fixed a few bugs for release 0.2.7

Author: falexwolf

scanpy/api/pp.py

@@ -1,3 +1,4 @@
+# TODO: this duplicates scanpy.preprocessing.__init__
 from ..preprocessing.recipes import recipe_zheng17, recipe_weinreb16
 from ..preprocessing.simple import filter_cells, filter_genes, filter_genes_dispersion
 from ..preprocessing.simple import log1p, pca, normalize_per_cell, regress_out, scale, subsample

scanpy/plotting/ann_data.py

@@ -209,7 +209,7 @@ def add_centroid(centroids, name, Y, mask):
     for i, icolor_key in enumerate(categoricals):
         palette = palettes[i]
         color_key = color_keys[icolor_key]
-        if len(adata.add[color_key + '_order']) != np.unique(adata.smp[color_key]):
+        if len(adata.add[color_key + '_order']) != len(np.unique(adata.smp[color_key])):
             from ..utils import unique_categories
             adata.add[color_key + '_order'] = unique_categories(adata.smp[color_key])
         if (not color_key + '_colors' in adata.add or not palette_was_none
@@ -226,7 +226,7 @@ def add_centroid(centroids, name, Y, mask):
                     mask_remaining[mask] = False
                     if legend_loc == 'on data': add_centroid(centroids, name, Y, mask)
         else:
-            for name in names:
+            for name in groups:
                 if name not in set(adata.add[color_key + '_order']):
                     raise ValueError('"' + name + '" is invalid!'
                                      + ' specify valid name, one of '

scanpy/preprocessing/__init__.py

@@ -0,0 +1,4 @@
+# this duplicates scanpy.api.pp
+from ..preprocessing.recipes import recipe_zheng17, recipe_weinreb16
+from ..preprocessing.simple import filter_cells, filter_genes, filter_genes_dispersion
+from ..preprocessing.simple import log1p, pca, normalize_per_cell, regress_out, scale, subsample

scanpy/readwrite.py

@@ -716,7 +716,8 @@ def postprocess_reading(key, value):
     if value.dtype.kind == 'S':
         value = value.astype(str)
         # recover a dictionary that has been stored as a string
-        if value[0] == '{' and value[-1] == '}': value = eval(value)
+        if len(value) > 0:
+            if value[0] == '{' and value[-1] == '}': value = eval(value)
     if (key != 'smp' and key != 'var'
         and not isinstance(value, dict) and value.dtype.names is not None):
         # TODO: come up with a better way of solving this, see also below
@@ -797,7 +798,12 @@ def write_dict_to_file(filename, d, ext='h5'):
         if not os.path.exists(dirname): os.makedirs(dirname)
         if not os.path.exists(dirname + 'add'): os.makedirs(dirname + 'add')
         from pandas import DataFrame
+        not_yet_raised_data_graph_warning = True
         for key, value in d_write.items():
+            if key.startswith('data_graph') and not_yet_raised_data_graph_warning:
+                logg.warn('Omitting to write neighborhood graph (`adata.add[\'data_graph...\']`).')
+                not_yet_raised_data_graph_warning = False
+                continue
             filename = dirname
             if key not in {'X', 'var', 'smp'}: filename += 'add/'
             filename += key + '.' + ext

scanpy/tools/sim.py

@@ -81,8 +81,6 @@ def sim(model,
     else:
         params = locals()
     adata = sample_dynamic_data(params)
-    if 'tools' not in adata.add:
-        adata.add['tools'] = np.array([], dtype=str)
     adata.add['xroot'] = adata.X[0]
     return adata