Improve Packaging

.githooks/pre-commit

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+#!/bin/sh
+
+echo "Script $0 triggered ..."
+
+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+echo "Starting ruff analysis..."
+
+# quietly run ruff
+ruff . --fix
+
+# use return code to abort commit if necessary
+if [ $? != "0" ]; then
+    echo "Commit aborted. Fix linter issues found by ruff before committing."
+    exit 1
+fi
+
+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+echo "Pre-commit checks completed successfully."
+exit 0

.github/workflows/build.yml

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+name: Python package
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+
+  build:
+    name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        python-version: ['3.8', '3.9', '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: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Run unit tests
+        run: python -m pytest -v
+      - name: Verify that we can build the package
+        run: python -m build
+
+  lint:
+    name: Linting build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+      - name: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Check style against standards using ruff
+        run: ruff .

.github/workflows/documentation.yml

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+name: documentation
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  build-documentation:
+    name: Build documentation
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+      - name: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Install pandoc using apt
+        run: sudo apt install pandoc        
+      - name: Build documentation
+        run: make coverage doctest html
+        working-directory: docs

CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.0.1] - 1900-12-31
+
+### Added
+
+### Removed
+
+### Changed
+
+[Unreleased]: https://github.com/olivierlacan/keep-a-changelog/compare/v1.0.0...HEAD
+[0.0.1]: https://github.com/olivierlacan/keep-a-changelog/releases/tag/v0.0.1

CITATION.cff

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+# YAML 1.2
+---
+cff-version: "1.2.0"
+title: "pads"
+authors:
+  -
+    family-names: Renaud
+    given-names: Nicolas
+    orcid: "https://orcid.org/0000-0000-0000-0000"
+date-released: 20??-MM-DD
+doi: <insert your DOI here>
+version: "0.1.0"
+repository-code: "https://github.com/QuantumApplicationLab/pads_pck"
+keywords:
+  - data
+  - algorithms
+message: "If you use this software, please cite it using these metadata."
+license: MIT

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+education, socio-economic status, nationality, personal appearance, race,
+religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at n.renaud@esciencecenter.nl. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

CONTRIBUTING.md

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+# Contributing guidelines
+
+We welcome any kind of contribution to our software, from simple comment or question to a full fledged [pull request](https://help.github.com/articles/about-pull-requests/). Please read and follow our [Code of Conduct](CODE_OF_CONDUCT.md).
+
+A contribution can be one of the following cases:
+
+1. you have a question;
+1. you think you may have found a bug (including unexpected behavior);
+1. you want to make some kind of change to the code base (e.g. to fix a bug, to add a new feature, to update documentation);
+1. you want to make a new release of the code base.
+
+The sections below outline the steps in each case.
+
+## You have a question
+
+1. use the search functionality [here](https://github.com/QuantumApplicationLab/pads_pck/issues) to see if someone already filed the same issue;
+2. if your issue search did not yield any relevant results, make a new issue;
+3. apply the "Question" label; apply other labels when relevant.
+
+## You think you may have found a bug
+
+1. use the search functionality [here](https://github.com/QuantumApplicationLab/pads_pck/issues) to see if someone already filed the same issue;
+1. if your issue search did not yield any relevant results, make a new issue, making sure to provide enough information to the rest of the community to understand the cause and context of the problem. Depending on the issue, you may want to include:
+    - the [SHA hashcode](https://help.github.com/articles/autolinked-references-and-urls/#commit-shas) of the commit that is causing your problem;
+    - some identifying information (name and version number) for dependencies you're using;
+    - information about the operating system;
+1. apply relevant labels to the newly created issue.
+
+## You want to make some kind of change to the code base
+
+1. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
+1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
+1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
+1. install dependencies (see the [development documentation](README.dev.md#development_install));
+1. make sure the existing tests still work by running ``pytest``;
+1. add your own tests (if necessary);
+1. update or expand the documentation;
+1. update the `CHANGELOG.md` file with your change;
+1. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the pads repository on GitHub;
+1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
+
+In case you feel like you've made a valuable contribution, but you don't know how to write or run tests for it, or how to generate the documentation: don't let this discourage you from making the pull request; we can help you! Just go ahead and submit the pull request, but keep in mind that you might be asked to append additional commits to your pull request.
+
+## You want to make a new release of the code base
+
+To create a release you need write permission on the repository.
+
+1. Check the author list in [`CITATION.cff`](CITATION.cff)
+1. Bump the version using `bump-my-version bump <major|minor|patch>`. For example, `bump-my-version bump major` will increase major version numbers everywhere it's needed (code, meta, etc.) in the repo. Alternatively the version can be manually changed in pads/__init__.py, pyproject.toml, CITATION.cff and docs/conf.py (and other places it was possibly added).
+1. Update the `CHANGELOG.md` to include changes made
+1. Go to the [GitHub release page](https://github.com/QuantumApplicationLab/pads_pck/releases)
+1. Press draft a new release button
+1. Fill version, title and description field
+1. Press the Publish Release button
+<!--
+For projects that automatically publish to PyPI using a release or publish workflow, something like the following could be useful to add (make sure to replace the names and links):
+
+1. Wait until [PyPi publish workflow](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/publish.yml) has completed
+1. Verify new release is on [PyPi](https://pypi.org/project/matchms/#history)
+-->
+<!--
+For projects that also build conda packages, e.g. on conda-forge or Bioconda, something like the following could be useful to add (example taken from matchms, make sure to replace the names and links):
+
+1. Wait until new release is also on Bioconda (https://anaconda.org/bioconda/pads) via a automaticly created PR on [bioconda recipes repo](https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Apr+is%3Aopen+pads)
+1. Test pads from bioconda by manually running [Conda verify](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/conda_verify.yml) workflow
+-->
+
+Also a Zenodo entry will be made for the release with its own DOI.

MANIFEST.in

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+include CITATION.cff
+include LICENSE
+include NOTICE
+include README.md

NOTICE

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+This product includes pads, software developed by
+Eppstein David.

README.md

@@ -1,10 +1,50 @@
-# PADS: Python Algorithms and Data Structures
+## Badges
 
-This repository is a fork of PADS, as implemented by David Eppstein and available at http://www.ics.uci.edu/~eppstein/PADS/.
+(Customize these badges with your own links, and check https://shields.io/ or https://badgen.net/ to see which other badges are available.)
 
-# Tests
+| fair-software.eu recommendations | |
+| :-- | :--  |
+| (1/5) code repository              | [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](https://github.com/QuantumApplicationLab/pads_pck) |
+| (2/5) license                      | [![github license badge](https://img.shields.io/github/license/QuantumApplicationLab/pads_pck)](https://github.com/QuantumApplicationLab/pads_pck) |
+| (3/5) community registry           | [![RSD](https://img.shields.io/badge/rsd-pads-00a3e3.svg)](https://www.research-software.nl/software/pads) [![workflow pypi badge](https://img.shields.io/pypi/v/pads.svg?colorB=blue)](https://pypi.python.org/project/pads/) |
+| (4/5) citation                     | [![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>) |
+| (5/5) checklist                    | [![workflow cii badge](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>/badge)](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>) |
+| howfairis                          | [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu) |
+| **Other best practices**           | &nbsp; |
+| Static analysis                    | [![workflow scq badge](https://sonarcloud.io/api/project_badges/measure?project=QuantumApplicationLab_pads_pck&metric=alert_status)](https://sonarcloud.io/dashboard?id=QuantumApplicationLab_pads_pck) |
+| Coverage                           | [![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=QuantumApplicationLab_pads_pck&metric=coverage)](https://sonarcloud.io/dashboard?id=QuantumApplicationLab_pads_pck) |
+| Documentation                      | [![Documentation Status](https://readthedocs.org/projects/pads_pck/badge/?version=latest)](https://pads_pck.readthedocs.io/en/latest/?badge=latest) |
+| **GitHub Actions**                 | &nbsp; |
+| Build                              | [![build](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/build.yml/badge.svg)](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/build.yml) |
+| Citation data consistency          | [![cffconvert](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/cffconvert.yml/badge.svg)](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/cffconvert.yml) |
+| SonarCloud                         | [![sonarcloud](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/sonarcloud.yml/badge.svg)](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/sonarcloud.yml) |
+| MarkDown link checker              | [![markdown-link-check](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/markdown-link-check.yml/badge.svg)](https://github.com/QuantumApplicationLab/pads_pck/actions/workflows/markdown-link-check.yml) |
 
-Run
-```bash
-python -m unittest -v pads/*.py
+## How to use pads
+
+Python Algorithms and Data Structure
+
+The project setup is documented in [project_setup.md](project_setup.md). Feel free to remove this document (and/or the link to this document) if you don't need it.
+
+## Installation
+
+To install pads from GitHub repository, do:
+
+```console
+git clone git@github.com:QuantumApplicationLab/pads_pck.git
+cd pads_pck
+python -m pip install .
 ```
+
+## Documentation
+
+Include a link to your project's full documentation here.
+
+## Contributing
+
+If you want to contribute to the development of pads,
+have a look at the [contribution guidelines](CONTRIBUTING.md).
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [NLeSC/python-template](https://github.com/NLeSC/python-template).

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = pads
+SOURCEDIR     = .
+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)