Major rewrite (#2)

* Add framework

* Start making environment

* Run make format

* Add dependencies

* Update some typing

* Ignore .orig files

* Run make validate

* Starting contexts

* Move utils into subpex dir

* Remove *.orig

* Update locks

* Move restart_subpex to sp_restart

* Update lock files

* Update ignores

* LFS for sim files

* Add prmtop to LFS

* Fix pre-commit

* Add m7g test

* Move wizard

* Add contexts module

* Cleanup westpa checks

* chore: fix subpex validator class name

* feat: add more subpex

* remove unnecessary scripts

* Add restart option for subpex context

* Reorganize wizard

* chore: remove unnecessary files

* Move some scripts

* refactor: create base context manager and validators

* chore: switch to ruff for linting

* feat: separate pocket and fop modules

* Add ruff check to make formatting

* remove ruff from pre-commit

* Start splitting pcoord.py

* chore: add jaccard function

* chore: update some data keys

* feat: add function to read FOP files

* chore: rename pocket radius of gyration function

* refactor: split subpex contexts

* fix: add missing pocket context manager

* chore: add composite sigma to data context

* chore: start reworking progress coords

* refactor: write_fop takes data_dir now

* feat: add data writer

* refactor: cleanup compute progress coords

* chore: remove unnecessary scripts

* Remove subpex from west.cfg

* tests: add simple FOP generation test

* Add black

* feat: put back calculate_distance_two_points

* tests: add pocket tests

* chore: fix gitignore

* chore: enable lfs for codecov.yml

* ci: Add CODECOV_TOKEN

* ci: fix build.yml

* ci: fix lfs with build

* chore: update README

* chore: cleanup some code

* feat: start templater

* feat: overhaul westpa context manager

* feat: render west.cfg file

* chore: cleanup some context

* build: bump minimum mkdocstrings versions

* chore: cleanup cli

* chore: update styling

* chore: update mkdocstrings

* chore: start updating westpa docs

* build: Add pydantic

* chore: add --unsafe-fixes to rust

* Start westpa context

* build: add pydantic-settings

* refactor: rename base -> main

* feat: change to pydantic

* refactor: start transition to pydantic

* fix: westpa config

* fix: improve westpa config implementation

* chore: remove duplicate scripts

* chore: rename spx_config -> subpex_config

* feat: start westpa init script

* chore: cleanup configs

* chore: update docstrings in FOP module

* refactor: get_fop_pocket and test

* feat: Provide get_rmsd function in utils

* feat: add function to compute backbone rmsd

* refactor: Do not remove directory during westpa setup when overwriting

* feat: add convenience functions for computing fop

* refactor: unify pocket computations

* refactor: revamp AuxData

* refactor: reorganize some config settings

* chore: small updates to render

* refactor: change pcoord -> data

* refactor: change m7g to path dict

* chore: add tmp for tests

* feat: compute traj data

* feat: improve interaction with aux data

* tests: write actual tests for computing traj data

* tests: add docstrings to tests

* chore: remove old get_rmsd function

* docs: improve data IO docstrings

* docs: improve FoP compute docstrings

* chore: ignore some mypy types

* fix: the c_alphas for get_fop_pocket

* refactor: add docstrings and clarify distance constraint

* chore: cleanup r"""

* chore: start lfs cleanup

* chore: move lfs files to git

* refactor: fix selection_dist -> water_dist

* tests: fix test path names

.editorconfig

@@ -0,0 +1,36 @@
+# Check http://editorconfig.org for more information
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.{py, pyi}]
+indent_style = space
+indent_size = 4
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[Makefile]
+indent_style = tab
+
+[*.{yml, yaml}]
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.md]
+indent_size = 4
+trim_trailing_whitespace = true
+
+[LICENSE]
+insert_final_newline = false
+
+[*.{diff,patch}]
+trim_trailing_whitespace = false

.gitattributes

@@ -0,0 +1,11 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.md text
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
+*.nc binary
+*.rst binary
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,42 @@
+---
+name: 🐛 Bug report
+about: If something isn't working 🔧
+title: ''
+labels: bug
+assignees:
+---
+
+## Bug Report
+
+<!-- A clear and concise description of what the bug is. -->
+
+## How To Reproduce
+
+Steps to reproduce the behavior:
+
+1.  ...
+
+### Code sample
+
+<!-- If applicable, attach a minimal code sample to reproduce the decried issue. -->
+
+### Environment
+
+-   OS: [e.g. Linux / Windows / macOS]
+-   Python version, get it with:
+
+```bash
+python --version
+```
+
+### Screenshots
+
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## Expected behavior
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,3 @@
+# Configuration: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository
+
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: 🚀 Feature request
+about: Suggest an idea for this project 🏖
+title: ''
+labels: enhancement
+assignees:
+---
+
+## Feature Request
+
+<!-- A clear and concise description of the feature proposal. -->
+
+## Motivation
+
+<!-- Please describe the motivation for this proposal. -->
+
+## Alternatives
+
+<!-- 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/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,25 @@
+---
+name: ❓ Question
+about: Ask a question about this project 🎓
+title: ''
+labels: question
+assignees:
+---
+
+## Checklist
+
+<!-- Mark with an `x` all the checkboxes that apply (like `[x]`) -->
+
+-   [ ] I've searched the project's [`issues`](https://github.com/durrantlab/subpex/issues?q=is%3Aissue).
+
+## Question
+
+<!-- What is your question? -->
+
+How can I [...]?
+
+Is it possible to [...]?
+
+## Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,29 @@
+## Description
+
+<!-- Add a more detailed description of the changes if needed. -->
+
+## Related Issue
+
+<!-- If your PR refers to a related issue, link it here. -->
+
+## Type of Change
+
+<!-- Mark with an `x` all the checkboxes that apply (like `[x]`) -->
+
+-   [ ] 📚 Examples / docs / tutorials / dependencies update
+-   [ ] 🔧 Bug fix (non-breaking change which fixes an issue)
+-   [ ] 🥂 Improvement (non-breaking change which improves an existing feature)
+-   [ ] 🚀 New feature (non-breaking change which adds functionality)
+-   [ ] 💥 Breaking change (fix or feature that would cause existing functionality to change)
+-   [ ] 🔐 Security fix
+
+## Checklist
+
+<!-- Mark with an `x` all the checkboxes that apply (like `[x]`) -->
+
+-   [ ] I have updated the code style using `make codestyle`.
+-   [ ] I have performed a self-review of my code.
+-   [ ] I have written tests for all new methods and classes that I created.
+-   [ ] New and existing unit tests pass locally with my changes.
+-   [ ] I have written the docstring in `NumPy` format for all the methods and classes that I used.
+-   [ ] I have made corresponding changes to the documentation.

.github/release-drafter.yml

@@ -0,0 +1,28 @@
+# Release drafter configuration https://github.com/release-drafter/release-drafter#configuration
+# Emojis were chosen to match the https://gitmoji.carloscuesta.me/
+
+name-template: "v$NEXT_PATCH_VERSION"
+tag-template: "v$NEXT_PATCH_VERSION"
+
+categories:
+  - title: ":rocket: Features"
+    labels: [enhancement, feature]
+  - title: ":wrench: Fixes & Refactoring"
+    labels: [bug, refactoring, bugfix, fix]
+  - title: ":package: Build System & CI/CD"
+    labels: [build, ci, testing]
+  - title: ":boom: Breaking Changes"
+    labels: [breaking]
+  - title: ":pencil: Documentation"
+    labels: [documentation]
+  - title: ":arrow_up: Dependencies updates"
+    labels: [dependencies]
+
+template: |
+  ## What's Changed
+
+  $CHANGES
+
+  ## :busts_in_silhouette: List of contributors
+
+  $CONTRIBUTORS

.github/workflows/build.yml

@@ -0,0 +1,43 @@
+
+name: build
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Install miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Initialize conda environment
+        run: make conda-create
+
+      - name: Setup conda
+        run: make conda-setup
+
+      - name: Install conda dependencies
+        run: make from-conda-lock
+
+      - name: Poetry install
+        run: make install
+
+      - name: Run tests
+        run: make test

.github/workflows/codecov.yml

@@ -0,0 +1,50 @@
+
+name: Codecov workflow
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  run:
+    name: codecov
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          # Set to the same as `PYTHON_VERSION` in `Makefile`
+          python-version: "3.12"
+
+      - name: Initialize conda environment
+        run: make conda-create
+
+      - name: Setup conda
+        run: make conda-setup
+
+      - name: Install conda dependencies
+        run: make from-conda-lock
+
+      - name: Poetry install
+        run: make install
+
+      - name: Run tests and coverage
+        run: make test
+
+      - name: Upload to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          verbose: true

.github/workflows/deploy-docs.yml

@@ -0,0 +1,71 @@
+
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  deploy:
+    name: docs
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          fetch-depth: 0
+
+      - name: Install miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: "3.12"
+
+      - name: Initialize conda environment
+        run: make conda-create
+
+      - name: Setup conda
+        run: make conda-setup
+
+      - name: Install conda dependencies
+        run: make from-conda-lock
+
+      - name: Poetry install
+        run: make install
+
+      - name: Build documentation
+        run: make docs-versioned
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          # Upload entire repository
+          path: './docs/html/'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2