Merge pull request #1 from softwaremill/feat/base_code_structure

WIP: Initial architecture and codebase structure

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

src/Makefile

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+MAX_LINE_LENGTH=120
+TARGET_PYTHON_VERSION=py38
+
+all: style lint type
+
+style:
+	# Check only
+	poetry run black --target-version ${TARGET_PYTHON_VERSION} \
+	--check \
+	--verbose \
+	--line-length ${MAX_LINE_LENGTH} \
+	src/ tests/
+
+format:
+	# Format all files
+	poetry run black --target-version ${TARGET_PYTHON_VERSION} \
+	--verbose \
+	--line-length ${MAX_LINE_LENGTH} \
+	src/ tests/
+
+type: 
+	poetry run mypy src/ tests/ \
+	--ignore-missing-imports \
+	--follow-imports=skip \
+	--show-error-context
+
+lint:
+	poetry run pylint src/ tests/ \
+	--disable=C,W,no-error,design,no-member,duplicate-code,unnecessary-comprehension,import-error,no-name-in-module \
+	--max-line-length=${MAX_LINE_LENGTH} \
+	--enable=C0303,W0613,R1705,C0303,C0305,W0601,W0641,W0611,W0613,W0614,W0631,W0602

src/README.md

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+# AutoXAI
+
+## Requirements
+
+This package was tested using `Python3.8`.
+
+## Environment
+
+To prepare virtual environment You can use `virtualenv`.
+```bash
+virtualenv -p python3.8 <ENV_NAME>
+```
+
+Activate new virtual environment:
+```bash
+source <ENV_NAME>/bin/activate
+```
+
+Firstly upgrade `pip` package:
+```bash
+python3 -m pip install --upgrade pip
+```
+
+Now You can install all dependencies from `requirements.txt` file:
+```bash
+python3 -m pip install -r requirements.txt
+```
+
+And finally, You can install all dependencies from `poetry.lock` file.
+```bash
+poetry install
+```
+
+## Development
+
+We are using `Makefile` to perform automatic linting, style and type checks.
+To perform them just type:
+```bash
+make all
+```
+
+# Note
+
+At the moment only explainable algorithms for image classification are 
+implemented to test design of the architecture. In future more algorithms 
+and more computer vision tasks will be introduces. In the end module should 
+work with all types of tasks (NLP, etc.).
+
+## Architecture
+
+Module is designed to operate in two modes: offline and online. In offline 
+mode user can explain already trained model against test data. In online 
+mode user can attach callback to training framework to perform explanations 
+of predictions during training at the end of each validation epochs.
+
+Module is using cache directory to store artifacts and configuration similar 
+to `Tensorboard`. There are many levels of directory structure:
+```bash
+cache_directory/
+└── <date>
+    ├── <uuid>
+    │   ├── data
+    │   │   ├── input_data
+    │   │   │   └── <data>.pkl
+    │   │   ├── normalized
+    │   │   │   └── <data>.pkl
+    │   │   ├── original
+    │   │   │   └── <data>.pkl
+    │   │   └── predictions
+    │   │       └── <data>.pkl
+    │   ├── explanations
+    │   │   ├── <method1>
+    │   │   │   └── figures
+    │   │   │       ├── attributes.npy
+    │   │   │       └── params.json.pkl
+    │   │   ├── <method2>
+    │   │   │   └── figures
+    │   │   │       ├── attributes.npy
+    │   │   │       └── params.json.pkl
+    │   │   ├── ...
+    └── ...
+```
+
+Another part of this module is GUI interface to view explanations and 
+modify parameters of explainable algorithms. As a PoC application in 
+`streamlit` is developed.