Merge branch 'dev_experimental' into dev_main

Author: PeterCalifano

.github/workflows/build_test_wheel.yml

@@ -0,0 +1,68 @@
+name: Python Package using Conda
+
+# Set run on push on main branches and only if src file has changed
+on: 
+  push:
+   branches:
+    - main 
+    - dev_main
+   paths:
+    - examples/**
+    - pyTorchAutoForge/**
+    - tests/**
+  pull_request:
+    branches:
+    - main
+    - dev_main
+  release: # Always
+    types:
+    - created
+    - published
+    - edited
+    - deleted
+    - prereleased
+    - released
+    - unpublished
+  
+jobs:
+  build-package:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        #conda env update --file environment.yml --name base
+        pip install .
+  verify-lint:
+    runs-on: ubuntu-latest
+    needs: build-package
+    steps:
+    - uses: actions/checkout@v4
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+  test-package:
+    runs-on: ubuntu-latest
+    needs: build-package
+    steps:
+    - uses: actions/checkout@v4
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest # TODO add specifications of test
+    

.gitignore

@@ -6,6 +6,7 @@ mlruns/*
 *.asv
 checkpoints/*
 pyTorchAutoForge/.experimental/*
+*autodoc*
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -131,11 +132,7 @@ celerybeat.pid
 
 # Environments
 .env
-<<<<<<< HEAD
-.venv*
-=======
 .venv*/
->>>>>>> fdfbee2 (Added script for automatic setup on Linux)*/
 env/
 venv/
 ENV/

.readthedocs.yaml

@@ -0,0 +1,26 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: doc/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: doc/requirements.txt
+    - method: pip
+      path: .
+        
+

README.md

@@ -1,16 +1,21 @@
 # pyTorchAutoForge
-PyTorchAutoForge library is based on raw PyTorch and designed to automate DNN development, model tracking and deployment, tightly integrated with MLflow and Optuna. It also supports spiking networks libraries (WIP). Model optimization and deployment can be performed using ONNx, pyTorch facilities or TensorRT (WIP). The library also aims to be compatible with Jetson Orin Nano Jetpack rev6.1. 
 
-# Installation using pip
+A library based on PyTorch (<https://pytorch.org/>) and designed to automate ML models development, tracking and deployment, integrated with MLflow and Optuna (<https://mlflow.org/>, <https://optuna.org/>). It also supports spiking networks libraries (WIP). Model optimization and deployment can be performed using ONNx, pyTorch facilities or TensorRT (WIP). The library also aims to be compatible with Jetson Orin Nano Jetpack rev6.1. ASeveral other functionalities and utilities for sklearn and pySR (<https://github.com/MilesCranmer/PySR>) are included (see README and documentation).
+
+## Installation using pip
+
 Run in a conda or virtual environment:
+
 ```bash
-pip install pyTorchAutoForge==0.1.0b1
+pip install pyTorchAutoForge
 ```
-Dependencies for the core modules should be installed automatically using pip. 
 
-# Manual installation (bash)
+Dependencies for the core modules should be installed automatically using pip.
+
+## Manual installation (bash)
+
 1) Clone the repository
 2) Create a virtual environment using python >= 3.10 (tested with 3.11), using `python -m venv <your_venv_name>`
-3) Activate the virtual environment using `source <your_venv_name>/bin/activate` on Linux 
+3) Activate the virtual environment using `source <your_venv_name>/bin/activate` on Linux
 4) Install the requirements using `pip install -r requirements.txt`
 5) Install the package using `pip install .` in the root folder of the repository

TODO

@@ -0,0 +1,35 @@
+# List of TODOs
+
+## Library management and config
+
+- [x] Review linters/code formatting tools and configure them properly to comply with standards
+
+- [ ] Add type annotations for mypy (currently disable no-untyped-defs due to too many errors)
+
+- [ ] Automate documentation building process
+
+- [ ] Implement CI/CD to run tests
+
+- [ ] Improve docstrings in src code
+
+- [x] Configure project to use hatch build for automatic versioning linked to git tags
+
+## Modules development
+
+### Evaluation
+
+- [ ] Improve ModelProfiler to provide more functionalities from torch_profiler
+
+- [ ]
+
+### Optimization
+
+- [ ]
+
+### API module
+
+- [ ] Add prototype implementation of mlflow api: MlflowHandler to replace manually written code in optimization module
+
+- [ ] Add prototype implementation of telegram bot api for training push notifications
+
+- [ ] Improve torch saving api

_version.py

@@ -0,0 +1,21 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.0.dev26+g7100b36.d20250330'
+__version_tuple__ = version_tuple = (0, 1, 0, 'dev26', 'g7100b36.d20250330')

conda_install.sh

@@ -174,6 +174,11 @@ if [ $jetson_target -eq 1 ]; then
       pip install -e .  # Install the package in editable mode
   else
     echo "Building and installing pyTorchAutoForge wheel..."
+    # Remove previous build 
+    rm -rf dist
+    rm -rf build
+    rm -rf pyTorchAutoForge.egg-info
+    # Build and install
     python3 -m build 
     pip install dist/*.whl  # Install pyTorchAutoForge wheel # FIXME editable mode does not work for this
   fi
@@ -197,6 +202,11 @@ else
       pip install -e .  # Install the package in editable mode
   else
     echo "Building and installing pyTorchAutoForge wheel..."
+    # Remove previous build 
+    rm -rf dist
+    rm -rf build
+    rm -rf pyTorchAutoForge.egg-info
+    # Build and install
     python3 -m build 
     pip install dist/*.whl  # Install pyTorchAutoForge wheel # FIXME editable mode does not work for this
   fi

deeplab1.png

@@ -0,0 +1,8 @@
+<<<<<<< HEAD
+html
+doctrees
+=======
+doctrees
+html
+>>>>>>> main
+sources