fix(docker): repair the Dockerfile as a legacy BNG2.pl image (#414)

.github/workflows/docker.yml

@@ -0,0 +1,39 @@
+name: docker
+
+# Build (and smoke-test) the legacy BNG2.pl container image so the Dockerfile
+# can't rot silently again (issue #414). Runs on demand and whenever the
+# Dockerfile or the dependency set it mirrors changes.
+on:
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - Dockerfile
+      - pyproject.toml
+      - .github/workflows/docker.yml
+  push:
+    branches: [main]
+    paths:
+      - Dockerfile
+      - pyproject.toml
+      - .github/workflows/docker.yml
+
+jobs:
+  build:
+    name: docker build (legacy BNG2.pl image)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build image
+        run: docker build -t pybnf:ci .
+
+      - name: Smoke-test the image
+        run: |
+          # PyBNF imports cleanly without bngsim (legacy BNG2.pl backend)...
+          docker run --rm pybnf:ci python -c "import pybnf; print('pybnf', pybnf.__version__)"
+          # ...the console script is wired...
+          docker run --rm pybnf:ci pybnf --help
+          # ...and BNG2.pl is on PATH via BNGPATH. Use a non-login shell: a
+          # login shell would re-source /etc/profile and reset PATH, dropping
+          # the image's BNGPATH entry.
+          docker run --rm pybnf:ci bash -c 'command -v BNG2.pl'

Dockerfile

@@ -1,45 +1,51 @@
 #
-# To build Docker image, run inside PyBNF directory:
-#     docker build -t pybnf .
+# PyBNF container image -- legacy BNG2.pl backend.
+#
+# This image bundles BioNetGen's BNG2.pl backend (the open-source rule-based
+# modeling engine) together with PyBNF and its public runtime dependencies.
 #
-# If BNGsim is hosted on a private package index, pass the index URL:
-#     docker build --build-arg PIP_EXTRA_INDEX_URL=https://... -t pybnf .
+# It deliberately does NOT install bngsim, PyBNF's modern simulation backend:
+# bngsim is a private, macOS-only wheel with no public Linux build, so it cannot
+# be installed in a Linux container today (issue #414). PyBNF imports cleanly
+# without bngsim and falls back to the legacy BNG2.pl path. When bngsim ships
+# public Linux wheels, a bngsim-backed image can replace this one.
 #
-# Run inside PyBNF to mount examples directory inside the image:
+# Build (run inside the PyBNF directory):
+#     docker build -t pybnf .
+#
+# Run with your examples directory mounted:
 #     docker run -it --rm -v $(pwd)/examples:/project/examples pybnf
 #
 # And then inside the image:
 #     cd examples/demo
 #     pybnf -c demo_bng.conf
 #
 
-ARG PYTHON_VERSION=3.12
+ARG PYTHON_VERSION=3.13
 ARG BIONETGEN_VERSION=BioNetGen-2.9.3
 
 
-### BioNetGen build container
-FROM python:${PYTHON_VERSION}-slim AS bionetgen-build
-
+### BioNetGen: fetch the prebuilt Linux release (no from-source compile)
+FROM python:${PYTHON_VERSION}-slim AS bionetgen
 ARG BIONETGEN_VERSION
 
 ENV DEBIAN_FRONTEND=noninteractive
 
-WORKDIR /usr/src
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    autoconf \
-    build-essential \
     ca-certificates \
-    cmake \
-    git \
-    libtool \
-    ninja-build \
-    perl && \
+    curl && \
     rm -rf /var/lib/apt/lists/*
 
-RUN git clone --depth 1 --recurse-submodules --branch "${BIONETGEN_VERSION}" https://github.com/RuleWorld/bionetgen.git
-
-WORKDIR /usr/src/bionetgen/bng2
-RUN ./make_dist.pl --build
+WORKDIR /usr/src
+# Use the official prebuilt Linux tarball (BNG2.pl plus its bundled
+# run_network/NFsim binaries) instead of compiling from source. This mirrors the
+# CI provisioning in .github/actions/setup-pybnf/action.yml and keeps the build
+# fast and robust (no autoconf/cmake/ninja toolchain needed).
+RUN curl -fsSL \
+      "https://github.com/RuleWorld/bionetgen/releases/download/${BIONETGEN_VERSION}/${BIONETGEN_VERSION}-linux.tar.gz" \
+      -o bionetgen.tar.gz && \
+    tar -xzf bionetgen.tar.gz && \
+    rm bionetgen.tar.gz
 
 
 ### PyBNF wheel build container
@@ -56,20 +62,34 @@ RUN python -m pip wheel --no-cache-dir --no-deps --wheel-dir /wheels .
 FROM python:${PYTHON_VERSION}-slim
 
 ARG BIONETGEN_VERSION
-ARG PIP_EXTRA_INDEX_URL
 
 ENV DEBIAN_FRONTEND=noninteractive
-ENV PIP_EXTRA_INDEX_URL=${PIP_EXTRA_INDEX_URL}
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     libgomp1 \
     perl && \
     rm -rf /var/lib/apt/lists/*
 
-COPY --from=bionetgen-build /usr/src/bionetgen/bng2/${BIONETGEN_VERSION} /usr/BioNetGen
+COPY --from=bionetgen /usr/src/${BIONETGEN_VERSION} /usr/BioNetGen
 COPY --from=pybnf-build /wheels /tmp/wheels
 
-RUN python -m pip install --no-cache-dir /tmp/wheels/*.whl && \
+# Install PyBNF's PUBLIC runtime dependencies explicitly, then install the wheel
+# with --no-deps. We must not let pip re-resolve PyBNF's dependency set here: it
+# pins bngsim>=0.5.0,<1, a private macOS-only wheel with no public Linux build,
+# which would make the install fail (issue #414). This list mirrors
+# pyproject.toml's [project.dependencies] minus bngsim; keep it in sync.
+RUN python -m pip install --no-cache-dir \
+      'dask>=2024.1.0' \
+      'distributed>=2024.1.0' \
+      'libroadrunner>=1.6.0' \
+      'msgpack>=0.6.2' \
+      'numpy>=1.24' \
+      'paramiko>=2.7' \
+      'pydantic>=2,<3' \
+      'pyparsing>=2.4,<4' \
+      'scipy>=1.10' \
+      'tornado>=6.1' && \
+    python -m pip install --no-cache-dir --no-deps /tmp/wheels/*.whl && \
     rm -rf /tmp/wheels
 
 ENV BNGPATH=/usr/BioNetGen