MesoHOPS 1.7.0

.coveragerc

@@ -0,0 +1,30 @@
+[run]
+source = mesohops
+relative_files = true
+omit =
+    */tests/*
+    */test_*
+    setup.py
+    */venv/*
+    */virtualenv/*
+    */site-packages/*
+    */timing/timing_analysis.py
+    */timing/helper_functions/*
+    */timing/timing_models/*
+    */timing/__init__.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    if self.debug:
+    if settings.DEBUG
+    raise AssertionError
+    raise NotImplementedError
+    if 0:
+    if __name__ == .__main__.:
+    class .*\bProtocol\):
+    @(abc\.)?abstractmethod
+
+[html]
+directory = htmlcov

.github/workflows/coverage.yml

@@ -0,0 +1,106 @@
+name: Code Coverage
+
+on:
+  pull_request:
+    branches: [ main, master ]
+
+permissions:
+  contents: read
+  pull-requests: write
+  checks: write  # Needed for test reporting
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.12', '3.13']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies (editable)
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+
+    - name: Run tests with coverage
+      continue-on-error: true
+      run: |
+        # Run tests and generate both coverage and test report
+        pytest --cov=mesohops --cov-report=xml --cov-report=term --junitxml=test-results.xml -v || true
+
+        # Show test results summary
+        echo "=== Test Results Summary ==="
+        if [ -f test-results.xml ]; then
+          echo "Test results file generated"
+          # Count total tests
+          total_tests=$(grep -c "<testcase" test-results.xml)
+          # Count failed tests
+          failed_tests=$(grep -c "<failure" test-results.xml)
+          echo "Total tests: $total_tests"
+          echo "Failed tests: $failed_tests"
+          echo "Passed tests: $((total_tests - failed_tests))"
+        else
+          echo "No test results file generated"
+        fi
+
+    - name: Upload coverage to Codecov
+      if: matrix.python-version == '3.12'
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+        flags: unittests
+        name: Python Coverage
+        fail_ci_if_error: false
+        verbose: true
+
+    - name: Publish Test Results
+      if: always()
+      uses: mikepenz/action-junit-report@v4
+      with:
+        report_paths: 'test-results.xml'
+        check_name: 'Python Unit Tests (${{ matrix.python-version }})'
+        fail_on_failure: false
+        require_tests: false
+
+  smoke-install:
+    # Validates that `pip install .` (non-editable) succeeds and that the
+    # installed package can run the test suite. Catches packaging bugs the
+    # editable-install coverage job hides — missing files in the wheel,
+    # broken pyproject.toml metadata, dependency-resolution failures.
+    # Gating: a failed clean install must block the PR.
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.12', '3.13']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Clean install (non-editable)
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+
+    - name: Run level-1 tests against installed package
+      run: |
+        # Override pytest.ini's addopts to disable coverage measurement here.
+        # Coverage is the editable-install job's responsibility; in the smoke
+        # job, the installed-package paths can't be reconciled with the
+        # `source = mesohops` setting in .coveragerc, so --cov-fail-under=70
+        # would always trip on a 0% reading.
+        pytest tests/ --level 1 -v -o addopts=""

codecov.yml

@@ -0,0 +1,25 @@
+comment:
+  layout: "diff, flags, files"  # Shows coverage diff, flags, and file list
+  behavior: default
+  require_changes: false  # Always post comment, even if no coverage changes
+  require_base: false    # Don't require base report
+  require_head: true     # Require head report
+  hide_project_coverage: false  # Show project coverage
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto  # Compare to previous base commit
+        threshold: 0%  # No threshold requirement
+        informational: true  # Don't block PRs
+    patch:
+      default:
+        target: auto
+        threshold: 0%
+        informational: true  # Don't block PRs
+
+codecov:
+  require_ci_to_pass: false  # Show coverage even if CI fails
+  notify:
+    wait_for_ci: false  # Send notifications immediately 

pyproject.toml

@@ -1,15 +1,20 @@
 [project]
 name = "mesohops"
-version = "1.6.0"
+version = "1.7.0"
+# 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
+# either dependency require running the level-2 test suite against the
+# candidate version.
 dependencies = [
-  "numpy",
-  "scipy",
-  "numba",
-  "pytest",
-  "pytest-level",
-  "pytest-cov"
+  "numpy>=2.3,<2.4",
+  "scipy>=1.15,<2.0",
+  "numba>=0.63,<0.64",
+  "pytest>=8.3,<9.0",
+  "pytest-level>=0.1,<0.2",
+  "pytest-cov>=6.0,<7.0",
 ]
-requires-python = ">=3.12"
+requires-python = ">=3.12,<3.14"
 authors = [
   {name = "Leonel Varvelo", email = "leonel_varvelo@yahoo.com"},
   {name = "Jacob Lynd", email = "jacobklynd@gmail.com"},
@@ -29,11 +34,15 @@ readme = "README.md"
 license = {file = "LICENSE"}
 keywords = ["open quantum systems", "mesoscale", "spectroscopy", "excited-state dynamics", "non-Markovian"]
 classifiers = [
-  "Development Status :: full release 1.6.0",
+  "Development Status :: 5 - Production/Stable",
   "Programming Language :: Python"
 ]
 
-
 [project.urls]
 Homepage = "https://captainexasperated.github.io/Readthedocs-Tutorial/"
 Repository = "https://github.com/MesoscienceLab/mesohops"
+
+[tool.pytest.ini_options]
+markers = [
+  "order: mark test to run in a specific order"
+]