small-fish-gui 2.0.3__py3-none-any.whl → 2.1.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (16) hide show
  1. small_fish_gui/__init__.py +1 -1
  2. small_fish_gui/batch/prompt.py +1 -1
  3. small_fish_gui/batch/values.txt +65 -0
  4. small_fish_gui/gui/_napari_widgets.py +18 -6
  5. small_fish_gui/gui/layout.py +10 -10
  6. small_fish_gui/gui/napari_visualiser.py +39 -16
  7. small_fish_gui/interface/settings.json +3 -3
  8. small_fish_gui/pipeline/detection.py +1 -1
  9. small_fish_gui/pipeline/segmentation.py +1 -1
  10. small_fish_gui/pipeline/testing.ipynb +3636 -0
  11. small_fish_gui/small_fish_gui.code-workspace +7 -0
  12. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.1.dist-info}/METADATA +18 -9
  13. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.1.dist-info}/RECORD +15 -13
  14. small_fish_gui/interface/testing.ipynb +0 -4354
  15. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.1.dist-info}/WHEEL +0 -0
  16. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.1.dist-info}/licenses/LICENSE +0 -0
small_fish_gui/small_fish_gui.code-workspace ADDED
@@ -0,0 +1,7 @@
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+ {
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+ "folders": [
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+ {
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+ "path": "src/small_fish_gui"
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+ }
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+ ]
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+ }
{small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.1.dist-info}/METADATA RENAMED
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  Metadata-Version: 2.4
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  Name: small_fish_gui
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- Version: 2.0.3
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+ Version: 2.1.1
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  Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
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  Project-URL: Homepage, https://github.com/SmallFishGUI/small_fish_gui
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  Project-URL: Wiki, https://github.com/SmallFishGUI/small_fish_gui/wiki
@@ -36,7 +36,7 @@ Description-Content-Type: text/markdown
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  # Small Fish - A User-Friendly Graphical Interface for smFISH Image Quantification
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  [![License: BSD-2-Clause](https://img.shields.io/badge/License-BSD_2--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
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- [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
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+ [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
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  **Small Fish** is a python application for smFish image analysis. It provides a ready to use graphical interface to synthetize state-of-the-art scientific packages into an automated workflow. Small Fish is designed to simplify images quantification and analysis for people without coding skills.
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@@ -83,22 +83,27 @@ Analysis can be performed either fully interactively throught a Napari interface
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  ### General setup
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- If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/).
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+ If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/); but any distribution should work.
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- It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
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+ It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.9/library/venv.html) environnement to install small fish.
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+ As of version 2.1.0 Small Fish runs on python 3.12.
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+ If you are using **conda** or **miniconda**
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  ```bash
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- conda create -n small_fish python=3.9
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+ conda create -n small_fish python=3.12
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  conda activate small_fish
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  ```
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- Then download the small_fish package :
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+ If you are using **venv**, after installing the official python 3.12, python-venv **and** *python-tk* .
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  ```bash
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- pip install small_fish_gui
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+ python3.12 -m venv python_env/small_fish
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+ source python_env/small_fish/bin/activate
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  ```
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- Results visualisation is achieved through *Napari* which you can install with :
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+ Then download and install the small_fish package with :
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  ```bash
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- pip install napari[all]
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+ pip install small_fish_gui
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  ```
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  ### Setting up GPU
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  ```
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  You are all set! Try it yourself or check the [get started](https://github.com/2Echoes/small_fish_gui/wiki/Get-started) section in the wiki.
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+
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+ ## Developement
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+ Bugs to fix :
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+ * Use of load button during co-localization quantification yields wrongs results
{small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.1.dist-info}/RECORD RENAMED
@@ -1,22 +1,24 @@
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- small_fish_gui/__init__.py,sha256=L_lJwkpdlIGo4eXl6wIvnwALDNwtZ0acL3OeWxoNi0Y,2163
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+ small_fish_gui/__init__.py,sha256=CeLyp2zV0AfjMKoP3uqVfIT1j05NhBfc90HKwtFJhCU,2163
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  small_fish_gui/__main__.py,sha256=xwpFMDuo0kkYvPamyhlTHJ68bymDfbRpPzKy3SKwezY,1639
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  small_fish_gui/hints.py,sha256=NEKqCbjXF3guHnc1dzq_LYYGlTxIV6z6wtdwVlmgHos,3349
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  small_fish_gui/main_menu.py,sha256=z0ZlidWNGHLYYnBx2Z1i2IX_EGQr-HtIlsOQl-yTw4o,6273
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+ small_fish_gui/small_fish_gui.code-workspace,sha256=GbzU4Vx0xJV2o86UOa-FA83na5mGxSD6Efeb1QFBMlM,60
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  small_fish_gui/utils.py,sha256=LM6QW2ono_LIRv7JXIIq7ZxxbDXqBtZ5uR9gjKJfwM8,1903
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  small_fish_gui/batch/__init__.py,sha256=ku2_Yate-UG89Q0BmE2B9kFV4kOz-u9Lf2lj6VsdFXs,127
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  small_fish_gui/batch/input.py,sha256=mqnP8LBhyNbtlcqjVlUiVeuHw4YxOX3GgzJbq03isKE,1477
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  small_fish_gui/batch/integrity.py,sha256=3m3faYeIM6-l5-6butv0sc56dKTz56GNiID0bps_mL8,5085
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  small_fish_gui/batch/output.py,sha256=cKZBsO48HaKfxfa6cwcBKw3YRILBCcdC8rpYd2OTEVs,520
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  small_fish_gui/batch/pipeline.py,sha256=oVylDQ3v88Wz1BuGoVBTchPGBkVFKRhMMXclSYkr6kY,14462
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- small_fish_gui/batch/prompt.py,sha256=LIjzVijpvZ9YShQ2-FRjit2RoJZhSMyebcKnsx_99vs,22001
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+ small_fish_gui/batch/prompt.py,sha256=_WZB-O3oYp8rRdEuf3r8o-ML0EWQn6UTuJVaW2OgpT8,21978
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  small_fish_gui/batch/test.py,sha256=FcoCngSeueociwVoG8V3C6lQO7rrRHUfIVA2hJKr4v4,213
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  small_fish_gui/batch/update.py,sha256=Gv1805-xUtrJ3BK0HdflBSnSFAEB5RmnAPk6peAR9CA,6169
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  small_fish_gui/batch/utils.py,sha256=apHxp72OdjTSUyj4ZwN75NYc12Am4m7N9Sw03TrjLMk,1870
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+ small_fish_gui/batch/values.txt,sha256=9QpmRfZ5AuDByZFzkHxTESKV6bnZMH5DtPIGbMmLsXY,999
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  small_fish_gui/gui/__init__.py,sha256=idpRSg2FFawF0ydfc7Y8ep6gQ4_jhroL_jZURlRE_BM,920
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- small_fish_gui/gui/_napari_widgets.py,sha256=xXa-da5MYEWCpwlnE7LkURXSjxvAcF2EHj9-jm482Rk,34934
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+ small_fish_gui/gui/_napari_widgets.py,sha256=9gfikNMLZmeWY9tosD19aGmw4Ulf-BMo8erehJ4KU1k,35321
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  small_fish_gui/gui/animation.py,sha256=MnYsA1kxQZ72L_H0knxOs41lG0ZZv1re7gSgYNmZY00,983
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- small_fish_gui/gui/layout.py,sha256=Js3fwYDQ8Ejxw_dAGN53gKSGCLNiIKxHyiv49vjLA7g,30905
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- small_fish_gui/gui/napari_visualiser.py,sha256=mipNwfcUDVZSZjlnZDbVe9E4p_2cBsxFDoQX6vqhsbk,13935
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+ small_fish_gui/gui/layout.py,sha256=CkQNmAWkpaz7WsdG-dp-IOaIxAFrJWLmA7cty3BkQzc,30878
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+ small_fish_gui/gui/napari_visualiser.py,sha256=5Dk9wJbnmxgNZ3upiQtOrtAr2CT700qkvNQvGsHHdsw,14834
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  small_fish_gui/gui/prompts.py,sha256=vWLLJZ7jdYIbjT71qHGiE1o9-pTrc607shnKW6EZi8I,18361
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  small_fish_gui/gui/testing.ipynb,sha256=2E51kT3BcXvOvOSdmYIy4Cxbe-4HtnOjzPTZQHDZJJw,69148
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  small_fish_gui/gui/theme.py,sha256=30nujS48ZRdD1HVbzdEBkiAWlhow1AGgXSQNZcGEsaQ,118
@@ -25,8 +27,7 @@ small_fish_gui/interface/__init__.py,sha256=nqMwHG-l1yMm8iaD6hhCdji5RiKImzNFQcbd
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  small_fish_gui/interface/default_settings.py,sha256=vI4-Pl_MpAGuCp7SjWdnpYvWwde_3rfvm9Mb_smaDho,3442
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  small_fish_gui/interface/image.py,sha256=0icuHuKFuSZ-YUTIskz-S2HcJ3wXtOrW37iPg8tknHg,3440
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  small_fish_gui/interface/inoutput.py,sha256=toB2SNNZNiupZTT2-zQKJ6ewI-_DJTVrXIkdq8TMWXY,5793
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- small_fish_gui/interface/settings.json,sha256=WqMjgN1Ex01hXruJ1Kkho4nPi9PbEPpOIplT5IIkHxQ,1366
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- small_fish_gui/interface/testing.ipynb,sha256=I8iGdcYsds4iBxL417D_PXt7bZcEkHAjWAgXA9DNlSM,323719
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+ small_fish_gui/interface/settings.json,sha256=8-PCnEJLsoFdkhAeJvKtOiuhBjTcA7CXqnG_IsZAqhI,1402
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  small_fish_gui/interface/testing.py,sha256=AUdqmFJ6kBvFTOLRfZZJBBe3nm1key2bGpUDXJRaueI,2561
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  small_fish_gui/interface/user_settings.py,sha256=vMpj-s9tzMKQy1CdJ3SO-6yAknU-ZIMT0RZQs8WAGPY,2620
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  small_fish_gui/pipeline/__init__.py,sha256=Oww6dcuvnktl5jFKLriz8ZXObKo9MkneE739A8C1reY,739
@@ -35,12 +36,13 @@ small_fish_gui/pipeline/_colocalisation.py,sha256=m6wRgf_nESqvkvkD2RRyTj3ekKKvk4
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  small_fish_gui/pipeline/_custom_errors.py,sha256=tQ-AUhgzIFpK30AZiQQrtHCHyGVRDdAoIjzL0Fk-1pA,43
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  small_fish_gui/pipeline/_preprocess.py,sha256=zfwhNoAUkVv1TYlyffNQkSTitMXTDokADabBeHuB58U,15766
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  small_fish_gui/pipeline/actions.py,sha256=lPKyX12qEJNnQ4ArYqCRkLrFzwzGgIEl1_HpSFtTMKo,20476
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- small_fish_gui/pipeline/detection.py,sha256=Gi1H01P8n7EsthY1NsyRR407DwXxvrJB9S91aMBfc0A,35961
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- small_fish_gui/pipeline/segmentation.py,sha256=rlDxHrbhokEJngmaGTjWHRp06XXraQWUWWUHA4sROq0,32065
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+ small_fish_gui/pipeline/detection.py,sha256=IE0Wf9NaHcxkCv1cjrOdyfnQUzv8SlXilIT7KI8INP4,35988
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+ small_fish_gui/pipeline/segmentation.py,sha256=m9XW8XiWCSpGFdi6It6RkeDYTiKtNhfj30kUSBG8pNo,32023
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  small_fish_gui/pipeline/spots.py,sha256=3kMe404RHOsNLRZQV6RdpxrHqaRRiGK4_qKSx6jesDM,6738
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  small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
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+ small_fish_gui/pipeline/testing.ipynb,sha256=zIjnWwsqCBUqydvFx3n4R3_SlrBSwgWjDt50zn4SNgI,339174
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  small_fish_gui/pipeline/utils.py,sha256=dYV7WAJ375xM5RdaljjxeKvBC1niQvBl1E55SeIiIYo,563
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- small_fish_gui-2.0.3.dist-info/METADATA,sha256=KBV5T--5i-x6ek7K1hVoQScF9p8Z3jWK2COHcoY_GE4,5817
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- small_fish_gui-2.0.3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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- small_fish_gui-2.0.3.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
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- small_fish_gui-2.0.3.dist-info/RECORD,,
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+ small_fish_gui-2.1.1.dist-info/METADATA,sha256=796rUUMhbnBHdlSsaXT0lkq4aO14MR5j4iQWxyX8064,6166
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+ small_fish_gui-2.1.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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+ small_fish_gui-2.1.1.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
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+ small_fish_gui-2.1.1.dist-info/RECORD,,