pyedr - pypi Package Compare versions

Comparing version 0.6.0 to 0.7.0

PKG-INFO

 Metadata-Version: 2.1
 Name: pyedr
-Version: 0.6.0
+Version: 0.7.0
 Summary: Read and manipulate Gromacs energy files
@@ -46,2 +46,4 @@ Home-page: https://github.com/MDAnalysis/panedr
   in a nested list
+- ``get_unit_dictionary``: Returns a dictionary that holds the units of each
+  energy term found in the EDR file.
 
@@ -54,6 +56,8 @@
 and returns its contents as a pandas_ dataframe. Panedr exposes the
-following function:
+following functions:
 
 - ``edr_to_df``: which gets the path to an EDR file and returns a
-  pandas DataFrame,
+  pandas DataFrame.
+- ``get_unit_dictionary``: Returns a dictionary that holds the units of each
+  energy term found in the EDR file.
 
@@ -82,3 +86,7 @@
 
+    # Get the units of the EDR entries
+    unit_dict = pyedr.get_unit_dictionary(path)
+    unit_dict["Temperature"]  # returns "K"
 
+
 Using ``panedr``:
@@ -102,3 +110,7 @@
 
+    # Get the units of the EDR entries
+    unit_dict = panedr.get_unit_dictionary(path)
+    unit_dict["Temperature"]  # returns "K"
 
+
 Install
@@ -111,3 +123,3 @@ -------
 
-    pip install pyedr 
+    pip install pyedr
 
@@ -114,0 +126,0 @@ # installing panedr automatically installs pyedr

pyedr.egg-info/pbr.json

@@ -1,1 +0,1 @@
-{"git_version": "ccfdc89", "is_release": false}
+{"git_version": "a66de99", "is_release": false}

pyedr.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: pyedr
-Version: 0.6.0
+Version: 0.7.0
 Summary: Read and manipulate Gromacs energy files
@@ -46,2 +46,4 @@ Home-page: https://github.com/MDAnalysis/panedr
   in a nested list
+- ``get_unit_dictionary``: Returns a dictionary that holds the units of each
+  energy term found in the EDR file.
 
@@ -54,6 +56,8 @@
 and returns its contents as a pandas_ dataframe. Panedr exposes the
-following function:
+following functions:
 
 - ``edr_to_df``: which gets the path to an EDR file and returns a
-  pandas DataFrame,
+  pandas DataFrame.
+- ``get_unit_dictionary``: Returns a dictionary that holds the units of each
+  energy term found in the EDR file.
 
@@ -82,3 +86,7 @@
 
+    # Get the units of the EDR entries
+    unit_dict = pyedr.get_unit_dictionary(path)
+    unit_dict["Temperature"]  # returns "K"
 
+
 Using ``panedr``:
@@ -102,3 +110,7 @@
 
+    # Get the units of the EDR entries
+    unit_dict = panedr.get_unit_dictionary(path)
+    unit_dict["Temperature"]  # returns "K"
 
+
 Install
@@ -111,3 +123,3 @@ -------
 
-    pip install pyedr 
+    pip install pyedr
 
@@ -114,0 +126,0 @@ # installing panedr automatically installs pyedr

pyedr/__init__.py

 # -*- coding: utf-8 -*-
-
+from .pyedr import edr_to_dict, read_edr, get_unit_dictionary
 import pbr.version
 __version__ = pbr.version.VersionInfo('pyedr').release_string()
 del pbr
-
-from .pyedr import edr_to_dict, read_edr

pyedr/pyedr.py

@@ -83,3 +83,3 @@ #-*- coding:utf-8 -*-
 
-__all__ = ['edr_to_dict', 'read_edr']
+__all__ = ['edr_to_dict', 'read_edr', 'get_unit_dictionary']
 
@@ -413,3 +413,5 @@ class EDRFile(object):
 times_type = List[float]
-read_edr_return_type = Tuple[all_energies_type, all_names_type, times_type]
+read_edr_return_type = Tuple[all_energies_type,
+                             all_names_type,
+                             times_type]
 
@@ -469,2 +471,24 @@
 
+def get_unit_dictionary(path: str) -> Dict[str, str]:
+    """Creates an EDRFile object which executes the :func:`do_enxnms`
+    method. This reads the names and units of the EDR data, which is returned
+    as a dictionary mapping column names (str) to unit names (str).
+
+    Parameters
+    ----------
+    path : str
+        path to EDR file to be read
+
+    Returns
+    -------
+    unit_dict: Dict[str, str]
+        A dictionary mapping the term names to their units.
+    """
+    edr_file = EDRFile(str(path))
+    unit_dict = {'Time': "ps"}
+    for nm in edr_file.nms:
+        unit_dict[nm.name] = nm.unit
+    return unit_dict
+
+
 def edr_to_dict(path: str, verbose: bool = False) -> Dict[str, np.ndarray]:
@@ -471,0 +495,0 @@ """Calls :func:`read_edr` and packs its return values into a dictionary

pyedr/tests/datafiles.py

@@ -33,10 +33,14 @@ #-*- coding:utf-8 -*-
 EDR_XVG = resource_filename(__name__, 'data/cat.xvg')
+EDR_UNITS = resource_filename(__name__, 'data/cat_units.p')
 
-EDR_IRREGULAR = resource_filename(__name__, 'data/irregular.edr')
-EDR_IRREGULAR_XVG = resource_filename(__name__, 'data/irregular.xvg')
+EDR_IRREG = resource_filename(__name__, 'data/irregular.edr')
+EDR_IRREG_XVG = resource_filename(__name__, 'data/irregular.xvg')
+EDR_IRREG_UNITS = resource_filename(__name__, 'data/irregular_units.p')
 
 EDR_DOUBLE = resource_filename(__name__, 'data/double.edr')
 EDR_DOUBLE_XVG = resource_filename(__name__, 'data/double.xvg')
+EDR_DOUBLE_UNITS = resource_filename(__name__, 'data/double_units.p')
 
 EDR_BLOCKS = resource_filename(__name__, 'data/blocks.edr')
 EDR_BLOCKS_XVG = resource_filename(__name__, 'data/blocks.xvg')
+EDR_BLOCKS_UNITS = resource_filename(__name__, 'data/blocks_units.p')

pyedr/tests/test_edr.py

@@ -13,2 +13,3 @@ #-*- coding: utf-8 -*-
 import unittest
+import pickle
 
@@ -21,4 +22,5 @@ import pytest
 from pyedr.tests.datafiles import (
-        EDR, EDR_XVG, EDR_IRREGULAR, EDR_IRREGULAR_XVG,
-        EDR_DOUBLE, EDR_DOUBLE_XVG, EDR_BLOCKS, EDR_BLOCKS_XVG
+        EDR, EDR_XVG, EDR_UNITS, EDR_IRREG, EDR_IRREG_XVG,
+        EDR_IRREG_UNITS, EDR_DOUBLE, EDR_DOUBLE_XVG, EDR_DOUBLE_UNITS,
+        EDR_BLOCKS, EDR_BLOCKS_XVG, EDR_BLOCKS_UNITS
 )
@@ -33,22 +35,26 @@
 # Data constants
-EDR_Data = namedtuple('EDR_Data', 
-                      ['edr_dict', 'xvgdata', 'xvgtime', 'xvgnames',
-                       'xvgcols', 'xvgprec', 'edrfile', 'xvgfile'])
+EDR_Data = namedtuple('EDR_Data',
+                      ['edr_dict', 'edr_units', 'xvgdata', 'xvgtime',
+                       'xvgnames', 'xvgcols', 'xvgprec', 'true_units',
+                       'edrfile', 'xvgfile'])
 
 
 @pytest.fixture(scope='module',
-                params=[(EDR, EDR_XVG),
-                        (EDR_IRREGULAR, EDR_IRREGULAR_XVG),
-                        (EDR_DOUBLE, EDR_DOUBLE_XVG),
-                        (EDR_BLOCKS, EDR_BLOCKS_XVG),
-                        (Path(EDR), EDR_XVG),])
+                params=[(EDR, EDR_XVG, EDR_UNITS),
+                        (EDR_IRREG, EDR_IRREG_XVG, EDR_IRREG_UNITS),
+                        (EDR_DOUBLE, EDR_DOUBLE_XVG, EDR_DOUBLE_UNITS),
+                        (EDR_BLOCKS, EDR_BLOCKS_XVG, EDR_BLOCKS_UNITS),
+                        (Path(EDR), EDR_XVG, EDR_UNITS), ])
 def edr(request):
-    edrfile, xvgfile = request.param
+    edrfile, xvgfile, unitfile = request.param
     edr_dict = pyedr.edr_to_dict(edrfile)
+    edr_units = pyedr.get_unit_dictionary(edrfile)
     xvgdata, xvgnames, xvgprec = read_xvg(xvgfile)
+    with open(unitfile, "rb") as f:
+        true_units = pickle.load(f)
     xvgtime = xvgdata[:, 0]
     xvgdata = xvgdata[:, 1:]
     xvgcols = np.insert(xvgnames, 0, u'Time')
-    return EDR_Data(edr_dict, xvgdata, xvgtime, xvgnames,
-                    xvgcols, xvgprec, edrfile, xvgfile)
+    return EDR_Data(edr_dict, edr_units, xvgdata, xvgtime, xvgnames,
+                    xvgcols, xvgprec, true_units, edrfile, xvgfile)
 
@@ -60,2 +66,3 @@
     """
+
     def test_output_type(self, edr):
@@ -68,2 +75,5 @@ """
 
+    def test_units(self, edr):
+        assert edr.edr_units == edr.true_units
+
     def test_columns(self, edr):
@@ -70,0 +80,0 @@ """

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Improved metrics

Total package byte prevSize

38255

6.72%

Lines of code

663

5.07%