Update Python version references to 3.9 in documentation and configuration files

- Updated .gitignore to include new input and test directories.
- Changed Python version from 3.8 to 3.9 in .readthedocs.yml, setup.cfg, and run script.
- Updated documentation to reflect the use of Python 3.9 in various tutorials.

Signed-off-by: M Q <[email protected]>

Author: MMelQin

.readthedocs.yml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.9"
     # You can also specify other tool versions:
     # nodejs: "20"
     # rust: "1.70"

CONTRIBUTING.md

@@ -138,7 +138,7 @@ MONAI Deploy App SDK's code coverage report is available at [CodeCov](https://co
 #### Building the documentation
 
 :::{note}
-Please note that the documentation builds successfully in Python 3.8 environment, but fails with Python 3.10.
+Please note that the documentation builds successfully in Python 3.9 environment, but fails with Python 3.10.
 :::
 
 MONAI's documentation is located at `docs/`.

docs/requirements.txt

@@ -1,6 +1,6 @@
 Sphinx==4.1.2
 sphinx-autobuild==2021.3.14
-myst-nb==0.17.2  # this version is fine in python 3.8 and avoids pulling in multiple nbformat packages
+myst-nb==0.17.2  # this version is fine in python 3.9 and avoids pulling in multiple nbformat packages
 myst-parser==0.18.0
 lxml_html_clean  # needed by myst-nb
 linkify-it-py==1.0.1  # https://myst-parser.readthedocs.io/en/latest/syntax/optional.html?highlight=linkify#linkify

docs/source/getting_started/tutorials/mednist_app.md

@@ -5,9 +5,9 @@ This tutorial demos the process of packaging up a trained model using MONAI Depl
 ## Setup
 
 ```bash
-# Create a virtual environment with Python 3.8.
+# Create a virtual environment with Python 3.9.
 # Skip if you are already in a virtual environment.
-conda create -n mednist python=3.8 pytorch jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
+conda create -n mednist python=3.9 pytorch jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
 conda activate mednist
 
 # Launch JupyterLab if you want to work on Jupyter Notebook

docs/source/getting_started/tutorials/monai_bundle_app.md

@@ -5,9 +5,9 @@ This tutorial shows how to create an organ segmentation application for a PyTorc
 ## Setup
 
 ```bash
-# Create a virtual environment with Python 3.8.
+# Create a virtual environment with Python 3.9.
 # Skip if you are already in a virtual environment.
-conda create -n monai python=3.8 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
+conda create -n monai python=3.9 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
 conda activate monai
 
 # Launch JupyterLab if you want to work on Jupyter Notebook

docs/source/getting_started/tutorials/multi_model_app.md

@@ -7,9 +7,9 @@ The models used in this example are trained with MONAI, and are packaged in the
 ## Setup
 
 ```bash
-# Create a virtual environment with Python 3.8.
+# Create a virtual environment with Python 3.9.
 # Skip if you are already in a virtual environment.
-conda create -n monai python=3.8 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
+conda create -n monai python=3.9 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
 conda activate monai
 
 # Launch JupyterLab if you want to work on Jupyter Notebook

docs/source/getting_started/tutorials/segmentation_app.md

@@ -7,9 +7,9 @@ Please note that the following steps are for demonstration purpose. The code pul
 ## Setup
 
 ```bash
-# Create a virtual environment with Python 3.8.
+# Create a virtual environment with Python 3.9.
 # Skip if you are already in a virtual environment.
-conda create -n monai python=3.8 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
+conda create -n monai python=3.9 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
 conda activate monai
 
 # Launch JupyterLab if you want to work on Jupyter Notebook

docs/source/getting_started/tutorials/segmentation_clara-viz_app.md

@@ -5,9 +5,9 @@ This tutorial shows how to create an organ segmentation application for a PyTorc
 ## Setup
 
 ```bash
-# Create a virtual environment with Python 3.8.
+# Create a virtual environment with Python 3.9.
 # Skip if you are already in a virtual environment.
-conda create -n monai python=3.8 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
+conda create -n monai python=3.9 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
 conda activate monai
 
 # Launch JupyterLab if you want to work on Jupyter Notebook

docs/source/getting_started/tutorials/simple_app.md

@@ -5,9 +5,9 @@ This tutorial shows how a simple image processing application can be created wit
 ## Setup
 
 ```bash
-# Create a virtual environment with Python 3.8.
+# Create a virtual environment with Python 3.9.
 # Skip if you are already in a virtual environment.
-conda create -n monai python=3.8 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
+conda create -n monai python=3.9 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
 conda activate monai
 
 # Launch JupyterLab if you want to work on Jupyter Notebook

run

@@ -344,10 +344,10 @@ install_python_dev_deps() {
         # Copy the cuda runtime library to the fixed location (workaround for readthedocs) so that
         # we can leverage the existing LD_LIBRARY_PATH (configured by the readthedocs UI) to locate the cuda runtime library.
         # (LD_LIBRARY_PATH is set to /home/docs/ for that purpose)
-        # Note that 'python3.8' is hard-coded here, it should be updated if the Python version changes by
+        # Note that 'python3.9' is hard-coded here, it should be updated if the Python version changes by
         # .readthedocs.yml or other configurations.
-        run_command ls -al /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.8/site-packages/nvidia/cuda_runtime/lib/
-        run_command cp /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.8/site-packages/nvidia/cuda_runtime/lib/*.so* /home/docs/
+        run_command ls -al /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.9/site-packages/nvidia/cuda_runtime/lib/
+        run_command cp /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.9/site-packages/nvidia/cuda_runtime/lib/*.so* /home/docs/
         run_command ls -al /home/docs/
     fi
 }