exprmat 0.1.44__tar.gz → 0.1.45__tar.gz

{exprmat-0.1.44 → exprmat-0.1.45}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.44
+Version: 0.1.45
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

{exprmat-0.1.44 → exprmat-0.1.45}/exprmat/ansi.py

@@ -160,6 +160,74 @@ def cyan(x): return '\033[36m' + x + '\033[0m'
 def annot(x): return '\033[90;3m' + x + '\033[0m'
 
 
+def dtypestr(dty):
+    string = str(dty)
+    if string == 'category': return 'cat'
+    elif 'float' in string: return string.replace('float', 'f')
+    elif 'int' in string: return string.replace('int', 'i')
+    elif string == 'object': return 'o'
+    return string
+
+
+def dtypemat(dty):
+    from numpy import matrix, ndarray
+    from scipy.sparse import csr_array, csr_matrix, csc_array, csc_matrix, coo_array, coo_matrix
+    from pandas import DataFrame
+
+    classdef = ''
+    if isinstance(dty, DataFrame): return 'df'
+    elif isinstance(dty, matrix): classdef = 'dense'
+    elif isinstance(dty, ndarray): classdef = 'arr'
+    elif isinstance(dty, csr_array): classdef = 'csra'
+    elif isinstance(dty, csr_matrix): classdef = 'csr'
+    elif isinstance(dty, csc_array): classdef = 'csca'
+    elif isinstance(dty, csc_matrix): classdef = 'csc'
+    elif isinstance(dty, coo_array): classdef = 'cooa'
+    elif isinstance(dty, coo_matrix): classdef = 'coo'
+    else: classdef = str(type(dty))
+    
+    size = ''
+    try:
+        if dty.shape[1] != dty.shape[0]: size = dty.shape[1]
+    except: pass
+    
+    ret = ':'.join([classdef, dtypestr(dty.dtype)])
+    if size != '': ret += f'({size})'
+    return ret
+
+
+def remove_ansi_escape_sequences(text):
+    ansi_escape = re.compile(r'\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])')
+    return ansi_escape.sub('', text)
+
+
+def lenp(string: str):
+    return len(remove_ansi_escape_sequences(string))
+
+
+def wrap(array: list[str], sep = ' ', n = 100) -> list[str]:
+    results = []
+    cumulative = ''
+    lencum = 0
+
+    for a in array:
+
+        lenprint = lenp(a)
+
+        if lencum + lenprint + len(sep) <= n:
+            cumulative += (sep + a)
+            lencum += (len(sep) + lenprint)
+        else:
+            results += [cumulative[1:] if cumulative[0] == ' ' else cumulative]
+            cumulative = a
+            lencum = lenprint
+
+    if cumulative[0] != '':
+        results += [cumulative[1:] if cumulative[0] == ' ' else cumulative]
+
+    return results
+
+
 progress_styles = {
     'ncols': 80,
     'ascii': '-━',

{exprmat-0.1.44 → exprmat-0.1.45}/exprmat/dynamics/moments.py

@@ -7,7 +7,12 @@ from exprmat.ansi import error, warning, info
 
 
 def not_yet_normalized(X):
-    return np.allclose(np.ravel(X[:5].data if issparse(X) else X[:5]) % 1, 0, atol=1e-3)
+
+    # this logic sometimes have bugs.
+    # just cancel it for now.
+    
+    return False
+    return np.allclose(np.ravel(X[:5].data if issparse(X) else X[:5]) % 1, 0, atol = 1e-3)
 
 
 def moments(

{exprmat-0.1.44 → exprmat-0.1.45}/exprmat/plotting/expression.py

@@ -12,7 +12,7 @@ def barplot(
     adata, *, gene, 
     slot = 'X', group = 'cell.type', selected_groups = None, selected_splits = None,
     split = 'treat', palette = ['red', 'black'], ax = None, style = 'box',
-    size = (6,3), dpi = 100, violin_kwargs = {}
+    size = (6,3), dpi = 100, violin_kwargs = {}, legend = True
 ):
     
     plt.rcParams["ytick.labelright"] = False
@@ -81,7 +81,8 @@ def barplot(
         grid_color = 'lightgray'
     )
             
-    axes.legend(bbox_to_anchor = (1, 1), loc = 'upper left', borderaxespad = 0, frameon = False)
+    if legend: axes.legend(bbox_to_anchor = (1, 1), loc = 'upper left', borderaxespad = 0, frameon = False)
+    else: axes.get_legend().remove()
     axes.set_xlabel('')
     axes.set_ylabel(gene)
     # axes.set_xticks(selected_groups)

{exprmat-0.1.44 → exprmat-0.1.45}/exprmat/reader/experiment.py

@@ -30,7 +30,7 @@ from exprmat.reader.matcher import (
     parse_tcr_10x, attach_splice_reads_mtx, attach_splice_reads_loom
 )
 from exprmat.reader.matcher import attach_tcr
-from exprmat.ansi import warning, info, error, red, green, pprog
+from exprmat.ansi import warning, info, error, red, green, pprog, wrap, dtypestr, dtypemat
 from exprmat import config as cfg
 import exprmat.reader.static as st
 import exprmat as em
@@ -2393,52 +2393,84 @@ class experiment:
             import textwrap
             if adata.obs is not None and len(adata.obs) > 0:
                 print(green('    obs'), ':', end = ' ', file = strio)
-                wrapped = textwrap.wrap(' '.join([
-                    x + ' ' + annot('<' + str(adata.obs[x].dtype) + '>')
+
+                wrapped = wrap([
+                    x + ' ' + annot('<' + dtypestr(adata.obs[x].dtype) + '>')
                     for x in adata.obs.keys()
-                ]), width = 90, replace_whitespace = False, drop_whitespace = True)
+                ], n = 90, sep = ' ')
+
                 for nline in range(len(wrapped)):
                     if nline == 0: print(wrapped[nline], file = strio)
                     else: print(' ' * 9, wrapped[nline], file = strio)
 
             if adata.var is not None and len(adata.var) > 0:
                 print(green('    var'), ':', end = ' ', file = strio)
-                wrapped = textwrap.wrap(' '.join(adata.var.keys()), width = 90)
+                
+                wrapped = wrap([
+                    x + ' ' + annot('<' + dtypestr(adata.var[x].dtype) + '>')
+                    for x in adata.var.keys()
+                ], n = 90, sep = ' ')
+
                 for nline in range(len(wrapped)):
                     if nline == 0: print(wrapped[nline], file = strio)
                     else: print(' ' * 9, wrapped[nline], file = strio)
             
             if adata.layers is not None and len(adata.layers) > 0:
                 print(green(' layers'), ':', end = ' ', file = strio)
-                wrapped = textwrap.wrap(' '.join(adata.layers.keys()), width = 90)
+                
+                wrapped = wrap([
+                    x + ' ' + annot('<' + dtypestr(adata.layers[x].dtype) + '>')
+                    for x in adata.layers.keys()
+                ], n = 90, sep = ' ')
+
                 for nline in range(len(wrapped)):
                     if nline == 0: print(wrapped[nline], file = strio)
                     else: print(' ' * 9, wrapped[nline], file = strio)
             
             if adata.obsm is not None and len(adata.obsm) > 0:
                 print(green('   obsm'), ':', end = ' ', file = strio)
-                wrapped = textwrap.wrap(' '.join(adata.obsm.keys()), width = 90)
+
+                wrapped = wrap([
+                    x + ' ' + annot('<' + dtypemat(adata.obsm[x]) + '>')
+                    for x in adata.obsm.keys()
+                ], n = 90, sep = ' ')
+
                 for nline in range(len(wrapped)):
                     if nline == 0: print(wrapped[nline], file = strio)
                     else: print(' ' * 9, wrapped[nline], file = strio)
             
             if adata.varm is not None and len(adata.varm) > 0:
                 print(green('   varm'), ':', end = ' ', file = strio)
-                wrapped = textwrap.wrap(' '.join(adata.varm.keys()), width = 90)
+                
+                wrapped = wrap([
+                    x + ' ' + annot('<' + dtypemat(adata.varm[x]) + '>')
+                    for x in adata.varm.keys()
+                ], n = 90, sep = ' ')
+
                 for nline in range(len(wrapped)):
                     if nline == 0: print(wrapped[nline], file = strio)
                     else: print(' ' * 9, wrapped[nline], file = strio)
 
             if adata.obsp is not None and len(adata.obsp) > 0:
                 print(green('   obsp'), ':', end = ' ', file = strio)
-                wrapped = textwrap.wrap(' '.join(adata.obsp.keys()), width = 90)
+                
+                wrapped = wrap([
+                    x + ' ' + annot('<' + dtypemat(adata.obsp[x]) + '>')
+                    for x in adata.obsp.keys()
+                ], n = 90, sep = ' ')
+
                 for nline in range(len(wrapped)):
                     if nline == 0: print(wrapped[nline], file = strio)
                     else: print(' ' * 9, wrapped[nline], file = strio)
 
             if adata.varp is not None and len(adata.varp) > 0:
                 print(green('   varp'), ':', end = ' ', file = strio)
-                wrapped = textwrap.wrap(' '.join(adata.varp.keys()), width = 90)
+                
+                wrapped = wrap([
+                    x + ' ' + annot('<' + dtypemat(adata.varp[x]) + '>')
+                    for x in adata.varp.keys()
+                ], n = 90, sep = ' ')
+
                 for nline in range(len(wrapped)):
                     if nline == 0: print(wrapped[nline], file = strio)
                     else: print(' ' * 9, wrapped[nline], file = strio)

{exprmat-0.1.44 → exprmat-0.1.45}/pyproject.toml

@@ -20,7 +20,7 @@ description = "exprmat: Routines for expression matrices"
 readme = "readme.md"
 license = {file = "license"}
 requires-python = ">=3.9, <3.13"
-version = "0.1.44"
+version = "0.1.45"
 authors = [
     {name = "Zheng Yang", email = "xornent@outlook.com"}
 ]