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owkin · Jun 12, 2024 · debd160 · debd160
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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 5a95befbf787dbab18242f13e781c7a1
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/contributing.doctree b/.doctrees/contributing.doctree
diff --git a/.doctrees/datasets.doctree b/.doctrees/datasets.doctree
diff --git a/.doctrees/docker.doctree b/.doctrees/docker.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/faq.doctree b/.doctrees/faq.doctree
diff --git a/.doctrees/fed_camelyon.doctree b/.doctrees/fed_camelyon.doctree
diff --git a/.doctrees/fed_heart.doctree b/.doctrees/fed_heart.doctree
diff --git a/.doctrees/fed_isic.doctree b/.doctrees/fed_isic.doctree
diff --git a/.doctrees/fed_ixi.doctree b/.doctrees/fed_ixi.doctree
diff --git a/.doctrees/fed_kits19.doctree b/.doctrees/fed_kits19.doctree
diff --git a/.doctrees/fed_lidc.doctree b/.doctrees/fed_lidc.doctree
diff --git a/.doctrees/fed_tcga_brca.doctree b/.doctrees/fed_tcga_brca.doctree
diff --git a/.doctrees/fedbiomed.doctree b/.doctrees/fedbiomed.doctree
diff --git a/.doctrees/fedml.doctree b/.doctrees/fedml.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/installation.doctree b/.doctrees/installation.doctree
diff --git a/.doctrees/quickstart.doctree b/.doctrees/quickstart.doctree
diff --git a/.doctrees/reproducing.doctree b/.doctrees/reproducing.doctree
diff --git a/.doctrees/strategies.doctree b/.doctrees/strategies.doctree
diff --git a/.doctrees/substra.doctree b/.doctrees/substra.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/_images/logo.png b/_images/logo.png
diff --git a/_images/output_27_0.png b/_images/output_27_0.png
diff --git a/_modules/flamby/datasets/fed_camelyon16/dataset.html b/_modules/flamby/datasets/fed_camelyon16/dataset.html
diff --git a/_modules/flamby/datasets/fed_heart_disease/dataset.html b/_modules/flamby/datasets/fed_heart_disease/dataset.html
diff --git a/_modules/flamby/datasets/fed_isic2019/dataset.html b/_modules/flamby/datasets/fed_isic2019/dataset.html
diff --git a/_modules/flamby/datasets/fed_ixi/dataset.html b/_modules/flamby/datasets/fed_ixi/dataset.html
diff --git a/_modules/flamby/datasets/fed_kits19/dataset.html b/_modules/flamby/datasets/fed_kits19/dataset.html
diff --git a/_modules/flamby/datasets/fed_lidc_idri/dataset.html b/_modules/flamby/datasets/fed_lidc_idri/dataset.html
diff --git a/_modules/flamby/datasets/fed_tcga_brca/dataset.html b/_modules/flamby/datasets/fed_tcga_brca/dataset.html
diff --git a/_modules/flamby/strategies/cyclic.html b/_modules/flamby/strategies/cyclic.html
diff --git a/_modules/flamby/strategies/fed_avg.html b/_modules/flamby/strategies/fed_avg.html
diff --git a/_modules/flamby/strategies/fed_opt.html b/_modules/flamby/strategies/fed_opt.html
diff --git a/_modules/flamby/strategies/fed_prox.html b/_modules/flamby/strategies/fed_prox.html
diff --git a/_modules/flamby/strategies/scaffold.html b/_modules/flamby/strategies/scaffold.html
diff --git a/_modules/index.html b/_modules/index.html
@@ -0,0 +1,156 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; FLamby 0.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
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+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=d45e8c67"></script>
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+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
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+
+          <a href="../index.html" class="icon icon-home">
+            FLamby
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
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+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Getting Started Instructions</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../quickstart.html">Quickstart</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Datasets informations</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../fed_tcga_brca.html">Fed-TCGA-BRCA</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fed_heart.html">Fed-Heart Disease</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fed_ixi.html">Fed-IXI</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fed_isic.html">Fed-ISIC 2019</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fed_camelyon.html">Fed-Camelyon16</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fed_lidc.html">Fed-LIDC-IDRI</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fed_kits19.html">Fed-KiTS19</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Integration with FL-frameworks</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../substra.html">Using FLamby with Substra</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fedbiomed.html">Using FLamby with Fed-BioMed</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../fedml.html">Using FLamby with FedML</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Reproducible results with docker</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../docker.html">Containerized execution</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Reproducing results</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../reproducing.html">Reproduction instructions</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">FAQ</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../faq.html">FAQ</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extending FLamby</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../contributing.html">Extending FLamby</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../contributing.html#contribution-guidelines">Contribution Guidelines</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Code Documentation</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../strategies.html">FL Strategies</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../datasets.html">Datasets</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
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+          <a href="../index.html">FLamby</a>
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+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="flamby/datasets/fed_camelyon16/dataset.html">flamby.datasets.fed_camelyon16.dataset</a></li>
+<li><a href="flamby/datasets/fed_heart_disease/dataset.html">flamby.datasets.fed_heart_disease.dataset</a></li>
+<li><a href="flamby/datasets/fed_isic2019/dataset.html">flamby.datasets.fed_isic2019.dataset</a></li>
+<li><a href="flamby/datasets/fed_ixi/dataset.html">flamby.datasets.fed_ixi.dataset</a></li>
+<li><a href="flamby/datasets/fed_kits19/dataset.html">flamby.datasets.fed_kits19.dataset</a></li>
+<li><a href="flamby/datasets/fed_lidc_idri/dataset.html">flamby.datasets.fed_lidc_idri.dataset</a></li>
+<li><a href="flamby/datasets/fed_tcga_brca/dataset.html">flamby.datasets.fed_tcga_brca.dataset</a></li>
+<li><a href="flamby/strategies/cyclic.html">flamby.strategies.cyclic</a></li>
+<li><a href="flamby/strategies/fed_avg.html">flamby.strategies.fed_avg</a></li>
+<li><a href="flamby/strategies/fed_opt.html">flamby.strategies.fed_opt</a></li>
+<li><a href="flamby/strategies/fed_prox.html">flamby.strategies.fed_prox</a></li>
+<li><a href="flamby/strategies/scaffold.html">flamby.strategies.scaffold</a></li>
+</ul>
+
+           </div>
+          </div>
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diff --git a/_sources/contributing.rst.txt b/_sources/contributing.rst.txt
@@ -0,0 +1,54 @@
+Extending FLamby
+----------------
+
+FLamby is a living project and contributions by the FL community are
+welcome.
+
+If you would like to add another cross-silo dataset **with natural
+splits**, please fork the repository and do a Pull-Request following the
+guidelines described below.
+
+Similarly, you can propose pull requests introducing novel training
+algorithms or models.
+
+Contribution Guidelines
+-----------------------
+
+After installing the package in dev mode
+(``pip install -e .[all_extra]``) You should also initialize
+``pre-commit`` by running:
+
+::
+
+    pre-commit install
+
+The ``pre-commit`` tool will automatically run
+`black <https://github.com/psf/black>`__ and
+`isort <https://github.com/PyCQA/isort>`__ and check
+`flake8 <https://flake8.pycqa.org/en/latest/>`__ compatibility. Which
+will format the code automatically making the code more homogeneous and
+helping catching typos and errors.
+
+Looking and or commenting the open issues is a good way to start. Once
+you have found a way to contribute the next steps are:
+
+-  Following the installation instructions (with -e and all_extra)
+-  Installing pre-commit by running: ``pre-commit install`` at the root of the repository
+-  Creating a new branch following the convention name\_contributor/short\_explicit\_name-wpi:
+   ``git checkout -b name_contributor/short_explicit_name-wpi``
+-  Potentially pushing the branch to origin with :
+   ``git push origin name_contributor/short_explicit_name-wpi`` 
+-  Working on the branch locally by making commits frequently:
+   ``git commit -m "explicit description of the commit's content"`` 
+-  Once the branch is ready or after considering you have made significant
+   progresses opening a Pull Request using Github interface, selecting your
+   branch as a source and the target to be the main branch and creating the
+   PR **in draft mode** after having made **a detailed description of the
+   content of the PR** and potentially linking to related issues. 
+-  Rebasing the branch onto main by doing ``git fetch origin`` and
+   ``git rebase origin/main``, solving potential conflicts adding the
+   resolved files ``git add myfile.py`` then continuing with
+   ``git rebase --continue`` until the rebase is complete. Then pushing the
+   branch to origin with ``git push origin --force-with-lease``. 
+-  Waiting for reviews then commiting and pushing changes to comply with the reviewer's requests 
+-  Once the PR is approved click on the arrow on the right of the merge button to select rebase and click on it
diff --git a/_sources/datasets.rst.txt b/_sources/datasets.rst.txt
@@ -0,0 +1,55 @@
+Datasets
+==========
+
+
+Fed-ISIC2019
+------------
+
+.. autoclass:: flamby.datasets.fed_isic2019.FedIsic2019
+   :members:
+   :undoc-members:
+
+Fed-Camelyon16
+--------------
+
+.. autoclass:: flamby.datasets.fed_camelyon16.FedCamelyon16
+   :members:
+   :undoc-members:
+
+Fed-LIDC-IDRI
+-------------
+
+.. autoclass:: flamby.datasets.fed_lidc_idri.FedLidcIdri
+   :members:
+   :undoc-members:
+
+
+Fed-TCGA_BRCA
+-------------
+
+.. autoclass:: flamby.datasets.fed_tcga_brca.FedTcgaBrca
+   :members:
+   :undoc-members:
+
+
+Fed-Heart-Disease
+-----------------
+
+.. autoclass:: flamby.datasets.fed_heart_disease.FedHeartDisease
+   :members:
+   :undoc-members:
+
+Fed-IXITiny
+-----------------
+
+.. autoclass:: flamby.datasets.fed_ixi.FedIXITiny
+   :members:
+   :undoc-members:
+
+Fed-Kits19
+-----------------
+
+.. autoclass:: flamby.datasets.fed_kits19.FedKits19
+   :members:
+   :undoc-members:
+
diff --git a/_sources/docker.rst.txt b/_sources/docker.rst.txt
@@ -0,0 +1,34 @@
+Containerized execution
+=======================
+
+A good step towards float-perfect reproducibility in your future
+benchmarks is to use docker. We give a base docker image and examples
+containing dataset download and benchmarking. For
+:any:`fed_heart`,
+``cd`` to the flamby dockers folder, replace ``myusername`` and
+``mypassword`` with your git credentials (OAuth token) in the command
+below and run:
+
+::
+
+    docker build -t flamby-heart -f Dockerfile.base --build-arg DATASET_PREFIX="heart" --build-arg GIT_USER="myusername" --build-arg GIT_PWD="mypassword" .
+    docker build -t flamby-heart-benchmark -f Dockerfile.heart .
+    docker run -it flamby-heart-benchmark
+
+If you are convinced you will use many datasets with docker, build the
+base image using ``all_extra`` option for flamby's install, you will be
+able to reuse it for all datasets with multi-stage build:
+
+::
+
+    docker build -t flamby-all -f Dockerfile.base --build-arg DATASET_PREFIX="all_extra" --build-arg GIT_USER="myusername" --build-arg GIT_PWD="mypassword" .
+    # modify Dockerfile.* line 1 to FROM flamby-all by replacing * with the dataset name of the dataset you are interested in
+    # Then run the following command replacing * similarly
+    #docker build -t flamby-* -f Dockerfile.* .
+    #docker run -it flamby-*-benchmark
+
+Checkout ``Dockerfile.tcga``. Similar dockerfiles can be theoretically
+easily built for the other datasets as well by replicating instructions
+found in each dataset folder following the model of
+``Dockerfile.heart``. Note that for bigger datasets execution can be
+prohibitively slow and docker can run out of time/memory.