Merge pull request #79 from cxhernandez/joss-review

Joss Review Suggestions

README.md

@@ -75,6 +75,8 @@ Dependencies
 
 ### Mandatory
 
+The latest versions of the following packages are required:
+
 -  [numpy](http://www.numpy.org/)
 
 -  [scipy](http://www.scipy.org/)
@@ -120,9 +122,18 @@ You may instead want to use the development version from Github, by running
 Development
 -----------
 
-https://github.com/msmexplorer/msmexplorer
+All development happens here, on
+[Github](https://github.com/msmexplorer/msmexplorer).
+
+If you're interested in contributing to MSMExplorer, please refer to our
+[Contributing](http://msmbuilder.org/msmexplorer/development/contributing.html)
+guide.
+
+Support
+-------
 
-Please [submit](https://github.com/msmexplorer/msmexplorer/issues/new) any bugs you encounter to the Github issue tracker.
+Please [submit](https://github.com/msmexplorer/msmexplorer/issues/new) any bugs
+or questions to the Github issue tracker.
 
 License
 -------

devtools/conda-recipe/meta.yaml

@@ -13,8 +13,6 @@ requirements:
   build:
     - python
     - setuptools
-    - cython
-    - numpy
 
   run:
     - python

docs/changelog.rst

@@ -4,12 +4,8 @@ Changelog
 =========
 
 
-v0.4.0 (Development)
---------------------
-
-API Changes
-~~~~~~~~~~~
-
+v1.0.0 (March 30, 2017)
+-----------------------
 
 New Features
 ~~~~~~~~~~~~
@@ -20,8 +16,9 @@ New Features
 
 Improvements
 ~~~~~~~~~~~~
-- The ``shade`` option now works for ``plot_free_energy`` in the 1D case.
-
+- The ``shade`` option now works for ``plot_free_energy`` in the 1D case (#76).
+- Fixed an issue where adding cluster centers would break the visualization
+if ``ndim`` > 2 (#70).
 
 v0.3.0 (October 24, 2016)
 -------------------------

docs/installing.rst

@@ -38,6 +38,8 @@ Dependencies
 Mandatory dependencies
 ^^^^^^^^^^^^^^^^^^^^^^
 
+The latest versions of the following packages are required:
+
 -  `numpy <http://www.numpy.org/>`__
 
 -  `scipy <http://www.scipy.org/>`__

examples/plot_chord.py

@@ -2,20 +2,29 @@
 Chord Diagram
 =============
 """
+from msmbuilder.example_datasets import FsPeptide
+
 import numpy as np
+import mdtraj as md
 
 import msmexplorer as msme
 from msmexplorer.utils import make_colormap
 
+# # Load Fs Peptide Data
+trajs = FsPeptide().get().trajectories
+
+# Compute Hydrogen Bonding Residue Pairs
+baker_hubbard = md.baker_hubbard(trajs[0])
+top = trajs[0].topology
+pairs = [(top.atom(di).residue.index, top.atom(ai).residue.index)
+         for di, _, ai in baker_hubbard]
 
-# Create a random square matrix
-rs = np.random.RandomState(42)
-n, p = 12, 12
-d = rs.normal(0, 2, (n, p))
-d += np.log(np.arange(1, p + 1)) * -5 + 10
+# Create Hydrogen Bonding Network
+hbonds = np.zeros((top.n_residues, top.n_residues))
+hbonds[list(zip(*pairs))] = 1.
 
-# Make a colormap
+# Make a Colormap
 cmap = make_colormap(['rawdenim', 'lightgray', 'pomegranate'])
 
 # Plot Chord Diagram
-msme.plot_chord(d, cmap=cmap, threshold=.2)
+msme.plot_chord(hbonds, cmap=cmap)

examples/plot_free_energy_1d.py

@@ -2,6 +2,7 @@
 Free Energy Plot (Univariate)
 =============================
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import DihedralFeaturizer
 from msmbuilder.decomposition import tICA
 from msmbuilder.cluster import MiniBatchKMeans
@@ -10,7 +11,6 @@
 import numpy as np
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
 
 rs = np.random.RandomState(42)
 

examples/plot_free_energy_2d.py

@@ -2,6 +2,7 @@
 Free Energy Plot (Bivariate)
 ============================
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import DihedralFeaturizer
 from msmbuilder.decomposition import tICA
 from msmbuilder.cluster import MiniBatchKMeans
@@ -10,7 +11,6 @@
 import numpy as np
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
 
 rs = np.random.RandomState(42)
 

examples/plot_histogram.py

@@ -2,13 +2,14 @@
 Histogram Plot
 ==============
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import DihedralFeaturizer
 from msmbuilder.decomposition import tICA
 
 import numpy as np
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
+
 
 # Load Fs Peptide Data
 trajs = FsPeptide().get().trajectories

examples/plot_msm_network.py

@@ -2,6 +2,7 @@
 MSM Network Plot
 ================
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import DihedralFeaturizer
 from msmbuilder.decomposition import tICA
 from msmbuilder.cluster import MiniBatchKMeans
@@ -10,7 +11,6 @@
 import numpy as np
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
 
 rs = np.random.RandomState(42)
 

examples/plot_pop_resids.py

@@ -2,6 +2,7 @@
 Population Residuals Plot
 =========================
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import DihedralFeaturizer
 from msmbuilder.decomposition import tICA
 from msmbuilder.cluster import MiniBatchKMeans
@@ -10,7 +11,6 @@
 import numpy as np
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
 
 rs = np.random.RandomState(42)
 

examples/plot_timescales.py

@@ -2,6 +2,7 @@
 Timescales Plot
 ===============
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import DihedralFeaturizer
 from msmbuilder.decomposition import tICA
 from msmbuilder.cluster import MiniBatchKMeans
@@ -10,7 +11,6 @@
 import numpy as np
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
 
 rs = np.random.RandomState(42)
 

examples/plot_tpaths.py

@@ -2,6 +2,7 @@
 Transition Pathway Plot
 =======================
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import DihedralFeaturizer
 from msmbuilder.decomposition import tICA
 from msmbuilder.cluster import MiniBatchKMeans
@@ -10,7 +11,6 @@
 import numpy as np
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
 
 rs = np.random.RandomState(42)
 

examples/plot_trace.py

@@ -2,10 +2,10 @@
 Trace Plot
 ==========
 """
+from msmbuilder.example_datasets import FsPeptide
 from msmbuilder.featurizer import RMSDFeaturizer
 
 import msmexplorer as msme
-from msmexplorer.example_datasets import FsPeptide
 
 # Load Fs Peptide Data
 traj = FsPeptide().get().trajectories[0]