sclab 0.1.7__py3-none-any.whl → 0.2.2__py3-none-any.whl

{sclab-0.1.7.dist-info → sclab-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: sclab
-Version: 0.1.7
+Version: 0.2.2
 Summary: sclab
 Author-email: Argenis Arriojas <ArriojasMaldonado001@umb.edu>
 Requires-Python: >=3.10,<3.13
@@ -10,23 +10,28 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+License-File: LICENSE
 Requires-Dist: anndata
 Requires-Dist: anywidget
 Requires-Dist: ipywidgets
 Requires-Dist: itables
 Requires-Dist: numpy<2.2
 Requires-Dist: pandas
-Requires-Dist: plotly
-Requires-Dist: scanpy
+Requires-Dist: plotly<6.0
+Requires-Dist: requests>=2.32.3
 Requires-Dist: scikit-learn
-Requires-Dist: scikit-misc
 Requires-Dist: svgpathtools
+Requires-Dist: tqdm>=4.67.1
+Requires-Dist: jupyterlab>=4.3.6 ; extra == "jupyter"
+Requires-Dist: scanpy[leiden, skmisc]>=1.10 ; extra == "scanpy"
 Requires-Dist: pytest>=8.3.4 ; extra == "test"
 Project-URL: Bug Tracker, https://github.com/umbibio/sclab/issues
 Project-URL: Changelog, https://github.com/umbibio/sclab/blob/main/CHANGELOG.md
 Project-URL: Documentation, https://github.com/umbibio/sclab/docs
 Project-URL: Homepage, https://github.com/umbibio/sclab
 Project-URL: Repository, https://github.com/umbibio/sclab.git
+Provides-Extra: jupyter
+Provides-Extra: scanpy
 Provides-Extra: test
 
 # SCLab
@@ -53,23 +58,29 @@ pip install sclab
 Open a Jupyter Notebook and run the following:
 
 ```python
+from IPython.display import display
 from sclab import SCLabDashboard
+from sclab.examples.processor_steps import QC, Preprocess, PCA, Neighbors, UMAP, Cluster
 import scanpy as sc
-from IPython.display import display
 
 # Load your data
 adata = sc.read_10x_h5("your_data.h5")
 
 # Create dashboard
 dashboard = SCLabDashboard(adata, name="My Analysis")
+# Add desired processing steps to the interface
+dashboard.pr.add_steps({"Processing": [QC, Preprocess, PCA, Neighbors, UMAP, Cluster]})
 
 # Display dashboard
 display(dashboard)
 
 # The dashboard provides easy access to components:
-dashboard.ds  # Dataset (wrapper for AnnData)
-dashboard.pl  # Plotter
-dashboard.pr  # Processor
+# dashboard.ds  # Dataset (wrapper for AnnData)
+# dashboard.pl  # Plotter
+# dashboard.pr  # Processor
+
+# the resulting AnnData object is found within the dataset object:
+# dashboard.ds.adata
 ```
 
 ## Components
@@ -129,10 +140,10 @@ This project is licensed under the BSD 3-Clause License - see the [LICENSE](LICE
 If you use SCLab in your research, please cite:
 
 ```bibtex
-@software{sclab2024,
+@software{sclab2025,
   author = {Arriojas, Argenis},
   title = {SCLab: Interactive Single-Cell Analysis Toolkit},
-  year = {2024},
+  year = {2025},
   publisher = {GitHub},
   url = {https://github.com/umbibio/sclab}
 }

sclab-0.2.2.dist-info/RECORD

@@ -0,0 +1,42 @@
+sclab/__init__.py,sha256=UaTIrqZIaNx_mwX7RPdk93mDBq1fkZaElCiMA-bvBIM,132
+sclab/_io.py,sha256=21EHrUvYV8WFRbBcdeuWXbApUIITHaXbqgDI8lqQgHo,2852
+sclab/_methods_registry.py,sha256=RcffyRuuLzHqsnAdbBL4W1GmZx80d9AxdGjUnx1mbNg,1704
+sclab/_sclab.py,sha256=Fq-GrhapzziTzJgkpPjdjYtjeQpBeXWYVUbPY6axg-A,8688
+sclab/dataset/__init__.py,sha256=f9PoXIMAPnC3Var1ODr3mXkotW6u6NRPQvlgcWYXk54,143
+sclab/dataset/_dataset.py,sha256=dJeiEfo-f6eM866-d53H6FUF9IR-OK4vwDojSq_og0Q,14248
+sclab/dataset/_exceptions.py,sha256=g8RJL8PiRmD4--PkOs5CZth_qeaduvieMlKJNkrUIYA,45
+sclab/dataset/plotter/__init__.py,sha256=pdWhAywnoc1_nnIcD-qNW0U364-yo4k5DwP79y9NVgA,129
+sclab/dataset/plotter/_controls.py,sha256=NBDdtY1wQbIEvE_WToigR5bEEoi3z30_67T_dLSOSIo,20295
+sclab/dataset/plotter/_plotter.py,sha256=EXwk6KSM7FOyLLJ8HCgIB_2m730t0kHsVKWfQOxL6kA,37023
+sclab/dataset/plotter/_utils.py,sha256=ANm_R9PJd33-QJtZzqXCN5pJ_XrJ7AA4AvSHaDRbOMA,11595
+sclab/dataset/processor/__init__.py,sha256=v8Qbusb6h8oSndv9q-12vzHrz5BDF3N2LCkQG9KC19I,104
+sclab/dataset/processor/_processor.py,sha256=H8smeuHPnJVToSxEgGNHUpyNwKYqP-Itp5jMVIgnjbc,41104
+sclab/dataset/processor/_results_panel.py,sha256=p2xmHgoYfpkPXj-SjRGTmAPAwL1VC8I70iFD_o-90AE,2342
+sclab/dataset/processor/step/__init__.py,sha256=j8j4oU9NMdWHn6kVjft7Klm6xme8M6wzebxJj_zNehg,179
+sclab/dataset/processor/step/_basic_processor_step.py,sha256=7NKC4W-I_EU3QBPi5BL9-NwAF_h6_oWl1l_kEk6gSAg,3640
+sclab/dataset/processor/step/_processor_step_base.py,sha256=DpbL4F53W1YPI_xHuQ0T3gcvDGwwKG2Xp-n8DkMUf90,4133
+sclab/event/__init__.py,sha256=unkfpmoxitPVZvWcc9YhkUwcXODdcd9cw_toVXVIDMU,126
+sclab/event/_broker.py,sha256=W4GgoBhJS1LxGQv8TYFg71o5jUQPO8BDLrKzahDUyEM,7121
+sclab/event/_client.py,sha256=Kx7pza-CzLySR0JBBneiZQAjtllUnjWKNKSfw3K2ZQE,2362
+sclab/event/_utils.py,sha256=LehiFhn7dopNEaTFERJhs6fiVgXCBvseRxWTSWc6u-k,456
+sclab/examples/__init__.py,sha256=uSu4DMfF2K7xlZbLC_CmANyS3D56khGLMSVt6x9XXiI,68
+sclab/examples/processor_steps/__init__.py,sha256=KhbgN0-WrIhpgDZhWJOHr2Vxo0FB1ZBvM2bJK2Mjdmg,372
+sclab/examples/processor_steps/_cluster.py,sha256=olbri3HWPBU8p__r9kP9tgWaJoUJ2bK48pmHfdvf11c,1120
+sclab/examples/processor_steps/_differential_expression.py,sha256=uEToPiACCgo42oZidAw5DFgWVcDnChWzVRlVzn53K34,11567
+sclab/examples/processor_steps/_neighbors.py,sha256=sEhLuuY-dCdwzqIarHpFVgM4tE1bW9Qa18xHOWA84Bk,2206
+sclab/examples/processor_steps/_pca.py,sha256=vit15FqHhWC-VSLSViduFt9V7dwakVvdnDOHxzJHiw0,4585
+sclab/examples/processor_steps/_preprocess.py,sha256=ffg8Vh-rSJPna08__xOlizu65QBBkRPinslnKRaRjbk,6336
+sclab/examples/processor_steps/_qc.py,sha256=KPWKxytu5YLXQ42uXe3ARKE36jqj5uidLhtyR-_TVBY,3238
+sclab/examples/processor_steps/_umap.py,sha256=Mzxj4LiZfh3WT5lS_BO_lTleC5jMoUm5_km_gvzU_I8,1402
+sclab/methods/__init__.py,sha256=FMxCemY8-TFHl-BUR6NNDUyOGAAGEhysIlXkSBQXV8g,646
+sclab/scanpy/_compat.py,sha256=VEdW4lWLtKmgLSrikRnfvYOz9EOa7e_iDt4Q88X9JKQ,2109
+sclab/scanpy/_settings.py,sha256=UVcJExVHsf_nvyZ5kTrBHPkddHCz7ARCzqAdZAM_A5E,16736
+sclab/scanpy/logging.py,sha256=VwSPeKjpXeopdcgEAlWDz2Wv4IGAAUv8GyMNpMART-0,8453
+sclab/scanpy/readwrite.py,sha256=yixHonShUZ2Ms3Sv3UXw_VXlY00XDApvmyN2mZWFAcs,37025
+sclab/scanpy/plotting/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sclab/scanpy/plotting/_rcmod.py,sha256=pc53dasHh2RFfTHVTbTb8v1z8vW032zjvum-WQLgjXA,1970
+sclab/scanpy/plotting/palettes.py,sha256=zHTM_CVfKazb32YreRx0-INllFssZP5rY_B7JTeaBhA,4782
+sclab-0.2.2.dist-info/licenses/LICENSE,sha256=LO7qldZoHIo9hc-HMBqclBh5800kZ9US9xTbLAQdHpg,1523
+sclab-0.2.2.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+sclab-0.2.2.dist-info/METADATA,sha256=GciGoDxIh9rPs3KVDs8EQqGq3fP_HfSxQxH4zBOuYVg,4289
+sclab-0.2.2.dist-info/RECORD,,

{sclab-0.1.7.dist-info → sclab-0.2.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: flit 3.10.1
+Generator: flit 3.12.0
 Root-Is-Purelib: true
 Tag: py3-none-any

sclab-0.2.2.dist-info/licenses/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2025 Argenis Arriojas
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

sclab-0.1.7.dist-info/RECORD

@@ -1,30 +0,0 @@
-sclab/__init__.py,sha256=0RUdbuZt9XoQgNmLnMCR4-LYIXnwXUgNyuLEL1Gu9Ms,95
-sclab/_io.py,sha256=mVazSViXfKpfY1iUNZXgQc1hutu6MXTaGZXF4rcqKLE,875
-sclab/_sclab.py,sha256=Eln0nWlnFpnDabW94UK8qOdxIys9FWSyqsm8lvlnk4A,2156
-sclab/dataset/__init__.py,sha256=f9PoXIMAPnC3Var1ODr3mXkotW6u6NRPQvlgcWYXk54,143
-sclab/dataset/_dataset.py,sha256=51E8iwiUFxFBvka8EsCuZrc-nfNxHcB4iEAy_Ja5qPg,14409
-sclab/dataset/_exceptions.py,sha256=g8RJL8PiRmD4--PkOs5CZth_qeaduvieMlKJNkrUIYA,45
-sclab/dataset/plotter/__init__.py,sha256=pdWhAywnoc1_nnIcD-qNW0U364-yo4k5DwP79y9NVgA,129
-sclab/dataset/plotter/_controls.py,sha256=NBDdtY1wQbIEvE_WToigR5bEEoi3z30_67T_dLSOSIo,20295
-sclab/dataset/plotter/_plotter.py,sha256=EXwk6KSM7FOyLLJ8HCgIB_2m730t0kHsVKWfQOxL6kA,37023
-sclab/dataset/plotter/_utils.py,sha256=ANm_R9PJd33-QJtZzqXCN5pJ_XrJ7AA4AvSHaDRbOMA,11595
-sclab/dataset/processor/__init__.py,sha256=v8Qbusb6h8oSndv9q-12vzHrz5BDF3N2LCkQG9KC19I,104
-sclab/dataset/processor/_processor.py,sha256=bvDdjcZDD7ighP-wvmebh4Tuc_-HyFT9KP8bFOB4POY,40811
-sclab/dataset/processor/step/__init__.py,sha256=j8j4oU9NMdWHn6kVjft7Klm6xme8M6wzebxJj_zNehg,179
-sclab/dataset/processor/step/_basic_processor_step.py,sha256=7NKC4W-I_EU3QBPi5BL9-NwAF_h6_oWl1l_kEk6gSAg,3640
-sclab/dataset/processor/step/_processor_step_base.py,sha256=Yk8nCDu4atk-txJcEEC6kravzP6FDBjcrdh6kNyZjdM,3909
-sclab/event/__init__.py,sha256=unkfpmoxitPVZvWcc9YhkUwcXODdcd9cw_toVXVIDMU,126
-sclab/event/_broker.py,sha256=W4GgoBhJS1LxGQv8TYFg71o5jUQPO8BDLrKzahDUyEM,7121
-sclab/event/_client.py,sha256=Kx7pza-CzLySR0JBBneiZQAjtllUnjWKNKSfw3K2ZQE,2362
-sclab/event/_utils.py,sha256=LehiFhn7dopNEaTFERJhs6fiVgXCBvseRxWTSWc6u-k,456
-sclab/examples/__init__.py,sha256=uSu4DMfF2K7xlZbLC_CmANyS3D56khGLMSVt6x9XXiI,68
-sclab/examples/processor_steps/__init__.py,sha256=tm2YWKIkBPcBoHp4VS78tLyQX44Y7zUj2dgzFH058DA,279
-sclab/examples/processor_steps/_cluster.py,sha256=fXI8J_ae8ZXjckmCff3WfwSa9HTdQmEDYQ3vTilmV9k,1124
-sclab/examples/processor_steps/_neighbors.py,sha256=-FxRBi5Uaywrn2fXnlgmwtQrTefPPdnfOuI6RhKw314,2210
-sclab/examples/processor_steps/_pca.py,sha256=XKEau9MtHr0LBDFTc9Y3QUQRv5fvNyKT8KeFujepypc,4589
-sclab/examples/processor_steps/_preprocess.py,sha256=ftuWt9asef_a5OU195UazfI34MjA82nE1LWTPjhXPPY,6340
-sclab/examples/processor_steps/_qc.py,sha256=VPiyY7o7YM8v6hetjxrSfnrn_fJhuC5EzeMi1bSUsw0,3242
-sclab/examples/processor_steps/_umap.py,sha256=Geyme_biIHxGE7zD8dsECUfQy31ff-w1BrAN55BW5Ug,1406
-sclab-0.1.7.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
-sclab-0.1.7.dist-info/METADATA,sha256=UTX_EmyQXRn0F2r69fnTKwju9H3PnMExTN08LuTfCkI,3767
-sclab-0.1.7.dist-info/RECORD,,