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Now compatible with Matplotlib 3.8.2 #34

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Dec 4, 2023
Merged

Now compatible with Matplotlib 3.8.2 #34

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5 changes: 0 additions & 5 deletions safep/AFEP_parse.py
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#Large datasets can be difficult to parse on a workstation due to inefficiencies in the way data is represented for pymbar. When possible, reduce the size of your dataset.
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes

from numpy.lib.stride_tricks import sliding_window_view
from scipy.stats import linregress as lr
from scipy.stats import norm

from glob import glob #file regexes
import pandas as pd
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1 change: 0 additions & 1 deletion safep/estimators.py
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@@ -1,6 +1,5 @@
# Import block
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes

import numpy as np
from numpy.lib.stride_tricks import sliding_window_view
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20 changes: 0 additions & 20 deletions safep/fileIO.py
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@@ -1,28 +1,8 @@
# Import block
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes

import numpy as np
from numpy.lib.stride_tricks import sliding_window_view

from scipy.stats import linregress as lr
from scipy.stats import norm
from scipy.special import erfc
from scipy.optimize import curve_fit as scipyFit
from scipy.stats import skew

import pandas as pd

from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.parsing import namd
from alchemlyb.estimators import BAR
from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.visualisation import plot_convergence

import re
from tqdm import tqdm #for progress bars
from natsort import natsorted #for sorting "naturally" instead of alphabetically
from glob import glob #file regexes

from .helpers import *

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21 changes: 0 additions & 21 deletions safep/helpers.py
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@@ -1,28 +1,7 @@
# Import block
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes

import numpy as np
from numpy.lib.stride_tricks import sliding_window_view

from scipy.stats import linregress as lr
from scipy.stats import norm
from scipy.special import erfc
from scipy.optimize import curve_fit as scipyFit
from scipy.stats import skew

import pandas as pd

from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.parsing import namd
from alchemlyb.estimators import BAR
from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.visualisation import plot_convergence

import re
from tqdm import tqdm #for progress bars
from natsort import natsorted #for sorting "naturally" instead of alphabetically
from glob import glob #file regexes

# Calculate the coefficient of determination:
def get_Rsq(X, Y, Yexpected):
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21 changes: 0 additions & 21 deletions safep/plotting.py
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@@ -1,30 +1,9 @@
# Import block
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes

import numpy as np
from numpy.lib.stride_tricks import sliding_window_view

from scipy.stats import linregress as lr
from scipy.stats import norm
from scipy.special import erfc
from scipy.optimize import curve_fit as scipyFit
from scipy.stats import skew
import scipy as sp

import pandas as pd

from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.parsing import namd
from alchemlyb.estimators import BAR
from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.visualisation import plot_convergence

import re
from tqdm import tqdm #for progress bars
from natsort import natsorted #for sorting "naturally" instead of alphabetically
from glob import glob #file regexes

from .helpers import *
from .processing import get_n_samples

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13 changes: 1 addition & 12 deletions safep/processing.py
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@@ -1,30 +1,19 @@
# Import block
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes

import numpy as np
from numpy.lib.stride_tricks import sliding_window_view

from scipy.stats import linregress as lr
from scipy.stats import norm
from scipy.special import erfc
from scipy.optimize import curve_fit as scipyFit
from scipy.stats import skew

import pandas as pd

from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.parsing import namd
from alchemlyb.estimators import BAR
from alchemlyb.visualisation.dF_state import plot_dF_state
from alchemlyb.visualisation import plot_convergence
from alchemlyb.preprocessing import subsampling

import re
from tqdm import tqdm # for progress bars
from natsort import (
natsorted,
) # for sorting "naturally" instead of alphabetically
from natsort import natsorted
from glob import glob # file regexes

from .helpers import *
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -2,7 +2,7 @@

setup(
name='safep',
version='0.1.2.3',
version='0.1.3',
description='Tools for Analyzing and Debugging (SA)FEP calculations',
url='https://github.com/BranniganLab/safep',
author='Brannigan Lab',
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