update dependencies

environment.yml

@@ -3,8 +3,11 @@ channels:
   - conda-forge
   - defaults
 dependencies: 
-  - python==3.7
-  - mdtraj==1.9.3 
-  - mdshare 
-  - pyemma 
+  - python==3.9
+  - scipy>=1.2
+  - numpy
+  - pandas
+  - matplotlib
   - MDAnalysis 
+  - deeptime
+  - biotite

pensa/clusters/clustering.py

@@ -1,9 +1,5 @@
 import numpy as np
-import scipy as sp
-import scipy.stats
-import mdshare
 import deeptime
-import MDAnalysis as mda
 import matplotlib.pyplot as plt
 
 

pensa/clusters/trajectory.py

@@ -1,13 +1,5 @@
 import numpy as np
-import scipy as sp
-import scipy.stats
-import mdshare
-import pyemma
-from pyemma.util.contexts import settings
 import MDAnalysis as mda
-import matplotlib.pyplot as plt
-
-
 
 
 def write_cluster_traj(cluster_idx, top_file, trj_file, out_name, start_frame=0):

pensa/clusters/wss.py

@@ -1,17 +1,9 @@
 import numpy as np
-import scipy as sp
-import scipy.stats
-import mdshare
-import pyemma
-from pyemma.util.contexts import settings
-import MDAnalysis as mda
 import matplotlib.pyplot as plt
 
 from pensa.clusters import obtain_clusters, obtain_combined_clusters
 
 
-
-
 def wss_over_number_of_clusters(data, algorithm='kmeans', 
                                 max_iter=100, num_repeats = 5, max_num_clusters = 12,
                                 plot_file = None):

pensa/comparison/metrics.py

@@ -2,8 +2,6 @@
 from pensa import *
 from pensa.comparison import *
 from pensa.dimensionality import *
-import random
-import math
 
 
 """

pensa/comparison/relative_entropy.py

@@ -3,9 +3,6 @@
 import scipy.stats
 import scipy.spatial
 import scipy.spatial.distance
-import MDAnalysis as mda
-import matplotlib.pyplot as plt
-import os
 from pensa.features import *
 
 

pensa/comparison/statespecific.py

@@ -1,5 +1,4 @@
-import numpy as np
-from tqdm import tqdm
+import numpy as np 
 from pensa.features import *
 from pensa.statesinfo import *
 

pensa/comparison/statistics.py

@@ -3,9 +3,6 @@
 import scipy.stats
 import scipy.spatial
 import scipy.spatial.distance
-import MDAnalysis as mda
-import matplotlib.pyplot as plt
-import os
 from pensa.features import *
 
 

pensa/comparison/visualization.py

@@ -5,7 +5,6 @@
 import scipy.spatial.distance
 import MDAnalysis as mda
 import matplotlib.pyplot as plt
-import os
 from pensa.features import *
 
 

pensa/dimensionality/pca.py

@@ -1,9 +1,8 @@
 import warnings
 import numpy as np
-import MDAnalysis as mda
 import matplotlib.pyplot as plt
 from sklearn.decomposition import PCA
-from pensa.preprocessing import sort_coordinates, merge_and_sort_coordinates
+from pensa.preprocessing import merge_and_sort_coordinates
 from pensa.comparison import feature_correlation
 from .visualization import project_on_eigenvector_pca, sort_traj_along_projection
 

pensa/dimensionality/tica.py

@@ -1,8 +1,7 @@
 import numpy as np
 import deeptime
-import MDAnalysis as mda
 import matplotlib.pyplot as plt
-from pensa.preprocessing import sort_coordinates, merge_and_sort_coordinates
+from pensa.preprocessing import merge_and_sort_coordinates
 from .visualization import project_on_eigenvector_tica, sort_traj_along_projection
 
 

pensa/dimensionality/visualization.py

@@ -1,11 +1,8 @@
 import numpy as np
-import pyemma
 from sklearn.decomposition import PCA
 import deeptime
-from pyemma.util.contexts import settings
-import MDAnalysis as mda
 import matplotlib.pyplot as plt
-from pensa.preprocessing import sort_coordinates, merge_and_sort_coordinates
+from pensa.preprocessing import sort_coordinates
 
 
 def project_on_eigenvector_tica(data, ev_idx, ana):

pensa/features/mda_distances.py

@@ -2,7 +2,6 @@
 import numpy as np
 import MDAnalysis as mda
 import MDAnalysis.lib.distances as ld
-import matplotlib.pyplot as plt
 import gpcrmining.gpcrdb as db
 
 

pensa/features/processing.py

@@ -3,10 +3,7 @@
 import scipy.stats
 import scipy.spatial
 import scipy.spatial.distance
-import MDAnalysis as mda
-import matplotlib.pyplot as plt
 import os
-import warnings
 from pensa.preprocessing import sort_coordinates
 
 

pensa/features/water_features.py

@@ -18,7 +18,6 @@
 
 import MDAnalysis as mda
 import numpy as np
-import itertools as it
 from gridData import Grid
 from tqdm import tqdm
 import os

pensa/preprocessing/coordinates.py

@@ -1,7 +1,5 @@
 import MDAnalysis as mda
 import numpy as np
-import os
-import requests
 from MDAnalysis.analysis import align
 
 

pensa/preprocessing/density.py

@@ -26,8 +26,6 @@
 from MDAnalysis.analysis import align
 import biotite.structure as struc
 import biotite.structure.io as strucio
-# from pensa import *
-# from pensa.features.processing import *
 from tqdm import tqdm
 
 # -- Processing trajectories for density analysis

pensa/preprocessing/download.py

@@ -1,5 +1,3 @@
-import MDAnalysis as mda
-import numpy as np
 import os
 import requests
 

pensa/preprocessing/selection.py

@@ -1,9 +1,4 @@
-import MDAnalysis as mda
-import pyemma
 import numpy as np
-import os
-import requests
-
 
 
 def range_to_string(a, b):

setup.py

@@ -20,9 +20,7 @@
       install_requires=[
         'numpy',
         'scipy>=1.2',
-        'mdtraj==1.9.9',
-        'mdshare',
-        'pyemma',
+        'deeptime',
         'MDAnalysis',
         'matplotlib',
         'biotite',