Merge pull request #3 from andrewtarzia/reorganise

Reorganise package and add centroid control.

.github/pull_request_template.md

@@ -0,0 +1,43 @@
+Related Issues: <!-- Add related issues here, e.g. #121 #341 -->
+Requested Reviewers: @andrewtarzia <!-- Add other reviewers here -->
+*Note for Reviewers: If you accept the review request add a :+1: to this post*
+
+<!--
+Talk about what a user would see (a big, a new feature) and what
+user goals weren't being met. If the commit fixes a bug, describe how
+the bug was discovered and steps to reproduce it, unless this is
+already covered by the related issues. If this is a bug fix, what was
+the mistake in the application logic? Be precise. Act like a detective
+and report your findings.
+-->
+
+<!--
+Why did you make the change this way? What other ways did you consider
+but reject? Explain how amazing your work is.
+-->
+
+<!--
+What risks are associated with making the changes in the commit? Will
+anything else break? Are the changes backwards-compatible? Is there
+any "tech debt"?
+-->
+
+<!--
+Explain the source code changes. Changes that are fully explained in
+code comments or the above paragraphs don't need to be repeated here.
+Use bullet points, e.g.
+
+* `src/stk/molecular/atoms/atom.py:Atom.get_id()`: The method
+  parameters were updated because <some reason>. The places where
+  the method was called were also updated.
+-->
+
+<!--
+Give evidence that the commit works. Did you visually inspect any
+changes to molecular structures yourself?
+-->
+
+<!--
+The suggested PR outline is taken from
+https://joshuatauberer.medium.com/write-joyous-git-commit-messages-2f98891114c4
+-->

.github/workflows/publish_release.yml

@@ -0,0 +1,24 @@
+name: Publish release
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+.[0-9]+'
+jobs:
+  publish-release:
+    runs-on: ubuntu-22.04
+    env:
+      VERSION: ${{ github.ref_name }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: python -m build
+      - name: Publish
+        run:
+          twine upload
+          -u ${{ secrets.PYPI_USERNAME }}
+          -p ${{ secrets.PYPI_PASSWORD }}
+          dist/*

.github/workflows/tests.yml

@@ -0,0 +1,48 @@
+name: Tests
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+  workflow_dispatch:
+jobs:
+  ruff:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: "pip install '.[dev]'"
+      - run: ruff .
+  mypy:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: "pip install -e '.[dev]'"
+      - run: mypy src
+  black:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: "pip install -e '.[dev]'"
+      - run: black --check .
+  pytest:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: "pip install -e '.[dev]'"
+      - run: pytest

.gitignore

@@ -129,4 +129,19 @@ dmypy.json
 .pyre/
 
 # Examples output.
-examples/min_example_output/
+examples/example_output/
+
+.vscode
+/dist
+/build
+src/pore_mapper.egg-info
+src/pore_mapper/_version.py
+/.coverage
+docs/source/_autosummary
+
+**/__pycache__/
+
+**/.cache
+.mypy_cache
+*.ipynb_checkpoints
+**/.vscode