Python project scaffolding (#1)

* python project scaffolding

* Updated documentation

.github/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, sex characteristics, 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 behaviour 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 behaviour 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
+behaviour and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behaviour.
+
+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 behaviours 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 behaviour may be
+reported by contacting the project team at [email protected]. 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][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

.github/CONTRIBUTING.md

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+Thank you for considering contributing to nsbi.
+
+If you have a new feature/bug report, make sure you create an [issue](https://github.com/handley-lab/nsbi/issues), and consult existing ones first, in case your suggestion is already being addressed.
+
+If you want to go ahead and create the feature yourself, you should fork the repository to you own github account and create a new branch with an appropriate name. Commit any code modifications to that branch, push to GitHub, and then create a pull request via your forked repository. More detail can be found [here](https://gist.github.com/Chaser324/ce0505fbed06b947d962).
+
+Note that a [code of conduct](https://github.com/handley-lab/nsbi/blob/master/CODE_OF_CONDUCT.md) applies to all spaces managed by the nsbi project, including issues and pull requests. 
+
+## Contributing - `pre-commit`
+
+nsbi uses black and isort to maintain a consistent style. To speed up linting, contributors can optionally use pre-commit to ensure their commits comply.
+
+First, ensure that pre-commit, black and isort are installed:
+```
+pip install pre-commit black isort
+```
+Then install the pre-commit to the .git folder:
+```
+pre-commit install
+```
+This will check changed files, and abort the commit if they do not comply. To uninstall, run:
+```
+pre-commit uninstall
+```

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+labels: 
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behaviour.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**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
+labels: 
+
+---
+
+**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/PULL_REQUEST_TEMPLATE.md

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+# Description
+
+Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context.
+
+Fixes # (issue)
+
+# Checklist:
+
+- [ ] I have performed a self-review of my own code
+- [ ] My code is black compliant (`black . --check`)
+- [ ] My code is isort compliant (`isort . --profile black --filter-files`)
+- [ ] My code contains compliant docstrings (`pydocstyle --convention=numpy nsbi`)
+- [ ] New and existing unit tests pass locally with my changes (`python -m pytest`)
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] I have appropriately incremented the [semantic version number](https://semver.org/) in both README.rst and nsbi/_version.py

.github/workflows/build.yaml

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+name: Build
+on:
+  push:
+    branches:
+      - master
+jobs:
+  get-version:
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.step1.outputs.v }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get version number
+        id: step1 
+        run: echo "v=$(grep ':Version:' README.rst | awk '{print $2}')" >> $GITHUB_OUTPUT
+
+  git-tag-and-release:
+    runs-on: ubuntu-latest
+    needs: get-version
+    steps:
+      - uses: actions/checkout@v4
+      - name: set version number
+        run: echo "DIST_VERSION=v${{ needs.get-version.outputs.version }}" >> $GITHUB_ENV
+      - name: Create Tag
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const {DIST_VERSION} = process.env
+            github.rest.git.createRef({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                ref: `refs/tags/${DIST_VERSION}`,
+                sha: context.sha
+            })
+      - name: Create GitHub Release
+        uses: ncipollo/release-action@v1
+        with:
+          name: "${{ env.DIST_VERSION }}"
+          tag: "${{ env.DIST_VERSION }}"
+          generateReleaseNotes: true
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+  pypi-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+      - name: Install pypa/build
+        run: python -m pip install build --user
+      - name: Build a binary wheel and a source tarball
+        run: python -m build --sdist --wheel --outdir dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+  pypi-public:
+    needs: 
+      - get-version
+      - pypi-release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Wait for PyPi
+        uses: nev7n/wait_for_response@v1
+        with:
+          url: "https://files.pythonhosted.org/packages/source/n/nsbi/nsbi-${{ needs.get-version.outputs.version }}.tar.gz"
+          responseCode: 200
+          timeout: 600000
+          interval: 10000
+
+  aur-release:
+    needs: pypi-public
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tomli
+      - name: Generate PKGBUILD
+        run: python ./bin/gen_PKGBUILD.py > ./PKGBUILD
+      - name: Publish AUR package
+        uses: KSXGitHub/[email protected]
+        with:
+          pkgname: python-nsbi
+          pkgbuild: ./PKGBUILD
+          updpkgsums: True
+          commit_username: ${{ secrets.AUR_USERNAME }}
+          commit_email: ${{ secrets.AUR_EMAIL }}
+          ssh_private_key: ${{ secrets.AUR_SSH_PRIVATE_KEY }}
+
+  conda-release:
+    needs: pypi-public
+    name: Build and deploy to conda
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: '3.9'
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+          channels: conda-forge,handley-lab
+      - name: install dependencies
+        shell: bash -el {0}
+        run: conda install grayskull conda-build anaconda-client
+      - name: Generate meta.yaml from grayskull
+        shell: bash -el {0}
+        run: grayskull pypi --strict-conda-forge nsbi
+      - name: Build and upload the conda packages
+        uses: uibcdf/[email protected]
+        with:
+          meta_yaml_dir: nsbi
+          python-version: '3.9'
+          user: handley-lab
+          label: 'main'
+          token: ${{ secrets.ANACONDA_TOKEN }} # Replace with the right name of your secret
+
+  conda-build:
+    needs: 
+      - conda-release
+      - get-version
+    name: test installation from conda
+    runs-on: ubuntu-latest
+    steps:
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: '3.9'
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+      - name: install from conda
+        shell: bash -el {0}
+        run: conda install -c handley-lab nsbi
+      - name: get install version
+        shell: bash -el {0}
+        run: echo "install_version=$(python -c 'import nsbi; print(nsbi.__version__)')" >> $GITHUB_ENV
+      - name: fail if versions not matching
+        if: ${{ env.install_version != needs.get-version.outputs.version }}
+        run: exit 1
+
+  pypi-build:
+    needs: 
+      - pypi-public
+      - get-version
+    name: test installation from pypi
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+      - name: Install from pypi
+        run: pip install nsbi
+      - name: get install version
+        run: echo "install_version=$(python -c 'import nsbi; print(nsbi.__version__)')" >> $GITHUB_ENV
+      - name: fail if versions not matching
+        if: ${{ env.install_version != needs.get-version.outputs.version }}
+        run: exit 1

.github/workflows/code_style.yaml

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+name: Code style
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install black
+        run: pip install black
+      - name: Run black
+        run: black . --check
+
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install isort
+        run: pip install isort
+      - name: Run isort
+        run: isort . --check-only
+
+  pydocstyle:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install pydocstyle
+        run: pip install pydocstyle
+      - name: run pydocstyle
+        run: python -m pydocstyle --convention=numpy anesthetic