Refactor configuration

* Configure conda installation

* Refactor the project code to be a package

* Add pylint dependency

* Remove flake8 configuration from setup.cfg

* Import the version as __version__ attribute in the package

* Ignore the _version.py file

* Add pyproject file to configure python tools

* Add editorconfig file to standardize the editors

* Add PyLint configuration

* Add .flake8 configuration file

* Remove PyLint configuration

* Add pydocstyle configuration

* Update isort configuration

* Add bandit configuration

* Add pre-commit configuration

* pre-commit configuration updated.

Co-authored-by: Valentino Maiorca <[email protected]>

* Remove the PROJECT_ROOT env variable and infer it

Co-authored-by: Valentino Maiorca <[email protected]>

* Disable hydra logging auto-configuration

* Add logging pretty printing

* Force logging configuration before pytorch lightning

See Lightning-AI/pytorch-lightning#1503

* Enable exceptions pretty printing

* Enable pin-memory if not on CPU

* Updated pin_memory policy to consider all "Trainer.gpus" data types.

Co-authored-by: Valentino Maiorca <[email protected]>

Simplify the mwe included in the template

https://stackoverflow.com/a/68172142

* Log the code used in the current experiment to wandb

* Improve files filtering when uploading the code to wandb

Functionalities decoupling via external library (nn-core).

* Disable pytest coverage uncompatible with PyCharm

See:
- https://stackoverflow.com/questions/40718760/unable-to-debug-in-pycharm-with-pytest
- https://youtrack.jetbrains.com/issue/PY-20186

* Update coverage configuration to ignore unreachable code

* Avoid executing the model test in fast_dev_run mode

* Add conftest to define basic configurations and training

* Add tests to validate configuration

* Add train loop tests

* Optimize fixture scoping

* Update template to be compatible with the tests

* Reorganize conftest fixtures

* Test the configuration is correctly stored on the storage folder

* Test the checkpoint are correctly saved in the storage

* Test the checkpoint can be loaded

* Test the configuration is stored in the checkpoint

* Rename test_resume into test_checkpoint

* Test on save checkpoint monkey patching

* Test PROJECT_ROOT resolution

* Test train loop in different regimens

* New fast_dev_run variable.

* Let's not forget the important things.

Co-authored-by: Valentino Maiorca <[email protected]>

* Remove unnecessary on save checkpoint hook injection

* Test the run path is stored in the checkpoint

* Implement resume logic

* Test resume behaviour

* Refactor resume with semantic options

* Refactor NNLogger usages

* Move NNTemplateCore callback from configuration to code

* Add github workflow to run pre-commits and tests

- Temporary change the nn-template-core to a git dependency
- Python 3.7 not supported
- Remove python dependency from environment

* Add publish workflow to deploy docs on release

* Update on condition of the Test Suite

* Add cache names

* Pin setuptools version

* Pin PyTorch version

* Fix nn_template import

* Downgrade setuptools

https://stackoverflow.com/questions/70520120/attributeerror-module-setuptools-distutils-has-no-attribute-version
pytorch/pytorch#69904

* Remove nn-template-core git dependency

* Add on push trigger for main and develop branches

Remove some trigger from the Test Suite workflow

Remove requirements.txt not necessary

Pre-initialize LICENSE correctly

* Add missing docstrings

* Fix pre-commit errors

* Update MetaData docstring

Co-authored-by: Valentino Maiorca <[email protected]>

* Add dynamic badges for tests, docs and nn-core version

* Remove unnecessary information in the README

* Update README

* Update structure in README

* Update checks badges

Co-authored-by: Valentino Maiorca <[email protected]>

* Add docs with mkdocs, material for mkdocs and mike

* Add Action to publish docs on release

* Update docs homepage

* Delete requirements.txt

Co-authored-by: Valentino Maiorca <[email protected]>

* Fix cache keys hashfiles

* Add cache keys echoing

* Move cache key generation after project generation

* Remove leading dot in conda env file

* Add a DAG in the post hook interactive setup

* Add pytest into suggested commands

* Initialize gh-pages branch in the post hook

* Remove mike set-default in ci/cd since it's set in post hook

* Improve "remember to" message

* Always in autorun if in interactive mode

* Improve git remote prompt

* Fix remote parametrization in the README

* Fix git remote parametrization

* Add cd command in develop setup

* Add Publications section in documentation

* Clean up documentation for release

* Update README.md

Co-authored-by: Valentino Maiorca <[email protected]>