Issue/105 improvments fixes

.devcontainer/Dockerfile

@@ -0,0 +1,6 @@
+FROM mcr.microsoft.com/devcontainers/python:3.12
+
+ENV PYTHONUNBUFFERED 1
+
+# Install Python Deps
+RUN pip install --upgrade pip pre-commit poetry

.devcontainer/devcontainer.json

@@ -0,0 +1,47 @@
+{
+	"name": "pyAKI",
+	"dockerComposeFile": "docker-compose.yml",
+	"service": "pyaki",
+	"workspaceFolder": "/workspaces",
+	"remoteUser": "vscode",
+	"postCreateCommand": "bash .devcontainer/scripts/post-create.sh",
+	"postStartCommand": "bash .devcontainer/scripts/post-start.sh",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-python.python",
+				"ms-python.mypy-type-checker",
+				"tamasfe.even-better-toml",
+				"charliermarsh.ruff",
+				"ryanluker.vscode-coverage-gutters",
+				"GitHub.copilot",
+				"GitHub.copilot-chat",
+				"ms-vsliveshare.vsliveshare",
+				"GitHub.vscode-pull-request-github",
+				"github.vscode-github-actions",
+				"ms-toolsai.jupyter"
+			],
+			"settings": {
+				"[python]": {
+					"editor.defaultFormatter": "charliermarsh.ruff",
+					"editor.codeActionsOnSave": {
+						"source.fixAll": true,
+						"source.organizeImports": true
+					},
+					"files.eol": "\n"
+				},
+				"mypy-type-checker.importStrategy": "fromEnvironment",
+				"mypy-type-checker.args": [
+					"--config-file=${workspaceFolder}/pyproject.toml"
+				],
+				"python.analysis.typeCheckingMode": "basic",
+				"coverage-gutters.coverageBaseDir": "/workspaces/pyAKI",
+				"coverage-gutters.coverageFileNames": [
+					"coverage.xml"
+				]
+			}
+		}
+	},
+	"forwardPorts": [],
+	"initializeCommand": "bash .devcontainer/scripts/initialize.sh"
+}

.devcontainer/docker-compose.yml

@@ -0,0 +1,17 @@
+version: '3.8'
+
+services:
+  pyaki:
+    container_name: pyaki
+
+    init: true
+    build:
+      context: ..
+      dockerfile: .devcontainer/Dockerfile
+    environment:
+      - no_proxy="127.0.0.1,localhost"
+      - NO_PROXY="127.0.0.1,localhost"
+    volumes:
+      - ..:/workspaces:cached
+    # Overrides default command so things don't shut down after the process ends.
+    command: sleep infinity

.devcontainer/scripts/initialize.sh

@@ -0,0 +1 @@
+docker pull mcr.microsoft.com/devcontainers/python:3.13

.devcontainer/scripts/post-create.sh

@@ -0,0 +1,5 @@
+# Add bash-completion's
+echo "source /usr/share/bash-completion/completions/git" >> ~/.bashrc
+
+# install deps
+pre-commit install

.devcontainer/scripts/post-start.sh

@@ -0,0 +1 @@
+poetry install --with dev

.github/dependabot.yml

@@ -5,11 +5,19 @@
 
 version: 2
 updates:
+  - package-ecosystem: "docker"
+    directory: "/"
+    schedule:
+      interval: "daily"
+  - package-ecosystem: "devcontainers"
+    directory: "/"
+    schedule:
+      interval: "daily"
   - package-ecosystem: "github-actions" # See documentation for possible values
     directory: "/" # Location of package manifests
     schedule:
       interval: "daily"
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
-      interval: "daily"
+      interval: "daily"

.github/workflows/python_cd.yml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Continuous Delivery (Python)
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    environment: pyaki
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]  # Add more Python versions to test here
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache Virtual Environment
+      uses: actions/cache@v4
+      with:
+        path: |
+          .venv
+          ~/.cache/pip
+          ~/.cache/pypoetry
+        key: ${{ runner.os }}-venv-${{ hashFiles('poetry.lock') }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry
+        poetry install --with dev
+
+    - name: Build and publish Package
+      run: |
+        poetry version ${{ github.ref_name }}
+        poetry publish --skip-existing --build
+      env:
+        POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}

.github/workflows/python_ci.yml

@@ -0,0 +1,52 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Continuous Integration (Python)
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  build:
+    environment: pyaki
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]  # Add more Python versions to test here
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache Virtual Environment
+      uses: actions/cache@v4
+      with:
+        path: |
+          .venv
+          ~/.cache/pip
+          ~/.cache/pypoetry
+        key: ${{ runner.os }}-venv-${{ hashFiles('poetry.lock') }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry
+        poetry install --with dev
+
+    - name: Lint with ruff
+      run: poetry run ruff check .
+    - name: Check types with mypy
+      run: poetry run mypy .
+    - name: Test with pytest
+      run: poetry run pytest .
+
+    - name: Coveralls
+      run: poetry run coveralls
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

.gitignore

@@ -1,5 +1,4 @@
 # env
-.vscode
 results
 paper
 .DS_Store
@@ -164,5 +163,3 @@ cython_debug/
 #  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/
-
-/tests/data/*

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+# https://pre-commit.com/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: fix-byte-order-marker
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: detect-private-key
+      - id: check-case-conflict
+      - id: check-toml
+      - id: check-json
+      - id: check-yaml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.1
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        exclude: "^tests/.*"

.ruff.toml

@@ -0,0 +1,76 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+line-length = 120
+indent-width = 4
+
+# Assume Python 3.12
+target-version = "py312"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = []
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"

.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

.vscode/tasks.json

@@ -0,0 +1,17 @@
+{
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "run pre-commit",
+            "type": "shell",
+            "command": "pre-commit run --all-files",
+            "problemMatcher": []
+        },
+        {
+            "label": "update pre-commit",
+            "type": "shell",
+            "command": "pre-commit autoupdate",
+            "problemMatcher": []
+        }
+    ]
+}

AUTHORS

@@ -1,6 +1,5 @@
 Christian Porschen <[email protected]>
 Jan Ernsting <[email protected]>
-Paul <[email protected]>
 Paul-B98 <[email protected]>
 aegis301 <[email protected]>
 dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>