Add GitHub Actions CI (lint + tests + manual integration)

.github/actions/setup-pybnf/action.yml

@@ -0,0 +1,75 @@
+name: Set up pybnf (bngsim-less)
+description: >-
+  Install BioNetGen (BNG2.pl) plus pybnf and its public runtime/test
+  dependencies into a uv venv, deliberately omitting the private, macOS-only
+  bngsim wheel. Tests run under PYBNF_NO_BNGSIM=1 so bngsim-marked tests skip
+  (see tests/conftest.py). BNG2.pl is still required: Configuration validation
+  execs `BNG2.pl -v` for any BNGLModel regardless of bngsim, and the analytical
+  tests aside, most of the suite builds such configs.
+
+inputs:
+  python-version:
+    description: Python version for the venv (e.g. "3.10", "3.12").
+    required: true
+
+runs:
+  using: composite
+  steps:
+    # Provision the interpreter with setup-python rather than uv's managed
+    # (python-build-standalone) builds: libroadrunner is a C++ extension that
+    # dlopen's libpython, and uv's standalone Python 3.10 does not expose
+    # libpython3.10.so.1.0 on the loader path (3.12's does). setup-python's
+    # Pythons are built --enable-shared with libpython discoverable, so
+    # roadrunner imports on every matrix leg.
+    - uses: actions/setup-python@v5
+      id: python
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+        # No uv.lock in this repo; key the cache on pyproject.toml so it can
+        # invalidate when deps change.
+        cache-dependency-glob: pyproject.toml
+
+    - name: Install BioNetGen 2.9.3
+      shell: bash
+      run: |
+        # BioNetGen is free/open-source and provides BNG2.pl (Perl is
+        # preinstalled on ubuntu runners). It is NOT vendored into the repo or
+        # the pybnf wheel -- it is fetched onto the ephemeral runner each run,
+        # mirroring the developer prerequisite (BNGPATH on a local machine).
+        curl -fsSL \
+          https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.3/BioNetGen-2.9.3-linux.tar.gz \
+          -o "$RUNNER_TEMP/bionetgen.tar.gz"
+        tar -xzf "$RUNNER_TEMP/bionetgen.tar.gz" -C "$RUNNER_TEMP"
+        echo "BNGPATH=$RUNNER_TEMP/BioNetGen-2.9.3" >> "$GITHUB_ENV"
+
+    - name: Create venv and install pybnf without bngsim
+      shell: bash
+      run: |
+        # Build the venv from the setup-python interpreter (see note above), not
+        # a uv-managed one.
+        uv venv --python "${{ steps.python.outputs.python-path }}"
+        # Mirror pyproject.toml's runtime deps MINUS bngsim (private, mac-only
+        # wheel, not on PyPI), plus the test stack and pytest-xdist. Keep these
+        # version bounds in sync with pyproject.toml; bngsim is the only
+        # intentional omission.
+        uv pip install \
+          'dask>=2021.5.0,<2023.0' \
+          'distributed>=2021.6.2,<2023.0' \
+          'libroadrunner>=1.6.0,<3' \
+          'msgpack>=0.6.2,<2' \
+          'numpy>=1.24,<3' \
+          'paramiko>=2.7,<5' \
+          'pyparsing>=2.4,<4' \
+          'scipy>=1.10,<2' \
+          'tornado>=6.1,<7' \
+          'pytest>=7,<10' \
+          'hypothesis>=6,<7' \
+          'pytest-xdist' \
+          'tomli>=2,<3; python_version < "3.11"'
+        # Install pybnf itself without re-resolving deps (which would pull
+        # bngsim and fail).
+        uv pip install --no-deps .

.github/workflows/integration.yml

@@ -0,0 +1,30 @@
+name: integration
+
+# Manual only. The slow tier is the 4 statistical-recovery tests against
+# analytical targets (AnalyticalModel) -- bngsim-free and BNG2.pl-free, ~8 min.
+#
+# NOTE: the bngsim *simulation* suites (true NFsim/RuleMonkey/SBML runs) are
+# deliberately NOT in hosted CI -- they need the private, macOS-only bngsim
+# wheel. They remain covered by the local pre-push hook (.pre-commit-config.yaml)
+# on a dev machine until bngsim ships Linux wheels.
+#
+# A nightly `schedule:` cron could be added here, but is intentionally omitted
+# pending a maintainer decision.
+on:
+  workflow_dispatch:
+
+jobs:
+  slow:
+    runs-on: ubuntu-latest
+    name: slow recovery tests
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/setup-pybnf
+        with:
+          python-version: '3.12'
+
+      - name: Run slow analytical recovery tests
+        env:
+          PYBNF_NO_BNGSIM: '1'
+        run: uv run --no-sync pytest -m slow -n auto

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: lint
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: ruff check
+        # Pin ruff so the rule set is reproducible: the [tool.ruff] config in
+        # pyproject.toml pins which rules run, but a newer ruff could add rules
+        # to the default selection and turn the gate red unexpectedly.
+        run: uvx ruff@0.15.14 check .
+
+      # NOTE: `ruff format --check` is intentionally NOT enforced in v1. The
+      # codebase predates ruff formatting; a repo-wide reformat is a large,
+      # behavior-adjacent diff best done in its own dedicated PR. Add a format
+      # check here once that lands.

.github/workflows/tests.yml

@@ -0,0 +1,35 @@
+name: tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # Min and max of the supported range (requires-python >= 3.10;
+        # classifiers list through 3.12).
+        python-version: ['3.10', '3.12']
+    name: pytest (py${{ matrix.python-version }})
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/setup-pybnf
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run unit tests (bngsim-less, parallel)
+        env:
+          # bngsim is a private mac-only wheel; with it absent, conftest.py
+          # auto-skips bngsim/nfsim/sbml/etc.-marked tests. The remaining suite
+          # runs against the bngsim-less code paths (and BNG2.pl from the
+          # composite action). -n auto parallelizes across the runner's cores.
+          PYBNF_NO_BNGSIM: '1'
+        # --no-sync: do NOT let `uv run` re-resolve the project env from
+        # pyproject.toml (that would pull the private bngsim and fail). The
+        # composite action already populated .venv.
+        run: uv run --no-sync pytest -m "not slow" -n auto

examples/sampler_benchmarking/run_all.py

@@ -159,7 +159,7 @@ def main():
         print(f"{submitted} jobs completed, {failed} failed.")
     else:
         print(f"{submitted} jobs submitted, {failed} failed.")
-        print(f"Monitor with: squeue -u $USER")
+        print("Monitor with: squeue -u $USER")
 
 
 if __name__ == "__main__":

pybnf/algorithms.py

@@ -8,7 +8,6 @@
 from subprocess import STDOUT
 from .pset import run_subprocess
 
-from numpy import mean
 
 from .bngsim_model import (
     BngsimModel,
@@ -24,9 +23,8 @@
 from .data import Data
 from .pset import PSet
 from .pset import Trajectory
-from .pset import TimeCourse
 from .pset import BNGLModel
-from .pset import NetModel, BNGLModel, SbmlModelNoTimeout
+from .pset import NetModel
 from .pset import OutOfBoundsException
 from .pset import FailedSimulationError
 from .printing import print0, print1, print2, PybnfError

pybnf/bngsim_model.py

@@ -14,13 +14,10 @@
 from ._bngsim_caps import (
     BNGSIM_AVAILABLE,
     BNGSIM_ERROR,
-    BNGSIM_FEATURES,
     BNGSIM_HAS_NFSIM,
     BNGSIM_HAS_RULEMONKEY,
-    BNGSIM_MISSING,
     BNGSIM_VERSION,
     bngsim,
-    feature_missing_reason,
 )
 from .data import Data
 from .pset import FreeParameter, Model, NetModel, PSet, _stage_and_rewrite_tfun_files
@@ -501,7 +498,6 @@ def _create_nf_session(session_backend, xml_path, molecule_limit=None):
     if molecule_limit is None:
         return session_cls(xml_path)
     return session_cls(xml_path, molecule_limit=molecule_limit)
-    return session
 
 
 def _destroy_nf_session(session):

pybnf/bngsim_sbml_model.py

@@ -29,8 +29,6 @@
 
 
 from ._bngsim_caps import (
-    BNGSIM_AVAILABLE,
-    BNGSIM_HAS_LIBSBML as LIBSBML_AVAILABLE,
     BNGSIM_HAS_SBML,
     BNGSIM_SBML_ERROR,
     bngsim,

pybnf/config.py

@@ -2,21 +2,19 @@
 
 
 from .data import Data, DuplicateColumnError
-from .objective import ChiSquareObjective, ChiSquareObjective_Dynamic, NegBinLikelihood_Dynamic, NegBinLikelihood, SumOfSquaresObjective, NormSumOfSquaresObjective, \
+from .objective import ChiSquareObjective, ChiSquareObjective_Dynamic, NegBinLikelihood_Dynamic, SumOfSquaresObjective, NormSumOfSquaresObjective, \
     AveNormSumOfSquaresObjective, SumOfDiffsObjective, NegBinLikelihood, KLLikelihood, DirectPassObjective
 
 from .pset import BNGLModel, ModelError, SbmlModel, SbmlModelNoTimeout, FreeParameter, TimeCourse, ParamScan, \
     Mutation, MutationSet
 from .bngsim_sbml_model import (
     BNGSIM_HAS_SBML,
     BNGSIM_SBML_ERROR,
-    BngsimSbmlModel,
     BngsimSbmlModelNoTimeout,
 )
 from .bngsim_antimony_model import (
     BNGSIM_HAS_ANTIMONY,
     BNGSIM_ANTIMONY_ERROR,
-    BngsimAntimonyModel,
     BngsimAntimonyModelNoTimeout,
 )
 from .printing import verbosity, print1, PybnfError

pybnf/pset.py

@@ -9,13 +9,12 @@
 import re
 import copy
 import signal
-from subprocess import run, Popen, STDOUT, PIPE, DEVNULL, CalledProcessError, TimeoutExpired
+from subprocess import Popen, STDOUT, PIPE, CalledProcessError, TimeoutExpired
 from .data import Data
 import heapq
 import traceback
 import roadrunner as rr
 import pickle
-from os.path import join
 import os
 import shutil
 import tempfile

pyproject.toml

@@ -66,6 +66,35 @@ packages = ["pybnf"]
 [tool.setuptools.dynamic]
 version = { attr = "pybnf.__version__" }
 
+[tool.ruff]
+target-version = "py310"
+# Pins ruff's default rule set (pycodestyle E4/E7/E9 + pyflakes F) so local runs
+# and CI agree. Line length (E501) and the broader style/lint families are
+# intentionally left off for v1; revisit once the codebase is reformatted.
+
+[tool.ruff.lint]
+# Pre-existing legacy style that PyBNF does not enforce. Each is either purely
+# cosmetic or a behavioral change to "fix", so it is out of scope for the lint
+# gate (which must stay mechanical). Items tied to dev/PUNCHLIST.md are tracked
+# and fixed there, not here.
+ignore = [
+    "E402",  # module-import-not-at-top: intentional (lazy backend guards, test bootstrap)
+    "E712",  # ==True/False: legacy; rewriting can change truthiness semantics (e.g. numpy bools)
+    "E721",  # type(x) == T comparisons: legacy, semantically fine in context
+    "E722",  # bare except: tracked as ROB-4 in dev/PUNCHLIST.md (behavioral fix)
+    "E741",  # ambiguous variable names (l/I/O): legacy
+    "F841",  # unused locals: several are CQ-5 dead code (tracked); common bind-then-assert in tests
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = [
+    "E702",  # multiple-statements-on-one-line (semicolons): established test-file style
+    "F402",  # import shadowed by loop variable
+]
+# context.py is a re-export shim: test modules do `from .context import data`,
+# so its imports are "unused" only within the file itself.
+"tests/context.py" = ["F401"]
+
 [tool.pytest.ini_options]
 minversion = "7.0"
 testpaths = ["tests"]

tests/test_bayes_mcmc.py

@@ -1,4 +1,4 @@
-from .context import data, algorithms, pset, objective, config
+from .context import data, algorithms, pset, config
 import os
 import shutil
 import numpy as np