sclab 0.1.8__py3-none-any.whl → 0.2.2__py3-none-any.whl

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Files changed (29) hide show
  1. sclab/__init__.py +3 -1
  2. sclab/_io.py +89 -12
  3. sclab/_methods_registry.py +65 -0
  4. sclab/_sclab.py +229 -21
  5. sclab/dataset/_dataset.py +2 -4
  6. sclab/dataset/processor/_processor.py +22 -15
  7. sclab/dataset/processor/_results_panel.py +80 -0
  8. sclab/dataset/processor/step/_processor_step_base.py +12 -6
  9. sclab/examples/processor_steps/__init__.py +2 -0
  10. sclab/examples/processor_steps/_cluster.py +2 -2
  11. sclab/examples/processor_steps/_differential_expression.py +328 -0
  12. sclab/examples/processor_steps/_neighbors.py +2 -2
  13. sclab/examples/processor_steps/_pca.py +2 -2
  14. sclab/examples/processor_steps/_preprocess.py +2 -2
  15. sclab/examples/processor_steps/_qc.py +2 -2
  16. sclab/examples/processor_steps/_umap.py +2 -2
  17. sclab/methods/__init__.py +28 -0
  18. sclab/scanpy/_compat.py +92 -0
  19. sclab/scanpy/_settings.py +526 -0
  20. sclab/scanpy/logging.py +290 -0
  21. sclab/scanpy/plotting/__init__.py +0 -0
  22. sclab/scanpy/plotting/_rcmod.py +73 -0
  23. sclab/scanpy/plotting/palettes.py +221 -0
  24. sclab/scanpy/readwrite.py +1108 -0
  25. {sclab-0.1.8.dist-info → sclab-0.2.2.dist-info}/METADATA +9 -4
  26. sclab-0.2.2.dist-info/RECORD +42 -0
  27. {sclab-0.1.8.dist-info → sclab-0.2.2.dist-info}/WHEEL +1 -1
  28. sclab-0.2.2.dist-info/licenses/LICENSE +29 -0
  29. sclab-0.1.8.dist-info/RECORD +0 -30
{sclab-0.1.8.dist-info → sclab-0.2.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.3
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+ Metadata-Version: 2.4
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  Name: sclab
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- Version: 0.1.8
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+ Version: 0.2.2
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  Summary: sclab
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  Author-email: Argenis Arriojas <ArriojasMaldonado001@umb.edu>
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  Requires-Python: >=3.10,<3.13
@@ -10,6 +10,7 @@ Classifier: Programming Language :: Python :: 3
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  Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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+ License-File: LICENSE
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  Requires-Dist: anndata
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  Requires-Dist: anywidget
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  Requires-Dist: ipywidgets
@@ -17,16 +18,20 @@ Requires-Dist: itables
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  Requires-Dist: numpy<2.2
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  Requires-Dist: pandas
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  Requires-Dist: plotly<6.0
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- Requires-Dist: scanpy
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+ Requires-Dist: requests>=2.32.3
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  Requires-Dist: scikit-learn
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- Requires-Dist: scikit-misc
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  Requires-Dist: svgpathtools
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+ Requires-Dist: tqdm>=4.67.1
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+ Requires-Dist: jupyterlab>=4.3.6 ; extra == "jupyter"
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+ Requires-Dist: scanpy[leiden, skmisc]>=1.10 ; extra == "scanpy"
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  Requires-Dist: pytest>=8.3.4 ; extra == "test"
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  Project-URL: Bug Tracker, https://github.com/umbibio/sclab/issues
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  Project-URL: Changelog, https://github.com/umbibio/sclab/blob/main/CHANGELOG.md
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  Project-URL: Documentation, https://github.com/umbibio/sclab/docs
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  Project-URL: Homepage, https://github.com/umbibio/sclab
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  Project-URL: Repository, https://github.com/umbibio/sclab.git
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+ Provides-Extra: jupyter
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+ Provides-Extra: scanpy
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  Provides-Extra: test
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  # SCLab
sclab-0.2.2.dist-info/RECORD ADDED
@@ -0,0 +1,42 @@
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+ sclab/__init__.py,sha256=UaTIrqZIaNx_mwX7RPdk93mDBq1fkZaElCiMA-bvBIM,132
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+ sclab/_io.py,sha256=21EHrUvYV8WFRbBcdeuWXbApUIITHaXbqgDI8lqQgHo,2852
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+ sclab/_methods_registry.py,sha256=RcffyRuuLzHqsnAdbBL4W1GmZx80d9AxdGjUnx1mbNg,1704
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+ sclab/_sclab.py,sha256=Fq-GrhapzziTzJgkpPjdjYtjeQpBeXWYVUbPY6axg-A,8688
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+ sclab/dataset/__init__.py,sha256=f9PoXIMAPnC3Var1ODr3mXkotW6u6NRPQvlgcWYXk54,143
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+ sclab/dataset/_dataset.py,sha256=dJeiEfo-f6eM866-d53H6FUF9IR-OK4vwDojSq_og0Q,14248
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+ sclab/dataset/_exceptions.py,sha256=g8RJL8PiRmD4--PkOs5CZth_qeaduvieMlKJNkrUIYA,45
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+ sclab/dataset/plotter/__init__.py,sha256=pdWhAywnoc1_nnIcD-qNW0U364-yo4k5DwP79y9NVgA,129
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+ sclab/dataset/plotter/_controls.py,sha256=NBDdtY1wQbIEvE_WToigR5bEEoi3z30_67T_dLSOSIo,20295
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+ sclab/dataset/plotter/_plotter.py,sha256=EXwk6KSM7FOyLLJ8HCgIB_2m730t0kHsVKWfQOxL6kA,37023
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+ sclab/dataset/plotter/_utils.py,sha256=ANm_R9PJd33-QJtZzqXCN5pJ_XrJ7AA4AvSHaDRbOMA,11595
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+ sclab/dataset/processor/__init__.py,sha256=v8Qbusb6h8oSndv9q-12vzHrz5BDF3N2LCkQG9KC19I,104
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+ sclab/dataset/processor/_processor.py,sha256=H8smeuHPnJVToSxEgGNHUpyNwKYqP-Itp5jMVIgnjbc,41104
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+ sclab/dataset/processor/_results_panel.py,sha256=p2xmHgoYfpkPXj-SjRGTmAPAwL1VC8I70iFD_o-90AE,2342
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+ sclab/dataset/processor/step/__init__.py,sha256=j8j4oU9NMdWHn6kVjft7Klm6xme8M6wzebxJj_zNehg,179
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+ sclab/dataset/processor/step/_basic_processor_step.py,sha256=7NKC4W-I_EU3QBPi5BL9-NwAF_h6_oWl1l_kEk6gSAg,3640
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+ sclab/dataset/processor/step/_processor_step_base.py,sha256=DpbL4F53W1YPI_xHuQ0T3gcvDGwwKG2Xp-n8DkMUf90,4133
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+ sclab/event/__init__.py,sha256=unkfpmoxitPVZvWcc9YhkUwcXODdcd9cw_toVXVIDMU,126
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+ sclab/event/_broker.py,sha256=W4GgoBhJS1LxGQv8TYFg71o5jUQPO8BDLrKzahDUyEM,7121
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+ sclab/event/_client.py,sha256=Kx7pza-CzLySR0JBBneiZQAjtllUnjWKNKSfw3K2ZQE,2362
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+ sclab/event/_utils.py,sha256=LehiFhn7dopNEaTFERJhs6fiVgXCBvseRxWTSWc6u-k,456
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+ sclab/examples/__init__.py,sha256=uSu4DMfF2K7xlZbLC_CmANyS3D56khGLMSVt6x9XXiI,68
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+ sclab/examples/processor_steps/__init__.py,sha256=KhbgN0-WrIhpgDZhWJOHr2Vxo0FB1ZBvM2bJK2Mjdmg,372
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+ sclab/examples/processor_steps/_cluster.py,sha256=olbri3HWPBU8p__r9kP9tgWaJoUJ2bK48pmHfdvf11c,1120
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+ sclab/examples/processor_steps/_differential_expression.py,sha256=uEToPiACCgo42oZidAw5DFgWVcDnChWzVRlVzn53K34,11567
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+ sclab/examples/processor_steps/_neighbors.py,sha256=sEhLuuY-dCdwzqIarHpFVgM4tE1bW9Qa18xHOWA84Bk,2206
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+ sclab/examples/processor_steps/_pca.py,sha256=vit15FqHhWC-VSLSViduFt9V7dwakVvdnDOHxzJHiw0,4585
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+ sclab/examples/processor_steps/_preprocess.py,sha256=ffg8Vh-rSJPna08__xOlizu65QBBkRPinslnKRaRjbk,6336
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+ sclab/examples/processor_steps/_qc.py,sha256=KPWKxytu5YLXQ42uXe3ARKE36jqj5uidLhtyR-_TVBY,3238
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+ sclab/examples/processor_steps/_umap.py,sha256=Mzxj4LiZfh3WT5lS_BO_lTleC5jMoUm5_km_gvzU_I8,1402
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+ sclab/methods/__init__.py,sha256=FMxCemY8-TFHl-BUR6NNDUyOGAAGEhysIlXkSBQXV8g,646
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+ sclab/scanpy/_compat.py,sha256=VEdW4lWLtKmgLSrikRnfvYOz9EOa7e_iDt4Q88X9JKQ,2109
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+ sclab/scanpy/_settings.py,sha256=UVcJExVHsf_nvyZ5kTrBHPkddHCz7ARCzqAdZAM_A5E,16736
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+ sclab/scanpy/logging.py,sha256=VwSPeKjpXeopdcgEAlWDz2Wv4IGAAUv8GyMNpMART-0,8453
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+ sclab/scanpy/readwrite.py,sha256=yixHonShUZ2Ms3Sv3UXw_VXlY00XDApvmyN2mZWFAcs,37025
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+ sclab/scanpy/plotting/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ sclab/scanpy/plotting/_rcmod.py,sha256=pc53dasHh2RFfTHVTbTb8v1z8vW032zjvum-WQLgjXA,1970
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+ sclab/scanpy/plotting/palettes.py,sha256=zHTM_CVfKazb32YreRx0-INllFssZP5rY_B7JTeaBhA,4782
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+ sclab-0.2.2.dist-info/licenses/LICENSE,sha256=LO7qldZoHIo9hc-HMBqclBh5800kZ9US9xTbLAQdHpg,1523
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+ sclab-0.2.2.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
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+ sclab-0.2.2.dist-info/METADATA,sha256=GciGoDxIh9rPs3KVDs8EQqGq3fP_HfSxQxH4zBOuYVg,4289
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+ sclab-0.2.2.dist-info/RECORD,,
{sclab-0.1.8.dist-info → sclab-0.2.2.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: flit 3.10.1
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+ Generator: flit 3.12.0
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  Root-Is-Purelib: true
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  Tag: py3-none-any
sclab-0.2.2.dist-info/licenses/LICENSE ADDED
@@ -0,0 +1,29 @@
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+ BSD 3-Clause License
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+
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+ Copyright (c) 2025 Argenis Arriojas
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+ All rights reserved.
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+
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+ Redistribution and use in source and binary forms, with or without
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+ modification, are permitted provided that the following conditions are met:
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+
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+ 1. Redistributions of source code must retain the above copyright notice, this
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+ list of conditions and the following disclaimer.
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+
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+ 2. Redistributions in binary form must reproduce the above copyright notice,
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+ this list of conditions and the following disclaimer in the documentation
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+ and/or other materials provided with the distribution.
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+
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+ 3. Neither the name of the copyright holder nor the names of its
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+ contributors may be used to endorse or promote products derived from
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+ this software without specific prior written permission.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
sclab-0.1.8.dist-info/RECORD DELETED
@@ -1,30 +0,0 @@
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- sclab/__init__.py,sha256=zrh5eCnp4YNbD2Y1-vTwnl4_9MIGLJ0HRsTZKI4inrM,95
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- sclab/_io.py,sha256=mVazSViXfKpfY1iUNZXgQc1hutu6MXTaGZXF4rcqKLE,875
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- sclab/_sclab.py,sha256=Eln0nWlnFpnDabW94UK8qOdxIys9FWSyqsm8lvlnk4A,2156
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- sclab/dataset/__init__.py,sha256=f9PoXIMAPnC3Var1ODr3mXkotW6u6NRPQvlgcWYXk54,143
5
- sclab/dataset/_dataset.py,sha256=rYzYxsUdlzaLYpvrvgxWuMxbM47_GjvCLAmHehUxhIc,14410
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- sclab/dataset/_exceptions.py,sha256=g8RJL8PiRmD4--PkOs5CZth_qeaduvieMlKJNkrUIYA,45
7
- sclab/dataset/plotter/__init__.py,sha256=pdWhAywnoc1_nnIcD-qNW0U364-yo4k5DwP79y9NVgA,129
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- sclab/dataset/plotter/_controls.py,sha256=NBDdtY1wQbIEvE_WToigR5bEEoi3z30_67T_dLSOSIo,20295
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- sclab/dataset/plotter/_plotter.py,sha256=EXwk6KSM7FOyLLJ8HCgIB_2m730t0kHsVKWfQOxL6kA,37023
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- sclab/dataset/plotter/_utils.py,sha256=ANm_R9PJd33-QJtZzqXCN5pJ_XrJ7AA4AvSHaDRbOMA,11595
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- sclab/dataset/processor/__init__.py,sha256=v8Qbusb6h8oSndv9q-12vzHrz5BDF3N2LCkQG9KC19I,104
12
- sclab/dataset/processor/_processor.py,sha256=bvDdjcZDD7ighP-wvmebh4Tuc_-HyFT9KP8bFOB4POY,40811
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- sclab/dataset/processor/step/__init__.py,sha256=j8j4oU9NMdWHn6kVjft7Klm6xme8M6wzebxJj_zNehg,179
14
- sclab/dataset/processor/step/_basic_processor_step.py,sha256=7NKC4W-I_EU3QBPi5BL9-NwAF_h6_oWl1l_kEk6gSAg,3640
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- sclab/dataset/processor/step/_processor_step_base.py,sha256=Yk8nCDu4atk-txJcEEC6kravzP6FDBjcrdh6kNyZjdM,3909
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- sclab/event/__init__.py,sha256=unkfpmoxitPVZvWcc9YhkUwcXODdcd9cw_toVXVIDMU,126
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- sclab/event/_broker.py,sha256=W4GgoBhJS1LxGQv8TYFg71o5jUQPO8BDLrKzahDUyEM,7121
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- sclab/event/_client.py,sha256=Kx7pza-CzLySR0JBBneiZQAjtllUnjWKNKSfw3K2ZQE,2362
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- sclab/event/_utils.py,sha256=LehiFhn7dopNEaTFERJhs6fiVgXCBvseRxWTSWc6u-k,456
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- sclab/examples/__init__.py,sha256=uSu4DMfF2K7xlZbLC_CmANyS3D56khGLMSVt6x9XXiI,68
21
- sclab/examples/processor_steps/__init__.py,sha256=tm2YWKIkBPcBoHp4VS78tLyQX44Y7zUj2dgzFH058DA,279
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- sclab/examples/processor_steps/_cluster.py,sha256=fXI8J_ae8ZXjckmCff3WfwSa9HTdQmEDYQ3vTilmV9k,1124
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- sclab/examples/processor_steps/_neighbors.py,sha256=-FxRBi5Uaywrn2fXnlgmwtQrTefPPdnfOuI6RhKw314,2210
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- sclab/examples/processor_steps/_pca.py,sha256=XKEau9MtHr0LBDFTc9Y3QUQRv5fvNyKT8KeFujepypc,4589
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- sclab/examples/processor_steps/_preprocess.py,sha256=ftuWt9asef_a5OU195UazfI34MjA82nE1LWTPjhXPPY,6340
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- sclab/examples/processor_steps/_qc.py,sha256=VPiyY7o7YM8v6hetjxrSfnrn_fJhuC5EzeMi1bSUsw0,3242
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- sclab/examples/processor_steps/_umap.py,sha256=Geyme_biIHxGE7zD8dsECUfQy31ff-w1BrAN55BW5Ug,1406
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- sclab-0.1.8.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
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- sclab-0.1.8.dist-info/METADATA,sha256=_vCAnf3Q-CTe-Q9oXPbf7X_vUQbYYqb2dP9tkmTlokc,4091
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- sclab-0.1.8.dist-info/RECORD,,