exprmat 0.1.50__tar.gz → 0.1.52__tar.gz

{exprmat-0.1.50 → exprmat-0.1.52}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.50
+Version: 0.1.52
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -101,7 +101,7 @@ Provides-Extra: cuda12
 License-File: license
 Summary: exprmat: Routines for expression matrices
 Author-email: Zheng Yang <xornent@outlook.com>
-Requires-Python: >=3.10, <3.13
+Requires-Python: >=3.10, <3.14
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 Project-URL: Repository, https://github.com/yang-z-03/exprmat
 
@@ -167,3 +167,115 @@ bsync-fetch --id <your-id> --secret <your-api-secret> \
 The authentication tokens passed to `--id` and `--secret` is provided by the
 Alibaba Cloud service (See the [Documentation](https://help.aliyun.com/zh/ram/user-guide/create-an-accesskey-pair)
 for details)
+
+### Licensing
+
+The original part of the source code is licensed under GNU GPLv3.
+The database download tool bsync-fetch (developed as a dependency package for
+exprmat, in python package `bincsync`) is only allowed for internal use and not
+for re-distribution.
+
+```
+exprmat - Routines to manipulate expression matrices
+Copyright (C) 2025 - 2026 Zheng Yang (杨政) <xornent@outlook.com>
+
+exprmat is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions. 
+You should have received a copy of the GNU General Public License
+version 3 along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+The GNU General Public License does not permit incorporating 
+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
+
+```
+

{exprmat-0.1.50 → exprmat-0.1.52}/exprmat/__init__.py

@@ -112,7 +112,7 @@ basepath = config['data']
 
 # core method exports
 from exprmat.utils import setup_styles, savefig
-from exprmat.ansi import pprog, pproga, info, error, warning
+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

{exprmat-0.1.50 → exprmat-0.1.52}/exprmat/ansi.py

@@ -7,7 +7,48 @@ from functools import partial
 from tqdm import tqdm
 from tqdm.auto import tqdm as tqdma
 
-SILENT = False
+
+class logger:
+
+    silent = False
+
+    def __init__(self, silent: bool = False) -> None:
+        self.silent = silent
+    
+    def error(self, text: str, error = None) -> None:
+
+        if self.silent: 
+            if error: raise Exception(text) from error
+            else: raise Exception(text)
+
+        fore_red()
+        print('[error]', end = ' ')
+        ansi_reset()
+        print(text)
+
+        if error is None: raise Exception(text)
+        else: raise Exception(text) from error
+
+
+    def warning(self, text: str) -> None:
+        if self.silent: return
+        fore_yellow()
+        print('[!]', end = ' ')
+        ansi_reset()
+        print(text)
+        ansi_reset()
+
+
+    def info(self, text: str) -> None:
+        if self.silent: return
+        fore_cyan()
+        print('[i]', end = ' ')
+        ansi_reset()
+        print(text)
+        ansi_reset()
+
+
+default_logger = logger()
 
 
 def fore_black() -> None:
@@ -114,32 +155,15 @@ 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()
-    print(text)
-
-    if error is None: raise Exception(text)
-    else: raise Exception(text) from error
+    default_logger.error(text, error)
 
 
 def warning(text: str) -> None:
-    if SILENT: return
-    fore_yellow()
-    print('[!]', end = ' ')
-    ansi_reset()
-    print(text)
-    ansi_reset()
+    default_logger.warning(text)
 
 
 def info(text: str) -> None:
-    if SILENT: return
-    fore_cyan()
-    print('[i]', end = ' ')
-    ansi_reset()
-    print(text)
-    ansi_reset()
+    default_logger.info(text)
 
 
 def clear():