Merge pull request #71 from DrDomenicoMarson/add-amber-mbar-none-non-…

…finished

Added the capability of loading a single test case for AMBER

docs/amber.rst

@@ -19,6 +19,7 @@ They can be accessed using the following accessor functions:
    load_bace_example
    load_simplesolvated
    load_invalidfiles
+   load_testfiles
 
 
 .. _amber_bace_improper:
@@ -44,6 +45,13 @@ They can be accessed using the following accessor functions:
 
 .. _amber_invalidfiles:
 
-.. include:: ../src/alchemtest/amber/invalidfiles/descr.rst
+.. include:: ../src/alchemtest/amber/testfiles/descr_invalid.rst
 
 .. autofunction:: alchemtest.amber.load_invalidfiles
+
+
+.. _load_testfiles:
+
+.. include:: ../src/alchemtest/amber/testfiles/descr.rst
+
+.. autofunction:: alchemtest.amber.load_testfiles

src/alchemtest/amber/__init__.py

@@ -6,3 +6,4 @@
 from .access import load_bace_example
 from .access import load_simplesolvated
 from .access import load_invalidfiles
+from .access import load_testfiles

src/alchemtest/amber/access.py

@@ -1,10 +1,8 @@
 """Accessors for Amber TI datasets.
 
 """
-
-from os.path import dirname, join
-from glob import glob
-
+import warnings
+from pathlib import Path
 from .. import Bunch
 
 
@@ -20,10 +18,10 @@ def load_bace_improper():
         - 'data' : the data files for improper solvated vdw alchemical leg
 
     """
-    module_path = dirname(__file__)
-    data = {'vdw': glob(join(module_path, 'bace_improper/solvated/vdw/*/ti-*.out.bz2'))}
+    module_path = Path(__file__).parent
+    data = {'vdw': list(map(str, module_path.glob('bace_improper/solvated/vdw/*/ti-*.out.bz2')))}
 
-    with open(join(module_path, 'bace_improper', 'descr.rst')) as rst_file:
+    with open(module_path / 'bace_improper' / 'descr.rst') as rst_file:
         fdescr = rst_file.read()
 
     return Bunch(data=data,
@@ -41,20 +39,20 @@ def load_bace_example():
         - 'data' : the data files by system and alchemical leg
 
     """
-    module_path = dirname(__file__)
+    module_path = Path(__file__).parent
     data = {'complex':
-                {'decharge': glob(join(module_path, 'bace_CAT-13d~CAT-17a/complex/decharge/*/ti-*.out.bz2')),
-                 'recharge': glob(join(module_path, 'bace_CAT-13d~CAT-17a/complex/recharge/*/ti-*.out.bz2')),
-                 'vdw': glob(join(module_path, 'bace_CAT-13d~CAT-17a/complex/vdw/*/ti-*.out.bz2'))
+                {'decharge': list(map(str, module_path.glob('bace_CAT-13d~CAT-17a/complex/decharge/*/ti-*.out.bz2'))),
+                 'recharge': list(map(str, module_path.glob('bace_CAT-13d~CAT-17a/complex/recharge/*/ti-*.out.bz2'))),
+                 'vdw': list(map(str, module_path.glob('bace_CAT-13d~CAT-17a/complex/vdw/*/ti-*.out.bz2')))
                  },
             'solvated':
-                {'decharge': glob(join(module_path, 'bace_CAT-13d~CAT-17a/solvated/decharge/*/ti-*.out.bz2')),
-                 'recharge': glob(join(module_path, 'bace_CAT-13d~CAT-17a/solvated/recharge/*/ti-*.out.bz2')),
-                 'vdw': glob(join(module_path, 'bace_CAT-13d~CAT-17a/solvated/vdw/*/ti-*.out.bz2'))
+                {'decharge': list(map(str, module_path.glob('bace_CAT-13d~CAT-17a/solvated/decharge/*/ti-*.out.bz2'))),
+                 'recharge': list(map(str, module_path.glob('bace_CAT-13d~CAT-17a/solvated/recharge/*/ti-*.out.bz2'))),
+                 'vdw': list(map(str, module_path.glob('bace_CAT-13d~CAT-17a/solvated/vdw/*/ti-*.out.bz2')))
                  }
             }
 
-    with open(join(module_path, 'bace_CAT-13d~CAT-17a', 'descr.rst')) as rst_file:
+    with open(module_path / 'bace_CAT-13d~CAT-17a' / 'descr.rst') as rst_file:
         fdescr = rst_file.read()
 
     return Bunch(data=data,
@@ -74,11 +72,11 @@ def load_simplesolvated():
 
     """
 
-    module_path = dirname(__file__)
-    data = {'charge': glob(join(module_path, 'simplesolvated/charge/*/ti-*.out')),
-            'vdw': glob(join(module_path, 'simplesolvated/vdw/*/ti-*.out'))}
+    module_path = Path(__file__).parent
+    data = {'charge': list(map(str, module_path.glob('simplesolvated/charge/*/ti-*.tar.bz2'))),
+            'vdw': list(map(str, module_path.glob('simplesolvated/vdw/*/ti-*.tar.bz2')))}
 
-    with open(join(module_path, 'simplesolvated', 'descr.rst')) as rst_file:
+    with open(module_path / 'simplesolvated' / 'descr.rst') as rst_file:
         fdescr = rst_file.read()
 
     return Bunch(data=data,
@@ -96,12 +94,60 @@ def load_invalidfiles():
         - 'data' : the example of invalid data files
         - 'DESCR': the full description of the dataset
 
+
+    .. deprecated:: 0.7
+       use :func:`load_testfiles` instead
+
     """
 
-    module_path = dirname(__file__)
-    data = [glob(join(module_path, 'invalidfiles/*.out.bz2'))]
+    warnings.warn(
+        "load_invalidfiles() was deprecated in 0.7.0 and will be removed in the following release."
+        " Use load_testfiles() instead",
+        DeprecationWarning)
+    module_path = Path(__file__).parent
+    data = [[
+        module_path / 'testfiles' / 'no_useful_data.out.bz2',
+        module_path / 'testfiles' / 'no_control_data.out.bz2',
+        module_path / 'testfiles' / 'no_temp0_set.out.bz2',
+        module_path / 'testfiles' / 'no_free_energy_info.out.bz2',
+        module_path / 'testfiles' / 'no_atomic_section.out.bz2',
+        module_path / 'testfiles' / 'no_results_section.out.bz2']]
+
+    with open(module_path / 'testfiles' / 'descr_invalid.rst') as rst_file:
+        fdescr = rst_file.read()
+
+    return Bunch(data=data,
+                 DESCR=fdescr)
+
+
+def load_testfiles():
+    """Load incomplete or wrongly formatted files to be used to test the AMBER parsers.
+
+    Returns
+    -------
+    data : Bunch
+        Dictionary-like object, the interesting attributes are:
+
+        - 'data' : the data files
+        - 'DESCR': the full description of all the files
+
+    """
 
-    with open(join(module_path, 'invalidfiles', 'descr.rst')) as rst_file:
+    testfiles_path = Path(__file__).parent / 'testfiles'
+
+    data = {
+        "not_finished_run": [testfiles_path / "not_finished_run.out.bz2"],
+        "none_in_mbar": [testfiles_path / "none_in_mbar.out.bz2"],
+        "no_useful_data": [testfiles_path / "no_useful_data.out.bz2"],
+        "no_temp0_set": [testfiles_path / "no_temp0_set.out.bz2"],
+        "no_results_section": [testfiles_path / "no_results_section.out.bz2"],
+        "no_free_energy_info": [testfiles_path / "no_free_energy_info.out.bz2"],
+        "no_dHdl_data_points": [testfiles_path / "no_dHdl_data_points.out.bz2"],
+        "no_control_data": [testfiles_path / "no_control_data.out.bz2"],
+        "no_atomic_section": [testfiles_path / "no_atomic_section.out.bz2"],
+        }
+
+    with open(testfiles_path / 'descr.rst') as rst_file:
         fdescr = rst_file.read()
 
     return Bunch(data=data,