Implement tests

.github/workflows/ci.yml

@@ -0,0 +1,40 @@
+name: CI
+
+on:
+  push:
+    branches: [main, uv_tests]
+  pull_request:
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python-version: ['3.14']
+        os: [ubuntu-latest]
+
+    name: Python ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6.5.0  # later versions crash locally: https://github.com/astral-sh/setup-uv/issues/535
+        with:
+          enable-cache: true
+
+      - name: Install Python
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --dev
+
+      - run: uv run ruff format .
+      - run: uv run ruff check .
+      - run: uv run ty check
+      - run: uv run pytest --cov --cov-report=xml
+
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v5
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -22,13 +22,20 @@ env/
 
 # Pytest cache
 .pytest_cache/
+ruff.out
+ty.out
+
+# ruff
+.ruff_cache/
 
 # mypy
 .mypy_cache/
 
 # Coverage reports
 htmlcov/
 .coverage
+.coverage.*
+coverage.xml
 
 # macOS files
 .DS_Store

README.md

@@ -4,6 +4,12 @@ Identify bond formation/breaking, angle changes, and dihedral rotations from vib
 
 [![PyPI Downloads](https://static.pepy.tech/badge/vib-analysis)](https://pepy.tech/projects/vib-analysis) 
 [![PyPI Downloads](https://static.pepy.tech/badge/graphrc)](https://pepy.tech/projects/graphrc)
+[![License](https://img.shields.io/github/license/aligfellow/graphrc)](https://github.com/aligfellow/graphrc/blob/main/LICENSE)
+[![Powered by: uv](https://img.shields.io/badge/-uv-purple)](https://docs.astral.sh/uv)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+[![Typing: ty](https://img.shields.io/badge/typing-ty-EFC621.svg)](https://github.com/astral-sh/ty)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/aligfellow/graphrc/ci.yml?branch=main&logo=github-actions)](https://github.com/aligfellow/graphrc/actions)
+[![Codecov](https://img.shields.io/codecov/c/github/aligfellow/graphrc)](https://codecov.io/gh/aligfellow/graphrc)
 
 ---
 
@@ -813,3 +819,21 @@ Must contain ≥2 frames.
 - Visualization examples with [v.2.0](https://github.com/briling/v) by Ksenia Briling
 
 ---
+
+## Developer Setup
+
+To develop with `xyzgraph`, you can clone the repo and use
+[`just`](https://github.com/casey/just) and [`uv`](https://docs.astral.sh) to setup the dev environment:
+
+```bash
+just setup
+```
+The cli can be used with:
+```bash
+uv run xyzgraph filename.xyz
+```
+
+Run the checks using:
+```bash
+just check
+```

examples/data/expected_results.py

@@ -8,49 +8,47 @@
 """
 
 EXPECTED_RESULTS = {
-    'ambh': {
-        'bonds': [(2, 11), (11, 18)] # C-H and H-N
+    "ambh": {
+        "bonds": [(2, 11), (11, 18)]  # C-H and H-N
     },
-    'atrop': {
-        'dihedrals': [(1, 5, 6, 7), (6, 7, 25, 27)]
+    "atrop": {"dihedrals": [(1, 5, 6, 7), (6, 7, 25, 27)]},
+    "bimp": {
+        "bonds": [(11, 12), (10, 14)],  # O-C and C-C
     },
-    'bimp': {
-        'bonds': [(11, 12), (10, 14)],  # O-C and C-C
+    "cpa": {
+        "bonds": [(23, 35), (35, 75), (70, 74)]  # O-H, H-O, C-C
     },
-    'cpa': {
-        'bonds': [(23, 35), (35, 75), (70, 74)] # O-H, H-O, C-C
+    "cycl": {
+        "bonds": [(2, 6)],  # C-N cyclisation
     },
-    'cycl': {
-        'bonds': [(2, 6)],  # C-N cyclisation
+    "dihedral": {
+        "dihedrals": [(6, 0, 3, 7)],  # F-C-C-F rotation
     },
-    'dihedral': {
-        'dihedrals': [(6, 0, 3, 7)],  # F-C-C-F rotation
+    "mn-h2": {
+        "bonds": [(1, 64), (5, 65), (63, 64), (64, 66), (65, 66)],  # Mn-H, N-H, H-H, H-O, H-O
     },
-    'mn-h2': {
-        'bonds': [(1, 64), (5, 65), (63, 64), (64, 66), (65, 66)],  # Mn-H, N-H, H-H, H-O, H-O
+    "mn-hy": {
+        "bonds": [(1, 67), (67, 77)]  # Mn-H, H-C
     },
-    'mn-hy': {
-        'bonds': [(1, 67), (67, 77)] # Mn-H, H-C
+    "ru-co-nuc": {
+        "bonds": [(3, 66), (64, 65), (65, 66)],  # N-H, C-N, N-H
     },
-    'ru-co-nuc': {
-        'bonds': [(3, 66), (64, 65), (65, 66)],  # N-H, C-N, N-H
+    "ru-co": {
+        "bonds": [(0, 63), (0, 64), (3, 66), (64, 66)],  # Ru-O, Ru-C, N-H, C-H
     },
-    'ru-co': {
-        'bonds': [(0, 63), (0, 64), (3, 66), (64, 66)],  # Ru-O, Ru-C, N-H, C-H
+    "sn2": {
+        "bonds": [(0, 4), (0, 5)],  # C-F and C-Cl
     },
-    'sn2': {
-        'bonds': [(0, 4), (0, 5)],  # C-F and C-Cl
+    "sn2_large": {
+        "bonds": [(0, 1), (0, 21)],  # C-I and C-N
     },
-    'sn2_large': {
-        'bonds': [(0, 1), (0, 21)],  # C-I and C-N
+    "spiro-ts1": {
+        "bonds": [(14, 15)],  # C-N
     },
-    'spiro-ts1': {
-        'bonds': [(14, 15)],  # C-N
+    "spiro-ts2": {
+        "bonds": [(13, 14)],  # O-C
     },
-    'spiro-ts2': {
-        'bonds': [(13, 14)],  # O-C
-    },
-    'thia-ma': {
-        'bonds': [(35, 47)],  # C-S
+    "thia-ma": {
+        "bonds": [(35, 47)],  # C-S
     },
 }

examples/example.ipynb

@@ -24,46 +24,45 @@
     }
    ],
    "source": [
-    "import os\n",
     "from graphrc import run_vib_analysis\n",
     "\n",
-    "vib_trj_dihedral = 'data/dihedral.v000.xyz'\n",
+    "vib_trj_dihedral = \"data/dihedral.v000.xyz\"\n",
     "\n",
     "# ORCA_PATH = os.system('which orca')\n",
     "# ORCA_PATH = '/path/to/orca'\n",
     "\n",
     "results = run_vib_analysis(\n",
-    "        input_file=vib_trj_dihedral,\n",
-    "        # bond_tolerance=1.5,\n",
-    "        # angle_tolerance=1.1,\n",
-    "        # dihedral_tolerance=1.0,\n",
-    "        # bond_threshold=0.5,\n",
-    "        # angle_threshold=10.0,\n",
-    "        # dihedral_threshold=20.0,\n",
-    "        # orca_pltvib_path=ORCA_PATH,\n",
-    "    )\n",
-    "vib = results['vibrational']\n",
+    "    input_file=vib_trj_dihedral,\n",
+    "    # bond_tolerance=1.5,\n",
+    "    # angle_tolerance=1.1,\n",
+    "    # dihedral_tolerance=1.0,\n",
+    "    # bond_threshold=0.5,\n",
+    "    # angle_threshold=10.0,\n",
+    "    # dihedral_threshold=20.0,\n",
+    "    # orca_pltvib_path=ORCA_PATH,\n",
+    ")\n",
+    "vib = results[\"vibrational\"]\n",
     "# print the results that have entries (dont print empty results)\n",
-    "if vib['bond_changes']:\n",
-    "    print('Bond changes:')\n",
-    "    for bond in vib['bond_changes']:\n",
+    "if vib[\"bond_changes\"]:\n",
+    "    print(\"Bond changes:\")\n",
+    "    for bond in vib[\"bond_changes\"]:\n",
     "        print(bond)\n",
-    "if vib['angle_changes']:\n",
-    "    print('Angle changes:')\n",
-    "    for angle in vib['angle_changes']:\n",
+    "if vib[\"angle_changes\"]:\n",
+    "    print(\"Angle changes:\")\n",
+    "    for angle in vib[\"angle_changes\"]:\n",
     "        print(angle)\n",
-    "if vib['dihedral_changes']:\n",
-    "    print('Dihedral changes:')\n",
-    "    for dihedral in vib['dihedral_changes']:\n",
+    "if vib[\"dihedral_changes\"]:\n",
+    "    print(\"Dihedral changes:\")\n",
+    "    for dihedral in vib[\"dihedral_changes\"]:\n",
     "        print(dihedral)\n",
     "\n",
-    "if vib['minor_angle_changes']:\n",
-    "    print('Minor angle changes:')\n",
-    "    for minor_angle in vib['minor_angle_changes']:\n",
+    "if vib[\"minor_angle_changes\"]:\n",
+    "    print(\"Minor angle changes:\")\n",
+    "    for minor_angle in vib[\"minor_angle_changes\"]:\n",
     "        print(minor_angle)\n",
-    "if vib['minor_dihedral_changes']:\n",
-    "    print('Minor dihedral changes:')\n",
-    "    for minor_dihedral in vib['minor_dihedral_changes']:\n",
+    "if vib[\"minor_dihedral_changes\"]:\n",
+    "    print(\"Minor dihedral changes:\")\n",
+    "    for minor_dihedral in vib[\"minor_dihedral_changes\"]:\n",
     "        print(minor_dihedral)"
    ]
   },
@@ -120,19 +119,19 @@
    "source": [
     "from graphrc import run_vib_analysis\n",
     "\n",
-    "out_file = 'data/spiro-ts1.log'\n",
+    "out_file = \"data/spiro-ts1.log\"\n",
     "\n",
     "results = run_vib_analysis(\n",
-    "        input_file=out_file,\n",
-    "        # mode=0, \n",
-    "        print_output=True,\n",
-    "        # bond_tolerance=1.5,\n",
-    "        # angle_tolerance=1.1,\n",
-    "        # dihedral_tolerance=1.0,\n",
-    "        # bond_threshold=0.5,\n",
-    "        # angle_threshold=10.0,\n",
-    "        # dihedral_threshold=20.0,\n",
-    "    )"
+    "    input_file=out_file,\n",
+    "    # mode=0,\n",
+    "    print_output=True,\n",
+    "    # bond_tolerance=1.5,\n",
+    "    # angle_tolerance=1.1,\n",
+    "    # dihedral_tolerance=1.0,\n",
+    "    # bond_threshold=0.5,\n",
+    "    # angle_threshold=10.0,\n",
+    "    # dihedral_threshold=20.0,\n",
+    ")"
    ]
   },
   {
@@ -153,18 +152,18 @@
    "source": [
     "from graphrc import run_vib_analysis\n",
     "\n",
-    "orca_out = 'data/bimp.v000.xyz'\n",
+    "orca_out = \"data/bimp.v000.xyz\"\n",
     "\n",
     "results = run_vib_analysis(\n",
-    "        input_file=orca_out,\n",
-    "    )\n",
+    "    input_file=orca_out,\n",
+    ")\n",
     "\n",
-    "vib = results['vibrational']\n",
+    "vib = results[\"vibrational\"]\n",
     "print(vib)\n",
     "\n",
-    "theoretical_bond_changes = [(11,12), (10,14)]\n",
-    "if all(bond in vib['bond_changes'] for bond in theoretical_bond_changes):\n",
-    "    print(f'True: All theoretical bond changes {theoretical_bond_changes} found in results.')\n"
+    "theoretical_bond_changes = [(11, 12), (10, 14)]\n",
+    "if all(bond in vib[\"bond_changes\"] for bond in theoretical_bond_changes):\n",
+    "    print(f\"True: All theoretical bond changes {theoretical_bond_changes} found in results.\")"
    ]
   },
   {
@@ -184,14 +183,14 @@
    "source": [
     "from graphRC import run_vib_analysis\n",
     "\n",
-    "orca_out = 'data/sn2_large.v000.xyz'\n",
+    "orca_out = \"data/sn2_large.v000.xyz\"\n",
     "\n",
     "results = run_vib_analysis(\n",
-    "        input_file=orca_out,\n",
-    "    )\n",
+    "    input_file=orca_out,\n",
+    ")\n",
     "\n",
-    "vib = results['vibrational']\n",
-    "print(vib)\n"
+    "vib = results[\"vibrational\"]\n",
+    "print(vib)"
    ]
   }
  ],