Reorganize and Refactor POVME (#2)

* refactor: Massive reorganization (broken)

* tests: Add basic povme tests

* docs: add start

* Fix docs title

* Fix docs code color

* Cleanup cli

* Reorganize some files

* Cleanup some test files

* Move pocket_id test info

* chore: fix mypy.ini

* tests: fix

* refactor: reorganize

* refactor: start migration to pydantic

* fix: get 4nss test running

* refactor: modular writing on POVME

* tests: Enable logging

* tests: cleanup

* refactor: fix pocket detection

* Cleanup docs

.black.toml

@@ -0,0 +1,7 @@
+[tool.black]
+target-version = [
+    "py312",
+]
+line-length = 88
+color = true
+exclude = "/(\n    \\.git\n    | \\.hg\n    | \\.mypy_cache\n    | \\.tox\n    | \\.venv\n    | _build\n    | buck-out\n    | build\n    | dist\n    | env\n    | venv\n)/\n"

.coveragerc

@@ -0,0 +1,9 @@
+[run]
+branch = true
+source = tests
+
+[paths]
+source = povme
+
+[report]
+show_missing = 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 +1,2 @@
+# SCM syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/workflows/codecov.yml

@@ -0,0 +1,37 @@
+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
+        with:
+          lfs: true
+
+      - name: Install pixi
+        uses: prefix-dev/[email protected]
+
+      - name: Setup environment
+        run: pixi install
+
+      - name: Get test coverage
+        run: pixi run tests
+
+      - name: Upload to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docs.yml

@@ -0,0 +1,55 @@
+name: Deploy documentation
+
+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/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install pixi
+        uses: prefix-dev/[email protected]
+
+      - name: Setup environment
+        run: pixi install
+
+      - 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

.github/workflows/tests.yml

@@ -0,0 +1,26 @@
+name: Tests
+
+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
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Install pixi
+        uses: prefix-dev/[email protected]
+
+      - name: Setup environment
+        run: pixi install
+
+      - name: Run tests
+        run: pixi run tests

.gitignore

@@ -1,2 +1,13 @@
 *.pyc
 .DS_Store
+
+# pixi environments
+.pixi
+*.egg-info
+
+# Documentation
+api
+public
+
+__pycache__
+.vscode

.isort.cfg

@@ -0,0 +1,9 @@
+[settings]
+py_version = 312
+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 +1,20 @@
+# 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
+MD036: false
+MD038: false
+MD041: false
+MD046: false

.mypy.ini

@@ -0,0 +1,24 @@
+[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
+exclude = (?x)(^public/*$)

.pytest.ini

@@ -0,0 +1,23 @@
+[pytest]
+norecursedirs =
+    povme
+    *.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
+pythonpaths = ./

.ruff.toml

@@ -0,0 +1,23 @@
+target-version = "py312"
+line-length = 88
+indent-width = 4
+exclude = [
+    ".git",
+    ".hg",
+    ".mypy_cache",
+    ".tox",
+    ".venv",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "env",
+    "venv",
+]
+
+[format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+docstring-code-format = true
+docstring-code-line-length = "dynamic"

CHANGES.md

@@ -10,58 +10,58 @@ NOTE: There is a MP error in python3. Need to fix. Use 1 processor for now.
 2.2.2
 -----
 
-1. Fixed text-encoding bug.
+1.  Fixed text-encoding bug.
 
 2.2.1
 -----
 
-1. Made minor changes to the `README.md` file to clarify the
+1.  Made minor changes to the `README.md` file to clarify the
    `ContiguousPointsCriteria`, `ContiguousPocketSeedSphere`, and
    `ContiguousPocketSeedBox` parameters.
-2. Otherwise identical to POVME 2.2.
+2.  Otherwise identical to POVME 2.2.
 
 2.2
 ---
 
-1. Updated version to 2.2.
-2. Fixed an error that prevented POVME from saving its output to uncompressed
+1.  Updated version to 2.2.
+2.  Fixed an error that prevented POVME from saving its output to uncompressed
    files. (Previously only writing output to compressed output succeeded.)
-3. POVME now throws a warning when using Python 3.5 or earlier.
-4. When the user does not specify any contiguous-pocket seed regions, POVME no
+3.  POVME now throws a warning when using Python 3.5 or earlier.
+4.  When the user does not specify any contiguous-pocket seed regions, POVME no
    longer outputs the default value of the ContiguousPointsCriteria parameter
    to the screen. In this case, POVME does not use the
    ContiguousPointsCriteria parameter anyway, so outputing its value to the
    screen only causes confusion.
-5. Applied [Black formatter](https://black.readthedocs.io/en/stable/) to all
+5.  Applied [Black formatter](https://black.readthedocs.io/en/stable/) to all
    Python code.
 
 2.1
 ---
 
-1. Updated version to 2.1.
-2. Now Python3 compatible. Python2 no longer officially supported.
-3. Refactored code so that it can now be called as a library.
-4. Moved GUI wrapper to new `depreciated/` folder. This feature is no longer
+1.  Updated version to 2.1.
+2.  Now Python3 compatible. Python2 no longer officially supported.
+3.  Refactored code so that it can now be called as a library.
+4.  Moved GUI wrapper to new `depreciated/` folder. This feature is no longer
    supported.
-5. Improved formatting (black) and docstrings.
-6. Fixed minor bug that assigned atoms with names like "HG21" to element "HG"
+5.  Improved formatting (black) and docstrings.
+6.  Fixed minor bug that assigned atoms with names like "HG21" to element "HG"
    rather than "H". No longer supporting element "HG".
-7. Moved examples directory to `povme/examples/`.
-8. Can now read both Windows and POSIX path names seamlessly (no need for
+7.  Moved examples directory to `povme/examples/`.
+8.  Can now read both Windows and POSIX path names seamlessly (no need for
    separate ini files).
-9. Easy testing now available: `python POVME2.py --test` and `python
+9.  Easy testing now available: `python POVME2.py --test` and `python
    POVME_pocket_id.py --test`
-10. Added project roadmap.
+10.  Added project roadmap.
 
 2.0.3
 -----
 
-1. Updated citation.
-2. Convex hull now calculated based on locations of all heavy atoms. In 2.0.1,
+1.  Updated citation.
+2.  Convex hull now calculated based on locations of all heavy atoms. In 2.0.1,
    it was all alpha carbons. Take care when comparing POVME 2.0.1 and POVME
    2.0.2/2.0.3 output.
-3. Fixed NumPy warning.
-4. Spelling error ("Angstroms").
+3.  Fixed NumPy warning.
+4.  Spelling error ("Angstroms").
 
 2.0.1
 -----