Add Python and R containers with reproducibility CI

.dockerignore

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+.git
+.github
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.Rhistory
+.RData
+.Rproj.user/
+.venv/
+venv/
+outputs_*/
+outputs_r/
+tables_r/

.github/workflows/container-ci.yml

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+name: Python, R, and container CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: container-ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  python-canonical:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --requirement requirements.txt
+      - name: Run scanner tests
+        run: python -m pytest -q
+      - name: Run a quick canonical Fe II scan
+        run: |
+          python scripts/nist_wct_log_spectral_scan_FIXED.py \
+            --csv data/Fe_lines.csv \
+            --ion 2 \
+            --bins 160 \
+            --null-n 10 \
+            --min-lines 100 \
+            --out-dir /tmp/nist-preview
+
+  python-container:
+    runs-on: ubuntu-24.04
+    needs: python-canonical
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build canonical Python image
+        run: docker build --tag nist-python-ci .
+      - name: Run a quick scan in the Python image
+        run: |
+          docker run --rm nist-python-ci \
+            python scripts/nist_wct_log_spectral_scan_FIXED.py \
+            --csv data/Fe_lines.csv \
+            --ion 2 \
+            --bins 160 \
+            --null-n 5 \
+            --min-lines 100 \
+            --out-dir /tmp/nist-preview
+
+  r-container:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build independent R image
+        id: r_build
+        shell: bash
+        run: |
+          set +e
+          set -o pipefail
+          docker build --progress=plain --file Dockerfile.r --tag nist-r-ci . \
+            2>&1 | tee r-build.log
+          status=${PIPESTATUS[0]}
+          echo "status=$status" >> "$GITHUB_OUTPUT"
+          exit 0
+      - name: Run R test suite
+        id: r_tests
+        if: steps.r_build.outputs.status == '0'
+        shell: bash
+        run: |
+          set +e
+          docker run --rm nist-r-ci > r-test.log 2>&1
+          status=$?
+          echo "status=$status" >> "$GITHUB_OUTPUT"
+          tail -n 250 r-test.log
+          exit 0
+      - name: Upload R diagnostics
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: nist-r-diagnostics-${{ github.sha }}
+          if-no-files-found: warn
+          path: |
+            r-build.log
+            r-test.log
+      - name: Enforce R image and test results
+        shell: bash
+        run: |
+          test "${{ steps.r_build.outputs.status }}" -eq 0
+          test "${{ steps.r_tests.outputs.status }}" -eq 0

Dockerfile

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+FROM python:3.12-slim
+
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    MPLBACKEND=Agg \
+    PIP_NO_CACHE_DIR=1
+
+WORKDIR /app
+
+COPY requirements.txt ./
+RUN python -m pip install --upgrade pip \
+    && python -m pip install --requirement requirements.txt
+
+COPY . .
+
+CMD ["python", "scripts/run_feii_bin_stability.py", "--null-n", "100"]

Dockerfile.r

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+FROM rocker/r-ver:4.4.2
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Rocker versioned images pin both R and the CRAN snapshot. Install only system
+# libraries with apt; install R packages into the Rocker R library with
+# install2.r so packages cannot be pulled from Ubuntu's separate R runtime.
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends libgmp-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN install2.r --error --skipinstalled --ncpus -1 \
+      jsonlite \
+      gmp \
+      testthat
+
+RUN Rscript -e "required <- c('jsonlite', 'gmp', 'testthat'); missing <- required[!vapply(required, requireNamespace, logical(1), quietly=TRUE)]; if (length(missing)) stop('missing R packages: ', paste(missing, collapse=', '))"
+
+WORKDIR /app
+COPY . .
+
+CMD ["Rscript", "tests/testthat.R"]