chore: bump dependencies for all examples (#441)

SdgJlbl · guilhem-barthes · web-flow · commit d2bad312cf05 · 2024-10-01T17:05:32.000+02:00
* chore: bump dependencies for all examples

Signed-off-by: SdgJlbl &lt;sarah.diot-girard@owkin.com&gt;

* chore: remove unused lines in `nitpick_ignore`

Signed-off-by: Guilhem Barthés &lt;guilhem.barthes@owkin.com&gt;

* feat: ignore remaining torch docstring

Signed-off-by: Guilhem Barthés &lt;guilhem.barthes@owkin.com&gt;

---------

Signed-off-by: SdgJlbl &lt;sarah.diot-girard@owkin.com&gt;
Signed-off-by: Guilhem Barthés &lt;guilhem.barthes@owkin.com&gt;
Co-authored-by: Guilhem Barthés &lt;guilhem.barthes@owkin.com&gt;
diff --git a/changes/441.changed b/changes/441.changed
@@ -0,0 +1 @@
+Bump all examples dependencies.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -358,9 +358,7 @@ def reformat_md_section_links(file_path: Path):
     ("py:class", "torch.nn.modules.module.Module"),
     ("py:class", "torch.nn.modules.Module"),
     ("py:class", "torch.nn.modules.loss._Loss"),
-    ("py:class", "torch.optim.optimizer.Optimizer"),
     ("py:class", "torch.optim.lr_scheduler._LRScheduler"),
-    ("py:class", "torch.utils.data.dataset.Dataset"),
     ("py:class", "torch.nn.modules.module.T"),
     ("py:class", "string"),
     ("py:class", "Module"),
@@ -378,7 +376,6 @@ def reformat_md_section_links(file_path: Path):
     ("py:attr", "strict"),
     ("py:attr", "grad_output"),
     ("py:attr", "requires_grad"),
-    ("py:attr", "device"),
     ("py:attr", "non_blocking"),
     ("py:attr", "dst_type"),
     ("py:attr", "dtype"),
@@ -399,6 +396,10 @@ def reformat_md_section_links(file_path: Path):
     ("py:class", "substrafl.algorithms.pytorch.torch_scaffold_algo.CUpdateRule"),
 ]
 
+nitpick_ignore_regex = [
+    # Used to ignore a torch.nn.Parameter`s\n... as we cannot identify the exact content of it
+    ("py:class", r"torch.nn.Parameter(?s:.)*"),
+]
 # This must be the name of an image file (path relative to the configuration
 # directory) that is the favicon of the docs. Modern browsers use this as
 # the icon for tabs, windows and bookmarks. It should be a Windows-style
diff --git a/docs/source/examples/substra_core/diabetes_example/assets/functions/aggregation/Dockerfile b/docs/source/examples/substra_core/diabetes_example/assets/functions/aggregation/Dockerfile
@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install 'pandas<2.0' 'numpy<2.0' substratools
+RUN pip3 install pandas numpy substratools
 
 # add your algorithm script to docker image
 ADD federated_analytics_functions.py .
diff --git a/docs/source/examples/substra_core/diabetes_example/assets/functions/local_first_order_computation/Dockerfile b/docs/source/examples/substra_core/diabetes_example/assets/functions/local_first_order_computation/Dockerfile
@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install 'pandas<2.0' 'numpy<2.0' substratools
+RUN pip3 install pandas numpy substratools
 
 # add your algorithm script to docker image
 ADD federated_analytics_functions.py .
diff --git a/docs/source/examples/substra_core/diabetes_example/assets/functions/local_second_order_computation/Dockerfile b/docs/source/examples/substra_core/diabetes_example/assets/functions/local_second_order_computation/Dockerfile
@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install 'pandas<2.0' 'numpy<2.0' substratools
+RUN pip3 install pandas numpy substratools
 
 # add your algorithm script to docker image
 ADD federated_analytics_functions.py .
diff --git a/docs/source/examples/substra_core/diabetes_example/assets/requirements.txt b/docs/source/examples/substra_core/diabetes_example/assets/requirements.txt
@@ -1,5 +1,5 @@
-matplotlib==3.6.3
-scikit-learn==1.5.0
+matplotlib==3.9.2
+scikit-learn==1.5.2
 pandas==2.2.2
 substra
 substratools
diff --git a/docs/source/examples/substra_core/titanic_example/assets/function_random_forest/predict/Dockerfile b/docs/source/examples/substra_core/titanic_example/assets/function_random_forest/predict/Dockerfile
@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas 'numpy<2.0' 'scikit-learn==1.5.0' substratools
+RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substratools
 
 # add your function script to docker image
 ADD titanic_function_rf.py .
diff --git a/docs/source/examples/substra_core/titanic_example/assets/function_random_forest/train/Dockerfile b/docs/source/examples/substra_core/titanic_example/assets/function_random_forest/train/Dockerfile
@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas 'numpy<2.0' 'scikit-learn==1.5.0' substratools
+RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substratools
 
 # add your function script to docker image
 ADD titanic_function_rf.py .
diff --git a/docs/source/examples/substra_core/titanic_example/assets/metric/Dockerfile b/docs/source/examples/substra_core/titanic_example/assets/metric/Dockerfile
@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas 'numpy<2.0' 'scikit-learn==1.5.0' substratools
+RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substratools
 
 # add your metrics script to docker image
 ADD titanic_metrics.py .
diff --git a/docs/source/examples/substra_core/titanic_example/assets/requirements.txt b/docs/source/examples/substra_core/titanic_example/assets/requirements.txt
@@ -1,5 +1,5 @@
-matplotlib==3.6.3
-scikit-learn==1.5.0
+matplotlib==3.9.2
+scikit-learn==1.5.2
 pandas==2.2.2
 substra
 substratools
diff --git a/docs/source/examples/substrafl/get_started/run_mnist_torch.ipynb b/docs/source/examples/substrafl/get_started/run_mnist_torch.ipynb
@@ -42,9 +42,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substra import Client\n",
@@ -78,9 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Create a dictionary to easily access each client from its human-friendly id\n",
@@ -117,9 +113,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import pathlib\n",
@@ -159,9 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substra.sdk.schemas import DatasetSpec\n",
@@ -224,9 +216,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from sklearn.metrics import accuracy_score\n",
@@ -283,9 +273,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import torch\n",
@@ -338,9 +326,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.index_generator import NpIndexGenerator\n",
@@ -375,9 +361,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "class TorchDataset(torch.utils.data.Dataset):\n",
@@ -422,9 +406,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.algorithms.pytorch import TorchFedAvgAlgo\n",
@@ -459,9 +441,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.strategies import FedAvg\n",
@@ -486,9 +466,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.nodes import TrainDataNode\n",
@@ -525,9 +503,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.nodes import TestDataNode\n",
@@ -564,14 +540,12 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.dependency import Dependency\n",
     "\n",
-    "dependencies = Dependency(pypi_dependencies=[\"numpy==1.26.4\", \"scikit-learn==1.5.0\", \"torch==2.2.1\", \"--extra-index-url https://download.pytorch.org/whl/cpu\"])"
+    "dependencies = Dependency(pypi_dependencies=[\"numpy==2.1.1\", \"scikit-learn==1.5.2\", \"torch==2.4.1\", \"--extra-index-url https://download.pytorch.org/whl/cpu\"])"
    ]
   },
   {
@@ -600,9 +574,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.experiment import execute_experiment\n",
@@ -651,9 +623,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# The results will be available once the compute plan is completed\n",
@@ -670,9 +640,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import pandas as pd\n",
@@ -692,9 +660,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
@@ -738,9 +704,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from substrafl.model_loading import download_algo_state\n",
@@ -762,7 +726,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -776,9 +740,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.10.9"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }
diff --git a/docs/source/examples/substrafl/get_started/torch_fedavg_assets/requirements.txt b/docs/source/examples/substrafl/get_started/torch_fedavg_assets/requirements.txt
@@ -1,7 +1,7 @@
-matplotlib==3.6.3
-numpy==1.26.4
+matplotlib==3.9.2
+numpy==2.1.1
 pandas==2.2.2
-scikit-learn==1.5.0
+scikit-learn==1.5.2
 substrafl
-torch==2.2.1
-torchvision==0.17.1
+torch==2.4.1
+torchvision==0.19.1
diff --git a/docs/source/examples/substrafl/go_further/diabetes_substrafl_assets/requirements.txt b/docs/source/examples/substrafl/go_further/diabetes_substrafl_assets/requirements.txt
@@ -1,5 +1,5 @@
-matplotlib==3.6.3
-scikit-learn==1.5.0
-numpy==1.26.4
+matplotlib==3.9.2
+scikit-learn==1.5.2
+numpy==2.1.1
 pandas==2.2.2
 substrafl
diff --git a/docs/source/examples/substrafl/go_further/run_diabetes_substrafl.ipynb b/docs/source/examples/substrafl/go_further/run_diabetes_substrafl.ipynb
diff --git a/docs/source/examples/substrafl/go_further/run_iris_sklearn.ipynb b/docs/source/examples/substrafl/go_further/run_iris_sklearn.ipynb
diff --git a/docs/source/examples/substrafl/go_further/run_mnist_cyclic.ipynb b/docs/source/examples/substrafl/go_further/run_mnist_cyclic.ipynb
diff --git a/docs/source/examples/substrafl/go_further/sklearn_fedavg_assets/requirements.txt b/docs/source/examples/substrafl/go_further/sklearn_fedavg_assets/requirements.txt
diff --git a/docs/source/examples/substrafl/go_further/torch_cyclic_assets/requirements.txt b/docs/source/examples/substrafl/go_further/torch_cyclic_assets/requirements.txt
