Merge dev into master

.dockerignore

@@ -0,0 +1,11 @@
+.git
+.cache
+.mypy_cache
+__pycache__
+build
+localizer/src/build
+localizer/src/install
+localizer/cpp
+.VSCodeCounter
+.vscode
+*archive*

.github/workflows/cross-compile.yml

@@ -7,11 +7,6 @@ on:
   push:
     tags:
       - 'v*'
-    branches:
-      - master
-      - main
-    paths-ignore:
-      - '**/*.md'
   pull_request:
   workflow_dispatch:
 
@@ -22,14 +17,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest, macos-14]
+        os: ${{ fromJSON(startsWith(github.ref, 'refs/tags/') && '["ubuntu-latest","windows-latest","macos-latest","macos-14"]' || '["ubuntu-latest","windows-latest"]') }}
 
     steps:
       - name: Checkout (with Git LFS)
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          lfs: true
+          lfs: ${{ startsWith(github.ref, 'refs/tags/') }}
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -41,14 +36,27 @@ jobs:
           python -m pip install --upgrade pip
           pip install conan
 
-      - name: Cache Conan packages
+      - name: Cache Conan packages (Windows/macOS)
+        if: runner.os != 'Linux'
         uses: actions/cache@v4
         with:
           path: ~/.conan2
           key: ${{ runner.os }}-conan-${{ hashFiles('localizer/src/conanfile.py') }}
           restore-keys: |
             ${{ runner.os }}-conan-
 
+      # Keep the legacy cache separate from the normal Linux cache: Conan may cache
+      # build tools such as Boost's b2, and tools built on ubuntu-latest can require
+      # newer glibc symbols than the manylinux2014/CentOS 7 container provides.
+      - name: Cache legacy Linux Conan packages
+        if: runner.os == 'Linux'
+        uses: actions/cache@v4
+        with:
+          path: ${{ runner.temp }}/dccc-conan2-legacy
+          key: ${{ runner.os }}-legacy-glibc217-conan-${{ hashFiles('localizer/src/conanfile.py', 'docker/Dockerfile.core.legacy', 'scripts/docker-build-core.sh', '.github/workflows/cross-compile.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-legacy-glibc217-conan-
+
       - name: Setup Ninja
         uses: seanmiddleditch/gha-setup-ninja@v4
 
@@ -60,8 +68,8 @@ jobs:
           echo "CC=gcc-12" >> $GITHUB_ENV
           echo "CXX=g++-12" >> $GITHUB_ENV
 
-      - name: Conan profile detect (Linux/macOS)
-        if: runner.os != 'Windows'
+      - name: Conan profile detect (macOS)
+        if: runner.os == 'macOS'
         working-directory: localizer/src
         shell: bash
         run: |
@@ -74,8 +82,8 @@ jobs:
         run: |
           conan profile detect --force
 
-      - name: Conan install (Linux/macOS)
-        if: runner.os != 'Windows'
+      - name: Conan install (macOS)
+        if: runner.os == 'macOS'
         working-directory: localizer/src
         shell: bash
         run: |
@@ -86,8 +94,8 @@ jobs:
             -o onetbb/*:tbbmalloc=False \
             -o onetbb/*:tbbproxy=False
 
-      - name: Configure with CMake (Linux/macOS)
-        if: runner.os != 'Windows'
+      - name: Configure with CMake (macOS)
+        if: runner.os == 'macOS'
         working-directory: localizer/src
         shell: bash
         run: |
@@ -98,20 +106,72 @@ jobs:
             -DCMAKE_BUILD_TYPE=Release \
             -DCMAKE_INSTALL_PREFIX="./install"
 
-      - name: Build with CMake (Linux/macOS)
-        if: runner.os != 'Windows'
+      - name: Build with CMake (macOS)
+        if: runner.os == 'macOS'
         working-directory: localizer/src
         shell: bash
         run: cmake --build build --config Release
 
-      - name: Install with CMake (Linux/macOS)
-        if: runner.os != 'Windows'
+      - name: Install with CMake (macOS)
+        if: runner.os == 'macOS'
         working-directory: localizer/src
         shell: bash
         run: cmake --install build --config Release
 
+      - name: Build legacy Linux Docker image
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          docker build \
+            --build-arg USER_UID="$(id -u)" \
+            --build-arg USER_GID="$(id -g)" \
+            -f docker/Dockerfile.core.legacy \
+            -t dccc-core-dev:legacy-glibc217 .
+
+      - name: Build and install with legacy Linux container
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          legacy_conan_home="$RUNNER_TEMP/dccc-conan2-legacy"
+          mkdir -p "$legacy_conan_home"
+          docker run --rm \
+            -v "$GITHUB_WORKSPACE:/workspace" \
+            -v "$legacy_conan_home:/home/dev/.conan2" \
+            -e CONAN_CPPSTD=gnu17 \
+            -e CONAN_BUILD_ARGS='--build=missing --build=b2/* --build=m4/* --build=autoconf/* --build=automake/* --build=libtool/* --build=pkgconf/*' \
+            -e BUILD_TYPE=Release \
+            -e INSTALL_PREFIX=./install \
+            dccc-core-dev:legacy-glibc217 \
+            /workspace/scripts/docker-build-core.sh
+
+      - name: Verify Linux glibc compatibility floor
+        if: runner.os == 'Linux'
+        working-directory: localizer/src
+        shell: bash
+        run: |
+          set -euo pipefail
+          mapfile -t elf_files < <(find install/bin -maxdepth 1 -type f -exec sh -c 'file "$1" | grep -q ELF' sh {} \; -print)
+          max_glibc=$(objdump -T "${elf_files[@]}" \
+            | sed -n 's/.*(GLIBC_\([0-9][0-9.]*\)).*/\1/p' \
+            | sort -V \
+            | tail -n 1)
+          echo "Maximum referenced GLIBC version: ${max_glibc:-none}"
+          if [[ -n "${max_glibc}" ]] && [[ "$(printf '%s\n%s\n' "2.17" "${max_glibc}" | sort -V | tail -n 1)" != "2.17" ]]; then
+            echo "Linux package references GLIBC_${max_glibc}; expected no symbols newer than GLIBC_2.17." >&2
+            exit 1
+          fi
+
+      - name: Run PR smoke tests on installed binary (Linux)
+        if: github.event_name == 'pull_request' && runner.os == 'Linux'
+        working-directory: localizer/src/tests
+        shell: bash
+        run: |
+          set -e
+          python -m pip install pytest pandas
+          python -m pytest -v test_ui_metric_command_builder.py test_quick_cli.py -k "help or version_information or no_subcommand"
+
       - name: Run pytest on installed binary (Linux/macOS)
-        if: runner.os != 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os != 'Windows'
         working-directory: localizer/src/tests
         shell: bash
         run: |
@@ -171,16 +231,24 @@ jobs:
         shell: pwsh
         run: cmake --install build --config Release
 
+      - name: Run PR smoke tests on installed binary (Windows)
+        if: github.event_name == 'pull_request' && runner.os == 'Windows'
+        working-directory: localizer/src/tests
+        shell: pwsh
+        run: |
+          python -m pip install pytest pandas
+          python -m pytest -v test_ui_metric_command_builder.py test_quick_cli.py -k "help or version_information or no_subcommand"
+
       - name: Run pytest on installed binary (Windows)
-        if: runner.os == 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os == 'Windows'
         working-directory: localizer/src/tests
         shell: pwsh
         run: |
           python -m pip install pytest pandas
           python -m pytest -v
 
       - name: Copy install/bin into localizer/cpp (Linux/macOS)
-        if: runner.os != 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os != 'Windows'
         shell: bash
         working-directory: localizer/src
         run: |
@@ -189,14 +257,15 @@ jobs:
           cp -a install/bin/. "$GITHUB_WORKSPACE/localizer/cpp/"
 
       - name: Copy install/bin into localizer/cpp (Windows)
-        if: runner.os == 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os == 'Windows'
         shell: pwsh
         working-directory: localizer/src
         run: |
           New-Item -ItemType Directory -Force -Path "$env:GITHUB_WORKSPACE/localizer/cpp" | Out-Null
           Copy-Item -Path install/bin/* -Destination "$env:GITHUB_WORKSPACE/localizer/cpp/" -Recurse -Force
 
       - name: Determine package metadata
+        if: startsWith(github.ref, 'refs/tags/')
         id: package-metadata
         shell: bash
         env:
@@ -244,7 +313,7 @@ jobs:
           echo "platform=${platform}" >> "$GITHUB_OUTPUT"
 
       - name: Assemble standalone core package (Linux/macOS)
-        if: runner.os != 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os != 'Windows'
         shell: bash
         working-directory: localizer/src
         run: |
@@ -257,7 +326,7 @@ jobs:
           cp "$GITHUB_WORKSPACE/LICENSE.md" "$package_dir/LICENSE.md"
 
       - name: Assemble standalone core package (Windows)
-        if: runner.os == 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os == 'Windows'
         shell: pwsh
         working-directory: localizer/src
         run: |
@@ -273,21 +342,23 @@ jobs:
           Copy-Item -Path (Join-Path $env:GITHUB_WORKSPACE 'LICENSE.md') -Destination (Join-Path $packageDir 'LICENSE.md') -Force
 
       - name: Create distributable zip (standalone core)
+        if: startsWith(github.ref, 'refs/tags/')
         uses: thedoctor0/zip-release@0.7.6
         with:
           type: 'zip'
           filename: DCCCcore-${{ env.PACKAGE_VERSION }}-${{ env.PACKAGE_PLATFORM }}.zip
           path: DCCCcore-${{ env.PACKAGE_VERSION }}-${{ env.PACKAGE_PLATFORM }}
 
       - name: Upload standalone core artifact
+        if: startsWith(github.ref, 'refs/tags/')
         uses: actions/upload-artifact@v4
         with:
           name: DCCCcore-${{ env.PACKAGE_VERSION }}-${{ env.PACKAGE_PLATFORM }}
           path: DCCCcore-${{ env.PACKAGE_VERSION }}-${{ env.PACKAGE_PLATFORM }}.zip
           if-no-files-found: error
 
       - name: Clean packaging workspace (Linux/macOS)
-        if: runner.os != 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os != 'Windows'
         shell: bash
         run: |
           set -euo pipefail
@@ -304,7 +375,7 @@ jobs:
           rm -f .gitmodules
 
       - name: Clean packaging workspace (Windows)
-        if: runner.os == 'Windows'
+        if: startsWith(github.ref, 'refs/tags/') && runner.os == 'Windows'
         shell: pwsh
         run: |
           $pathsToRemove = @(
@@ -330,13 +401,15 @@ jobs:
           }
 
       - name: Create distributable zip (entire project)
+        if: startsWith(github.ref, 'refs/tags/')
         uses: thedoctor0/zip-release@0.7.6
         with:
           type: 'zip'
           filename: DCCCSlicer-${{ env.PACKAGE_VERSION }}-${{ env.PACKAGE_PLATFORM }}.zip
           path: .
 
       - name: Upload artifact
+        if: startsWith(github.ref, 'refs/tags/')
         uses: actions/upload-artifact@v4
         with:
           name: DCCCSlicer-${{ env.PACKAGE_VERSION }}-${{ env.PACKAGE_PLATFORM }}
@@ -365,5 +438,3 @@ jobs:
           generate_release_notes: true
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-

.gitignore

@@ -9,6 +9,7 @@ localizer/Normalized*.nii
 localizer/tmp.nii
 localizer/ref.nii
 localizer/roi.nii
+localizer/templates/fetch_template.ipynb
 tracked_files.txt
 *archive*
 
@@ -29,4 +30,7 @@ localizer/cpp
 .cache/
 
 # code for generating seg.nrrd atlases
-localizer/templates/*.ipynb
+localizer/templates/*.ipynb
+
+# codex
+.codex

AGENTS.md

@@ -0,0 +1,13 @@
+每次递增版本号时，更新以下文件（写路径全名，避免改错同名文件）：
+- `localizer/src/CMakeLists.txt`
+  - `project(DCCCcore VERSION X.Y.Z)` 只写纯数字版本。
+  - 如果是预发布版本，再同步更新 `DCCCCORE_VERSION_SUFFIX`（例如 `-alpha`）。
+- `localizer/src/conanfile.py`
+  - `version = "X.Y.Z"` 或 `version = "X.Y.Z-alpha"`，需要与对外发布版本保持一致。
+- `localizer/src/core/config/Version.h`
+  - 当前仓库会提交这个生成后的头文件，里面的 `SOFTWARE_VERSION` 也要同步更新，避免 `--version` 或批处理日志显示旧版本。
+
+补充说明：
+- `localizer/src/core/config/Version.h.in` 是模板文件，日常递增版本号时不需要手改具体版本号；它会从 `localizer/src/CMakeLists.txt` 里的完整软件版本变量生成。
+- 仓库根目录的 `CMakeLists.txt` 当前没有单独的项目版本号，不属于版本递增时必须同步的文件。
+- 发布时还要注意 Git tag。`.github/workflows/cross-compile.yml` 会优先用 tag 名 `vX.Y.Z` 生成发布包版本；如果源码版本已经更新但 tag 没跟上，发布产物版本仍可能不一致。

CMakeLists.txt

@@ -4,10 +4,10 @@ project(DCCCSlicer)
 
 #-----------------------------------------------------------------------------
 # Extension meta-information
-set(EXTENSION_HOMEPAGE "https://www.slicer.org/wiki/Documentation/Nightly/Extensions/ACPCLocalizer")
+set(EXTENSION_HOMEPAGE "https://github.com/tctco/DCCCSlicer")
 set(EXTENSION_CATEGORY "Examples")
 set(EXTENSION_CONTRIBUTORS "Cheng Tang")
-set(EXTENSION_DESCRIPTION "This is an example of a simple extension")
+set(EXTENSION_DESCRIPTION "An open-source, super-simple, ultra-fast, fully-automated, fairly-accurate and PET-only solution to conduct spatial normalization and semi-quantification for almost any brain PET modalities.")
 set(EXTENSION_ICONURL "https://www.example.com/Slicer/Extensions/ACPCLocalizer.png")
 set(EXTENSION_SCREENSHOTURLS "https://www.example.com/Slicer/Extensions/ACPCLocalizer/Screenshots/1.png")
 set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies