Merge pull request #1242 from marscher/minor

Bugfixes and export_to_hdf5

Author: marscher

.travis.yml

@@ -29,6 +29,13 @@ env:
     - CONDA_PY=3.5
     - CONDA_PY=3.6
 
+matrix:
+  exclude: # test only 2.7 on osx.
+    - env: CONDA_PY=3.5
+      os: osx
+    - os: osx
+      env: CONDA_PY=3.6
+
 before_install:
 - source devtools/ci/travis/install_miniconda.sh
 

conftest.py

@@ -24,3 +24,12 @@ def add_np(doctest_namespace):
         np.set_printoptions(legacy='1.13')
     except TypeError:
         pass
+
+
+@pytest.fixture(autouse=True)
+def filter_warnings():
+    import warnings
+    old_filters = warnings.filters[:]
+    warnings.filterwarnings('ignore', message='You have not selected any features. Returning plain coordinates.')
+    yield
+    warnings.filters = old_filters

devtools/conda-recipe/meta.yaml

@@ -27,12 +27,12 @@ requirements:
     - python
     - scipy
     - setuptools
-    - gcc # [ not win ]
+    - toolchain
+
   run:
     - bhmm >=0.6,<0.7
     - decorator >=4.0.0
     - h5py
-    - libgcc # [linux or osx]
     - matplotlib
     - mdtraj
     - mock # TODO: remove when py3k only.
@@ -59,6 +59,7 @@ test:
   requires:
     - pytest
     - pytest-cov
+    - coverage
    # TODO: disabled on win64, until https://bugs.python.org/issue31701 is fixed.
     - pytest-faulthandler # [not win]
     - pytest-xdist

devtools/conda-recipe/run_test.py

@@ -22,6 +22,7 @@
                "{njobs_args} "
                "--junit-xml={junit_xml} "
                "-c {pytest_cfg}"
+               #"--durations=20 "
                .format(test_pkg=test_pkg, cover_pkg=cover_pkg,
                        junit_xml=junit_xml, pytest_cfg='setup.cfg',
                        dest_report=os.path.join(os.path.expanduser('~/'), 'coverage.xml'),

doc/source/CHANGELOG.rst

@@ -19,7 +19,7 @@ your Python installation to at least version 3.5 to catch future updates.
   extracted per iteration from a data source. This is invariant to the dimension of data sets. #1190
 - datasets: added Prinz potential (quadwell). #1226
 - coordinates: added VAMP estimator. #1237
-
+- coordinates: added method 'write_to_hdf5' for easy exporting streams to HDF5. #1242
 
 - References:
 

pyemma-ipython

@@ -61,10 +61,6 @@ def logger(self):
             self.__create_logger()
             return self._logger_instance
 
-    @property
-    def _logger(self):
-        return self.logger
-
     def _logger_is_active(self, level):
         """ @param level: int log level (debug=10, info=20, warn=30, error=40, critical=50)"""
         return self.logger.level >= level

pyemma/_base/loggable.py

@@ -194,7 +194,8 @@ def _get_interpolation_map(cls):
         return map
 
     def save(self, file_name, model_name='default', overwrite=False, save_streaming_chain=False):
-        r"""
+        r""" saves the current state of this object to given file and name.
+
         Parameters
         -----------
         file_name: str

pyemma/_base/serialization/serialization.py

@@ -80,13 +80,16 @@ def _check_old_chunksize_arg(chunksize, chunk_size_default, **kw):
         chosen_chunk_size = chunksize
     else:
         import warnings
+        from pyemma.util.annotators import get_culprit
+        filename, lineno = get_culprit(3)
         if is_default:  # case 2.
-            warnings.warn('Passed deprecated argument "chunk_size", please use "chunksize"',
-                          category=_PyEMMA_DeprecationWarning)
+            warnings.warn_explicit('Passed deprecated argument "chunk_size", please use "chunksize"',
+                                   category=_PyEMMA_DeprecationWarning, filename=filename, lineno=lineno)
             chosen_chunk_size = kw.pop('chunk_size')  # remove this argument to avoid further passing to other funcs.
         else:  # case 3.
-            warnings.warn('Passed two values for chunk size: "chunk_size" and "chunksize", while the first one'
-                          ' is deprecated. Please use "chunksize" in the future.', category=_PyEMMA_DeprecationWarning)
+            warnings.warn_explicit('Passed two values for chunk size: "chunk_size" and "chunksize", while the first one'
+                                   ' is deprecated. Please use "chunksize" in the future.',
+                                   category=_PyEMMA_DeprecationWarning, filename=filename, lineno=lineno)
             chosen_chunk_size = chunksize
     assert chosen_chunk_size is not NotImplemented
     return chosen_chunk_size

pyemma/coordinates/api.py

@@ -87,10 +87,11 @@ KMeans<dtype>::cluster(const np_array &np_chunk, const np_array &np_centers, int
         }
 #else
         {
+            std::mutex mutex;
+
             std::vector<scoped_thread> threads;
             threads.reserve(static_cast<std::size_t>(n_threads));
 
-            std::mutex mutex;
             std::size_t grainSize = n_frames / n_threads;
 
             auto worker = [&](std::size_t tid, std::size_t begin, std::size_t end, std::mutex& m) {