refactor(everything): Refactor for easier to maintain code

CI based on Github workflows, EyeVolume class as a standard way for handling OCT volumes, support for HEXEX VOL/XML, Bscans from folder, DUKE and RETOUCH data

BREAKING CHANGE:

.github/workflows/_quality.yaml

@@ -0,0 +1,55 @@
+name: Test
+
+on: workflow_call
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: [ "3.8" ]#, "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache Poetry
+        uses: actions/cache@v2
+        id: poetry-cache
+        with:
+          path: |
+            ~/.local
+          key: poetry-1.1.13
+          restore-keys: |
+            poetry-1.1.13
+
+      - name: Cache virtualenv
+        uses: actions/cache@v2
+        id: virtualenv-cache
+        with:
+          path: |
+            ~/.cache
+          key: virtualenv-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            virtualenv-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install and configure Poetry
+        if: steps.poetry-cache.outputs.cache-hit != 'true'
+        uses: snok/install-poetry@v1.3
+        with:
+          version: 1.1.13
+          virtualenvs-create: true
+          virtualenvs-in-project: false
+          installer-parallel: true
+
+      - name: Install Dependencies
+        if: steps.virtualenv-cache.outputs.cache-hit != 'true'
+        run: poetry install
+
+      - name: Test with pytest
+        run: poetry run pytest --cov .

.github/workflows/_release.yaml

@@ -0,0 +1,26 @@
+name: Semantic release
+
+on:
+  workflow_call:
+    secrets:
+      PYPI_PASSWORD:
+        required: true
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - name: Python Semantic Release
+        uses: relekang/python-semantic-release@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          repository_username: __token__
+          repository_password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/ci.yaml

@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Quality:
+    uses: MedVisBonn/eyepy/.github/workflows/_quality.yaml@master
+
+  Release:
+    needs: Quality
+    uses: MedVisBonn/eyepy/.github/workflows/_release.yaml@master
+    secrets:
+      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -1,3 +1,6 @@
+.idea/
+examples/notebooks
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -102,4 +105,4 @@ ENV/
 .mypy_cache/
 
 # Pycharm
-.idea/
+old/.idea/

.pre-commit-config.yaml

@@ -1,39 +1,17 @@
-# See https://pre-commit.com for more information
-# See https://pre-commit.com/hooks.html for more hooks
-minimum_pre_commit_version: 1.20.0
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
-    -   id: requirements-txt-fixer
-    -   id: fix-encoding-pragma
-    -   id: check-docstring-first
--   repo: https://github.com/asottile/blacken-docs
-    rev: v1.3.0
-    hooks:
-    -   id: blacken-docs
--   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.4.2
-    hooks:
-    -   id: python-use-type-annotations
--   repo: https://github.com/myint/docformatter
-    rev: v1.3.1
-    hooks:
-    -   id: docformatter
--   repo: https://github.com/pycqa/isort
-    rev: 5.6.3
-    hooks:
-    -   id: isort
-        name: isort (python)
-    -   id: isort
-        name: isort (cython)
-        types: [cython]
--   repo: https://github.com/psf/black
-    rev: 19.10b0
-    hooks:
-    -   id: black
-        language_version: python3 # Should be a command that runs python3.6+
+- hooks:
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.1.0
+- hooks:
+  - id: black
+  repo: https://github.com/psf/black
+  rev: 21.12b0
+- hooks:
+  - id: commitizen
+    stages:
+    - commit-msg
+  repo: https://github.com/commitizen-tools/commitizen
+  rev: v2.20.4

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020, Olivier Morelle
+Copyright (c) 2022, Olivier Morelle
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal