %s \033[0;0m\n'%args.HDU)
+
+    ###get greeping from command line
+    if args.grep:
+        grep = args.grep
+    else:
+        grep = False
+
+    if not args.key:
+        print('\n\033[1m[DFISTPY Error]>no keywords given...exit... \033[0;0m')
+        sys.exit()
+    else:
+        ##get all keywords
+        list_keys = get.get_keys(args.key)
+
+    ##get all values for each keys and each files
+    allvalues = readfits.dfitsort(list_files, list_keys, args.exact, grep, int(args.HDU))
+
+    ##display them in terminal
+    dp.dfitsort_view(allvalues)
+
+    print('\n\033[1m[DFITSPY INFO]> %s files used in output \033[0;0m'%len(allvalues))
+    if args.save:
+        ###if we want to save the list of files into a file:
+        with open('dfitspy_file_list.txt', 'w') as finalfile:
+            finalfile.write('##file produced by dfitspy %s\n'%(datetime.datetime.now()))
+            finalfile.write('##Current directory: %s\n'%os.getcwd())
+            for i in allvalues.keys():
+                finalfile.write('%s\n'%i)
+        if os.path.isfile('dfitspy_file_list.txt'):
+            print('\033[1m[DFITSPY INFO]> File saved: dfitspy_file_list.txt \033[0;0m')
+
+
+if __name__ == "__main__":
+    main()

dfitspy/cli.py

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+'''
+---dfitspy---
+
+dfitspy is a program aimed at reproducing the dfits program in python.
+the functions can be used inside another program or it can also be called
+as an executable
+
+This file organises the command line interface (and nunit test it)
+
+@place: ESO - La Silla - Paranal Observatory
+@author(s): Romain Thomas
+@year(s):  2018
+@First version: 18.09-0
+@Current version: 20.7.1
+@Telescope(s): ALL
+@Instrument(s): ALL
+@Valid for SciOpsPy: v0.1-b
+@Documentation url:
+@Last SciOps review [date + name]: 18-09-2018 - Romain Thomas
+@Usage: inside another code (dfitspy)
+@Licence: GPL
+@Testable: Yes
+@Test data place (if any required): N.A.
+'''
+
+
+##standard library
+import argparse
+
+##testing
+import unittest
+
+#local import
+from . import __info__ as info
+
+
+def command_line(args):
+    '''
+    This function defines the command line interface of the program.
+    It is used only if dfitspy is used as an executable
+
+    Parameters
+    -----------
+    None
+
+    Returns
+    -------
+    args    Namespace with arguments
+    '''
+
+    ##create parser object
+    parser = argparse.ArgumentParser(description='dfitspy: dfits|fitsort in python, version %s, \
+            Licence: GPL'%(info.__version__))
+
+    mand = parser.add_argument_group("Mandatory arguments if you want to dfitsort your files")
+    mand.add_argument('-file', nargs='*', help='a file, a list of file separated by coma,\
+            *.fits is accepted, * as well, test* as well, testdir/test* as well')
+    mand.add_argument('-key', help='Header keyword or list of header keywords\
+            (separated by coma)')
+
+
+    ###optional arguments
+    #parser.add_argument('--dir', help='Directory where we search for files. \
+    #        If none given, the default directory is the one from where dfitspy \
+    #        is started.', default=os.getcwd())
+    opt = parser.add_argument_group("Optional arguments")
+    opt.add_argument('--list', help='List all keywords in a given file \
+            (if a list of file is given the first one is used)', action='store_true')
+    opt.add_argument('--grep', help='Restrain the files to the one with a given \
+            value of a given parameter. It can be used multiple times with different values', \
+            type=str, action='append')
+    opt.add_argument('--exact', '-e', help='Consider only exact matches for keywords',
+                     action='store_true')
+    opt.add_argument('--HDU', '-H', help='HDU extension, default is 0 (primary header)', type=int, default=0) 
+    opt.add_argument('--save', help='Save the list of files into an ascii file',\
+            action='store_true')
+    opt.add_argument('--test', help='Start the testing of the program', \
+            action='store_true')
+    opt.add_argument('--version', help='Display the version of the program', \
+            action='version', version=info.__version__)
+    opt.add_argument('--docs', help='Diplay the online or local documentation program', \
+            action='store_true')
+
+    ##create a group of arguments that are mandatory
+    return parser.parse_args(args)
+
+
+
+class Interfacetest(unittest.TestCase):
+    '''
+    Class that define the test for the command line interface
+    '''
+    def test_cli(self):
+        '''
+        This method tests the command line interface
+        The principle is that we send some argument configuration
+        and see what the interface is giving back
+        '''
+        options = command_line(['--grep', 'testobject',\
+                                '--list', '--test'])
+        self.assertEqual(options.grep, ['testobject'])
+        self.assertEqual(options.list, True)
+        self.assertEqual(options.test, True)
+
+        options2 = command_line(['-file', '/home/file', \
+                                 '-key', 'testkey'])
+        self.assertEqual(options2.key, 'testkey')
+        self.assertEqual(options2.file, ['/home/file'])