Merge pull request #54 from chrisburr/develop

Add support for columns of arrays and general tidying

.travis.yml

@@ -1,36 +1,27 @@
-#sudo: false
-# travis-ci.org build & test configuration
 language: python
 
 matrix:
-    include:
-        - python: 2.7
-          env: PYTHON=2.7 ROOT=5.34.32
-        - python: 2.7
-          env: PYTHON=2.7 ROOT=6.04
-        - python: 3.4
-          env: PYTHON=3.4 ROOT=5.34.32
-        - python: 3.4
-          env: PYTHON=3.4 ROOT=6.04
-        - python: 3.5
-          env: PYTHON=3.4 ROOT=5.34.32
-        - python: 3.5
-          env: PYTHON=3.4 ROOT=6.04
-        - python: 3.6
-          env: PYTHON=3.4 ROOT=5.34.32
-        - python: 3.6
-          env: PYTHON=3.4 ROOT=6.04
-#install: source ci/install.sh
-install:
-  - if [ "${TRAVIS_OS_NAME}" == "osx" ]; then curl --silent http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh -o miniconda.sh; fi
-  - if [ "${TRAVIS_OS_NAME}" == "linux" ]; then wget -nv http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
+  include:
+    - python: 2.7
+      env: PYTHON=2.7 ROOT=5.34.32
+    - python: 2.7
+      env: PYTHON=2.7 ROOT=6.04
+    - python: 3.4
+      env: PYTHON=3.4 ROOT=5.34.32
+    - python: 3.4
+      env: PYTHON=3.4 ROOT=6.04
 
+install:
+  - if [ "${TRAVIS_OS_NAME}" == "osx" ]; then curl --silent http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh
+    -o miniconda.sh; fi
+  - if [ "${TRAVIS_OS_NAME}" == "linux" ]; then wget -nv http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    -O miniconda.sh; fi
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
-  - conda info -a # Useful for debugging any issues with conda
+  - conda info -a
   - conda config --add channels http://conda.anaconda.org/NLeSC
   - conda config --set show_channel_urls yes
   - conda create -q -n testenv python=${PYTHON} root=${ROOT} rootpy pandas nose
@@ -41,7 +32,16 @@ install:
 script: nosetests --with-coverage --cover-package=root_pandas
 
 after_success:
-    - time coveralls
+  - time coveralls
 
 notifications:
-    email: false
+  email: false
+
+deploy:
+  provider: pypi
+  user: chrisburr
+  password:
+    secure: MyD2Q4zASzpXWaOBnbkGGm7luYB2SrrBVdX4faN0JmSmDcssn/exu2XDAIwhbZhg3uZC4bq7mBUpPiw/3Mx1f5kFgWlnjpnSRDaGhGLLc6rBp9Kqt6IOWcQ64yQ+S6LIuJ+tjbTMJAlNZgy3HDEwBWXKBvectWKJPZdVCenfMPA=
+  on:
+    tags: true
+    branch: master

root_pandas/__init__.py

@@ -1,2 +1,7 @@
 from .readwrite import read_root
 from .readwrite import to_root
+
+__all__ = [
+    'read_root',
+    'to_root',
+]

root_pandas/readwrite.py

@@ -28,7 +28,7 @@
 
 
 def expand_braces(orig):
-    r = r'.*(\{.+?[^\\]\})'
+    r = r'.*?(\{.+[^\\]\})'
     p = re.compile(r)
 
     s = orig[:]
@@ -40,12 +40,10 @@ def expand_braces(orig):
         open_brace = s.find(sub)
         close_brace = open_brace + len(sub) - 1
         if sub.find(',') != -1:
-            for pat in sub.strip('{}').split(','):
+            for pat in sub[1:-1].split(','):
                 res.extend(expand_braces(s[:open_brace] + pat + s[close_brace+1:]))
-
         else:
             res.extend(expand_braces(s[:open_brace] + sub.replace('}', '\\}') + s[close_brace+1:]))
-
     else:
         res.append(s.replace('\\}', '}'))
 
@@ -59,6 +57,7 @@ def get_nonscalar_columns(array):
     bad_names = col_names[bad_cols]
     return list(bad_names)
 
+
 def get_matching_variables(branches, patterns, fail=True):
     selected = []
 
@@ -93,6 +92,30 @@ def filter_noexpand_columns(columns):
     return other, noexpand
 
 
+def do_flatten(arr, flatten):
+    if flatten is True:
+        warnings.warn(" The option flatten=True is deprecated. Please specify the branches you would like "
+                      "to flatten in a list: flatten=['foo', 'bar']", FutureWarning)
+        arr_, idx = stretch(arr, return_indices=True)
+    else:
+        nonscalar = get_nonscalar_columns(arr)
+        fields = [x for x in arr.dtype.names if (x not in nonscalar or x in flatten)]
+
+        for col in flatten:
+            if col in nonscalar:
+                pass
+            elif col in fields:
+                raise ValueError("Requested to flatten {col} but it has a scalar type"
+                                 .format(col=col))
+            else:
+                raise ValueError("Requested to flatten {col} but it wasn't loaded from the input file"
+                                 .format(col=col))
+
+        arr_, idx = stretch(arr, fields=fields, return_indices=True)
+    arr = append_fields(arr_, '__array_index', idx, usemask=False, asrecarray=True)
+    return arr
+
+
 def read_root(paths, key=None, columns=None, ignore=None, chunksize=None, where=None, flatten=False, *args, **kwargs):
     """
     Read a ROOT file, or list of ROOT files, into a pandas DataFrame.
@@ -175,22 +198,6 @@ def read_root(paths, key=None, columns=None, ignore=None, chunksize=None, where=
         for var in ignored:
             all_vars.remove(var)
 
-    def do_flatten(arr, flatten):
-        if flatten is True:
-            warnings.warn(" The option flatten=True is deprecated. Please specify the branches you would like "
-                          "to flatten in a list: flatten=['foo', 'bar']", FutureWarning)
-            arr_, idx = stretch(arr, return_indices=True)
-        else:
-            nonscalar = get_nonscalar_columns(arr)
-            fields = [x for x in arr.dtype.names if (x not in nonscalar or x in flatten)]
-            will_drop = [x for x in arr.dtype.names if x not in fields]
-            if will_drop:
-                warnings.warn("Ignored the following non-scalar branches: {bad_names}"
-                      .format(bad_names=", ".join(will_drop)), UserWarning)
-            arr_, idx = stretch(arr, fields=fields, return_indices=True)
-        arr = append_fields(arr_, '__array_index', idx, usemask=False, asrecarray=True)
-        return arr
-
     if chunksize:
         tchain = ROOT.TChain(key)
         for path in paths:
@@ -216,26 +223,45 @@ def genchunks():
 
 def convert_to_dataframe(array, start_index=None):
     nonscalar_columns = get_nonscalar_columns(array)
-    if nonscalar_columns:
-        warnings.warn("Ignored the following non-scalar branches: {bad_names}"
-                      .format(bad_names=", ".join(nonscalar_columns)), UserWarning)
-    indices = list(filter(lambda x: x.startswith('__index__') and x not in nonscalar_columns, array.dtype.names))
+
+    # Columns containing 2D arrays can't be loaded so convert them 1D arrays of arrays
+    reshaped_columns = {}
+    for col in nonscalar_columns:
+        if array[col].ndim >= 2:
+            reshaped = np.zeros(len(array[col]), dtype='O')
+            for i, row in enumerate(array[col]):
+                reshaped[i] = row
+            reshaped_columns[col] = reshaped
+
+    indices = list(filter(lambda x: x.startswith('__index__'), array.dtype.names))
     if len(indices) == 0:
         index = None
         if start_index is not None:
             index = RangeIndex(start=start_index, stop=start_index + len(array))
-        df = DataFrame.from_records(array, exclude=nonscalar_columns, index=index)
+        df = DataFrame.from_records(array, exclude=reshaped_columns, index=index)
     elif len(indices) == 1:
         # We store the index under the __index__* branch, where
         # * is the name of the index
-        df = DataFrame.from_records(array, index=indices[0], exclude=nonscalar_columns)
+        df = DataFrame.from_records(array, exclude=reshaped_columns, index=indices[0])
         index_name = indices[0][len('__index__'):]
         if not index_name:
             # None means the index has no name
             index_name = None
         df.index.name = index_name
     else:
         raise ValueError("More than one index found in file")
+
+    # Manually the columns which were reshaped
+    for key, reshaped in reshaped_columns.items():
+        df[key] = reshaped
+
+    # Reshaping can cause the order of columns to change so we have to change it back
+    if reshaped_columns:
+        # Filter to remove __index__ columns
+        columns = [c for c in array.dtype.names if c in df.columns]
+        assert len(columns) == len(df.columns), (columns, df.columns)
+        df = df.reindex_axis(columns, axis=1, copy=False)
+
     return df
 
 

root_pandas/utils.py

@@ -1,15 +1,15 @@
 # Copyright (c) 2012 rootpy developers and contributors
-# 
+#
 # Permission is hereby granted, free of charge, to any person obtaining a copy of
 # this software and associated documentation files (the "Software"), to deal in
 # the Software without restriction, including without limitation the rights to
 # use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
 # the Software, and to permit persons to whom the Software is furnished to do so,
 # subject to the following conditions:
-# 
+#
 # The above copyright notice and this permission notice shall be included in all
 # copies or substantial portions of the Software.
-# 
+#
 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 # FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
@@ -24,6 +24,7 @@
 import numpy as np
 VLEN = np.vectorize(len)
 
+
 def stretch(arr, fields=None, return_indices=False):
     """Stretch an array.
     Stretch an array by ``hstack()``-ing  multiple array fields while
@@ -104,5 +105,5 @@ def stretch(arr, fields=None, return_indices=False):
     if return_indices:
         idx = np.concatenate(list(map(np.arange, len_array)))
         return ret, idx
-    
+
     return ret

tests/samples/README.md

@@ -0,0 +1,3 @@
+# Files for testing `root_pandas`
+
+These files are taken from [uproot](https://github.com/scikit-hep/uproot/).