Merge pull request #1 from BrainLesion/foundation_work

new: init

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Install '....'
+3. Run commands '....'
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment**
+
+### operating system and version?
+e.g. Ubuntu 23.10 LTS
+
+### Python environment and version?
+e.g. Conda environment with Python 3.10. Check your Python version with:
+```sh
+python --version
+```
+
+### version of brainles_preprocessing ?
+please specify your version of brainles_preprocessing (please make sure you run the latest version):
+```sh
+pip freeze | grep brainles_preprocessing
+```
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question.md

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+---
+name: Question
+about: Please ask your question, make sure to read the FAQ before
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Your question**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

.github/workflows/release.yml

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+name: release
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+
+jobs:
+   publish:
+    name: Publish to test PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository 
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          pip install build
+          pip install twine
+      - name: Build package
+        run: python -m build
+      - name: Upload to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: | 
+          twine upload dist/*.whl

.github/workflows/tests.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11","3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # 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
+    - name: Test with pytest
+      run: |
+        pytest

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+      # Tell poetry to not use a virtual environment
+      - poetry config virtualenvs.create false
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      - poetry install --with docs
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs

docs/Makefile

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+# 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

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%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
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

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+# 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("../../"))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'panoptica'
+copyright = '2023, florian kofler et al.'
+author = 'Florian Kofler et al.'
+
+
+# -- 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.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx_copybutton",
+    "myst_parser",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# 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 = "sphinx_rtd_theme"
+
+# 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']
+
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "private-members": True,
+    "show-inheritance": True,
+}

docs/source/index.rst

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+.. panoptica documentation master file, created by
+   sphinx-quickstart on Tue Nov 21 12:02:41 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to panoptica's documentation!
+=====================================
+
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Panoptica:
+
+   panoptica.rst
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Metrics:
+
+   panoptica.metrics.rst
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Utils:
+
+   panoptica.utils.rst

docs/source/panoptica.metrics.rst

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+panoptica.utils
+===========================
+
+
+panoptica.metrics.assd
+--------------------------------------------
+
+.. automodule:: panoptica.metrics.assd
+
+
+panoptica.metrics.dice
+--------------------------------------
+
+.. automodule:: panoptica.metrics.dice
+
+
+
+panoptica.metrics.iou
+--------------------------------------
+
+.. automodule:: panoptica.metrics.iou
+