Adding "G5repack" (#21)

.appveyor.yml

@@ -42,4 +42,5 @@ build_script:
   - python test/cli/G5compare.py
   - python test/cli/G5list.py
   - python test/cli/G5repair.py
+  - python test/cli/G5repack.py
 

.travis.yml

@@ -15,4 +15,5 @@ script:
   - python test/cli/G5list.py
   - python test/cli/G5print.py
   - python test/cli/G5repair.py
+  - python test/cli/G5repack.py
 

GooseHDF5/__init__.py

@@ -3,7 +3,7 @@
 warnings.filterwarnings("ignore")
 
 
-__version__ = '0.5.1'
+__version__ = '0.6.0'
 
 
 def abspath(path):

GooseHDF5/cli/G5repack.py

@@ -0,0 +1,47 @@
+'''G5repack
+    Read and write a HDF5 file, to write it more efficiently by removing features like
+    extendible datasets.
+
+Usage:
+    G5repack [options] <source>...
+
+Arguments:
+    <source>    HDF5-file.
+
+Options:
+    -h, --help      Show help.
+        --version   Show version.
+
+(c - MIT) T.W.J. de Geus | tom@geus.me | www.geus.me | github.com/tdegeus/GooseHDF5
+'''
+
+from .. import getpaths
+from .. import __version__
+import docopt
+import h5py
+import os
+import tempfile
+import warnings
+warnings.filterwarnings("ignore")
+
+def check_isfile(fname):
+    if not os.path.isfile(fname):
+        raise IOError('"{0:s}" does not exist'.format(fname))
+
+def main():
+
+    args = docopt.docopt(__doc__, version=__version__)
+    tempname = next(tempfile._get_candidate_names())
+
+    for filename in args['<source>']:
+
+        print(filename)
+
+        check_isfile(filename)
+
+        with h5py.File(filename, 'r') as source:
+            with h5py.File(tempname, 'w') as tmp:
+                for path in getpaths(source):
+                    tmp[path] = source[path][...]
+
+        os.replace(tempname, filename)

docs/tools.rst

@@ -12,20 +12,20 @@ G5check
 
 .. code-block:: none
 
-  G5check
-    Try reading datasets. In case of reading failure the path is printed (otherwise nothing is
-    printed).
+    G5check
+        Try reading datasets. In case of reading failure the path is printed (otherwise nothing is
+        printed).
 
-  Usage:
-    G5check <source> [options]
+    Usage:
+        G5check <source> [options]
 
-  Arguments:
-    <source>        HDF5-file.
+    Arguments:
+        <source>        HDF5-file.
 
-  Options:
-    -b, --basic     Only try getting a list of datasets, skip trying to read them.
-    -h, --help      Show help.
-        --version   Show version.
+    Options:
+        -b, --basic     Only try getting a list of datasets, skip trying to read them.
+        -h, --help      Show help.
+            --version   Show version.
 
 G5list
 ------
@@ -34,20 +34,23 @@ G5list
 
 .. code-block:: none
 
-  G5list
-    List datasets (or groups of datasets) in a HDF5-file.
+    G5list
+        List datasets (or groups of datasets) in a HDF5-file.
 
-  Usage:
-    G5list [options] [--fold ARG]... <source>
+    Usage:
+        G5list [options] [--fold ARG]... <source>
 
-  Arguments:
-    <source>    HDF5-file.
+    Arguments:
+        <source>    HDF5-file.
 
-  Options:
-    -f, --fold=ARG        Fold paths.
-    -d, --max-depth=ARG   Maximum depth to display.
-    -h, --help            Show help.
-        --version         Show version.
+    Options:
+        -f, --fold=ARG        Fold paths.
+        -d, --max-depth=ARG   Maximum depth to display.
+        -r, --root=ARG        Start a certain point in the path-tree. [default: /]
+        -i, --info            Print information: shape, dtype.
+        -l, --long            As above but will all attributes.
+        -h, --help            Show help.
+            --version         Show version.
 
 G5print
 ------
@@ -56,21 +59,21 @@ G5print
 
 .. code-block:: none
 
-  G5print
-    Print datasets in a HDF5-file.
+    G5print
+        Print datasets in a HDF5-file.
 
-  Usage:
-    G5print [options] <source> <dataset>...
+    Usage:
+        G5print [options] <source> <dataset>...
 
-  Arguments:
-    <source>    HDF5-file.
-    <dataset>   Path to the dataset.
+    Arguments:
+        <source>    HDF5-file.
+        <dataset>   Path to the dataset.
 
-  Options:
-    -r, --regex           Evaluate dataset name as a regular expression.
-        --info            Print information: shape, dtype.
-    -h, --help            Show help.
-        --version         Show version.
+    Options:
+        -r, --regex     Evaluate dataset name as a regular expression.
+        -i, --info      Print information: shape, dtype.
+        -h, --help      Show help.
+            --version   Show version.
 
 G5repair
 --------
@@ -79,20 +82,20 @@ G5repair
 
 .. code-block:: none
 
-  G5repair
-    Extract readable data from a HDF5-file and copy it to a new HDF5-file.
+    G5repair
+        Extract readable data from a HDF5-file and copy it to a new HDF5-file.
 
-  Usage:
-    G5repair [options] <source> <destination>
+    Usage:
+        G5repair [options] <source> <destination>
 
-  Arguments:
-    <source>        Source HDF5-file, possibly containing corrupted data.
-    <destination>   Destination HDF5-file.
+    Arguments:
+        <source>        Source HDF5-file, possibly containing corrupted data.
+        <destination>   Destination HDF5-file.
 
-  Options:
-    -f, --force     Force continuation, overwrite existing files.
-    -h, --help      Show help.
-        --version   Show version.
+    Options:
+        -f, --force     Force continuation, overwrite existing files.
+        -h, --help      Show help.
+            --version   Show version.
 
 G5compare
 ---------
@@ -101,19 +104,40 @@ G5compare
 
 .. code-block:: none
 
-  G5compare
-    Compare two HDF5 files. If the function does not output anything all datasets are present in both
-    files, and all the content of the datasets is equals
+    G5compare
+      Compare two HDF5 files. If the function does not output anything all datasets are present in both
+      files, and all the content of the datasets is equals
 
-  Usage:
-    G5compare [options] [--renamed ARG]... <source> <other>
+    Usage:
+      G5compare [options] [--renamed ARG]... <source> <other>
 
-  Arguments:
-    <source>    HDF5-file.
-    <other>     HDF5-file.
+    Arguments:
+      <source>    HDF5-file.
+      <other>     HDF5-file.
 
-  Options:
-    -r, --renamed=ARG     Renamed paths, separated by a separator (see below).
-    -s, --ifs=ARG         Separator used to separate renamed fields. [default: :]
-    -h, --help            Show help.
-        --version         Show version.
+    Options:
+      -r, --renamed=ARG     Renamed paths, separated by a separator (see below).
+      -s, --ifs=ARG         Separator used to separate renamed fields. [default: :]
+      -h, --help            Show help.
+          --version         Show version.
+
+G5repack
+---------
+
+[:download:`G5repack <../GooseHDF5/cli/G5repack.py>`]
+
+.. code-block:: none
+
+    G5repack
+        Read and write a HDF5 file, to write it more efficiently by removing features like
+        extendible datasets.
+
+    Usage:
+        G5repack [options] <source>...
+
+    Arguments:
+        <source>    HDF5-file.
+
+    Options:
+        -h, --help      Show help.
+            --version   Show version.

setup.py

@@ -25,4 +25,5 @@
             'G5compare = GooseHDF5.cli.G5compare:main',
             'G5list = GooseHDF5.cli.G5list:main',
             'G5print = GooseHDF5.cli.G5print:main',
+            'G5repack = GooseHDF5.cli.G5repack:main',
             'G5repair = GooseHDF5.cli.G5repair:main']})

test/cli/G5repack.py

@@ -0,0 +1,24 @@
+import subprocess
+import os
+import h5py
+import numpy as np
+
+def run(cmd):
+    out = list(filter(None, subprocess.check_output(cmd, shell=True).decode('utf-8').split('\n')))
+    return out
+
+a = np.random.random(5)
+
+with h5py.File('a.hdf5', 'w') as source:
+    source['/a'] = a
+
+output = run('G5repack a.hdf5')
+
+with h5py.File('a.hdf5', 'r') as source:
+    b = source['/a'][...]
+
+os.remove('a.hdf5')
+
+if not np.all(a == b):
+    raise IOError('Test failed')
+