Merge pull request #1 from edadaltocg/dev

Merge dev branch into master

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+insert_final_newline = false
+
+[*.py]
+indent_size = 4

.env.example

@@ -1,3 +1,3 @@
-export DATASETS_DIR="storage/"
+export DATA_DIR="storage/"
 export CHECKPOINTS_DIR="checkpoints/"
 export RESULTS_DIR="results/"

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8"]
 
     steps:
     - uses: actions/checkout@v3
@@ -27,14 +27,17 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install -r requirements_dev.txt
+        python -m pip install -e .
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
+    - name: Format and Lint
       run: |
+        black --config pyproject.toml .
+        isort --settings pyproject.toml .
         # 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
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=120 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        coverage run -m pytest -vv tests/models.py

.gitignore

@@ -147,10 +147,13 @@ dmypy.json
 /results
 /storage
 /logs
-/checkpoints
+/checkpoints*
 
 # .lock
 *.lock
 
 # github releases
 /releases
+
+/deprecated
+/scripts/bash

CHANGELOG.md

@@ -0,0 +1,9 @@
+# Changelog
+
+## Template
+
+Date: YYYY-MM-DD, Version: X.Y.Z, Author: @username, PR: #PR/Issue: #ISSUE (optional), Milestone: description
+
+## History
+
+2023-02-28, 0.1.0, @edadaltocg, Initial release.

README.md

@@ -1,6 +1,6 @@
 <p align="center">
     <br>
-    <img src="./face-with-monocle.svg" width="150" height="150" /> 
+    <img src="./face-with-monocle.svg" width="150" height="150" />
     <br>
 </p>
 
@@ -10,3 +10,56 @@
 Package to accelerate research on out-of-distribution (OOD) detection inspired by Huggingface's transformers.
 
 Under development.
+
+## Deployment & Documentation & Stats & License
+
+[![PyPi version](https://badgen.net/pypi/v/pip/)](https://pypi.org/project/pip)
+
+[![Documentation Status](https://readthedocs.org/projects/ansicolortags/badge/?version=latest)](http://ansicolortags.readthedocs.io/?badge=latest)
+
+[![GitHub stars](https://img.shields.io/github/stars/Naereen/StrapDown.js.svg?style=social&label=Star&maxAge=2592000)](https://GitHub.com/Naereen/StrapDown.js/stargazers/)
+
+
+[![GitHub forks](https://badgen.net/github/forks/Naereen/Strapdown.js/)](https://GitHub.com/Naereen/StrapDown.js/network/)
+
+[![PyPI download month](https://img.shields.io/pypi/dm/ansicolortags.svg)](https://pypi.python.org/pypi/ansicolortags/)
+
+[![GitHub contributors](https://img.shields.io/github/contributors/Naereen/badges.svg)](https://GitHub.com/Naereen/badges/graphs/contributors/)
+
+[![DOI:10.1007/978-3-319-76207-4_15](https://zenodo.org/badge/DOI/10.1007/978-3-319-76207-4_15.svg)](https://doi.org/10.1007/978-3-319-76207-4_15)
+
+[![PyPi license](https://badgen.net/pypi/license/pip/)](https://pypi.org/project/pip/)
+
+-----
+
+<!--
+## Examples
+
+```python
+``` -->
+
+## Features
+
+- Datasets with md5 checksums.
+- Models pre-trained on CIFAR and integrated in `timm`.
+- Pipeline for evaluating OOD detectors on CIFAR and ImageNet benchmarks.
+- Multiple seed simulations.
+- Diverse aggregation methods for OOD detection.
+- Efficient OOD detection metrics.
+
+## Installation
+
+```bash
+pip install detectors
+```
+
+<!-- ## TODO
+
+- Pipeline for generating results table.
+
+## Contributing
+
+## Citing detectors
+
+```bibtex
+``` -->

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,84 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../../src/"))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "detectors"
+copyright = "2023, Eduardo Dadalto"
+author = "Eduardo Dadalto"
+
+# The full version, including alpha/beta/rc tags
+release = "0.1.0"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.autosummary",
+    "myst_parser",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.imgmath",
+    "sphinx.ext.viewcode",
+    "sphinxcontrib.bibtex",
+]
+
+source_suffix = [".rst", ".md"]
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_preprocess_types = False
+napoleon_type_aliases = None
+napoleon_attr_annotations = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "classic"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,18 @@
+Welcome to detectors's documentation!
+=====================================
+
+.. automodule:: detectors.config
+    :members:
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

pyproject.toml

@@ -1,3 +1,10 @@
+[tool.isort]
+atomic = true
+profile = "black"
+line_length = 120
+skip_gitignore = true
+src_paths = ["src", "tests", "scripts", "examples", "demo", "setup.py"]
+
 [tool.black]
-line-length = 119
-target-version = ['py35']
+line-length = 120
+include = '\.pyi?$'

requirements_dev.txt

@@ -0,0 +1,12 @@
+setuptools
+black
+isort
+pytest
+pytest-timeout
+pytest-xdist
+coverage
+twine
+sphinx
+six
+myst-parser
+flake8