Bootstrap the library (#1)

* Basic repo structure

* Basic skeleton code

* First implementation of all major components: Action, Curator, Report, Broadcaster

* Added a functional module and added discretization

* Added deduplication

* Add stereoisomer AC detection

* Ported over test cases

* Made a good start on visualizations

* Tested with an integrated example - Added it as a tutorial

* Basic setup of docs

* Add HTML broadcaster

* Added chemspace visualization

* Added basic, untested CLI implementation

* Added visualization to stereoisomers with ACs

* Update README

* Fix bug

* Fix another bug

* Enhancement (#2)

* dev refactor

* fix test

* fix tests

* remove unused code

* refactor repo name

* Reviewed @zhu0619's changes. Switched to jinja2 for HTML  broadcaster

* Fixed bug in LoggerBroadcaster

* Fixed release CICD

* Fix CICD

---------

Co-authored-by: cwognum <caswognum@outlook.com>

---------

Co-authored-by: Lu Zhu <lu@valencediscovery.com>

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @cwognum

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible 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.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,59 @@
+name: 🐛 File a bug report
+description: X's behavior is deviating from its documented behavior.
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Please provide the following information.
+  - type: input
+    id: auroris-version
+    attributes:
+      label: Auroris version
+      description: Value of ``auroris.__version__``
+      placeholder: 0.2.5, 0.3.0, 0.3.1, etc.
+    validations:
+      required: true
+  - type: input
+    id: Python-version
+    attributes:
+      label: Python Version
+      description: Version of Python interpreter
+      placeholder: 3.9, 3.10, 3.11, etc.
+    validations:
+      required: true
+  - type: input
+    id: OS
+    attributes:
+      label: Operating System
+      description: Operating System
+      placeholder: (Linux/Windows/Mac)
+    validations:
+      required: true
+  - type: input
+    id: installation
+    attributes:
+      label: Installation
+      description: How was Auroris installed?
+      placeholder: e.g., "using pip into virtual environment", or "using conda"
+    validations:
+      required: true
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: Explain why the current behavior is a problem, what the expected output/behaviour is, and why the expected output/behaviour is a better solution.
+    validations:
+      required: true
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: Minimal, reproducible code sample, a copy-pastable example if possible.
+    validations:
+      required: true
+  - type: textarea
+    id: additional-output
+    attributes:
+      label: Additional output
+      description: If you think it might be relevant, please provide the output from ``pip freeze`` or ``conda env export`` depending on which was used to install Auroris.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: ❓ Discuss something on Discord
+    url: https://discord.gg/vBFd8p6H7u
+    about: For more interactive discussions, you can join the Polaris Discord server.

.github/ISSUE_TEMPLATE/default-template.md

@@ -0,0 +1,23 @@
+---
+name: Default Template
+about: Default, generic issue template
+title: ''
+labels: ''
+assignees: ''
+---
+
+# Context
+
+_Provide some context for this issue: why is this change being requested, what constraint are there on the solution, are there any relevant artifacts(design documents, discussions, others) to this issue, etc._
+
+# Description
+
+_Describe the expected work that will be needed to address the issue, leading into the following acceptance criteria. Add any relevant element that could impact the solution: limits, performance, security, compatibility, etc._
+
+# Acceptance Criteria
+
+- List what needs to be checked and valid to determine that this issue can be closed
+
+# Links
+
+- [Link to other issues/PRs/external tasks](www.example.com)

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,19 @@
+---
+name: 🚀 Feature request
+about: Suggest an idea for a new Polaris feature
+title: ''
+labels: feature
+assignees: ''
+---
+
+### 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

@@ -0,0 +1,17 @@
+## Changelogs
+
+- _enumerate the changes of that PR._
+
+---
+
+_Checklist:_
+
+- [ ] _Was this PR discussed in an issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR._
+- [ ] _Add tests to cover the fixed bug(s) or the newly introduced feature(s) (if appropriate)._
+- [ ] _Update the API documentation if a new function is added, or an existing one is deleted._
+- [ ] _Write concise and explanatory changelogs above._
+- [ ] _If possible, assign one of the following labels to the PR: `feature`, `fix` or `test` (or ask a maintainer to do it for you)._
+
+---
+
+_discussion related to that PR_

.github/changelog_config.json

@@ -0,0 +1,22 @@
+{
+    "categories": [
+        {
+            "title": "## 🚀 Features",
+            "labels": ["feature"]
+        },
+        {
+            "title": "## 🐛 Fixes",
+            "labels": ["fix"]
+        },
+        {
+            "key": "tests",
+            "title": "## 🧪 Tests",
+            "labels": ["test"]
+        },
+        {
+            "key": "docs",
+            "title": "## 📚 Documentation",
+            "labels": ["documentation"]
+        }
+    ]
+}

.github/workflows/code-check.yml

@@ -0,0 +1,34 @@
+name: code-check
+
+on:
+  push:
+    branches: ["main"]
+    tags: ["*"]
+  pull_request:
+    branches:
+      - "*"
+      - "!gh-pages"
+
+jobs:
+
+  python-lint-ruff:
+    name: Python lint [ruff]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install ruff
+        run: |
+          pip install ruff
+
+      - name: Lint
+        run: ruff .
+
+      - name: Format
+        run: ruff format . --check

.github/workflows/doc.yml

@@ -0,0 +1,51 @@
+name: doc
+
+on:
+  push:
+    branches: ["main"]
+
+# Prevent doc action on `main` to conflict with each others.
+concurrency:
+  group: doc-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  doc:
+    runs-on: "ubuntu-latest"
+    timeout-minutes: 30
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@v4
+
+      - name: Setup mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: env.yml
+          environment-name: my_env
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Install library
+        run: |
+          python -m pip install --no-deps .
+          # Note: Temporarily upgrade mkdocs-jupyter through PyPi
+          # See https://github.com/conda-forge/mkdocs-jupyter-feedstock/pull/30
+          python -m pip install mkdocs-jupyter -U --force-reinstall
+
+      - name: Configure git
+        run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+
+      - name: Deploy the doc
+        run: |
+          echo "Get the gh-pages branch"
+          git fetch origin gh-pages
+
+          echo "Build and deploy the doc on main"
+          mike deploy --push main