Prepare napari-curvealign for merge and fix ROI mode-switch desync

.github/ci_setup_curvelab.sh

@@ -0,0 +1,168 @@
+#!/usr/bin/env bash
+
+# CI helper: build FFTW 2.1.5 and CurveLab 2.1.3 from source and export env vars.
+# Requires three secrets: RESTRICTED_USER, RESTRICTED_PASSWORD, RESTRICTED_URL.
+
+set -euo pipefail
+
+FFTW_VERSION="${FFTW_VERSION:-2.1.5}"
+CURVELAB_VERSION="${CURVELAB_VERSION:-2.1.3}"
+CURVELAB_ARCHIVE="${CURVELAB_ARCHIVE:-CurveLab-${CURVELAB_VERSION}.tar.gz}"
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+UTILS_DIR="${ROOT_DIR}/utils"
+
+mkdir -p "${UTILS_DIR}"
+cd "${UTILS_DIR}"
+
+echo "== Preparing FFTW ${FFTW_VERSION} =="
+if [ -n "${FFTW:-}" ]; then
+  if [ ! -d "${FFTW}" ]; then
+    echo "::error title=Invalid FFTW path::FFTW is set to '${FFTW}' but the directory does not exist."
+    exit 1
+  fi
+  FFTW_PATH="${FFTW}"
+  echo "Using pre-installed FFTW at ${FFTW_PATH}"
+else
+  if [ ! -d "fftw-${FFTW_VERSION}" ]; then
+    if [ ! -f "fftw-${FFTW_VERSION}.tar.gz" ]; then
+      curl -fsSL "http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz" -o "fftw-${FFTW_VERSION}.tar.gz"
+    fi
+    tar xzf "fftw-${FFTW_VERSION}.tar.gz"
+    pushd "fftw-${FFTW_VERSION}" >/dev/null
+    CFLAGS="-fPIC" CXXFLAGS="-fPIC" ./configure --prefix="$(pwd)" --disable-fortran --enable-shared --disable-static
+    make -j"$(nproc)"
+    make install
+    popd >/dev/null
+    ln -sf "fftw-${FFTW_VERSION}" fftw
+  else
+    echo "FFTW already present, skipping rebuild."
+  fi
+  FFTW_PATH="${UTILS_DIR}/fftw-${FFTW_VERSION}"
+fi
+
+# Some CurveLab makefiles expect headers/libs under FFTW_DIR/fftw
+mkdir -p "${FFTW_PATH}/fftw"
+if [ -f "${FFTW_PATH}/include/fftw.h" ]; then
+  ln -sf "${FFTW_PATH}/include/fftw.h" "${FFTW_PATH}/fftw/fftw.h"
+fi
+if [ -d "${FFTW_PATH}/lib" ]; then
+  ln -sf "${FFTW_PATH}/lib/"* "${FFTW_PATH}/fftw/" || true
+fi
+
+ARCHIVE_NAME="$(basename "${RESTRICTED_URL:-CurveLab-${CURVELAB_VERSION}.tar.gz}")"
+DEFAULT_ARCHIVE="CurveLab-${CURVELAB_VERSION}.tar.gz"
+
+if [ -n "${FDCT:-}" ]; then
+  if [ ! -d "${FDCT}" ]; then
+    echo "::error title=Invalid CurveLab path::FDCT is set to '${FDCT}' but the directory does not exist."
+    exit 1
+  fi
+  FDCT_PATH="${FDCT}"
+  echo "Using pre-installed CurveLab at ${FDCT_PATH}"
+else
+  echo "== Preparing CurveLab ${CURVELAB_VERSION} archive =="
+  if [ -f "${DEFAULT_ARCHIVE}" ]; then
+    ARCHIVE_NAME="${DEFAULT_ARCHIVE}"
+  elif [ ! -f "${ARCHIVE_NAME}" ]; then
+    if [ -n "${RESTRICTED_USER:-}" ] && [ -n "${RESTRICTED_PASSWORD:-}" ] && [ -n "${RESTRICTED_URL:-}" ]; then
+      curl --fail-with-body -fL --retry 3 --retry-all-errors --connect-timeout 20 --max-time 600 \
+        -A "Mozilla/5.0 (GitHub Actions)" \
+        -u "${RESTRICTED_USER}:${RESTRICTED_PASSWORD}" \
+        -O "${RESTRICTED_URL}"
+    else
+      echo "::error title=CurveLab archive missing::Provide FETCH_FDCT secret (preferred) or define RESTRICTED_USER/RESTRICTED_PASSWORD/RESTRICTED_URL."
+      exit 1
+    fi
+  fi
+
+  if [ ! -d "CurveLab-${CURVELAB_VERSION}" ]; then
+    echo "== Extracting ${ARCHIVE_NAME} =="
+    if command -v file >/dev/null 2>&1; then
+      MIME_TYPE=$(file -b --mime-type "${ARCHIVE_NAME}")
+    else
+      MIME_TYPE=""
+    fi
+    if [[ "${MIME_TYPE}" == text/html* ]]; then
+      echo "::error title=CurveLab download failed::${ARCHIVE_NAME} is HTML (likely an auth error or redirect)."
+      if command -v head >/dev/null 2>&1; then
+        echo "First 40 lines of response:"
+        head -n 40 "${ARCHIVE_NAME}"
+      fi
+      echo "Ensure FETCH_FDCT runs a curl command that downloads the actual CurveLab-${CURVELAB_VERSION} archive."
+      exit 1
+    fi
+    case "${MIME_TYPE}" in
+      application/gzip|application/x-gzip)
+        tar xzf "${ARCHIVE_NAME}"
+        ;;
+      application/x-tar|"")
+        # Fallback to plain tar if mime type unknown
+        tar xf "${ARCHIVE_NAME}"
+        ;;
+      application/zip)
+        unzip -q "${ARCHIVE_NAME}"
+        ;;
+      *)
+        echo "::error title=Unknown archive format::Don't know how to extract ${ARCHIVE_NAME} (${MIME_TYPE})."
+        exit 1
+        ;;
+    esac
+  fi
+
+  echo "== Building CurveLab binaries =="
+  export FFTW_DIR="${FFTW_PATH}"
+  export FFTW="${FFTW_PATH}"
+  export CPPFLAGS="-I${FFTW_PATH}/include"
+  export LDFLAGS="-L${FFTW_PATH}/lib"
+  pushd "CurveLab-${CURVELAB_VERSION}" >/dev/null
+  pushd fdct_wrapping_cpp/src >/dev/null
+  make FFTW_DIR="${FFTW_PATH}" FFTW="${FFTW_PATH}" FFTW_INC="${FFTW_PATH}/include" FFTW_INCLUDE="${FFTW_PATH}/include" FFTW_LIB="${FFTW_PATH}/lib" FFTW_LIBDIR="${FFTW_PATH}/lib"
+  popd >/dev/null
+  pushd fdct3d/src >/dev/null
+  make FFTW_DIR="${FFTW_PATH}" FFTW="${FFTW_PATH}" FFTW_INC="${FFTW_PATH}/include" FFTW_INCLUDE="${FFTW_PATH}/include" FFTW_LIB="${FFTW_PATH}/lib" FFTW_LIBDIR="${FFTW_PATH}/lib"
+  popd >/dev/null
+  popd >/dev/null
+
+  FDCT_WRAPPING_LIB="CurveLab-${CURVELAB_VERSION}/fdct_wrapping_cpp/src/libfdct_wrapping.a"
+  FDCT3D_LIB="CurveLab-${CURVELAB_VERSION}/fdct3d/src/libfdct3d.a"
+  if [ ! -f "${FDCT_WRAPPING_LIB}" ]; then
+    echo "::error title=CurveLab build missing::libfdct_wrapping.a not found after build."
+    echo "Contents of fdct_wrapping_cpp/src:"
+    ls -la "CurveLab-${CURVELAB_VERSION}/fdct_wrapping_cpp/src" || true
+    exit 1
+  fi
+  if [ ! -f "${FDCT3D_LIB}" ]; then
+    echo "::error title=CurveLab build missing::libfdct3d.a not found after build."
+    echo "Contents of fdct3d/src:"
+    ls -la "CurveLab-${CURVELAB_VERSION}/fdct3d/src" || true
+    exit 1
+  fi
+
+  FDCT_PATH="${UTILS_DIR}/CurveLab-${CURVELAB_VERSION}"
+fi
+
+echo "FFTW path: ${FFTW_PATH}"
+echo "CurveLab path: ${FDCT_PATH}"
+
+LD_LIBRARY_PATH_VAL="${FFTW_PATH}/lib"
+if [ -n "${LD_LIBRARY_PATH:-}" ]; then
+  LD_LIBRARY_PATH_VAL="${FFTW_PATH}/lib:${LD_LIBRARY_PATH}"
+fi
+
+if [ -n "${GITHUB_ENV:-}" ]; then
+  {
+    echo "FFTW=${FFTW_PATH}"
+    echo "FDCT=${FDCT_PATH}"
+    echo "CPPFLAGS=-I${FFTW_PATH}/include"
+    echo "LDFLAGS=-L${FFTW_PATH}/lib"
+    echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH_VAL}"
+  } >> "${GITHUB_ENV}"
+else
+  export FFTW="${FFTW_PATH}"
+  export FDCT="${FDCT_PATH}"
+  export CPPFLAGS="-I${FFTW_PATH}/include"
+  export LDFLAGS="-L${FFTW_PATH}/lib"
+  export LD_LIBRARY_PATH="${LD_LIBRARY_PATH_VAL}"
+fi
+
+echo "CurveLab setup complete."

.github/workflows/ci.yml

@@ -8,36 +8,124 @@ on:
     branches: [main]
 
 jobs:
-  test:
+  test-basic:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
 
-      # Install system dependencies (like in your Docker container)
       - name: Install system dependencies
-        run: sudo apt-get update && sudo apt-get install -y libgl1 libglib2.0-0 python3-venv
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgl1 libglib2.0-0 python3-venv
 
-      # Set up Python
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      # Create virtual environment
-      - name: Create virtual environment
+      - name: Install dependencies
         run: |
-          python -m venv venv
-          source venv/bin/activate
-          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install --upgrade pip
           python -m pip install -e .
           python -m pip install pytest ruff
 
-      # Run tests in the venv
-      - name: Run tests
+      - name: Run basic tests
+        env:
+          TMEQ_RUN_CURVELETS: "0"
+          QT_QPA_PLATFORM: "offscreen"
+        run: |
+          pytest -q -rs
+
+  # Secure build with CurveLab; skip on forked PRs (no secrets on forks).
+  test-curvelab:
+    if: ${{ github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential gcc g++ make wget curl unzip libgl1 libglib2.0-0
+
+      - name: Fetch CurveLab archive
+        shell: bash
+        env:
+          FETCH_FDCT: ${{ secrets.FETCH_FDCT }}
+        run: |
+          set -euo pipefail
+          if [ -z "${FETCH_FDCT}" ]; then
+            echo "::error title=Missing secret::FETCH_FDCT is empty. It must download utils/CurveLab-2.1.3.tar.gz."
+            exit 1
+          fi
+          mkdir -p utils
+          cd utils
+          echo "-- Pre eval --"
+          ls -la
+          echo "Downloading CurveLab archive via FETCH_FDCT..."
+          eval "${FETCH_FDCT}"
+          echo "-- Post eval --"
+          ls -la
+          if [ ! -f "CurveLab-2.1.3.tar.gz" ]; then
+            echo "::error title=CurveLab archive missing after FETCH_FDCT::Expected utils/CurveLab-2.1.3.tar.gz to exist after running FETCH_FDCT."
+            echo "Files in utils/:"
+            ls -la
+            exit 1
+          fi
+          if command -v file >/dev/null 2>&1; then
+            echo "Downloaded archive mime-type:"
+            MIME="$(file -b --mime-type "CurveLab-2.1.3.tar.gz" || true)"
+            echo "${MIME}"
+            if [[ "${MIME}" == text/html* ]]; then
+              echo "::error title=CurveLab download returned HTML::Likely a 403/redirect. Showing first 40 lines:"
+              head -n 40 "CurveLab-2.1.3.tar.gz" || true
+              echo "Fix: update FETCH_FDCT to use 'curl --fail-with-body -fL ... -o CurveLab-2.1.3.tar.gz <URL>' so it fails on 403 instead of saving HTML."
+              exit 1
+            fi
+          fi
+
+      - name: Prepare FFTW + CurveLab toolchain
+        env:
+          FDCT: ""
+          FFTW: ""
+          CPPFLAGS: ""
+          LDFLAGS: ""
+        run: |
+          unset FDCT FFTW CPPFLAGS LDFLAGS
+          bash .github/ci_setup_curvelab.sh
+
+      - name: Validate CurveLab libraries
+        run: |
+          echo "Testing CurveLab compilation..."
+          if [ -z "${FDCT:-}" ]; then
+            echo "❌ FDCT environment variable not set by ci_setup_curvelab.sh"
+            exit 1
+          fi
+          echo "FDCT=${FDCT}"
+          ls -la "${FDCT}" || true
+          ls -la "${FDCT}/fdct_wrapping_cpp/src" || true
+          ls -la "${FDCT}/fdct3d/src" || true
+          test -f "${FDCT}/fdct_wrapping_cpp/src/libfdct_wrapping.a" && echo "✅ libfdct_wrapping.a built" || (echo "❌ libfdct_wrapping.a missing"; exit 1)
+          test -f "${FDCT}/fdct3d/src/libfdct3d.a" && echo "✅ libfdct3d.a built" || (echo "❌ libfdct3d.a missing"; exit 1)
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[curvelops]"
+          python -m pip install pytest ruff
+
+      - name: Run tests with CurveLab
         env:
+          TMEQ_RUN_CURVELETS: "1"
           QT_QPA_PLATFORM: "offscreen"
         run: |
-          source venv/bin/activate
-          pytest -rs
+          pytest -q -rs