Convert to Python package with entry_points (#11)

.travis.yml

@@ -1,15 +1,14 @@
 language: python
+
 python:
   - "3.4"
   - "3.5"
   - "3.6"
   - "3.7"
-# command to install dependencies
+
 install:
-  - pip install h5py numpy docopt
-  - pip install .
-  - export PATH="${PWD}"/bin:"${PATH}"
-# command to run tests
+  - python -m pip install .
+
 script:
   - python test/bin/G5check.py
   - python test/bin/G5compare.py

GooseHDF5/__init__.py

@@ -1,7 +1,9 @@
 import warnings
 warnings.filterwarnings("ignore")
 
-import os, re, h5py
+import os
+import re
+import h5py
 
 # ==================================================================================================
 
@@ -343,8 +345,10 @@ def verify(data, datasets, error=False):
     try:
       tmp = data[path][...]
     except:
-      if error: raise IOError('Error reading "{path:s}"'.format(path=path))
-      else    : continue
+      if error:
+        raise IOError('Error reading "{path:s}"'.format(path=path))
+      else:
+        continue
 
     # - add to output
     out += [path]

bin/G5check → GooseHDF5/cli/G5check.py

@@ -24,7 +24,13 @@
 warnings.filterwarnings("ignore")
 
 import numpy as np
-import sys, os, re, h5py, docopt, GooseHDF5
+import sys
+import os
+import re
+import h5py
+import docopt
+
+from .. import *
 
 # ==================================================================================================
 
@@ -38,28 +44,32 @@ def check_isfile(fname):
 
 # ==================================================================================================
 
-def read(filename, verify):
+def read(filename, check):
   r'''
-Read (and verify) all datasets
+Read (and check) all datasets
   '''
 
   with h5py.File(filename, 'r') as source:
 
-    paths = list(GooseHDF5.getdatasets(source))
+    paths = getdatasets(source)
 
-    if verify:
-      GooseHDF5.verify(source, paths, error=True)
+    if check:
+      verify(source, paths, error=True)
 
 # ==================================================================================================
 
-# parse command-line options
-args = docopt.docopt(__doc__,version='0.0.2')
+def main():
+
+  # parse command-line options
+  args = docopt.docopt(__doc__,version='0.0.2')
 
-# check that file exists
-check_isfile(args['<source>'])
+  # check that file exists
+  check_isfile(args['<source>'])
 
-# read datasets
-try:
   read(args['<source>'], not args['--basic'])
-except:
-  print(args['<source>'])
+
+  # read datasets
+  try:
+    read(args['<source>'], not args['--basic'])
+  except:
+    print(args['<source>'])

bin/G5compare → GooseHDF5/cli/G5compare.py

@@ -26,7 +26,13 @@
 warnings.filterwarnings("ignore")
 
 import numpy as np
-import sys, os, re, h5py, docopt, GooseHDF5
+import sys
+import os
+import re
+import h5py
+import docopt
+
+from .. import *
 
 # ==================================================================================================
 
@@ -90,17 +96,17 @@ def check_plain(source_name, other_name):
     with h5py.File(other_name, 'r') as other:
 
       # check missing dataset
-      for path in GooseHDF5.getpaths(source):
+      for path in getpaths(source):
         if path not in other:
           print('-> {0:s}'.format(path))
 
       # check missing dataset
-      for path in GooseHDF5.getpaths(other):
+      for path in getpaths(other):
         if path not in source:
           print('<- {0:s}'.format(path))
 
       # check values
-      for path in GooseHDF5.getpaths(source):
+      for path in getpaths(source):
         if path in other:
           check_dataset(path, source[path][...], other[path][...])
 
@@ -118,8 +124,8 @@ def check_renamed(source, other, renamed):
     with h5py.File(other, 'r') as other:
 
       # get list of all datasets
-      s2o = {i:i for i in list(GooseHDF5.getpaths(source))}
-      o2s = {i:i for i in list(GooseHDF5.getpaths(other))}
+      s2o = {i:i for i in list(getpaths(source))}
+      o2s = {i:i for i in list(getpaths(other))}
 
       # rename
       for s, o in renamed:
@@ -143,22 +149,22 @@ def check_renamed(source, other, renamed):
 
 # ==================================================================================================
 
-# parse command-line options
-args = docopt.docopt(__doc__,version='0.0.1')
-
-# check that file exists
-check_isfile(args['<source>'])
-check_isfile(args['<other>'])
+def main():
 
-# check without accounting for renamed field
-if len(args['--renamed']) == 0:
-  check_plain(args['<source>'], args['<other>'])
-  sys.exit(0)
+  # parse command-line options
+  args = docopt.docopt(__doc__,version='0.0.1')
 
-# unpack renaming
-renamed = [i.split(args['--ifs']) for i in args['--renamed']]
+  # check that file exists
+  check_isfile(args['<source>'])
+  check_isfile(args['<other>'])
 
-# check with accounting for renamed field
-check_renamed(args['<source>'], args['<other>'], renamed)
+  # check without accounting for renamed field
+  if len(args['--renamed']) == 0:
+    check_plain(args['<source>'], args['<other>'])
+    sys.exit(0)
 
+  # unpack renaming
+  renamed = [i.split(args['--ifs']) for i in args['--renamed']]
 
+  # check with accounting for renamed field
+  check_renamed(args['<source>'], args['<other>'], renamed)

bin/G5list → GooseHDF5/cli/G5list.py

@@ -21,12 +21,17 @@
 
 # ==================================================================================================
 
-# temporary fix: suppress warning from h5py
 import warnings
 warnings.filterwarnings("ignore")
 
 import numpy as np
-import sys, os, re, h5py, docopt, GooseHDF5
+import sys
+import os
+import re
+import h5py
+import docopt
+
+from .. import *
 
 # ==================================================================================================
 
@@ -90,23 +95,25 @@ def print_info(source, paths):
 
 # ==================================================================================================
 
-# parse command-line options
-args = docopt.docopt(__doc__,version='0.0.3')
+def main():
+
+  # parse command-line options
+  args = docopt.docopt(__doc__,version='0.0.3')
 
-# check that file exists
-check_isfile(args['<source>'])
+  # check that file exists
+  check_isfile(args['<source>'])
 
-# open file and read
-with h5py.File(args['<source>'], 'r') as source:
+  # open file and read
+  with h5py.File(args['<source>'], 'r') as source:
 
-  # get iterator to data-sets
-  paths = GooseHDF5.getpaths(source,
-    root      = args['--root'],
-    max_depth = args['--max-depth'],
-    fold      = args['--fold'])
+    # get iterator to data-sets
+    paths = getpaths(source,
+      root      = args['--root'],
+      max_depth = args['--max-depth'],
+      fold      = args['--fold'])
 
-  # print
-  if args['--info']:
-    print_info(source, paths)
-  else:
-    print_plain(source, paths)
+    # print
+    if args['--info']:
+      print_info(source, paths)
+    else:
+      print_plain(source, paths)

bin/G5repair → GooseHDF5/cli/G5repair.py

@@ -19,12 +19,17 @@
 
 # ==================================================================================================
 
-# temporary fix: suppress warning from h5py
 import warnings
 warnings.filterwarnings("ignore")
 
 import numpy as np
-import sys, os, re, h5py, docopt, GooseHDF5
+import sys
+import os
+import re
+import h5py
+import docopt
+
+from .. import *
 
 # ==================================================================================================
 
@@ -38,23 +43,25 @@ def check_isfile(fname):
 
 # ==================================================================================================
 
-# parse command-line options
-args = docopt.docopt(__doc__,version='0.0.2')
+def main():
+
+  # parse command-line options
+  args = docopt.docopt(__doc__,version='0.0.2')
 
-# check that file exists
-check_isfile(args['<source>'])
+  # check that file exists
+  check_isfile(args['<source>'])
 
-# check to overwrite
-if os.path.isfile(args['<destination>']) and not args['--force']:
-  if not click.confirm('File "{0:s}" already exists, continue [y/n]? '.format(args['<destination>'])):
-    sys.exit(1)
+  # check to overwrite
+  if os.path.isfile(args['<destination>']) and not args['--force']:
+    if not click.confirm('File "{0:s}" already exists, continue [y/n]? '.format(args['<destination>'])):
+      sys.exit(1)
 
-# read the 'damaged' file
-with h5py.File(args['<source>'], 'r') as source:
+  # read the 'damaged' file
+  with h5py.File(args['<source>'], 'r') as source:
 
-  # get paths that can be read
-  paths = GooseHDF5.verify(source, GooseHDF5.getdatasets(source))
+    # get paths that can be read
+    paths = verify(source, getdatasets(source))
 
-  # copy datasets
-  with h5py.File(args['<destination>'], 'w') as dest:
-    GooseHDF5.copydatasets(source, dest, paths)
+    # copy datasets
+    with h5py.File(args['<destination>'], 'w') as dest:
+      copydatasets(source, dest, paths)

README.md

@@ -1,5 +1,4 @@
 [![Travis](https://travis-ci.com/tdegeus/GooseHDF5.svg?branch=master)](https://travis-ci.com/tdegeus/GooseHDF5)
-
 [![Documentation Status](https://readthedocs.org/projects/goosehdf5/badge/?version=latest)](http://goosehdf5.readthedocs.io/en/latest/?badge=latest)
 
 # GooseHDF5