exprmat 0.1.39__tar.gz → 0.1.41__tar.gz

{exprmat-0.1.39 → exprmat-0.1.41}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.39
+Version: 0.1.41
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -54,10 +54,9 @@ Requires-Dist: hdbscan
 Requires-Dist: graphtools
 Requires-Dist: bincsync>=0.3.0
 Requires-Dist: pybigwig
+Requires-Dist: spatialdata
 Requires-Dist: loompy
-Requires-Dist: squidpy
 Requires-Dist: zarr
-Requires-Dist: spatialdata-io
 Requires-Dist: scikit-image
 Requires-Dist: spatial-image
 Requires-Dist: multiscale-spatial-image
@@ -76,11 +75,26 @@ Requires-Dist: pyfastx
 Requires-Dist: genomicranges
 Requires-Dist: rustworkx
 Requires-Dist: xgboost
+Requires-Dist: dask-expr>=2.0
 Requires-Dist: sphinx ; extra == 'dev'
 Requires-Dist: twine ; extra == 'dev'
 Requires-Dist: ipykernel ; extra == 'dev'
 Requires-Dist: ipytree ; extra == 'dev'
+Requires-Dist: cudf-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: dask-cudf-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: cuml-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: cugraph-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: nx-cugraph-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: cuxfilter-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: cucim-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: pylibraft-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: raft-dask-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: cuvs-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: nx-cugraph-cu12==25.8.* ; extra == 'cuda12'
+Requires-Dist: cupy-cuda12x ; extra == 'cuda12'
+Requires-Dist: rapids-singlecell ; extra == 'cuda12'
 Provides-Extra: dev
+Provides-Extra: cuda12
 License-File: license
 Summary: exprmat: Routines for expression matrices
 Author-email: Zheng Yang <xornent@outlook.com>

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/__init__.py

@@ -65,9 +65,11 @@ except ImportError:
     info('compilation finished.')
 
 
-from exprmat.configuration import default as config
+from exprmat.configuration import Configuration as configuration
 from exprmat.ansi import warning, info
 
+config = configuration()
+
 mu.set_options(pull_on_update = False)
 Image.MAX_IMAGE_PIXELS = config['max.image']
 
@@ -107,9 +109,10 @@ basepath = config['data']
 
 # core method exports
 from exprmat.utils import setup_styles
+from exprmat.ansi import error, warning, info, pprog, pproga
 from exprmat.reader.experiment import experiment, load_experiment
 from exprmat.reader.metadata import metadata, load_metadata
-from exprmat.ansi import error, warning, info, pprog, pproga
+
 
 setup_styles()
 
@@ -139,8 +142,8 @@ if PERFORM_DATABASE_CHECK:
 
 
 def cuda():
-
     import torch
+    from exprmat.utils import supports_tensorcore
     info(f'PyTorch version: {torch.__version__}')
     info(f'GPU acceleration availability: {"YES" if torch.cuda.is_available() else "NO"}')
     if torch.cuda.is_available():
@@ -154,7 +157,7 @@ def cuda():
             info(f'[{i}] {torch.cuda.get_device_name(i)} {"*" if torch.cuda.current_device() == i else ""}')
             info(f'    CUDA capability: {torch.cuda.get_device_capability(i)}')
             info(f'    Installed VRAM (GiB): {total_mem:.2f} GiB')
-            info(f'    Supporting TensorCore: {"YES" if torch.cuda.get_device_properties(0).major >= 7 else "NO"}')
+            info(f'    Supporting TensorCore: {"YES" if supports_tensorcore() else "NO"}')
             info(f'    Current dedicated memory: {dedicated_mem:.2f} / {total_mem:.2f} GiB ({100 * dedicated_mem / total_mem:.1f}%)')
 
 
@@ -186,7 +189,6 @@ def memory():
 
 setwd = os.chdir
 getwd = os.getcwd
-def locate_data(dir): config.update_config('data', dir)
 
 
 __all__ = [

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/ansi.py

@@ -6,6 +6,8 @@ from functools import partial
 from tqdm import tqdm
 from tqdm.auto import tqdm as tqdma
 
+SILENT = False
+
 
 def fore_black() -> None:
     print('\033[30m', end = '')
@@ -111,6 +113,7 @@ def format_file_size(size):
 
 
 def error(text: str, error = None) -> None:
+    if SILENT: raise Exception(text) from error
     fore_red()
     print('[error]', end = ' ')
     ansi_reset()
@@ -121,6 +124,7 @@ def error(text: str, error = None) -> None:
 
 
 def warning(text: str) -> None:
+    if SILENT: return
     fore_yellow()
     print('[!]', end = ' ')
     ansi_reset()
@@ -129,6 +133,7 @@ def warning(text: str) -> None:
 
 
 def info(text: str) -> None:
+    if SILENT: return
     fore_cyan()
     print('[i]', end = ' ')
     ansi_reset()

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/clustering/leiden.py

@@ -18,6 +18,8 @@ def leiden(
     neighbors_key: str | None = None,
     obsp: str | None = None,
     flavor = 'igraph',
+    use_gpu = False,
+    theta = 1,
     ** clustering_args,
 ) -> ad.AnnData | None:
     '''
@@ -86,11 +88,27 @@ def leiden(
         passes arguments to the `partition_type`) or `igraph.Graph.community_leiden` from `igraph`.
     '''
     
-    return sc.tl.leiden(
-        adata, resolution = resolution,
-        restrict_to = restrict_to, random_state = random_state,
-        key_added = key_added, adjacency = adjacency, directed = directed,
-        use_weights = use_weights, n_iterations = n_iterations,
-        partition_type = partition_type, neighbors_key = neighbors_key,
-        copy = False, flavor = flavor, **clustering_args
-    )
+    if use_gpu:
+        import rapids_singlecell as rsc
+        return rsc.tl.leiden(
+            adata, resolution = resolution,
+            restrict_to = restrict_to, random_state = random_state,
+            key_added = key_added, adjacency = adjacency,
+            use_weights = use_weights, 
+            # the n_iterations in igraph takes -1, 0, 1 and 2 as magic numbers
+            # not real number of iterations. indeed, the gpu implementation
+            # supports only real iterations, by default 200.
+            n_iterations = n_iterations if n_iterations > 2 else 200,
+            neighbors_key = neighbors_key, theta = theta,
+            copy = False
+        )
+
+    else:
+        return sc.tl.leiden(
+            adata, resolution = resolution,
+            restrict_to = restrict_to, random_state = random_state,
+            key_added = key_added, adjacency = adjacency, directed = directed,
+            use_weights = use_weights, n_iterations = n_iterations,
+            partition_type = partition_type, neighbors_key = neighbors_key,
+            copy = False, flavor = flavor, **clustering_args
+        )

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/configuration.py

@@ -17,8 +17,9 @@ class Configuration:
             'Ubuntu', 
             'Verdana'
         ]
-        
-        self.config['backend'] = 'TkAgg'
+
+        self.config['plotting.flavor'] = 'light'
+        self.config['plotting.backend'] = 'TkAgg'
         self.config['data'] = os.path.join(os.path.dirname(__file__), 'data')
 
         # target taxa
@@ -56,6 +57,3 @@ class Configuration:
 
     def update_config(self, conf_name, value):
         self.config[conf_name] = value
-
-
-default = Configuration()

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/data/finders.py

@@ -3,7 +3,7 @@ import os
 import pandas
 from exprmat import basepath
 from exprmat.ansi import warning, info
-from exprmat.configuration import default as cfg
+from exprmat import config as cfg
 
 genome = {}
 

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/data/geneset.py

@@ -4,7 +4,7 @@ import pandas
 import numpy as np
 
 from exprmat.ansi import warning, info
-from exprmat.configuration import default as cfg
+from exprmat import config as cfg
 from exprmat.data.finders import basepath, genome, get_genome
 
 

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/lr/utils.py

@@ -10,7 +10,6 @@ from exprmat.ansi import warning, error, pprog
 
 
 class default_params():
-    
     logbase = exp(1)
     min_cells = 5
     expr_prop = 0.1

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/peaks/motif.py

@@ -21,7 +21,7 @@ from pynndescent import NNDescent
 
 from exprmat.ansi import error, warning, info, pprog
 from exprmat.data.finders import basepath
-from exprmat.configuration import default
+from exprmat import config as default
 
 
 # genomic background sequencing

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/peaks/sequence.py

@@ -2,7 +2,7 @@
 import os
 from exprmat import pprog
 from exprmat.data.finders import basepath
-from exprmat.configuration import default
+from exprmat import config as default
 
 
 def query_sequence(adata, seqlen = None):

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/cnmf.py

@@ -3,6 +3,8 @@ import matplotlib.pyplot as plt
 import pandas as pd
 import numpy as np
 
+from exprmat.plotting.palettes import mpl, get_palette
+
 
 def cnmf_silhoutte(adata, nmf_slot = 'cnmf', figsize = (3, 2), dpi = 100):
 
@@ -38,11 +40,11 @@ def cnmf_density(adata, k, nmf_slot = 'cnmf', figsize = (3, 2), dpi = 100):
     return fig
 
 
-def cnmf_distance_comps(adata, k, nmf_slot = 'cnmf', cmap = 'Reds_r', figsize = (3, 3), dpi = 100):
+def cnmf_distance_comps(adata, k, nmf_slot = 'cnmf', cmap = 'reds', figsize = (3, 3), dpi = 100):
     
     fig = plt.figure(figsize = figsize, dpi = dpi)
     df = adata.uns[f'{nmf_slot}.dist.{k}']
-    fig.gca().imshow(df, cmap = cmap)
+    fig.gca().imshow(df, cmap = mpl(cmap))
 
     return fig
 
@@ -50,7 +52,7 @@ def cnmf_distance_comps(adata, k, nmf_slot = 'cnmf', cmap = 'Reds_r', figsize =
 def cnmf_distance_usages(
     adata, k, nmf_slot = 'cnmf', metrics = 'cosine', downsample = 0.1, method = 'single',
     annotations = None, show_indices = False, legend_cols = 1,
-    cmap = 'Reds_r', cmap_annotations = 'Set1', figsize = (3, 3), dpi = 100
+    cmap = 'reds', cmap_annotations = 'set1', figsize = (3, 3), dpi = 100
 ):
     
     import numpy as np
@@ -80,8 +82,8 @@ def cnmf_distance_usages(
 
 def cnmf_distance_modules(
     adata, k, nmf_slot = 'cnmf', metrics = 'cosine', downsample = 1, method = 'complete',
-    annotations = None, cmap_annotations = 'Set1', show_indices = False,
-    cmap = 'Reds_r', figsize = (3, 3), dpi = 100, legend_cols = 1
+    annotations = None, cmap_annotations = 'set1', show_indices = False,
+    cmap = 'reds', figsize = (3, 3), dpi = 100, legend_cols = 1
 ):
     
     import numpy as np
@@ -109,12 +111,12 @@ def cnmf_distance_modules(
 
 def matrix_plot(
     mat, labels = None, annotations = None, 
-    cmap = 'Reds_r', cmap_annotations = 'Set1',
+    cmap = 'reds', cmap_annotations = 'set1',
     show_indices = True,
     figsize = (3, 3), dpi = 100, legend_cols = 1
 ):
     fig = plt.figure(figsize = figsize, dpi = dpi)
-    fig.gca().imshow(mat, cmap = cmap)
+    fig.gca().imshow(mat, cmap = mpl(cmap))
     ax = fig.gca()
     ax.set_yticks([])
     ax.set_xticks([])
@@ -130,9 +132,7 @@ def matrix_plot(
         annot_n = [annot_u.index(x) for x in annotations]
 
         from exprmat.plotting import palettes
-        colors = list(palettes.linear_palette(palettes.all_palettes[cmap_annotations][
-            list(palettes.all_palettes[cmap_annotations].keys())[-1]
-        ], len(annot_u)))
+        colors = get_palette(cmap_annotations, len(annot_u))
         colormap = {x: y for x, y in zip(annot_u, colors)}
 
         ax_annot.set_xlim(-0.5, 0.5)
@@ -175,7 +175,7 @@ def matrix_plot(
         ncol = annotations.shape[1]
         ax_annot = ax.inset_axes([1.05, 0, max(0.3, 0.07 * ncol), 1], sharey = ax)
         
-        ax_annot.imshow(annotations, cmap = cmap_annotations, aspect = 'auto', interpolation = 'nearest')
+        ax_annot.imshow(annotations, cmap = mpl(cmap_annotations), aspect = 'auto', interpolation = 'nearest')
         # ax_annot.set_yticks([])
         if xn: 
             ax_annot.set_xticks([x for x in range(len(xn))])

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/cnv.py

@@ -5,6 +5,7 @@ import numpy as np
 import scanpy as sc
 from matplotlib.colors import Colormap, TwoSlopeNorm
 from exprmat.ansi import error
+from exprmat.plotting.palettes import mpl
 
 
 def chromosome_heatmap(
@@ -66,7 +67,7 @@ def chromosome_heatmap(
         var_names = tmp_adata.var.index.values,
         groupby = groupby,
         figsize = figsize,
-        cmap = cmap,
+        cmap = mpl(cmap),
         show_gene_labels = False,
         var_group_positions = var_group_positions,
         var_group_labels = list(chr_pos_dict.keys()),
@@ -139,7 +140,7 @@ def chromosome_heatmap_summary(
         var_names = tmp_adata.var.index.values,
         groupby = groupby,
         figsize = figsize,
-        cmap = cmap,
+        cmap = mpl(cmap),
         show_gene_labels = False,
         var_group_positions = var_group_positions,
         var_group_labels = list(chr_pos_dict.keys()),

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/gse.py

@@ -15,6 +15,7 @@ from matplotlib.colors import Normalize
 from matplotlib.category import UnitData
 from matplotlib.lines import Line2D
 
+from exprmat.plotting.palettes import mpl
 from exprmat.ansi import error, info
 
 
@@ -218,7 +219,7 @@ class nesplot:
             mat[np.newaxis, :],
             rasterized = True,
             norm = midnorm,
-            cmap = self.cmap,
+            cmap = mpl(self.cmap),
         )
 
         ax3.spines["bottom"].set_visible(False)
@@ -425,7 +426,7 @@ class heatmapplot(object):
         
         matrix = ax.pcolormesh(
             df.values,
-            cmap = self.cmap,
+            cmap = mpl(self.cmap),
             norm = norm,
             rasterized=True,
         )
@@ -751,7 +752,7 @@ class dotplot(object):
         sc = ax.scatter(
             x = x, y = y, data = df,
             s = "area", edgecolors = "none",
-            c = self.colname, cmap = self.cmap,
+            c = self.colname, cmap = mpl(self.cmap),
             vmin = vmin,
             vmax = vmax,
             marker = self.marker,

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/lr.py

@@ -11,6 +11,7 @@ from exprmat.lr.utils import default_anndata_keys as K
 from exprmat.lr.utils import default_primary_columns as D
 from exprmat.lr.utils import default_params as V
 from exprmat.utils import error, warning, info
+from exprmat.plotting.palettes import mpl
 
 
 def check_variable(liana_res, var_name, var):
@@ -434,7 +435,7 @@ def lr_dotplot(
 
     p = ax.scatter(
         x = 'x', y = 'y', s = 's',
-        edgecolors = "lightgrey", c = 'c', cmap = cmap,
+        edgecolors = "lightgrey", c = 'c', cmap = mpl(cmap),
         data = pd.DataFrame(df), marker = 'o'
     )
 
@@ -517,7 +518,7 @@ def heatmap(
     sns.heatmap(
         pvt, ax = ax, annot = annotate, linewidths = .5, 
         fmt = 'd' if pivot_mode == 'counts' else '.1f',
-        cmap = cmap
+        cmap = mpl(cmap)
     )
 
     ax.set_xlabel('Receiver (receptors)')

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/palettes.py

@@ -1439,7 +1439,7 @@ d3 = {
     'category20c' : Category20c,
 }
 
-mpl = {
+matpl = {
     'magma'   : Magma,
     'inferno' : Inferno,
     'plasma'  : Plasma,
@@ -1655,7 +1655,7 @@ def cividis(n: int) -> palette:
 def turbo(n: int) -> palette:
     return linear_palette(Turbo256, n)
 
-def cmdiv_wyj(n: int) -> palette:
+def wyj(n: int) -> palette:
     return interp_palette(palette((
         rgb_color(78, 42, 135).to_hex(),
         rgb_color(162, 184, 198).to_hex(),
@@ -1722,12 +1722,13 @@ def demo_colormap(ncols = 6, dpi = 100):
     for i, feat in enumerate(list(all_palettes.keys())):
         if len(axes.shape) == 2:
             plot_colormap(
-                get_palette(feat, 256), 
+                get_palette(feat), 
                 axes[i // ncols, i % ncols], 
                 title = feat
             )
+
         elif len(axes.shape) == 1:
-            plot_colormap(get_palette(feat, 256), axes[i], title = feat)
+            plot_colormap(get_palette(feat), axes[i], title = feat)
     
     for icol in range(ncols):
         for irow in range(nrows):
@@ -1752,11 +1753,17 @@ def to_rgba_array(palette: palette):
     return rgba_array
 
 
-def get_palette_tuple(name, n):
+def get_palette_tuple(name, n = None):
     
     if name not in all_palettes.keys():
         error(f'can not find a palette named `{name}`.')
     
+    # find if there is a defined n set if n is None.
+    if (n is None) and isinstance(all_palettes[name], dict):
+        keys = list(all_palettes[name].keys())
+        return all_palettes[name][keys[-1]]
+    elif n is None: n = 256
+    
     if isinstance(all_palettes[name], dict):
         if n in all_palettes[name].keys():
             return all_palettes[name][n]
@@ -1764,10 +1771,74 @@ def get_palette_tuple(name, n):
     else: return interp_palette(all_palettes[name], n)
 
 
-def get_palette(name, n):
-    return list(get_palette_tuple(name, n))
+def get_palette(name, n = None):
+
+    if '/' in name: name, suffix = name.split('/')
+    else: suffix = None
+    
+    pal = list(get_palette_tuple(name, n))
+    if suffix: # modification suffices.
+        if suffix == 'r': pal = pal[::-1]
+    
+    return pal
+
+
+def mpl(name, n = 256):
+    return to_matplotlib(get_palette(name, n))
+
 
-# custom palettes
-all_palettes['cmdiv_wyj']  = cmdiv_wyj(256)
 all_palettes['modlight']   = modlight(256)
-all_palettes['moddark']    = moddark(256)
+all_palettes['moddark']    = moddark(256)
+
+# inherit from matplotlib
+import matplotlib
+
+def get_mpl_discrete_colormap(name):
+    l, names = len(matplotlib.colormaps[name].colors), matplotlib.colormaps[name].colors
+    colors = []
+    for i in range(l):
+        r, g, b = names[i][0:3]
+        colors.append(rgb_color(int(r * 255), int(g * 255), int(b * 255)).to_hex())
+    return l, colors
+
+def get_mpl_continuous_colormap(name):
+    names = matplotlib.colormaps[name](np.linspace(0, 1, 256))
+    colors = []
+    for i in range(256):
+        r, g, b = names[i, 0:3]
+        colors.append(rgb_color(int(r * 255), int(g * 255), int(b * 255)).to_hex())
+    return 256, colors
+
+discretes = [
+    'tab10', 'tab20', 'tab20b', 'tab20c'
+]
+
+continuous = [
+    # cyclic
+    'twilight', 'twilight_shifted', 'hsv',
+
+    # diverging
+    'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu', 'RdYlBu', 'RdYlGn',
+    'Spectral', 'coolwarm', 'bwr', 'seismic', 'berlin', 'managua', 'vanimo',
+
+    # sequential
+    'bone', 'pink', 'spring', 'summer', 'autumn', 'winter', 'cool', 'Wistia',
+    'hot', 'afmhot', 'gist_heat', 'copper',
+
+    # misc
+    'flag', 'prism', 'ocean', 'gist_earth', 'terrain', 'gist_stern',
+    'gnuplot', 'gnuplot2', 'CMRmap', 'cubehelix', 'brg', 'gist_rainbow',
+    'rainbow', 'jet', 'gist_ncar', 'nipy_spectral'
+]
+
+for d in discretes:
+    k, v = get_mpl_discrete_colormap(d)
+    all_palettes[d.lower().replace('_', '.')] = { k : v }
+
+for d in continuous:
+    k, v = get_mpl_continuous_colormap(d)
+    all_palettes[d.lower().replace('_', '.')] = v
+
+
+# custom palettes
+all_palettes['wyj']  = wyj(256)

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/sankey.py

@@ -6,7 +6,7 @@ import matplotlib.pyplot as plt
 import seaborn as sns
 
 from exprmat.ansi import error
-from exprmat.plotting.palettes import linear_palette, all_palettes
+from exprmat.plotting.palettes import linear_palette, all_palettes, get_palette
 
 
 def check_data_matches_labels(labels, data, side):
@@ -69,9 +69,7 @@ def sankey(
     # if no colorDict given, make one
     if colors is None:
         colors = {}
-        pal = linear_palette(all_palettes[cmap][
-            list(all_palettes[cmap].keys())[-1]
-        ], len(all_labels))
+        pal = get_palette(cmap, len(all_labels))
         for i, label in enumerate(all_labels):
             colors[label] = pal[i]
     

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/track.py

@@ -230,7 +230,7 @@ def gene_track(
     show_gene_name = True
 ):
     from exprmat.data.finders import get_genome, get_genome_model
-    from exprmat.configuration import default as cfg
+    from exprmat import config as cfg
     model = get_genome_model(assembly)
     gtable = get_genome(cfg['taxa.reference'][assembly.lower()])
 
@@ -575,7 +575,7 @@ def genes(
         return fig
     
     elif where is not None:
-        from exprmat.configuration import default as cfg
+        from exprmat import config as cfg
         gtable = get_genome(cfg['taxa.reference'][assembly.lower()])
         ens = gtable['id'].tolist()
         name = gtable['gene'].tolist()
@@ -606,7 +606,7 @@ def genes(
 
 def whereis(assembly, where, upstream = 10000, downstream = 10000):
 
-    from exprmat.configuration import default as cfg
+    from exprmat import config as cfg
     from exprmat.data.finders import get_genome, get_genome_model
     from exprmat.ansi import error
 

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/utils.py

@@ -3,6 +3,7 @@ import seaborn as sns
 import numpy as np
 import matplotlib.pyplot as plt
 import pandas as pd
+from exprmat.plotting.palettes import mpl
 
 
 def linregress(
@@ -286,7 +287,7 @@ def density(
         y = yscale(y),
         s = size,
         c = clist,
-        cmap = cmap,
+        cmap = mpl(cmap),
         alpha = alpha
     )
 

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/plotting/velocity.py

@@ -17,6 +17,7 @@ from exprmat.dynamics.moments import second_order_moments
 from exprmat.plotting import embedding
 from exprmat.utils import translate_variables
 from exprmat.ansi import error, warning, info
+from exprmat.plotting.palettes import mpl
 
 
 def make_unique_list(key, allow_array = False):
@@ -499,7 +500,7 @@ def proportions(
     counts_layers = np.array([counts / counts_total for counts in counts_layers])
 
     gspec = pl.GridSpec(1, 2, pl.figure(None, figsize, dpi=dpi))
-    colors = pl.get_cmap("tab20b")(np.linspace(0.10, 0.65, len(layers_keys)))
+    colors = mpl("tab20b")(np.linspace(0.10, 0.65, len(layers_keys)))
 
     # pie chart of total abundances
     ax = pl.subplot(gspec[0])

{exprmat-0.1.39 → exprmat-0.1.41}/exprmat/preprocessing/filter.py

@@ -5,6 +5,7 @@ import scipy.sparse as sparse
 import pandas as pd
 import numba
 from numba import njit
+import warnings
 
 from exprmat.ansi import warning, info, error
 import exprmat.snapatac as internal
@@ -96,9 +97,13 @@ def vscore(E, min_mean = 0, n_bins = 50, fit_percentile = 0.1, error_weight = 1)
     a = c / (1 + b) - 1
 
     v_scores = ff_gene / ((1 + a) * (1 + b) + b * mu_gene)
-    cv_eff = np.sqrt((1 + a) * (1 + b) - 1)
-    cv_input = np.sqrt(b)
 
+    with warnings.catch_warnings():
+        warnings.simplefilter('ignore')
+        # encounter invalid values (inf/nan)
+        cv_eff = np.sqrt((1 + a) * (1 + b) + 1e-300 - 1) # add a small sigma
+
+    cv_input = np.sqrt(b)
     return v_scores, cv_eff, cv_input, min_expr_filter, mu_gene, ff_gene, a, b