refactor attempted imports

scprep/io/fcs.py

@@ -3,29 +3,15 @@
 
 import pandas as pd
 import numpy as np
-from decorator import decorator
 import struct
 from io import BytesIO
 import string
 import warnings
 
 from .utils import _matrix_to_data_frame
+from .. import utils
 
-try:
-    import fcsparser
-except ImportError:
-    pass
-
-
-@decorator
-def _with_fcsparser(fun, *args, **kwargs):
-    try:
-        fcsparser
-    except NameError:
-        raise ImportError(
-            "fcsparser not found. "
-            "Please install it with e.g. `pip install --user fcsparser`")
-    return fun(*args, **kwargs)
+fcsparser = utils._try_import("fcsparser")
 
 
 def _channel_names_from_meta(meta, channel_numbers, naming="N"):
@@ -236,7 +222,7 @@ def _fcsextract(filename, channel_naming="$PnS", reformat_meta=True):
     return meta, events
 
 
-@_with_fcsparser
+@utils._with_pkg("fcsparser")
 def load_fcs(filename, gene_names=True, cell_names=True,
              sparse=None,
              metadata_channels=['Time', 'Event_length', 'DNA1', 'DNA2',

scprep/io/hdf5.py

@@ -2,14 +2,10 @@
 # (C) 2018 Krishnaswamy Lab GPLv2
 from decorator import decorator
 
-try:
-    import tables
-except ImportError:
-    pass
-try:
-    import h5py
-except ImportError:
-    pass
+from .. import utils
+
+tables = utils._try_import("tables")
+h5py = utils._try_import("h5py")
 
 
 @decorator

scprep/plot/histogram.py

@@ -2,12 +2,12 @@
 import pandas as pd
 
 from .. import measure, utils
-from .utils import (_with_matplotlib, _get_figure, show,
+from .utils import (_get_figure, show,
                     temp_fontsize, parse_fontsize)
 from .tools import label_axis
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def histogram(data,
               bins=100, log=False,
               cutoff=None, percentile=None,
@@ -89,7 +89,7 @@ def histogram(data,
     return ax
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def plot_library_size(data,
                       bins=100, log=True,
                       cutoff=None, percentile=None,
@@ -146,7 +146,7 @@ def plot_library_size(data,
                      xlabel=xlabel, title=title, fontsize=fontsize, **kwargs)
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def plot_gene_set_expression(data, genes=None,
                              starts_with=None, ends_with=None, regex=None,
                              bins=100, log=False,

scprep/plot/jitter.py

@@ -1,8 +1,8 @@
 import numpy as np
 import pandas as pd
 
-from .. import utils, stats, select
-from .utils import (_with_matplotlib, _get_figure, show,
+from .. import utils
+from .utils import (_get_figure, show,
                     temp_fontsize, parse_fontsize, _with_default)
 from .tools import label_axis, generate_colorbar, generate_legend
 
@@ -26,7 +26,7 @@ def x_coords(self):
         return self._x_coords[self.plot_idx]
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def jitter(labels, values, sigma=0.1,
            c=None, cmap=None, cmap_scale='linear',
            s=None,

scprep/plot/marker.py

@@ -2,12 +2,12 @@
 import pandas as pd
 
 from .. import utils, stats, select
-from .utils import (_with_matplotlib, _get_figure, show,
+from .utils import (_get_figure, show,
                     temp_fontsize, parse_fontsize, shift_ticklabels)
 from .tools import label_axis
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def marker_plot(data, clusters, markers, gene_names=None,
                 normalize_expression=True, cmap='magma',
                 title=None, figsize=(8, 6),

scprep/plot/scatter.py

@@ -2,20 +2,18 @@
 import numbers
 import pandas as pd
 import warnings
-try:
-    import matplotlib.pyplot as plt
-    import matplotlib as mpl
-    from matplotlib import animation
-except ImportError:
-    pass
 
 from .. import utils, select
-from .utils import (_get_figure, _with_matplotlib, _is_color_array,
+from .utils import (_get_figure, _is_color_array,
                     show, _in_ipynb, parse_fontsize, temp_fontsize,
                     _with_default)
 from .tools import (create_colormap, create_normalize,
                     label_axis, generate_colorbar, generate_legend)
 
+plt = utils._try_import("matplotlib.pyplot")
+mpl = utils._try_import("matplotlib")
+animation = utils._try_import("matplotlib.animation")
+
 
 class _ScatterParams(object):
 
@@ -350,7 +348,7 @@ def check_cmap_scale(self):
                 self._cmap_scale = 'linear'
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def scatter(x, y, z=None,
             c=None, cmap=None, cmap_scale='linear', s=None, discrete=None,
             ax=None,
@@ -556,7 +554,7 @@ def scatter(x, y, z=None,
     return ax
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def scatter2d(data,
               c=None, cmap=None, cmap_scale='linear', s=None, discrete=None,
               ax=None, legend=None, colorbar=None,
@@ -708,7 +706,7 @@ def scatter2d(data,
                    **plot_kwargs)
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def scatter3d(data,
               c=None, cmap=None, cmap_scale='linear', s=None, discrete=None,
               ax=None, legend=None, colorbar=None,
@@ -875,7 +873,7 @@ def scatter3d(data,
                    **plot_kwargs)
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def rotate_scatter3d(data,
                      filename=None,
                      rotation_speed=30,

scprep/plot/scree.py

@@ -1,11 +1,13 @@
 import numpy as np
 
-from .utils import (_with_matplotlib, _get_figure, show,
+from .. import utils
+
+from .utils import (_get_figure, show,
                     temp_fontsize)
 from .tools import label_axis
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def scree_plot(singular_values, cumulative=False, ax=None, figsize=None,
                xlabel='Principal Component', ylabel='Explained Variance (%)',
                fontsize=None,

scprep/plot/style.py

@@ -1,8 +1,8 @@
-from .utils import _with_matplotlib
+from .. import utils
 from .tools import label_axis
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def style_phate(ax, label_prefix="PHATE"):
     """Removes ticks from `ax` and adds axis labels.
 

scprep/plot/tools.py

@@ -1,15 +1,14 @@
 import numpy as np
 import warnings
-try:
-    import matplotlib as mpl
-    import matplotlib.pyplot as plt
-except ImportError:
-    pass
 
-from .utils import _with_matplotlib, _get_figure, parse_fontsize, temp_fontsize
+from .. import utils
+from .utils import _get_figure, parse_fontsize, temp_fontsize
 
+plt = utils._try_import("matplotlib.pyplot")
+mpl = utils._try_import("matplotlib")
 
-@_with_matplotlib
+
+@utils._with_pkg("matplotlib")
 def create_colormap(colors, name="scprep_custom_cmap"):
     """Create a custom colormap from a list of colors
 
@@ -39,7 +38,7 @@ def create_colormap(colors, name="scprep_custom_cmap"):
     return cmap
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def create_normalize(vmin, vmax, scale=None):
     """Create a colormap normalizer
 
@@ -76,7 +75,7 @@ def create_normalize(vmin, vmax, scale=None):
     return norm
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def generate_legend(cmap, ax, title=None, marker='o', markersize=10,
                     loc='best', bbox_to_anchor=None,
                     fontsize=None, title_fontsize=None,
@@ -133,7 +132,7 @@ def generate_legend(cmap, ax, title=None, marker='o', markersize=10,
     return legend
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def generate_colorbar(cmap=None, vmin=None, vmax=None, scale=None, ax=None,
                       title=None, title_rotation=270, fontsize=None,
                       n_ticks='auto', labelpad=10, mappable=None, **kwargs):

scprep/plot/utils.py

@@ -1,24 +1,11 @@
 import numpy as np
-from decorator import decorator
 import platform
-try:
-    import matplotlib.pyplot as plt
-    import matplotlib as mpl
-    from mpl_toolkits.mplot3d import Axes3D
-except ImportError:
-    pass
 
+from .. import utils
 
-@decorator
-def _with_matplotlib(fun, *args, **kwargs):
-    try:
-        assert int(mpl.__version__[0]) >= 3
-    except (NameError, AssertionError):
-        raise ImportError(
-            "matplotlib>=3.0 not found. "
-            "Please install it with e.g. "
-            "`pip install --user --upgrade matplotlib`")
-    return fun(*args, **kwargs)
+plt = utils._try_import("matplotlib.pyplot")
+mpl = utils._try_import("matplotlib")
+mplot3d = utils._try_import("mpl_toolkits.mplot3d")
 
 
 def _with_default(param, default):
@@ -49,7 +36,8 @@ def _get_figure(ax=None, figsize=None, subplot_kw=None):
             else:
                 raise e
         if 'projection' in subplot_kw:
-            if subplot_kw['projection'] == '3d' and not isinstance(ax, Axes3D):
+            if subplot_kw['projection'] == '3d' and \
+                    not isinstance(ax, mplot3d.Axes3D):
                 raise TypeError("Expected ax with projection='3d'. "
                                 "Got 2D axis instead.")
         show_fig = False
@@ -73,7 +61,7 @@ def _in_ipynb():
         return False
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def show(fig):
     """Show a matplotlib Figure correctly, regardless of platform
 
@@ -148,7 +136,7 @@ def __exit__(self, type, value, traceback):
         plt.rcParams['font.size'] = self.old_size
 
 
-@_with_matplotlib
+@utils._with_pkg("matplotlib")
 def shift_ticklabels(axis, dx=0, dy=0):
     """Shifts ticklabels on an axis
 

scprep/stats.py

@@ -8,10 +8,7 @@
 from . import plot, utils
 import warnings
 
-try:
-    import matplotlib.pyplot as plt
-except ImportError:
-    pass
+plt = utils._try_import("matplotlib.pyplot")
 
 
 def EMD(x, y):
@@ -286,7 +283,7 @@ def knnDREMI(x, y, k=10, n_bins=20, n_mesh=3, n_jobs=1,
         return dremi
 
 
-@plot.utils._with_matplotlib
+@utils._with_pkg("matplotlib")
 def plot_knnDREMI(dremi, mutual_info, x, y, n_bins, n_mesh,
                   density, bin_density, drevi,
                   figsize=(12, 3.5), filename=None,

scprep/utils.py

@@ -3,10 +3,30 @@
 import numbers
 from scipy import sparse
 import warnings
-import re
+import importlib
+from decorator import decorator
+
 from . import select
 
 
+def _try_import(pkg):
+    try:
+        return importlib.import_module(pkg)
+    except ImportError:
+        return None
+
+
+@decorator
+def _with_pkg(fun, pkg=None, *args, **kwargs):
+    try:
+        importlib.import_module(pkg)
+    except ImportError:
+        raise ImportError(
+            "{0} not found. "
+            "Please install it with e.g. `pip install --user {0}`".format(pkg))
+    return fun(*args, **kwargs)
+
+
 def toarray(x):
     """Convert an array-like to a np.ndarray