Merge pull request #45 from moldyn/main

Merge main into py312

CHANGELOG.md

@@ -18,6 +18,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Supporting latest Python 3.12 🎉
 
 
+## [1.1.1] - 2023-11-10
+### Bugfix 🐛:
+- Fix mutable properties of `mh.StateTraj` and `mh.LumpedStateTraj`, #43
+
+### Other changes:
+- Improved performance of `mh.LumpedStateTraj.microtrajs`
+
+
 ## [1.1.0] - 2023-11-03
 ### API changes warning ⚠️:
 - Python 3.7 support was dropped!
@@ -185,7 +193,8 @@ Chapman-Kolmogorov test
 - Initial release
 
 
-[Unreleased]: https://github.com/moldyn/msmhelper/compare/v1.1.0...main
+[Unreleased]: https://github.com/moldyn/msmhelper/compare/v1.1.1...main
+[1.1.1]: https://github.com/moldyn/msmhelper/compare/v1.1.0...v1.1.1
 [1.1.0]: https://github.com/moldyn/msmhelper/compare/v1.0.4...v1.1.0
 [1.0.4]: https://github.com/moldyn/msmhelper/compare/v1.0.3...v1.0.4
 [1.0.3]: https://github.com/moldyn/msmhelper/compare/v1.0.2...v1.0.3

docs/css/extra.css

@@ -65,6 +65,7 @@ a[href^="https://"]::after
 
 a[href^="https://github.com/moldyn/msmhelper"]::after,
 a[href^="https://moldyn.github.io/msmhelper"]::after,
+a[href^="https://joss.theoj.org"]::after,
 a[href^="https://github.com/wemake-services"]::after,
 a[href^="https://pypi.org"]::after,
 a[href^="https://anaconda.org"]::after,

setup.py

@@ -58,7 +58,7 @@ def remove_gh_dark_mode_only_tags(text, tag='#gh-dark-mode-only'):
 # This call to setup() does all the work
 setuptools.setup(
     name='msmhelper',
-    version='1.1.0',
+    version='1.1.1',
     description='Helper functions for Markov State Models.',
     long_description=README,
     long_description_content_type='text/markdown',

src/msmhelper/__init__.py

@@ -30,4 +30,4 @@
     unique,
 )
 
-__version__ = '1.1.0'
+__version__ = '1.1.1'

src/msmhelper/statetraj.py

@@ -60,11 +60,14 @@ def __init__(self, trajs):
         # get number of states
         self._states = mh.utils.unique(self._trajs)
 
+        # enforce true copy of trajs
+        if np.array_equal(self._states, np.arange(self.nstates)):
+            self._trajs = [traj.copy() for traj in self._trajs]
         # shift to indices
-        if np.array_equal(self._states, np.arange(1, self.nstates + 1)):
+        elif np.array_equal(self._states, np.arange(1, self.nstates + 1)):
             self._states = np.arange(1, self.nstates + 1)
             self._trajs = [traj - 1 for traj in self._trajs]
-        elif not np.array_equal(self._states, np.arange(self.nstates)):
+        else:  # not np.array_equal(self._states, np.arange(self.nstates)):
             self._trajs, self._states = mh.utils.rename_by_index(
                 self._trajs,
                 return_permutation=True,
@@ -80,7 +83,7 @@ def states(self):
             Numpy array holding active set of states.
 
         """
-        return self._states
+        return self._states.copy()
 
     @property
     def nstates(self):
@@ -108,7 +111,7 @@ def ntrajs(self):
 
     @property
     def nframes(self):
-        """Return cummulative length of all trajectories.
+        """Return cumulative length of all trajectories.
 
         Returns
         -------
@@ -131,7 +134,7 @@ def trajs(self):
         if np.array_equal(self.states, np.arange(1, self.nstates + 1)):
             return [traj + 1 for traj in self._trajs]
         if np.array_equal(self.states, np.arange(self.nstates)):
-            return self._trajs
+            return self.index_trajs
         return mh.shift_data(
             self._trajs,
             np.arange(self.nstates),
@@ -160,7 +163,7 @@ def index_trajs(self):
             List of ndarrays holding the input data.
 
         """
-        return self._trajs
+        return [traj.copy() for traj in self._trajs]
 
     @property
     def index_trajs_flatten(self):
@@ -338,7 +341,7 @@ def states(self):
             Numpy array holding active set of states.
 
         """
-        return self._macrostates
+        return self._macrostates.copy()
 
     @property
     def nstates(self):
@@ -362,8 +365,10 @@ def microstate_trajs(self):
             List of ndarrays holding the input data.
 
         """
-        if np.array_equal(self.microstates, np.arange(self.nmicrostates)):
-            return self._trajs
+        if np.array_equal(self.microstates, np.arange(1, self.nstates + 1)):
+            return [traj + 1 for traj in self._trajs]
+        elif np.array_equal(self.microstates, np.arange(self.nmicrostates)):
+            return self.microstate_index_trajs
         return mh.shift_data(
             self._trajs,
             np.arange(self.nmicrostates),
@@ -392,7 +397,7 @@ def microstate_index_trajs(self):
             List of ndarrays holding the microstate index trajectory.
 
         """
-        return self._trajs
+        return [traj.copy() for traj in self._trajs]
 
     @property
     def microstate_index_trajs_flatten(self):
@@ -448,7 +453,7 @@ def microstates(self):
             Numpy array holding active set of states.
 
         """
-        return self._states
+        return self._states.copy()
 
     @property
     def nmicrostates(self):
@@ -472,7 +477,7 @@ def state_assignment(self):
             Micro to macrostate assignment vector.
 
         """
-        return self._state_assignment
+        return self._state_assignment.copy()
 
     @property
     def _state_assignment_idx(self):

test/test_statetraj.py

@@ -96,6 +96,14 @@ def test_StateTraj_constructor(statetraj):
     lumpedTraj = LumpedStateTraj(statetraj, statetraj)
     assert lumpedTraj is StateTraj(lumpedTraj)
 
+    # check that immutable
+    assert traj._trajs[0] is not StateTraj(traj.trajs)._trajs[0]
+    # check for index trajs
+    assert (
+        StateTraj(traj.index_trajs)._trajs[0] is not
+        StateTraj(traj.index_trajs)._trajs[0]
+    )
+
 
 def test_LumpedStateTraj_constructor(macrotraj, statetraj):
     """Test construction of object."""
@@ -127,6 +135,14 @@ def test_nstates(state_traj, statetraj, macro_traj, macrotraj):
         state_traj.nstates = 5
 
 
+def test_states(state_traj):
+    """Test immutability of states property."""
+    assert state_traj.states is not state_traj.states
+
+    with pytest.raises(AttributeError):
+        state_traj.states = state_traj.states
+
+
 def test_nframes(state_traj):
     """Test nframes property."""
     assert state_traj.nframes == len(state_traj[0])