Update to HOOMD 5 (#95)

* Support HOOMD 5 build configuration

* Add new required method to anisotropic pair potentials

* Update readthedocs environment

* Run pre-commit on all files

* Cleanup automock list

.github/workflows/unit-test.yaml

@@ -8,7 +8,7 @@ env:
 
   #############################################################################################
   # HOOMD-blue version to build.
-  HOOMD_BLUE_VERSION: v4.8.2
+  HOOMD_BLUE_VERSION: v5.0.0
   # prevent deadlocked MPI tests from causing the job to cancel
   MPIEXEC_TIMEOUT: 3000
   # allow mpirun to execute as root in the tests

.pre-commit-config.yaml

@@ -14,9 +14,6 @@ repos:
   - id: check-json
   - id: check-yaml
   - id: check-case-conflict
-  - id: fix-encoding-pragma
-    args:
-    - --remove
   - id: mixed-line-ending
 - repo: https://github.com/glotzerlab/fix-license-header
   rev: v0.4.1
@@ -48,12 +45,14 @@ repos:
     - --keep-after=.. automodule
     - --comment-prefix=..
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v19.1.1
+  rev: v19.1.4
   hooks:
   - id: clang-format
     types_or: [c, c++, cuda, inc]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.9
+  rev: v0.8.1
   hooks:
     - id: ruff-format
+      types_or: [python]
     - id: ruff
+      types_or: [python]

.readthedocs.yaml

@@ -5,14 +5,14 @@ sphinx:
   fail_on_warning: true
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
   jobs:
     post_install:
-      - wget https://github.com/glotzerlab/hoomd-blue/releases/download/v4.8.2/hoomd-4.8.2.tar.gz
-      - tar -xzvf hoomd-4.8.2.tar.gz
-      - python doc/mock_install.py hoomd-4.8.2/hoomd src
+      - wget https://github.com/glotzerlab/hoomd-blue/releases/download/v5.0.0/hoomd-5.0.0.tar.gz
+      - tar -xzvf hoomd-5.0.0.tar.gz
+      - python doc/mock_install.py hoomd-5.0.0/hoomd src
 
 conda:
   environment: doc/environment.yaml

CMakeLists.txt

@@ -5,7 +5,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 3.9 FATAL_ERROR)
 project(azplugins LANGUAGES C CXX)
 
 # Find the installed HOOMD.
-find_package(HOOMD 4.0.0 REQUIRED)
+find_package(HOOMD 5.0.0 REQUIRED)
 
 message(STATUS "Found HOOMD ${HOOMD_VERSION}: ${HOOMD_INSTALL_PREFIX}/${PYTHON_SITE_INSTALL_DIR}")
 

doc/conf.py

@@ -14,79 +14,76 @@
 import datetime
 import os
 
-project = 'azplugins'
+project = "azplugins"
 year = datetime.date.today().year
-copyright = f'2018-2020, Michael P. Howard. 2021-{year}, Auburn University.'  # noqa: A001
-author = 'Michael P. Howard'
-release = '1.0.0'
+copyright = f"2018-2020, Michael P. Howard. 2021-{year}, Auburn University."
+author = "Michael P. Howard"
+release = "1.0.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-default_role = 'any'
+default_role = "any"
 
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 extensions = [
-    'sphinx.ext.mathjax',
+    "sphinx.ext.mathjax",
 ]
 
-extensions += ['sphinx.ext.autodoc', 'sphinx.ext.autosummary']
+extensions += ["sphinx.ext.autodoc", "sphinx.ext.autosummary"]
 autodoc_docstring_signature = True
-autodoc_typehints_format = 'short'
-autodoc_mock_imports = ['hoomd.azplugins._azplugins']
-if os.getenv('READTHEDOCS'):
+autodoc_typehints_format = "short"
+autodoc_mock_imports = ["hoomd.azplugins._azplugins"]
+if os.getenv("READTHEDOCS"):
     autodoc_mock_imports += [
-        'hoomd._hoomd',
-        'hoomd.version_config',
-        'hoomd.md._md',
-        'hoomd.metal._metal',
-        'hoomd.mpcd._mpcd',
-        'hoomd.minimize._minimize',
-        'hoomd.hpmc._jit',
-        'hoomd.hpmc._hpmc',
+        "hoomd._hoomd",
+        "hoomd.version_config",
+        "hoomd.hpmc._hpmc",
+        "hoomd.md._md",
+        "hoomd.mpcd._mpcd",
     ]
 
-extensions += ['sphinx.ext.napoleon']
+extensions += ["sphinx.ext.napoleon"]
 napoleon_include_special_with_doc = True
 
-extensions += ['sphinx.ext.intersphinx']
+extensions += ["sphinx.ext.intersphinx"]
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
-    'numpy': ('https://numpy.org/doc/stable', None),
-    'gsd': ('https://gsd.readthedocs.io/en/stable/', None),
-    'hoomd': ('https://hoomd-blue.readthedocs.io/en/stable/', None),
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "gsd": ("https://gsd.readthedocs.io/en/stable/", None),
+    "hoomd": ("https://hoomd-blue.readthedocs.io/en/stable/", None),
 }
 
-extensions += ['sphinx.ext.todo']
+extensions += ["sphinx.ext.todo"]
 todo_include_todos = False
 
-extensions += ['sphinx_copybutton']
-copybutton_prompt_text = '$ '
+extensions += ["sphinx_copybutton"]
+copybutton_prompt_text = "$ "
 copybutton_remove_prompts = True
-copybutton_line_continuation_character = '\\'
+copybutton_line_continuation_character = "\\"
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'furo'
-html_static_path = ['_static']
+html_theme = "furo"
+html_static_path = ["_static"]
 # html_logo = "hoomdblue-logo-vertical.svg"
 html_theme_options = {
     # "sidebar_hide_name": True,
-    'top_of_page_buttons': [],
-    'navigation_with_keys': True,
-    'dark_css_variables': {
-        'color-brand-primary': '#5187b2',
-        'color-brand-content': '#5187b2',
+    "top_of_page_buttons": [],
+    "navigation_with_keys": True,
+    "dark_css_variables": {
+        "color-brand-primary": "#5187b2",
+        "color-brand-content": "#5187b2",
     },
-    'light_css_variables': {
-        'color-brand-primary': '#406a8c',
-        'color-brand-content': '#406a8c',
+    "light_css_variables": {
+        "color-brand-primary": "#406a8c",
+        "color-brand-content": "#406a8c",
     },
 }
 # html_favicon = "hoomdblue-logo-favicon.svg"
 
-pygments_style = 'friendly'
-pygments_dark_style = 'native'
+pygments_style = "friendly"
+pygments_dark_style = "native"

doc/environment.yaml

@@ -4,8 +4,8 @@ channels:
   - defaults
 dependencies:
   - python=3.12
-  - numpy=2.1.2
+  - numpy=2.1.3
   - sphinx=8.1.3
   - furo=2024.8.6
-  - tornado=6.4.1
+  - tornado=6.4.2
   - sphinx-copybutton=0.5.2

doc/mock_install.py

@@ -13,13 +13,13 @@
 install_dir = Path(site.getsitepackages()[0])
 
 hoomd_dir = Path(sys.argv[1])
-for file in hoomd_dir.rglob('*.py'):
+for file in hoomd_dir.rglob("*.py"):
     relative_file = file.relative_to(hoomd_dir.parent)
     os.makedirs(install_dir / relative_file.parent, exist_ok=True)
     shutil.copy(file, install_dir / relative_file.parent)
 
 azplugins_dir = Path(sys.argv[2])
-for file in azplugins_dir.rglob('*.py'):
-    relative_file = Path('hoomd') / 'azplugins' / file.relative_to(azplugins_dir)
+for file in azplugins_dir.rglob("*.py"):
+    relative_file = Path("hoomd") / "azplugins" / file.relative_to(azplugins_dir)
     os.makedirs(install_dir / relative_file.parent, exist_ok=True)
     shutil.copy(file, install_dir / relative_file.parent)

ruff.toml

@@ -0,0 +1,43 @@
+include = ["*.py"]
+extend-exclude = [".git",
+  "__pycache__",
+  "build",
+  ]
+line-length = 88
+indent-width = 4
+
+[lint]
+select = [
+    "E",
+    "F",
+    "N",
+    "W",
+    "D",
+    "NPY",
+    "RUF",
+]
+ignore = [
+  "D105", # Magic methods don't require documentation
+  "D107", # do not document __init__ separately from the class
+  "D301", # Allow backslashes in docstrings
+  "D205", "D415", # Allow no summary line. The rendered Sphinx documentation is cleaner without them.
+  "N816", "N806","N803", # allow occasional use of uppercase variable and argument names
+  "D214", # ignore overindented sections in Trigger - this is Google napoleon formatting
+  "RUF012", # hoomd does not use typing annotations
+  "NPY002", # TODO: refactor tests to use modern numpy Generator API.
+]
+
+[lint.pydocstyle]
+convention = "google"
+
+[lint.per-file-ignores]
+# allow unused imports in init files
+"__init__.py" = ["F401"]
+# do not require docstrings in unit test or documentation example files
+"**/pytest/*" = ["D", "F811", "N999"]
+
+[format]
+indent-style = "space"
+line-ending = "auto"
+docstring-code-line-length = 72
+docstring-code-format = true

src/AnisoPairEvaluator.h

@@ -196,6 +196,11 @@ class AnisoPairEvaluator
         throw std::runtime_error("Name not defined for this pair potential.");
         }
 
+    static std::string getShapeParamName()
+        {
+        throw std::runtime_error("Shape name not defined for this pair potential.");
+        }
+
     std::string getShapeSpec() const
         {
         throw std::runtime_error("Shape definition not supported for this pair potential.");

src/AnisoPairEvaluatorTwoPatchMorse.h

@@ -220,6 +220,11 @@ class AnisoPairEvaluatorTwoPatchMorse : public AnisoPairEvaluator
         {
         return std::string("TwoPatchMorse");
         }
+
+    static std::string getShapeParamName()
+        {
+        return std::string("");
+        }
 #endif
 
     private:

src/__init__.py

@@ -6,4 +6,4 @@
 
 from hoomd.azplugins import bond, flow, pair
 
-__version__ = '1.0.0'
+__version__ = "1.0.0"

src/bond.py

@@ -51,13 +51,13 @@ class DoubleWell(bond.Bond):
     """
 
     _ext_module = _azplugins
-    _cpp_class_name = 'PotentialBondDoubleWell'
+    _cpp_class_name = "PotentialBondDoubleWell"
 
     def __init__(self):
         super().__init__()
         params = TypeParameter(
-            'params',
-            'bond_types',
+            "params",
+            "bond_types",
             TypeParameterDict(
                 r_0=float, r_1=float, U_1=float, U_tilt=float, len_keys=1
             ),
@@ -135,13 +135,13 @@ class Quartic(bond.Bond):
     """
 
     _ext_module = _azplugins
-    _cpp_class_name = 'PotentialBondQuartic'
+    _cpp_class_name = "PotentialBondQuartic"
 
     def __init__(self):
         super().__init__()
         params = TypeParameter(
-            'params',
-            'bond_types',
+            "params",
+            "bond_types",
             TypeParameterDict(
                 k=float,
                 r_0=float,

src/conftest.py

@@ -7,13 +7,13 @@
 import pytest
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope="session")
 def bonded_two_particle_snapshot_factory(two_particle_snapshot_factory):
     """Fixture for a single bond."""
 
     def make_snapshot(bond_types=None, **kwargs):
         if bond_types is None:
-            bond_types = ['A-A']
+            bond_types = ["A-A"]
         snap = two_particle_snapshot_factory(**kwargs)
         if snap.communicator.rank == 0:
             snap.bonds.types = bond_types