snakeframed

.coveragerc

@@ -0,0 +1,11 @@
+[run]
+branch = true
+data_file = .coverage
+source = "tests"
+
+[paths]
+source = censible
+
+[report]
+show_missing = true
+skip_empty = true

.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 +1,13 @@
+# 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
+*.rst text
+
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
+
+pixi.lock linguist-language=YAML linguist-generated=true

.github/workflows/docs.yml

@@ -0,0 +1,57 @@
+name: Documentation
+
+on:
+  push:
+    branches: ["main"]
+
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+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/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.8.8
+        with:
+          locked: false
+          frozen: false
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+
+      - name: Setup environment
+        run: pixi install -e docs
+
+      - name: Build documentation
+        run: pixi run docs
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'public/'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+

.gitignore

@@ -1,26 +1,33 @@
+**/.DS_Store
 __pycache__
-imgs
+.venv
+.env
 
-t
-smina/
-pdbid_bins.json
-pdbbind2020.hdf5
-*.molcache2
-create_caches2.py
-cache/
-1.pdbbind2020/
-*.old
-*.types
+# Jupyter Notebook
+**/.ipynb_checkpoints
 
-train/*.npy
+# IDE settings
 .vscode/
-.fuse*
-train/pdbbind
-.DS_Store
-*.converted.pdb
+.idea/
+
+public/
+
+.cache
+
+node_modules
+package-lock.json
+package.json
 
-*.png
-*.xyz
-tmp.*
-tmp
-src
+# pixi environments
+.pixi
+*.egg-info
+
+# coverage
+coverage.xml
+report.xml
+.coverage
+
+test_*
+*.molcache2
+cache/
+*.converted.pdb

.isort.cfg

@@ -0,0 +1,10 @@
+[settings]
+py_version = 313
+skip=.bzr,.direnv,.eggs,.git,.hg,.mypy_cache,.nox,.pants.d,.svn,.tox,.venv,__pypackages__,_build,buck-out,build,dist,node_modules,venv,.pixi
+line_length = 88
+known_typing = typing,types,typing_extensions,mypy,mypy_extensions
+sections = FUTURE,TYPING,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
+profile = black
+include_trailing_comma = true
+multi_line_output = 3
+indent = 4

.markdownlint.yaml

@@ -0,0 +1,23 @@
+# https://github.com/DavidAnson/markdownlint/blob/main/schema/.markdownlint.yaml
+MD007:
+  indent: 4
+MD013: false
+MD022: false
+MD024: false
+MD026: false
+MD028: false
+MD030:
+  ol_multi: 2
+  ol_single: 2
+  ul_multi: 3
+  ul_single: 3
+MD031: false
+MD032: false
+MD033: false
+MD034: false
+MD036: false
+MD038: false
+MD041: false
+MD046: false
+MD052: false
+MD053: false

.mypy.ini

@@ -0,0 +1,23 @@
+[mypy]
+python_version = "3.12"
+pretty = true
+show_traceback = true
+color_output = true
+allow_redefinition = false
+check_untyped_defs = true
+disallow_any_generics = true
+disallow_incomplete_defs = true
+ignore_missing_imports = true
+implicit_reexport = false
+no_implicit_optional = true
+show_column_numbers = true
+show_error_codes = true
+show_error_context = true
+strict_equality = true
+strict_optional = true
+warn_no_return = true
+warn_redundant_casts = true
+warn_return_any = true
+warn_unreachable = true
+warn_unused_configs = true
+warn_unused_ignores = true

.pytest.ini

@@ -0,0 +1,22 @@
+[pytest]
+norecursedirs =
+    censible
+    *.egg
+    .eggs
+    dist
+    build
+    docs
+    .tox
+    .git
+    __pycache__
+doctest_optionflags =
+    NUMBER
+    NORMALIZE_WHITESPACE
+    IGNORE_EXCEPTION_DETAIL
+addopts =
+    --strict-markers
+    --tb=short
+    --doctest-modules
+    --doctest-continue-on-failure
+    --maxfail=2 -rf
+testpaths = tests

.ruff.toml

@@ -0,0 +1,42 @@
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+    ".pixi",
+    ".pytest_cache",
+]
+
+line-length = 88
+indent-width = 4
+
+[format]
+quote-style = "double"
+indent-style = "space"
+line-ending = "lf"
+docstring-code-format = true
+docstring-code-line-length = "dynamic"
+skip-magic-trailing-comma = true
+

CHANGES.md → CHANGELOG.md

@@ -1,16 +1,24 @@
-# Changes
+# Changelog
 
-## Version 1.0 (2023-10-21)
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-The initial version.
+## [Unreleased]
 
-## Version 1.1 (2024-02-09)
+## [1.2.0] - 2024-05-10
+
+### Added
+
+- Added parameter to use CPU for inference.
+
+## [1.1.0] - 2024-02-09
+
+### Changed
 
 - When training a new CENsible model, the code now saves the Pearson correlation
   coefficients (per epoch) on the training-set data, in addition to the
   testing-set data as before. This change aims to help users diagnose
   overfitting and other issues during training.
 
-## Version 1.2 (2024-05-10)
+## [1.0.0] - 2023-10-21
 
-- Added parameter to use CPU for inference.
+Initial release!