mBuild 2.0 polymer and simulation improvements: Introduce Path class, Polymer.build_from_path() and add new HOOMD-Blue simulation methods.

.github/workflows/CI.yaml

@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - "main"
+      - "develop"
   pull_request:
     branches:
       - "main"
+      - "develop"
   schedule:
     - cron:  "0 0 * * *"
 
@@ -19,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     defaults:
       run:
@@ -39,6 +41,10 @@ jobs:
       - name: Install Package
         run: python -m pip install -e .
 
+      - name: Conditionally install OpenBabel
+        if: ${{ matrix.python-version != '3.13' }}
+        run: micromamba install -y openbabel
+
       - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
         run: python -m pytest -v --cov=mbuild --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs mbuild
 
@@ -57,7 +63,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, macOS-13, ubuntu-latest]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     defaults:
       run:
@@ -89,7 +95,7 @@ jobs:
       - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
-      - uses: Vampire/setup-wsl@v4
+      - uses: Vampire/setup-wsl@v6
         with:
           distribution: Ubuntu-24.04
           wsl-shell-user: runner

.github/workflows/codeql.yml

@@ -2,9 +2,9 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "develop" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "develop" ]
   schedule:
     - cron: "50 6 * * 0"
 
@@ -27,15 +27,15 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"

.gitignore

@@ -3,6 +3,7 @@ test-output.xml
 *.pymon
 *.ipynb_checkpoints
 *DS_Store*
+__pycache__
 
 # C extensions
 *.so

.pre-commit-config.yaml

@@ -10,15 +10,15 @@ ci:
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.11.13
+  rev: v0.12.10
   hooks:
     # Run the linter.
     - id: ruff
       args: [--line-length=80, --fix]
     # Run the formatter.
     - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer

README.md

@@ -61,6 +61,8 @@ conda activate mbuild-dev
 pip install .
 ```
 
+NOTE: [openbabel](https://github.com/openbabel/openbabel) is required for some energy minimization methods in `mbuild.compound.Compound()`. It can be installed into your mBuild environment from conda-forge with `conda install -c conda-forge openbabel`; however, openbabel does not yet support python 3.13.
+
 #### Install an editable version from source
 
 Once all dependencies have been installed and the ``conda`` environment has been created, the ``mBuild`` itself can be installed.

codecov.yml

@@ -1,3 +1,4 @@
 ignore:
   - "mbuild/examples"
   - "mbuild/tests"
+  - "mbuild/__init__.py"

docs/conf.py

@@ -158,8 +158,8 @@
 # built documents.
 #
 
-version = "1.2.0"
-release = "1.2.0"
+version = "1.2.1"
+release = "1.2.1"
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

environment-dev.yml

@@ -2,26 +2,26 @@ name: mbuild-dev
 channels:
   - conda-forge
 dependencies:
-  - python>=3.9,<=3.12
+  - python>=3.10,<=3.13
   - boltons
-  - numpy=1.26.4
+  - numba
+  - numpy>=2.0,<2.3
   - sympy
   - unyt>=2.9.5
   - boltons
   - lark>=1.2
   - lxml
-  - freud>=3.0
   - intermol
   - mdtraj
   - pydantic>=2
   - networkx
   - nglview>=3
   - pytest
   - garnett>=0.7.1
-  - openbabel>=3.0.0
-  - openff-toolkit-base >=0.11,<0.16.7
+  - openff-toolkit-base>0.16.7
   - openmm
   - gsd>=2.9
+  - freud>=3.2
   - parmed>=3.4.3
   - packmol>=20.15
   - pytest-cov
@@ -39,8 +39,8 @@ dependencies:
   - pandas
   - symengine
   - python-symengine
-  - hoomd>=4.0,<5.0
   - py3Dmol
+  - hoomd>=4.0
   - pip:
       - git+https://github.com/mosdef-hub/gmso.git@main
       - git+https://github.com/mosdef-hub/foyer.git@main

environment.yml

@@ -3,13 +3,14 @@ channels:
   - conda-forge
 dependencies:
   - ele
-  - numpy=1.26.4
+  - numpy>=2.0,<2.3
   - packmol>=20.15
-  - gmso>=0.9.0
+  - gmso>=0.12.0
   - garnett
+  - numba
   - parmed>=3.4.3
   - pycifrw
-  - python>=3.8
+  - python>=3.10,<=3.13
   - rdkit>=2021
   - scipy
   - networkx

mbuild/__init__.py

@@ -2,6 +2,10 @@
 # ruff: noqa: F403
 """mBuild: a hierarchical, component based molecule builder."""
 
+import logging
+import sys
+from logging.handlers import RotatingFileHandler
+
 from mbuild.box import Box
 from mbuild.coarse_graining import coarse_grain
 from mbuild.compound import *
@@ -10,8 +14,124 @@
 from mbuild.lattice import Lattice
 from mbuild.packing import *
 from mbuild.pattern import *
+from mbuild.polymer import Polymer
 from mbuild.port import Port
 from mbuild.recipes import recipes
 
-__version__ = "1.2.0"
+__version__ = "1.2.1"
 __date__ = "2025-01-23"
+
+
+class DeduplicationFilter(logging.Filter):
+    """A logging filter that suppresses duplicate messages."""
+
+    def __init__(self):
+        super().__init__()
+        self.logged_messages = set()
+
+    def filter(self, record):
+        log_entry = (record.name, record.levelno, record.msg)
+        if log_entry not in self.logged_messages:
+            self.logged_messages.add(log_entry)
+            return True
+        return False
+
+
+class HeaderRotatingFileHandler(RotatingFileHandler):
+    def __init__(
+        self,
+        filename,
+        mode="w",
+        maxBytes=0,
+        backupCount=0,
+        encoding=None,
+        delay=False,
+        header="",
+    ):
+        self.header = header
+        super().__init__(filename, mode, maxBytes, backupCount, encoding, delay)
+
+    def _open(self):
+        """
+        Open the current base log file, with the header written.
+        """
+        stream = super()._open()
+        if stream.tell() == 0 and self.header:  # Only write header if file is empty
+            stream.write(self.header + "\n")
+        return stream
+
+
+class mBuildLogger:
+    def __init__(self):
+        self.library_logger = logging.getLogger("mbuild")
+        self.library_logger.setLevel(logging.DEBUG)
+
+        # Create handlers
+        self.console_handler = logging.StreamHandler(sys.stdout)
+        self.console_handler.setLevel(logging.WARNING)
+
+        # Create a formatter
+        self.formatter = logging.Formatter(
+            "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+        )
+
+        # Add formatter to handlers
+        self.console_handler.setFormatter(self.formatter)
+
+        # Initialize and add the deduplication filter
+        self.dedup_filter = DeduplicationFilter()
+        self.console_handler.addFilter(self.dedup_filter)
+
+        # Clear any previous handlers to avoid duplicates in Jupyter
+        self._clear_handlers()
+
+        # Add handlers to the library logger
+        self.library_logger.addHandler(self.console_handler)
+
+    def _clear_handlers(self):
+        handlers = self.library_logger.handlers[:]
+        for handler in handlers:
+            self.library_logger.removeHandler(handler)
+
+    def debug_file(self, filename: str):
+        """Print logging Debug messages to file `filename`."""
+        # Get the path to the Python interpreter
+        python_executable = sys.executable
+
+        # Get the list of command-line arguments
+        command_arguments = sys.argv
+
+        # Construct the full command
+        full_command = [python_executable] + command_arguments
+        header = f"Log details for mBuild {__version__} from running \n{full_command}"
+        self.file_handler = HeaderRotatingFileHandler(
+            filename, mode="a", maxBytes=10**6, backupCount=2, header=header
+        )
+        self.file_handler.setLevel(logging.DEBUG)
+
+        self.file_handler.addFilter(DeduplicationFilter())  # fresh duplication handler
+        self.file_handler.setFormatter(self.formatter)
+        self.library_logger.addHandler(self.file_handler)
+
+    def print_level(self, level: str):
+        """Print sys.stdout screen based on the logging `level` passed."""
+        levelDict = {
+            "notset": logging.NOTSET,
+            "debug": logging.DEBUG,
+            "info": logging.INFO,
+            "warning": logging.WARNING,
+            "error": logging.ERROR,
+            "critical": logging.CRITICAL,
+        }
+        logLevel = levelDict.get(level.lower())
+        if logLevel:
+            self.console_handler.setLevel(logLevel)  # sets stdout
+        else:
+            raise ValueError(
+                f"INCORRECT {level=}. Please set level of {levelDict.keys()}"
+            )
+
+
+# Example usage in __init__.py
+mbuild_logger = mBuildLogger()
+mbuild_logger.library_logger.setLevel(logging.INFO)

mbuild/box.py

@@ -1,13 +1,15 @@
 """mBuild box module."""
 
-from warnings import warn
+import logging
 
 import numpy as np
 
 from mbuild.exceptions import MBuildError
 
 __all__ = ["Box"]
 
+logger = logging.getLogger(__name__)
+
 
 class Box(object):
     """A box representing the bounds of the system.
@@ -350,7 +352,7 @@ def _normalize_box(vectors):
             f"3D region in space.\n Box vectors evaluated: {vectors}"
         )
     if det < 0.0:
-        warn(
+        logger.warning(
             "Box vectors provided for a left-handed basis, these will be "
             "transformed into a right-handed basis automatically."
         )