MesoHOPS 1.8.0

.github/CODEOWNERS

@@ -0,0 +1,3 @@
+# ABOUTME: Gates master merges - required approval must come from a listed owner.
+# ABOUTME: Works with branch protection require_code_owner_reviews; admins may bypass.
+* @digbennett @alexiahartzell

.github/workflows/coverage.yml

@@ -3,6 +3,11 @@ name: Code Coverage
 on:
   pull_request:
     branches: [ main, master ]
+  # Codecov needs a coverage report on the base branch to compute a diff and to
+  # render the badge. Without push builds there is no baseline, so PR comments
+  # show "unknown" and the badge never populates.
+  push:
+    branches: [ main, master ]
 
 permissions:
   contents: read
@@ -33,8 +38,12 @@ jobs:
     - name: Run tests with coverage
       continue-on-error: true
       run: |
-        # Run tests and generate both coverage and test report
-        pytest --cov=mesohops --cov-report=xml --cov-report=term --junitxml=test-results.xml -v || true
+        # Run tests and generate both coverage and test report.
+        # --level 3 overrides the --level=1 in pytest.ini's addopts so that
+        # coverage reflects the whole suite. At level 1 the level-2 and
+        # level-3 tests are deselected and contribute nothing, which
+        # understates coverage.
+        pytest --level 3 --cov=mesohops --cov-report=xml --cov-report=term --junitxml=test-results.xml -v || true
 
         # Show test results summary
         echo "=== Test Results Summary ==="
@@ -53,13 +62,16 @@ jobs:
 
     - name: Upload coverage to Codecov
       if: matrix.python-version == '3.12'
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
         flags: unittests
         name: Python Coverage
-        fail_ci_if_error: false
+        # Fail loudly. Previously this was false, so a rejected upload (missing
+        # token, sunset uploader) left the job green while Codecov received
+        # nothing -- the failure was invisible for several releases.
+        fail_ci_if_error: true
         verbose: true
 
     - name: Publish Test Results

.gitignore

@@ -1,5 +1,198 @@
-*.pyc
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+cover/
+
+# 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/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm / JetBrains
+.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
 .DS_Store
-mesohops.egg-info
-.idea
-.idea
+
+# AI coding tools
+.claude/
+.private-journal/
+.zencoder/
+.tldr/

README.md

@@ -1,3 +1,5 @@
+[![codecov](https://codecov.io/gh/MesoscienceLab/mesohops/graph/badge.svg?token=EZAW5BW4P4)](https://codecov.io/gh/MesoscienceLab/mesohops)
+
 # What is MesoHOPS?
 
 MesoHOPS is a Python library for running simulations with the Hierarchy of Pure States (HOPS), a formally exact trajectory-based approach for solving the time-evolution of open quantum systems coupled to non-Markovian thermal environments. The main feature of MesoHOPS is the implementation of adaptive HOPS (adHOPS), an extension of the HOPS formalism that leverages the dynamic localization of excitations to construct an adaptive basis. The moving adHOPS basis significantly reduces the computational cost of simulations and exhibits a size-invariant scaling in large systems.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mesohops"
-version = "1.7.0"
+version = "1.8.0"
 # numba and numpy are pinned to a single minor version. numba minor
 # releases have introduced stochastic test failures and memory issues,
 # and numba binds against a specific numpy ABI. Upper-bound bumps for