chore: init commit py-vibracore

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+omit = */tests/*
+source = src/pyvibracore

.flake8

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+[flake8]
+# just stop shouting as black decides line lengths.
+max-line-length = 180
+# E203, W504: due to black fmt
+ignore = E203,W503
+exclude = ["test*"]

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/deploy_docs.yaml

@@ -0,0 +1,33 @@
+name: deploy docs
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy_docs:
+    name: Deploy docs
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install -r requirements.txt
+          pip install .
+
+      - name: Build docs
+        run: sphinx-build -b html docs public
+
+      - name: Publish docs
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./public

.github/workflows/release_pypi.yaml

@@ -0,0 +1,43 @@
+name: Release
+
+on:
+  push:
+    tags: ['*']
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/py-vibracore
+
+    # Mandatory permission for trusted publishing to PyPi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          pip install setuptools build
+
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v3
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test.yaml

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+name: Test
+
+on:
+  push:
+    paths-ignore:
+      - "docs/**"
+      - "**.md"
+  pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "**.md"
+  workflow_call:
+
+jobs:
+  test:
+    name: Unit test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - '3.9'
+          - '3.10'
+          - '3.11'
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          # shellcheck disable=SC2102
+          pip install -e .[test]
+
+      - name: Test
+        run: coverage run -m pytest
+
+      - name: Post coverage results
+        uses: coverallsapp/github-action@v2
+        with:
+          flag-name: run-${{ matrix.python-version }}
+          parallel: true
+
+  finish:
+    needs: test
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel-finished: true
+
+  lint:
+    name: Formatting check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # Full git history is needed to get a proper list of changed test_files within `super-linter`
+          fetch-depth: 0
+
+      - name: Lint
+        uses: github/super-linter@v5
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+
+          VALIDATE_JSCPD: false
+          VALIDATE_CSS: false
+          VALIDATE_BASH: false
+          VALIDATE_YAML: false
+          VALIDATE_PYTHON_PYLINT: false
+          VALIDATE_NATURAL_LANGUAGE: false
+          VALIDATE_MARKDOWN: false
+
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+          LINTER_RULES_PATH: /
+          PYTHON_BLACK_CONFIG_FILE: pyproject.toml
+          PYTHON_ISORT_CONFIG_FILE: pyproject.toml
+          PYTHON_MYPY_CONFIG_FILE: pyproject.toml
+          PYTHON_FLAKE8_CONFIG_FILE: .flake8
+
+  test_docs:
+    name: Test docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install -r requirements.txt
+          pip install .
+
+      - name: Build docs
+        run: sphinx-build -b html docs public

README.md

@@ -1,2 +1,104 @@
 # py-vibracore
 Public python SDK for the CEMS VibraCore web-API
+
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+
+
+This repository is created by [CEMS BV](https://cemsbv.nl/) and is a public python wrapper around the CEMS [VibraCore web-API](https://nuclei.cemsbv.io/#/vibracore/api).
+
+# Installation
+
+To install a package in this repository run:
+
+`$ pip install py-vibracore`
+
+
+## ENV VARS
+
+To use `py-vibracore` add the follow ENV vars to your environment. Or provide them when asked.
+
+```
+* NUCLEI_TOKEN
+    - Your NUCLEI user token
+```
+
+You can obtain your `NUCLEI_TOKEN` on [NUCLEI](https://nuclei.cemsbv.io/#/). 
+Go to `personal-access-tokens` and create a new user token.
+
+# Contribution
+
+## Environment
+
+We recommend developing in Python3.9 with a clean virtual environment (using `virtualenv` or `conda`), installing the requirements from the requirements.txt file:
+
+Example using `virtualenv` and `pip` to install the dependencies in a new environment .env on Linux:
+
+```bash
+python -m venv .env
+source .env/bin/activate
+python -m pip install --upgrade pip setuptools
+pip install -r requirements.txt
+pip install -e .
+```
+
+## Documentation
+
+Build the docs:
+
+```bash
+python -m pip install --upgrade pip setuptools
+pip install -r requirements.txt
+pip install .
+
+sphinx-build -b html docs public
+```
+
+## Format
+
+We format our code with black and isort.
+
+```bash
+black --config "pyproject.toml" src/pyvibracore tests notebooks
+isort --settings-path "pyproject.toml" src/pyvibracore tests notebooks
+```
+
+## Lint
+
+To maintain code quality we use the GitHub super-linter.
+
+To run the linters locally, run the `run_super_linters.sh` bash script from the root directory.
+
+## UnitTest
+
+Test the software with the use of coverage:
+
+```bash
+python -m pip install --upgrade pip setuptools
+pip install -r requirements.txt
+pip install -e .
+coverage run -m pytest
+```
+
+## Requirements
+
+Requirements are autogenerated by the `pip-compile` command with python 3.9
+
+Install pip-tools with:
+
+```bash
+pip install pip-tools
+```
+
+Generate requirements.txt file with:
+
+```bash
+pip-compile --extra=test --extra=lint --extra=docs --extra=notebook --output-file=requirements.txt pyproject.toml
+```
+
+Update the requirements within the defined ranges with:
+
+```bash
+pip-compile --upgrade --extra=test --extra=lint --extra=docs --extra=notebook --output-file=requirements.txt pyproject.toml
+```

docs/_static/css/index.css

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+
+
+.red {
+    color: red;
+}
+
+.blue {
+    color: blue;
+}
+
+.green {
+    color: green;
+}
+.body {
+    max-width: 1200px !important;
+}

docs/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
+from typing import List
+
+sys.path.insert(0, os.path.abspath("../src"))
+os.environ["DOC_PATH"] = os.path.dirname(__file__)
+
+import pyvibracore  # noqa: E402
+
+project = "py-vibracore"
+copyright = "2023, CEMS BV"
+author = "Robin Wimmers"
+
+# The full version, including alpha/beta/rc tags
+release = pyvibracore.__version__
+
+# 'sphinx.ext.napoleon' Used for numpy docstring support
+extensions = [
+    "IPython.sphinxext.ipython_console_highlighting",
+    "IPython.sphinxext.ipython_directive",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx_autodoc_typehints",
+    "matplotlib.sphinxext.plot_directive",
+]
+
+# 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: List = []
+
+# -- 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"]
+
+html_css_files = ["css/index.css"]