pico-ml 2.0.0__py3-none-any.whl

pico/ui/tabs/__init__.py

@@ -0,0 +1,6 @@
+from .InfoTab import InfoTab
+from .SplitsTab import SplitsTab
+from .MLTab import MLTab
+from .ResultsTab import ResultsTab
+from .AggregatedResultsTab import AggregatedResultsTab
+from .InterpretTab import InterpretTab

pico/ui/tabs/utils.py

@@ -0,0 +1,101 @@
+import numpy as np
+
+from ...conf import parameters as cfg
+
+
+def update_marks(custom_value: int, add_all_value: bool = False) -> dict:
+    """
+    Update the marks of the features slider to include a custom value.
+    
+    If the custom value is already in the default marks, it will be used and
+    marked as "(used)".
+    
+    If the custom value is not in the default marks, it will be added to the
+    marks at a position that is the closest to its value.
+    
+    If add_all_value is True, the "All" mark will be added to the marks.
+    
+    Returns a tuple containing the updated marks and the location of the custom
+    value.
+    """
+    locations = [int(l) for l in cfg.default_marks.keys()]
+    values = np.array([int(v) for v in cfg.default_marks.values()])
+    
+    # If the custom value is already there, we use it a used feature
+    if custom_value in values:
+        marks = cfg.default_marks.copy()
+        idx = np.where(values == custom_value)[0].item()
+        location_key = str(locations[idx])
+        marks[location_key] = marks[location_key] + " (used)"
+        
+        if add_all_value:
+            marks.update(cfg.all_mark)
+        
+        return marks, location_key
+    
+    greater_indicator = values > custom_value
+    if np.all(greater_indicator):
+        # The value is on the far left
+        custom_location = locations[0] - cfg.custom_mark_offset
+    elif not np.any(greater_indicator):
+        # The value is on the far right
+        custom_location = locations[-1] + cfg.custom_mark_offset
+    else:
+        greater_idx = np.argmax(greater_indicator)
+        distance_from_greater = values[greater_idx] - custom_value
+        distance_from_smaller = custom_value - values[greater_idx - 1]
+        if distance_from_smaller < distance_from_greater:
+            # Closer to the left, we will add the offset on the left mark
+            custom_location = locations[greater_idx - 1] + cfg.custom_mark_offset
+        elif distance_from_smaller == distance_from_greater:
+            # Equal distance
+            custom_location = (locations[greater_idx - 1] + locations[greater_idx]) / 2
+        else:
+            # Closer the the right, we will remove the offset from the right mark
+            custom_location = locations[greater_idx] - cfg.custom_mark_offset
+    
+    marks = cfg.default_marks.copy()
+    value_label = {
+        'label': str(custom_value) + ' (used)', 
+        'style': {
+            "top": "-3em"
+        }
+    }
+    marks[str(custom_location)] = value_label
+
+    if add_all_value:
+        marks = {**marks, **cfg.all_mark}
+
+    return marks, custom_location
+
+
+
+def get_index_from_marks(number: float, marks: dict) -> int:
+    """This is really specific to how the results are saved. 
+    See pico.domain.Results._produce_PCA (or _produce_UMAP).
+
+    The first results are from cfg.features, then used_features, then all.
+
+    The result differs when there is "All" features (e.g. strip chart doesnt not include All).
+    """
+    contain_all = False
+    for v in marks.values():
+        if isinstance(v, str) and v == "All":
+            contain_all = True
+
+    match marks[str(number)]:
+        case dict(value):
+            # We have the used feature case, index is -2 or -1 when 
+            index = -2 if contain_all else -1
+        case "All":
+            # We have the "All" case, index is -1
+            index = -1
+        case str(value) if "used" in value:
+            # We have the feature case
+            index = -2 if contain_all else -1
+        case _:
+            # The number is the index
+            index = int(number)
+
+
+    return index

pico_ml-2.0.0.dist-info/METADATA

@@ -0,0 +1,86 @@
+Metadata-Version: 2.4
+Name: pico-ml
+Version: 2.0.0
+Summary: Pipeline for Interpretable Classification on Omics
+Project-URL: Homepage, https://elinaff.github.io/PICO/
+Project-URL: Issues, https://github.com/ElinaFF/PICO/issues
+Project-URL: Source, https://github.com/ElinaFF/PICO
+Author-email: Elina Francovic-Fontaine <elina.francovic-fontaine.1@ulaval.ca>
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: <3.13,>=3.8
+Requires-Dist: coloredlogs
+Requires-Dist: dash
+Requires-Dist: dash-bio
+Requires-Dist: dash-bootstrap-components
+Requires-Dist: dash-core-components
+Requires-Dist: dash-cytoscape
+Requires-Dist: dash-html-components
+Requires-Dist: dash-interactive-graphviz
+Requires-Dist: dash-renderer
+Requires-Dist: dash-table
+Requires-Dist: matplotlib
+Requires-Dist: numba
+Requires-Dist: numpy<2
+Requires-Dist: openpyxl
+Requires-Dist: pandas
+Requires-Dist: plotly
+Requires-Dist: pyscm-ml>=1.1.2
+Requires-Dist: randomscm>=0.1.2
+Requires-Dist: rich
+Requires-Dist: scikit-learn>1.4
+Requires-Dist: scipy
+Requires-Dist: typer
+Requires-Dist: umap-learn
+Provides-Extra: dev
+Requires-Dist: dash[testing]; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# PICO
+Pipeline for Interpretable Classification on Omics
+
+## Description
+The PICO is a tool to apply machine learning algorithms to omics datasets. The goal is to extract the most important features because they are potential novel biomarkers.
+The interface is made to be easy to use and intuitive even for those with small to nonexistant experience in programming and AI.
+
+More generally, it is a tool to apply interpretable machine learning algorithms to tabular data. It focuses on analyzing the features selected by the models.
+
+## The documentation
+You can find the documentation [here](https://elinaff.github.io/PICO/).
+It explains how to use PICO but also how it works.
+
+## Authors and contributors
+ - [Élina Francovic-Fontaine](https://github.com/ElinaFF)
+ - [Vincent Primpied](https://github.com/le-smog)
+ - [Vincent Vilain](https://github.com/VincentVilain)
+ - [Gabriel Leclerc](https://github.com/PandaGab)
+ - [Thierry Moszkowicz](https://github.com/ThierryAM)
+ - [Mathieu Bazinet](https://github.com/MathieuBazinet)
+ - [Thibaud Godon](https://github.com/thibgo)
+ - [Pier-Luc Plante](https://github.com/plpla)
+ - [Baptiste Bauvin](https://github.com/babau1)
+ - [Louis-Philippe Vignault](https://scholar.google.com/citations?user=QXye6lEAAAAJ&hl=fr)
+
+## Disclaimer
+PICO is still in development. If you encounter any issue or have any suggestion, feel free to contact us at [elina.francovic-fontaine.1@ulaval.ca](mailto:elina.francovic-fontaine.1@ulaval.ca). Or you can leave an issue [here](https://github.com/ElinaFF/PICO/issues) with the tag "bug".
+
+## For developers
+
+### Setup
+
+Clone the project with :
+```shell
+git clone https://github.com/ElinaFF/PICO.git
+```
+
+It is recommanded to setup a virtual environment. When it's done, use your isolated python and install `pico` package locally and in editable mode with :
+```shell
+python -m pip install -e ".[dev]"
+```
+
+## License
+<a href="https://github.com/ElinaFF/PICO">Pipeline for Interpretable Classification on Omics (PICO)</a> © 2025 by <a href="https://creativecommons.org">Elina Francovic-Fontaine</a> is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA 4.0</a>
+

pico_ml-2.0.0.dist-info/RECORD

@@ -0,0 +1,52 @@
+pico/__init__.py,sha256=PIFwmFSIbz4T6kPrvSr90M8Dj7WCndTv1oph5kCGO_U,43
+pico/__main__.py,sha256=2pEnS7f2JU7U3_GHXrmNWAIzXhPqN27zSHCZT6Ij4KE,33
+pico/cli/__init__.py,sha256=0m1GuS3w88DNt0kc72N_ugOxa5LH4ibYqrw92To5qWg,53
+pico/cli/main.py,sha256=1crrzeupD3Cb6QgW24nbDzMUB6Rt_nVrwq6SvQVSK04,3368
+pico/conf/SupportedCV.py,sha256=jJftCmsXwZWQOfshCcjxHYd1YFgx2z4qvYuDy82Y0pA,402
+pico/conf/SupportedModels.py,sha256=YTVAd8-ltYFqXGQwEIvL-P5gNCr7TkCkZYhDS3cU1cs,2766
+pico/conf/algo_sklearn.json,sha256=gbX8EJ-f7IrpgmbkH0BqwgONn_TFtbMsK4k33Xcxr8E,664
+pico/conf/parameters.py,sha256=s4gqg4rZlb-iVi7GC2yUmSwcYnQQlAWZsqhK-EuupAM,398
+pico/domain/ClassificationDesign.py,sha256=VED0xqONvnxFFl-Y6b6fVclqkIa7eXvpnmwL98xoyCo,4740
+pico/domain/Controller.py,sha256=xoJ1q0C4mWKVIpVhsbSsm6g1aRGyvxRAxbzJCiQT0Yg,16103
+pico/domain/DataMatrix.py,sha256=ABMFbbLnZ2Nj4TCNyHs9kwySBSWm5AW78uzLRVS5jA0,5720
+pico/domain/ExperimentDTO.py,sha256=hkFyBTD7gfkolO-9uGNyqlEi5st2RnT8yrGEflTiqXI,691
+pico/domain/MetaData.py,sha256=cGqdbrCyr2T4tSjfs63CJEa4PL3F_jnig6a1dTa7VhQ,8967
+pico/domain/MetaboExperiment.py,sha256=io0Jeu-Hx5KT_CCpwgo_Xmz5lTaWoTCaEDjeLX_fOHU,30808
+pico/domain/MetaboModel.py,sha256=Re1gffN_it8n2N5i7l-Ag4ZZiyal1LzKoSz6baBsMWc,1784
+pico/domain/ModelFactory.py,sha256=Y2KpeZVEgfhU-1SA9_e3GmwGGhSLrqI50qeKrf_B2yo,1735
+pico/domain/Results.py,sha256=4JY9BaGxIT35cPQkGTCBlXN9jGv_T2rpSuVWWBMGowQ,23988
+pico/domain/SplitGroup.py,sha256=kTjvAZ_Q3osqKO2peq6DNpIHtGEsXNmEhLL_geJXgsM,11388
+pico/domain/__init__.py,sha256=7WLgTGrvDDxiFyRTLXvP707E47rYnz-2VrK_MI8PffQ,343
+pico/domain/dumps/metadata/.gitkeep,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pico/domain/dumps/splits/.gitkeep,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pico/service/DataFormat.py,sha256=nzC_e9OI7ST6WSxVRWOx-rawUikoiYyW24oGIEQuEWo,8136
+pico/service/ExperimentDesign.py,sha256=A81A0gP6Z0WmLEhjwEtAKqjgFWfwHyksw_vdHvqmS6Q,685
+pico/service/LoggerConfig.py,sha256=i3_mutoK9NNj97DePF33YQk7PS2BbsT79zwd7hon86Q,5524
+pico/service/Plots.py,sha256=KHwNhYPe1-zubPI-4BSJ3nCp2B0M6ASyg6sznnBA1XI,16756
+pico/service/RunMLalgo.py,sha256=ujpGYMszxoLvWzCsg0nctKnA7UebPeeg3Re6rm477Ks,3450
+pico/service/SamplesPairing.py,sha256=3_AS1yl90v420wynwxDbw010ziqwGzAwneWmHIYRpzE,16121
+pico/service/Utils.py,sha256=RHGSCB3vfGnvaQXi38WzTtKmPvD_KFnzSd-T66oDudg,18973
+pico/service/__init__.py,sha256=M5R-zD4k2ow1Z8cRJzHFEg6Fu3Aopt8E65wIgWrlf5Y,228
+pico/ui/__init__.py,sha256=8G-rLhbTJsxt8QMNfYPDILcn9K1Psojh3Vq-lntPyS4,21
+pico/ui/app.py,sha256=UqMeDGM6a_UYnQzkEswH8bO2-p0u7kGHVMF_IPXsUz4,5565
+pico/ui/assets/000_Stylesheet.css,sha256=saRlyjSuwxFeE29eATw6cDRruHvlmNfAjl6R_Iwkgls,6530
+pico/ui/assets/DecisionTree.png,sha256=JNVvyvjOuAka4e_ic7njqUrhOZe20RFovUQribFXCAA,203270
+pico/ui/assets/Figure_home_wider.png,sha256=Tv424vLbQ7Fjtw8jO8ffyrLDRnvLyQ-Da_7PeRaoBrA,60314
+pico/ui/assets/favicon.ico,sha256=BwmZGm94ENHB2CPfb4AKTDqH286JLSHPVP04_LTBzo8,8532
+pico/ui/assets/help_icon.png,sha256=jhVapWHX6nZ7qwEdwp9WC7LW-kkWVaWA_08SCbB2s84,10134
+pico/ui/assets/help_icon.svg,sha256=l1z39WE4nG5duOb30Tl89hK520yzrt5E5UOAWJqLvuo,755
+pico/ui/assets/update_figure_steps_MeDIC_4.svg,sha256=2wDhHeM5sBjmBLCD7KTjKmFTVjqV5x6y20vvXSDqBUI,9721
+pico/ui/tabs/AggregatedResultsTab.py,sha256=xiaBhLYToBK72wGaRokOXpj6nmROgElK0whK-ITQo58,15108
+pico/ui/tabs/InfoTab.py,sha256=CWldI9f3Ll2gZ7dW80sz2y8L3ZCslUiXGN_TiRHiC0Q,19786
+pico/ui/tabs/InterpretTab.py,sha256=yJeNDtBOiY2FINVdxkXVKbmVf5b2wJ6E-GchNfShMhw,543
+pico/ui/tabs/MLTab.py,sha256=Oqnc8_4-eu-qQhzcX3uuuqtmovqkGVf83vSgCDV1JII,21106
+pico/ui/tabs/MetaTab.py,sha256=g7fELzDs5VHj_1FfxQX1s6mznI_dKwSmIBY8cTIXM08,537
+pico/ui/tabs/ResultsTab.py,sha256=sJS3w9Kgvqo6rBlYsUl7pvO8ZS3CbMvClDCBhmsZNfk,39867
+pico/ui/tabs/SplitsTab.py,sha256=ybIY09foDoHyR25o6y8iEn5UHyd6SOy0eIXuvsdKh_0,52517
+pico/ui/tabs/__init__.py,sha256=snlgOGrMRN9hgg7jXFM2g7TaoIwA1ufkZxdI9DOLNxY,216
+pico/ui/tabs/utils.py,sha256=BTDgNQV1FqCEKqkeIjr2Zcee6FDHZcHL9EY5NdLqpNo,3606
+pico_ml-2.0.0.dist-info/METADATA,sha256=AmRVytsVhQMpzH7wbvzeGeS2mI5aj4UFhRRghwuoMXc,3503
+pico_ml-2.0.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+pico_ml-2.0.0.dist-info/entry_points.txt,sha256=uSuwbxFEWXXiwg-TQsAEwcHshBOo-0hj1AWupayX46s,43
+pico_ml-2.0.0.dist-info/licenses/LICENSE,sha256=E0mkthSEkrRPYp5k7tZ2YS4jT-moOeTzsnfBSCyISfE,20849
+pico_ml-2.0.0.dist-info/RECORD,,

pico_ml-2.0.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

pico_ml-2.0.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+pico = pico.cli.main:app