htpolynet 2.0.0__tar.gz

htpolynet-2.0.0/.claude/settings.json

@@ -0,0 +1,23 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(wc -l /home/cfa/Git/HTPolyNet/src/htpolynet/*.py)",
+      "Bash(grep -rn \"^\\\\s*\\\\\\(from\\\\|import\\\\\\)\" /home/cfa/Git/HTPolyNet/src/htpolynet/core/*.py)",
+      "Bash(grep -rn \"^\\\\s*\\\\\\(from\\\\|import\\\\\\)\" /home/cfa/Git/HTPolyNet/src/htpolynet/cure/*.py)",
+      "Bash(grep -rn \"^\\\\s*\\\\\\(from\\\\|import\\\\\\)\" /home/cfa/Git/HTPolyNet/src/htpolynet/geometry/*.py)",
+      "Bash(sort grep:*)",
+      "Bash(grep -rn \"^\\\\s*\\\\\\(from\\\\|import\\\\\\)\" /home/cfa/Git/HTPolyNet/src/htpolynet/analysis/*.py)",
+      "Bash(BASE=/home/cfa/Git/HTPolyNet __NEW_LINE_9d067e0cee514a78__ SED_CMD=':*)",
+      "Bash(xargs sed:*)",
+      "Bash(wc -l /home/cfa/Git/htpolynet/src/htpolynet/cure/*.py /home/cfa/Git/htpolynet/src/htpolynet/external/*.py /home/cfa/Git/htpolynet/src/htpolynet/geometry/*.py /home/cfa/Git/htpolynet/src/htpolynet/utils/*.py /home/cfa/Git/htpolynet/src/htpolynet/driver.py /home/cfa/Git/htpolynet/src/htpolynet/resources/__init__.py)",
+      "Bash(grep -rل \"Args:\" /home/cfa/Git/htpolynet/src/htpolynet --include=\"*.py\" -l)",
+      "Bash(/home/cfa/anaconda3/envs/panacea/bin/pip index:*)",
+      "Read(//home/cfa/Git/**)",
+      "Bash(gh run:*)",
+      "Bash(git ls-tree:*)"
+    ],
+    "additionalDirectories": [
+      "/home/cfa/Git/HTPolyNet/.github/workflows"
+    ]
+  }
+}

htpolynet-2.0.0/.github/workflows/docker.yml

@@ -0,0 +1,35 @@
+name: Build and push Docker image
+
+on:
+  push:
+    tags:
+      - "v*"
+      - "d*"
+  schedule:
+    # Rebuild weekly (Monday 03:00 UTC) to pick up latest Gromacs/AmberTools
+    - cron: '0 3 * * 1'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Log in to GitHub Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Build and push
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        push: true
+        tags: |
+          ghcr.io/abramsgroup/htpolynet:latest
+          ghcr.io/abramsgroup/htpolynet:${{ github.sha }}

htpolynet-2.0.0/.github/workflows/release.yaml

@@ -0,0 +1,102 @@
+name: Release & Upload to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install package
+        run: pip install -e .
+
+      - name: Install Hatch
+        run: python -m pip install --upgrade hatch
+
+      - name: Verify tag matches pyproject version and CHANGELOG
+        if: startsWith(github.ref, 'refs/tags/v')
+        run: |
+          TAG="${GITHUB_REF_NAME#v}"
+          VER="$(grep '^version = ' pyproject.toml | sed 's/version = "\(.*\)"/\1/')"
+          echo "Tag version:     $TAG"
+          echo "Project version: $VER"
+          test "$TAG" = "$VER" || { echo "ERROR: tag $TAG != pyproject version $VER"; exit 1; }
+          grep -q "^## \[$VER\]" CHANGELOG.md || { echo "ERROR: no CHANGELOG entry for $VER"; exit 1; }
+
+      - name: Clean previous builds
+        run: rm -rf dist/
+
+      - name: Build the package with Hatch
+        run: hatch build
+
+      - name: Extract release notes from CHANGELOG.md
+        run: |
+          echo 'RELEASE_BODY<<EOF' >> $GITHUB_ENV
+          awk '
+            BEGIN {found=0; capture=0}
+            /^## \[Unreleased\]/ {next}
+            /^## \[/ {
+              if (found) exit;
+              found = 1;
+              capture = 1;
+              next
+            }
+            /^## / {capture=0}
+            capture {print}
+          ' CHANGELOG.md >> $GITHUB_ENV
+          echo 'EOF' >> $GITHUB_ENV
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ github.ref_name }}
+          name: Release ${{ github.ref_name }}
+          body: ${{ env.RELEASE_BODY }}
+          files: |
+            dist/*.tar.gz
+            dist/*.whl
+
+      - name: Upload dist artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Trigger ReadTheDocs build
+        run: |
+          curl -X POST \
+            -H "Authorization: Token ${{ secrets.RTD_SECRET }}" \
+            https://readthedocs.org/api/v3/projects/htpolynet/versions/latest/builds/
+          curl -X POST \
+            -H "Authorization: Token ${{ secrets.RTD_SECRET }}" \
+            https://readthedocs.org/api/v3/projects/htpolynet/versions/${{ github.ref_name }}/builds/
+
+  publish:
+    needs: release
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

htpolynet-2.0.0/.gitignore

@@ -0,0 +1,145 @@
+# Singularity/Apptainer images and Docker artifacts
+*.sif
+*.simg
+*.img
+docker-*.tar
+
+*.bak
+__defunct__/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.idea/
+*tmp*
+*/results
+.vscode/
+# C extensions
+*.so
+
+CLAUDE.md
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/source/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+.vscode/settings.json
+

htpolynet-2.0.0/.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

htpolynet-2.0.0/CHANGELOG.md

@@ -0,0 +1,41 @@
+# Changelog
+
+All notable changes to htpolynet will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [2.0.0] - 2026-05-07
+
+### Changed
+
+- Package renamed from `HTPolyNet` to `htpolynet` (fully lowercase) for PEP 8 compliance and PyPI consistency.
+- Runtime now logs the HTPolyNet git commit hash at startup, with a warning when uncommitted changes are present.
+
+### Added
+
+- Apptainer/Singularity container support: distributed as a `.sif` image for reproducible execution on HPC clusters.
+- New `gen-slurm-script` subcommand generates a ready-to-submit SLURM batch script from an htpolynet YAML config file.
+
+### Fixed
+
+- Chain-expansion bug: bond-chain `ChainManager` was not rebuilt for monomers on the fetch path, causing `bondchain_expand_reactions` to produce no chain-extended oligomers in runs that reused cached parameterizations.
+
+## [1.0.9] - 2025-01-01
+
+### Added
+
+- `minimum_bondcycle_length` parameter to allow for cyclic polymerization above a certain threshold length.
+
+### Fixed
+
+- Rings not transferred from monomer templates if they are pre-parameterized.
+- Atom indexes in bondchain structure not remapped after atom deletion.
+
+## [1.0.8] - 2024-01-04
+
+### Changed
+
+- Uses `chordless_cycles` to find rings; `ringidx` is no longer a unique atom attribute; improved ring-pierce detection.

htpolynet-2.0.0/Dockerfile

@@ -0,0 +1,35 @@
+# HTPolyNet container image
+# Includes Gromacs, AmberTools (antechamber, tleap, parmchk2), and OpenBabel via conda-forge.
+#
+# Usage:
+#   docker run --rm -v $(pwd):/work ghcr.io/abramsgroup/htpolynet htpolynet run config.yaml
+#
+# To avoid files being written as root, pass your host uid/gid:
+#   docker run --rm -v $(pwd):/work --user $(id -u):$(id -g) ghcr.io/abramsgroup/htpolynet htpolynet run config.yaml
+#
+# GPU support (requires nvidia-container-toolkit):
+#   docker run --rm --gpus all -v $(pwd):/work ghcr.io/abramsgroup/htpolynet htpolynet run config.yaml
+
+FROM continuumio/miniconda3:latest
+
+# Install Gromacs and AmberTools (latest available on conda-forge)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        openbabel \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN conda install -y -c conda-forge \
+        ambertools \
+        gromacs \
+        parmed \
+    && conda clean -afy
+
+# Install HTPolyNet
+COPY . /htpolynet
+WORKDIR /htpolynet
+RUN pip install --no-cache-dir .
+
+# User data is mounted here at runtime
+WORKDIR /work
+
+ENTRYPOINT ["htpolynet"]
+CMD ["--help"]

htpolynet-2.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Cameron Abrams
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

htpolynet-2.0.0/MANIFEST.in

@@ -0,0 +1 @@
+recursive-include htpolynet resources

htpolynet-2.0.0/PKG-INFO

@@ -0,0 +1,78 @@
+Metadata-Version: 2.4
+Name: htpolynet
+Version: 2.0.0
+Summary: Automated MD System Builder for Amorphous Network Polymers
+Project-URL: Source, https://github.com/AbramsGroup/htpolynet
+Project-URL: Documentation, https://htpolynet.readthedocs.io/
+Project-URL: Bug Tracker, https://github.com/AbramsGroup/htpolynet/issues
+Author-email: Cameron F Abrams <cfa22@drexel.edu>
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.9
+Requires-Dist: gputil>=1.4
+Requires-Dist: networkx>=3.2
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2
+Requires-Dist: parmed>=4
+Requires-Dist: pyyaml>=6
+Requires-Dist: requests>=2.28
+Requires-Dist: scipy>=1.10
+Provides-Extra: dev
+Requires-Dist: pytest; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# htpolynet
+> High-Throughput Polymer Network Atomistic Simulations
+
+htpolynet is a Python utility for generating atomistic models of cross-linked polymer networks together with appropriate topology and parameter files required for molecular dynamics simulations using Gromacs.  It is intended as a fully automated system builder requiring as inputs only the molecular structures of any monomer species, a description of the polymerization chemistry, and a handful of options describing desired system size and composition.  htpolynet uses the Generalized Amber Force Field for atom-typing and parameter generation.
+
+## Installation
+
+From PyPI:
+```bash
+pip install htpolynet
+```
+
+From conda-forge:
+```bash
+conda install -c conda-forge htpolynet
+```
+
+From source:
+```bash
+git clone git@github.com:AbramsGroup/htpolynet.git
+cd htpolynet
+pip install -e .
+```
+
+Once installed, the user has access to the main ``htpolynet`` command.
+
+IMPORTANT NOTES: The programs ``antechamber``, ``parmchk2`` and ``tleap`` from AmberTools must be in your path.  These can be installed using the ``ambertools`` package from ``conda-forge`` or compiled from source.  You also need Gromacs installed so ``gmx`` is in your path.  The examples show how to build input monomer structures using OpenBabel, so to use them you need ``obabel`` in your path as well.
+
+## Documentation
+
+Please consult documentation at [abramsgroup.github.io/htpolynet](https://abramsgroup.github.io/htpolynet/).
+
+## Meta
+
+Cameron F. Abrams – cfa22@drexel.edu
+
+Distributed under the MIT license. See ``LICENSE`` for more information.
+
+[https://github.com/cameronabrams](https://github.com/cameronabrams/)
+
+[https://github.com/AbramsGroup](https://github.com/AbramsGroup/)
+
+## Contributing
+
+1. Fork it (<https://github.com/AbramsGroup/htolynet/fork>)
+2. Create your feature branch (`git checkout -b feature/fooBar`)
+3. Commit your changes (`git commit -am 'Add some fooBar'`)
+4. Push to the branch (`git push origin feature/fooBar`)
+5. Create a new Pull Request
+

htpolynet-2.0.0/README.md

@@ -0,0 +1,50 @@
+# htpolynet
+> High-Throughput Polymer Network Atomistic Simulations
+
+htpolynet is a Python utility for generating atomistic models of cross-linked polymer networks together with appropriate topology and parameter files required for molecular dynamics simulations using Gromacs.  It is intended as a fully automated system builder requiring as inputs only the molecular structures of any monomer species, a description of the polymerization chemistry, and a handful of options describing desired system size and composition.  htpolynet uses the Generalized Amber Force Field for atom-typing and parameter generation.
+
+## Installation
+
+From PyPI:
+```bash
+pip install htpolynet
+```
+
+From conda-forge:
+```bash
+conda install -c conda-forge htpolynet
+```
+
+From source:
+```bash
+git clone git@github.com:AbramsGroup/htpolynet.git
+cd htpolynet
+pip install -e .
+```
+
+Once installed, the user has access to the main ``htpolynet`` command.
+
+IMPORTANT NOTES: The programs ``antechamber``, ``parmchk2`` and ``tleap`` from AmberTools must be in your path.  These can be installed using the ``ambertools`` package from ``conda-forge`` or compiled from source.  You also need Gromacs installed so ``gmx`` is in your path.  The examples show how to build input monomer structures using OpenBabel, so to use them you need ``obabel`` in your path as well.
+
+## Documentation
+
+Please consult documentation at [abramsgroup.github.io/htpolynet](https://abramsgroup.github.io/htpolynet/).
+
+## Meta
+
+Cameron F. Abrams – cfa22@drexel.edu
+
+Distributed under the MIT license. See ``LICENSE`` for more information.
+
+[https://github.com/cameronabrams](https://github.com/cameronabrams/)
+
+[https://github.com/AbramsGroup](https://github.com/AbramsGroup/)
+
+## Contributing
+
+1. Fork it (<https://github.com/AbramsGroup/htolynet/fork>)
+2. Create your feature branch (`git checkout -b feature/fooBar`)
+3. Commit your changes (`git commit -am 'Add some fooBar'`)
+4. Push to the branch (`git push origin feature/fooBar`)
+5. Create a new Pull Request
+

htpolynet-2.0.0/compose.yml

@@ -0,0 +1,7 @@
+services:
+  htpolynet:
+    image: ghcr.io/abramsgroup/htpolynet:latest
+    volumes:
+      - .:/work
+    working_dir: /work
+    user: "${UID:-0}:${GID:-0}"

htpolynet-2.0.0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+# i've changed this?
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

htpolynet-2.0.0/docs/README.rst

@@ -0,0 +1,6 @@
+htpolynet
+=========
+
+htpolynet is a tool for building atomically resolved models of amorphous network polymers.
+It uses the Generalized Amber Force Field and produces output that can be simulated 
+using Gromacs.

htpolynet-2.0.0/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

htpolynet-2.0.0/docs/requirements.txt

@@ -0,0 +1,7 @@
+sphinx
+myst-parser
+furo
+sphinxcontrib-bibtex
+sphinx-copybutton
+matplotlib
+pytrr

htpolynet-2.0.0/docs/source/changelog.rst

@@ -0,0 +1,7 @@
+.. _changelog:
+
+Changelog
+=========
+
+.. include:: ../../CHANGELOG.md
+   :parser: myst_parser.sphinx_