exprmat 0.1.58__tar.gz → 0.2.73__tar.gz

{exprmat-0.1.58 → exprmat-0.2.73}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.58
+Version: 0.2.73
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -57,7 +57,7 @@ Requires-Dist: bincsync>=0.4.0
 Requires-Dist: pybigwig
 Requires-Dist: spatialdata
 Requires-Dist: loompy
-Requires-Dist: zarr
+Requires-Dist: zarr<3
 Requires-Dist: scikit-image
 Requires-Dist: spatial-image
 Requires-Dist: multiscale-spatial-image
@@ -82,6 +82,13 @@ Requires-Dist: dask-expr>=2.0
 Requires-Dist: einops==0.8.1
 Requires-Dist: lxml
 Requires-Dist: arviz>=0.23
+Requires-Dist: pyvips
+Requires-Dist: openslide-python
+Requires-Dist: tissuumaps<4
+Requires-Dist: opencv-python
+Requires-Dist: marsilea
+Requires-Dist: qnorm
+Requires-Dist: torch-geometric
 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'
@@ -109,16 +116,14 @@ Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 Project-URL: Repository, https://github.com/yang-z-03/exprmat
 
 
-# Exprmat
+# exprmat
 
 ![wheels](https://img.shields.io/pypi/wheel/exprmat)
 ![version](https://img.shields.io/pypi/v/exprmat)
 
-Exprmat (short for **expr**ession **mat**rix) is a routine package for manipulation 
-of single cell expression matrices. It is built based on commonly accepted python
-infrastructures for single cell data management (Scanpy, SnapAtac2, and MuData) and
-provides integration and wrappers of common routines for preprocessing, annotating,
-clustering, visualizations, and downstream analyses with a common interface.
+exprmat (short for **expr**ession **mat**rix) is a routine package for manipulation 
+of sparse expression matrices. It provides a ***structured***, ***introspective***
+mudular interface for man and machine.
 
 You may refer to these places:
 
@@ -180,7 +185,7 @@ for re-distribution.
 
 ```
 exprmat - Routines to manipulate expression matrices
-Copyright (C) 2025 - 2026 Zheng Yang (杨政) <xornent@outlook.com>
+Copyright (C) 2025 - 2026 Zheng Yang <xornent@outlook.com>
 
 exprmat is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions. 
@@ -194,91 +199,34 @@ your program into proprietary programs.
 I acknowledge the following author(s) for modifying and integrating their work
 in the form of source code to this package.
 
-```
-parts of the source code under /preprocessing comes from the scanpy project.
-
-  BSD 3-Clause License. For full text of the license, see 
-  <https://opensource.org/license/BSD-3-clause>
-  Copyright (c) 2025 scverse®
-  Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab
-
-function embedding_atlas (file /reduction/plot.py) comes from the omicverse project.
-
-  GNU GPLv3. (same as this project)
-  Copyright (c) 2024 112 Lab
-
-most of the code from /snapatac2 and /snapatac2-core comes from the SnapATAC
-project, including the rust build system and the compiled binaries.
-
-  The MIT license. For full text of the license, see
-  <https://opensource.org/license/MIT>
-  Copyright (c) 2022-2024 Kai Zhang
-
-file /clustering/sc3.py comes from the sc3s project.
-
-  GNU GPLv3. (same as this project)
-  Copyright (c) Quah, F.X. and Hemberg, M. and contributors.
-
-file /clustering/nmf.py comes from cNMF project.
-
-  The MIT license
-  Copyright (c) 2019 Dylan Kotliar
-
-directory /cnv comes from infercnvpy project.
-  
-  BSD 3-Clause License
-  Copyright (c) 2022, Gregor Sturm
-
-directory /deconv comes from the TAPE project.
-
-  GNU GPLv3. (same as this project)
-  Copyright (c) The contributors.
-
-directory /metacell comes from the MetaQ project.
-  
-  MIT License
-  Copyright (c) 2024 XLearning Group
-
-directory /grn comes from the scenicplus project.
-
-  Academic Non-commercial Software License Agreement.
-  For full text of the license, see <https://github.com/aertslab/scenicplus>
-  Copyright (c) The contributors.
-
-directory /lr (but not /lr/icnet) comes from the lianapy project
-
-  BSD 3-Clause License
-  Copyright (c) 2025, Daniel Dimitrov
-
-directory /peaks/idr.py comes from the idr project
-
-  GNU GPLv2. For copyright details, see <https://github.com/nboley/idr>
-  Copyright (c) The contributors
-
-function diffmap comes from the pydiffmap project
-
-  MIT License
-  Copyright (c) 2018 Ralf Banisch, Erik Henning Thiede, Zofia Trstanova
-
-principle tree fitting and trajectory analysis comes from the scFates project
-
-  BSD 3-Clause License
-  Copyright (c) 2020, Louis Faure
-
-file /trajectory/cytotrace.py comes from the CytoTRACE2 project
-
-  Stanford Non-commercial Software License Agreement
-  Copyright (c) The contributors.
-
-rna velocity fitting comes from the scvelo project
-
-  BSD 3-Clause License
-  Copyright (c) 2018, Theis Lab
-
-directory /deseq comes from the pyDEseq2 project
-
-  MIT License
-  Copyright (c) 2022 Owkin
-
-```
-
+- **scanpy**, BSD 3-Clause, Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab
+- **snapatac2**, MIT, Copyright (c) 2022-2024 Kai Zhang
+- **sc3s**, GNU GPLv3, Copyright (c) Quah, F.X. and Hemberg, M. and contributors.
+- **cnmf**, MIT, Copyright (c) 2019 Dylan Kotliar
+- **infercnvpy**, BSD 3-Clause, Copyright (c) 2022, Gregor Sturm
+- **tape**, GNU GPLv3, Copyright (c) The contributors.
+- **metaq**, MIT, Copyright (c) 2024 XLearning Group
+- **scenicplus**, Academic Non-commercial Software License Agreement, Copyright (c) The contributors.
+- **lianapy**, BSD 3-Clause, Copyright (c) 2025, Daniel Dimitrov
+- **idr**, GNU GPLv2, Copyright (c) The contributors
+- **omicverse**, GNU GPLv3, Copyright (c) 2024 112 Lab
+- **pydiffmap**, MIT, Copyright (c) 2018 Ralf Banisch, Erik Henning Thiede, Zofia Trstanova
+- **scfates**, BSD 3-Clause, Copyright (c) 2020, Louis Faure
+- **cytotrace2**, Stanford Non-commercial Software License Agreement, Copyright (c) The contributors.
+- **scvelo**, BSD 3-Clause, Copyright (c) 2018, Theis Lab
+- **pydeseq2**, MIT, Copyright (c) 2022 Owkin
+- **decoupler**, GNU GPLv3, Copyright (c) The contributors.
+- **scvitools**, BSD 3-Clause, Copyright (c) 2026, Yosef Lab, Weizmann Institute of Science
+- **spacec**, Academic Software License Agreement, Copyright (c) The contributors.
+- **squidpy**, BSD 3-Clause, Copyright (c) 2021, Theis Lab
+- **sctransformpy**, GNU GPLv3, Copyright (c) David DeTomaso
+- **magic**, GNU GPLv2, Copyright (c) The contributors.
+- **scrublet**, MIT, Copyright (c) 2018 Samuel Wolock
+- **py8rds**, MIT, Copyright (c) 2024 Cellular Genetics Informatics
+- **nimfa**, New BSD, Copyright (c) 2016 The Nimfa developers.
+- **cellnest**, GNU GPLv3, Copyright (c) The contributors.
+- **tangram**, BSD 3-Clause, Copyright (c) 2020, Broad Institute All rights reserved.
+- **deepst**, MIT, Copyright (c) 2022 spatial-Transcriptomics
+- **spagcn**, MIT, Copyright (c) 2020 JianHu
+- **spatialde**, MIT, Copyright (c) 2018 Teichmann Group
+- **omnipathdb**, See source licenses and permissions.

{exprmat-0.1.58 → exprmat-0.2.73}/exprmat/__init__.py

@@ -4,15 +4,16 @@
 # continuous. historically taken [1, 39]
 
 SPECIFICATION = 39
+ENABLE_AGENT_PROMPT = True
 
 import importlib.metadata
 ver_string = importlib.metadata.version("exprmat")
 MAJOR, MINOR, REVISION = [int(x) for x in ver_string.split('.')]
 
-import os
-os.environ['OPENBLAS_NUM_THREADS'] = '1'
-os.environ['GOTO_NUM_THREADS'] = '1'
-os.environ['OMP_NUM_THREADS'] = '1'
+import os as _os
+_os.environ['OPENBLAS_NUM_THREADS'] = '1'
+_os.environ['GOTO_NUM_THREADS'] = '1'
+_os.environ['OMP_NUM_THREADS'] = '1'
 
 # public expose references
 import mudata as mu
@@ -21,8 +22,8 @@ import scanpy as sc
 import pandas as pd
 import numpy as np
 
-import pathlib
-from PIL import Image
+import pathlib as _pathlib
+from PIL import Image as _image
 
 # build cython package
 
@@ -43,14 +44,14 @@ except ImportError:
     # change to the project source directory
     # thus we can build the extension in the source directory.
     sys.argv = ['', 'build_ext', '--inplace']
-    cwd = os.getcwd()
-    os.chdir(os.path.dirname(__file__))
-    info(f'entering working directory: {os.getcwd()}')
+    cwd = _os.getcwd()
+    _os.chdir(_os.path.dirname(__file__))
+    info(f'entering working directory: {_os.getcwd()}')
 
     extensions = [
         Extension(
             'peaks.idr.invcdf',
-            [__file__.replace('__init__.py', os.path.join('peaks', 'idr', 'invcdf.pyx'))],
+            [__file__.replace('__init__.py', _os.path.join('peaks', 'idr', 'invcdf.pyx'))],
             include_dirs = [numpy.get_include()],
             define_macros = [('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')]
         )
@@ -62,9 +63,9 @@ except ImportError:
         ext_modules = cythonize(extensions, language_level = 3, quiet = True)
     )
 
-    os.chdir(cwd)
+    _os.chdir(cwd)
     # remove the autogenerated build directory. since we compile inplace.
-    os.system(f'rm -r {os.path.join(os.path.dirname(__file__), "build")}')
+    _os.system(f'rm -r {_os.path.join(_os.path.dirname(__file__), "build")}')
     info('compilation finished.')
 
 
@@ -74,7 +75,7 @@ from exprmat.ansi import warning, info
 config = configuration()
 
 mu.set_options(pull_on_update = False)
-Image.MAX_IMAGE_PIXELS = config['max.image']
+_image.MAX_IMAGE_PIXELS = config['max.image']
 
 DATABASE_SETUP_MESSAGE = """
 The exprmat package do not come with an included database after version 0.1.25, 
@@ -105,14 +106,14 @@ default_finders = [
     'exprmat.config',
     '.exprmat.config',
     '.exprmatrc',
-    os.path.join(str(pathlib.Path.home()), 'exprmat.config'),
-    os.path.join(str(pathlib.Path.home()), '.exprmat.config'),
-    os.path.join(str(pathlib.Path.home()), '.exprmatrc')
+    _os.path.join(str(_pathlib.Path.home()), 'exprmat.config'),
+    _os.path.join(str(_pathlib.Path.home()), '.exprmat.config'),
+    _os.path.join(str(_pathlib.Path.home()), '.exprmatrc')
 ]
 
 DEFAULT_CONFIG = '[internals]'
 for finder in default_finders:
-    if os.path.exists(finder):
+    if _os.path.exists(finder):
         DEFAULT_CONFIG = finder
         if False: info(f'load configuration from {finder}')
         with open(finder, 'r') as f:
@@ -124,21 +125,21 @@ for finder in default_finders:
 basepath = config['data']
 
 # core method exports
-from exprmat.utils import setup_styles, savefig
+from exprmat.utils import savefig
+from exprmat.utils import setup_styles as _setup_styles
 from exprmat.ansi import pprog, pproga, info, error, warning, default_logger, logger
 from exprmat.reader.experiment import experiment, load_experiment
 from exprmat.reader.metadata import metadata, load_metadata
-import exprmat.reader.static as st
 
 
-setup_styles()
+_setup_styles()
 
 
 def version_db():
     dbpath = config['data']
-    version_file = os.path.join(dbpath, '.bsync', 'current')
+    version_file = _os.path.join(dbpath, '.bsync', 'current')
 
-    if not os.path.exists(version_file): 
+    if not _os.path.exists(version_file): 
         db_ver = None
     else:
         with open(version_file, 'r') as vf:
@@ -207,25 +208,26 @@ def memory():
 
 def license(): print(LICENSE_MESSAGE)
 
-def view(fpath, cmd = 'less -S'): os.system(
-    cmd + ' "' + os.path.join(os.path.dirname(__file__), fpath) + '"'
+def view(fpath, cmd = 'less -S'): _os.system(
+    cmd + ' "' + _os.path.join(_os.path.dirname(__file__), fpath) + '"'
 )
     
-setwd = os.chdir
-getwd = os.getcwd
+setwd = _os.chdir
+getwd = _os.getcwd
 
+from .help import help
 
-import tqdm
+import tqdm as _tqdm
 # https://github.com/tqdm/tqdm/issues/457
-tqdm.tqdm(disable = True, total = 0)
+_tqdm.tqdm(disable = True, total = 0)
 
 
 # show version info after any install or update of the database.
 # this always synchronizes with the package update.
 
 try:
-    fd = os.open(os.path.join(basepath, '.license'), os.O_CREAT | os.O_EXCL | os.O_WRONLY)
-    with os.fdopen(fd, "w") as f: f.write(ver_string)
+    fd = _os.open(_os.path.join(basepath, '.license'), _os.O_CREAT | _os.O_EXCL | _os.O_WRONLY)
+    with _os.fdopen(fd, "w") as f: f.write(ver_string)
     license()
 
 except FileExistsError: 
@@ -237,7 +239,7 @@ __all__ = [
     'np', 'mu', 'ad', 'sc', 'pd',
     
     # exposed internal namespace
-    'st',
+    # 'st',
 
     # expose classes
     'experiment',
@@ -259,5 +261,6 @@ __all__ = [
     'savefig',
 
     # constants
-    'SPECIFICATION'
+    'SPECIFICATION',
+    'ENABLE_AGENT_PROMPT'
 ]

{exprmat-0.1.58 → exprmat-0.2.73}/exprmat/clustering/gating.py

@@ -6,10 +6,6 @@ from shapely import Point, Polygon
 def polygon_gate(
     adata, gene_x, gene_y, 
     layer = 'X',
-    
-    remove_zero_expression = False,
-    scale = 'asis', arcsinh_divider = None,
-
     polygon = [(0, 0), (1, 0), (1, 1), (0, 1)],
     key_added = 'gate'
 ):
@@ -33,26 +29,6 @@ def polygon_gate(
         'y': gy
     })
 
-    if remove_zero_expression:
-        df = df.loc[(df['x'] > 0) & (df['y'] > 0), :].copy()
-
-    if scale == 'asis': pass
-    elif scale == 'log':
-        df['x'] = np.log1p(df['x'])
-        df['y'] = np.log1p(df['y'])
-    elif scale == 'expm1':
-        df['x'] = np.expm1(df['x'])
-        df['y'] = np.expm1(df['y'])
-    elif scale == 'arcsinh':
-        lx = np.expm1(df['x']).loc[df['x'] > 0]
-        ly = np.expm1(df['y']).loc[df['x'] > 0]
-        df['x'] = np.arcsinh(np.expm1(df['x']) / (
-            arcsinh_divider if arcsinh_divider is not None 
-            else (np.median(lx) / 20)))
-        df['y'] = np.arcsinh(np.expm1(df['y']) / (
-            arcsinh_divider if arcsinh_divider is not None 
-            else (np.median(ly) / 20)))
-
     poly = Polygon(polygon)
     df['gate'] = [
         poly.contains(Point(x, y))

{exprmat-0.1.58 → exprmat-0.2.73}/exprmat/clustering/sc3.py

@@ -405,8 +405,15 @@ def consensus(
         random_state = random_state
     )
 
+    from exprmat.reader.introspect import fill_automatic_slots
+    from exprmat.reader.introspect import output_obs, output_uns
+    outputs = []
+
     # write the individual trials into AnnData object
-    adata.uns[f'{key_added}.trials'] = trials_dict
+    # adata.uns[f'{key_added}.trials'] = trials_dict
+    # outputs.append(output_uns(
+    #     ['sc3-trials'], f'{key_added}.trials', desc = 'Dictionary of individual clustering trials for SC3 consensus clustering'
+    # ))
 
     # run different number of clusters
     for K in n_clusters:
@@ -434,5 +441,9 @@ def consensus(
         # write results into AnnData object
         adata.obs[f'{key_added}.{K}'] = cell_labels
         adata.obs[f'{key_added}.{K}'] = adata.obs[f'{key_added}.{K}'].astype('str').astype('category')
+        outputs.append(output_obs(
+            ['category'], f'{key_added}.{K}', desc = f'SC3 clustering, K = {K}'
+        ))
 
+    fill_automatic_slots(adata, manual = outputs)
     return adata

exprmat-0.2.73/exprmat/deconv/__init__.py

@@ -0,0 +1,5 @@
+"""
+exprmat.deconv - cell-type deconvolution and cell-to-spot mapping methods.
+"""
+
+from . import tangram

exprmat-0.2.73/exprmat/deconv/tangram/__init__.py

@@ -0,0 +1,36 @@
+"""
+tangram - mapping single-cell expression onto spatial transcriptomics. ported
+from https://github.com/broadinstitute/Tangram.
+
+the upstream gene-selection / highly-variable-gene helpers and plotting
+modules are not ported here; users are expected to supply their own training
+gene list (or rely on the intersection of shared genes computed by
+`pp_adatas`).
+"""
+
+from .mapping import (
+    pp_adatas,
+    adata_to_cluster_expression,
+    map_cells_to_space,
+)
+from .utils import (
+    annotate_gene_sparsity,
+    one_hot_encoding,
+    project_cell_annotations,
+    project_genes,
+)
+from .spatial import spatial_weights
+from .optimizer import mapper, mapper_constrained
+
+__all__ = [
+    'pp_adatas',
+    'adata_to_cluster_expression',
+    'map_cells_to_space',
+    'annotate_gene_sparsity',
+    'one_hot_encoding',
+    'project_cell_annotations',
+    'project_genes',
+    'spatial_weights',
+    'mapper',
+    'mapper_constrained',
+]