Fix remaining CI failures: rc.exe flags, LTO archives, R proxies, docs deps

- Conda Build win: /GR /EHsc moved out of ADD_DEFINITIONS into
  CXX-scoped compile options. With the Ninja generator, cmcldeps forwards
  directory definitions to rc.exe, which aborted with RC1203 on the
  bundled libtiff version resource (the VS generator used by the pip
  build does not forward them, which is why only conda failed).
- Docs/pip TIFF symbols: build the bundled libtiff without LTO. When the
  static archive is created by an 'ar' without the LTO plugin (conda's
  binutils, MinGW), slim LTO members have invisible symbols and the final
  link silently leaves TIFFSetErrorHandler/TIFFSetWarningHandler
  undefined, failing at import.
- R interface: only pass SWIGWORDSIZE64 to SWIG >= 4.4. Older SWIG keeps
  int64_t literal (flag unnecessary) and SWIG 4.2's R backend mishandles
  'long long' returns under the flag: the C side returns a native vector
  while the R proxy wraps it as an external pointer, so every
  burst_search call died in validObject.
- Docs Build: render the documentation against the freshly built tttrlib
  conda package instead of pip-building from source. The docs job now
  depends on the Linux conda build, downloads its conda-bld artifact and
  passes it to rattler-build as a local channel; the recipe drops the
  compiler toolchain and gains tttrlib/pooch/tqdm host dependencies.

Author: tpeulen

.github/workflows/ci.yml

@@ -702,7 +702,7 @@ jobs:
 
   build_conda_docs:
     name: Docs Build (rattler)
-    needs: setup
+    needs: [setup, build_conda_lnx]
     if: needs.setup.outputs.is_main == 'true'
     runs-on: ubuntu-latest
     timeout-minutes: 120
@@ -721,20 +721,28 @@ jobs:
       - name: Install rattler-build
         shell: bash -l {0}
         run: conda install -y rattler-build -c conda-forge
+      # The docs recipe consumes the tttrlib conda package built by
+      # build_conda_lnx instead of rebuilding from source, so the docs are
+      # rendered against exactly what gets shipped.
+      - uses: actions/download-artifact@v4
+        with:
+          name: conda-packages-ubuntu-latest
+          path: local-channel
       - name: Build documentation package (rattler)
         shell: bash -l {0}
         run: |
           export PKG_VERSION=$(python -c "import re; v=re.search(r'version\s*=\s*\"([^\"]+)\"', open('pyproject.toml').read()); print(v.group(1))")
           rattler-build build --recipe recipes/docs \
             --output-dir ./conda-bld \
+            -c "file://$PWD/local-channel" \
             -c conda-forge
       # PRD-003 M1: extract the built HTML from the docs package (install it into a
       # throwaway prefix, then copy) so the gh-pages deploy job can consume the
       # rattler-built docs instead of re-running Sphinx.
       - name: Extract built HTML
         shell: bash -l {0}
         run: |
-          mamba create -y -p ./docsenv -c ./conda-bld -c conda-forge tttrlib-docs
+          mamba create -y -p ./docsenv -c ./conda-bld -c ./local-channel -c conda-forge tttrlib-docs
           mkdir -p docs-html
           cp -r ./docsenv/share/doc/tttrlib/html/. docs-html/
           ls docs-html | head

CMakeLists.txt

@@ -174,7 +174,11 @@ IF (MSVC)
     ADD_DEFINITIONS(-D_USE_MATH_DEFINES)
     # Issue with MSVC exceptions (https://stackoverflow.com/questions/6832666/lnk2019-when-including-asio-headers-solution-generated-with-cmake)
     # https://github.com/microsoft/vcpkg/discussions/25414
-    ADD_DEFINITIONS(/DWIN32 /D_WINDOWS /GR /EHsc)
+    ADD_DEFINITIONS(/DWIN32 /D_WINDOWS)
+    # /GR /EHsc are cl-only flags: keep them out of ADD_DEFINITIONS, or the
+    # Ninja generator (cmcldeps) forwards them to rc.exe, which then fails
+    # with RC1203 on the bundled libtiff version resource.
+    ADD_COMPILE_OPTIONS("$<$<COMPILE_LANGUAGE:CXX>:/GR;/EHsc>")
 ENDIF (MSVC)
 if(APPLE)
     FIND_PACKAGE(Threads)
@@ -290,6 +294,13 @@ IF(WITH_TIFF)
     SET(webp          OFF CACHE BOOL "" FORCE)
     SET(pixarlog      OFF CACHE BOOL "" FORCE)
     ADD_SUBDIRECTORY(thirdparty/libtiff EXCLUDE_FROM_ALL)
+    IF(NOT MSVC)
+      # libtiff.a may be archived by an 'ar' without the LTO plugin (conda's
+      # binutils, MinGW). Slim LTO members then have invisible symbols and the
+      # final link silently leaves TIFF* symbols undefined (import error at
+      # runtime). Always put real machine code into the bundled archive.
+      TARGET_COMPILE_OPTIONS(tiff PRIVATE -fno-lto)
+    ENDIF()
     LINK_LIBRARIES(TIFF::tiff)
     ADD_COMPILE_DEFINITIONS(BUILD_TIFF)
     MESSAGE(STATUS "TIFF support: bundled libtiff 4.7.0 (static, built-in codecs; Deflate/ZIP=${WITH_TIFF_ZLIB})")

ext/CMakeLists.txt

@@ -15,12 +15,15 @@ MESSAGE(STATUS "SWIG_VERSION: ${SWIG_VERSION}")
 INCLUDE(${SWIG_USE_FILE})
 INCLUDE_DIRECTORIES(.)
 
-# glibc on LP64 Linux defines int64_t as 'long', but SWIG's stdint.i typedefs
-# (applied by SWIG >= 4.4 whenever stdint.i is included) resolve int64_t to
-# 'long long' unless SWIGWORDSIZE64 is defined. Without this flag the
-# generated wrappers mix std::vector<long long> with the library's
-# std::vector<long> and do not compile on Linux.
-IF(UNIX AND NOT APPLE AND CMAKE_SIZEOF_VOID_P EQUAL 8)
+# glibc on LP64 Linux defines int64_t as 'long', but SWIG >= 4.4 eagerly
+# resolves the stdint.i typedefs and picks 'long long' unless SWIGWORDSIZE64
+# is defined. Without this flag the generated wrappers mix
+# std::vector<long long> with the library's std::vector<long> and do not
+# compile on Linux. Only define it for SWIG >= 4.4: older SWIG keeps int64_t
+# literal in generated code (so the flag is unnecessary), and SWIG 4.2's R
+# backend mishandles 'long long' returns under SWIGWORDSIZE64 (the C side
+# returns a native vector while the R proxy expects an external pointer).
+IF(UNIX AND NOT APPLE AND CMAKE_SIZEOF_VOID_P EQUAL 8 AND NOT SWIG_VERSION VERSION_LESS "4.4")
     SET(TTTRLIB_SWIG_INT64_FLAG "-DSWIGWORDSIZE64")
     LIST(APPEND CMAKE_SWIG_FLAGS ${TTTRLIB_SWIG_INT64_FLAG})
 ENDIF()

recipes/docs/build.sh

@@ -1,18 +1,18 @@
 #!/usr/bin/env bash
 set -euxo pipefail
 
-# 1. Build & install tttrlib into the host python (needed for autodoc/gallery).
-export CMAKE_ARGS="-DWITH_AVX=OFF"
-"${PYTHON}" -m pip install . --no-deps --no-build-isolation -vv
+# tttrlib itself comes from the freshly built conda package (host dependency);
+# the CI docs job passes its conda-bld channel to rattler-build. Nothing is
+# compiled here - this recipe only runs Sphinx against the installed package.
+"${PYTHON}" -c "import tttrlib; print('tttrlib', tttrlib.__version__ if hasattr(tttrlib, '__version__') else 'imported')"
 
-# 2. Reference data for the example gallery (examples are NOT executed).
+# 1. Reference data for the example gallery (examples are NOT executed).
 export TTTRLIB_DATA="${SRC_DIR}/tttr-data"
 export TTTRLIB_DOCS_EXECUTE_EXAMPLES=0
-"${PYTHON}" -m pip install --no-build-isolation pooch tqdm || true
 "${PYTHON}" test/download_test_data.py --output-dir "${TTTRLIB_DATA}" --quiet || \
   echo "warning: reference data download failed; gallery thumbnails may be missing"
 
-# 3. Build the HTML documentation.
+# 2. Build the HTML documentation.
 export BUILD_TIER="${BUILD_TIER:-4}"
 cd doc
 mkdir -p _build/api
@@ -22,6 +22,6 @@ rm -rf _build/html/stable/api
 [ -d _build/api ] && cp -r _build/api _build/html/stable/ || true
 cd ..
 
-# 4. Install the built HTML into the package.
+# 3. Install the built HTML into the package.
 mkdir -p "${PREFIX}/share/doc/tttrlib"
 cp -r doc/_build/html/stable "${PREFIX}/share/doc/tttrlib/html"

recipes/docs/recipe.yaml

@@ -1,6 +1,10 @@
 # rattler-build recipe that builds the tttrlib HTML documentation (Sphinx +
 # Doxygen) reproducibly and packages it under share/doc/tttrlib/html.
-# Build with:  rattler-build build --recipe recipes/docs -c conda-forge
+# tttrlib itself is NOT built here: it is consumed as a conda package from the
+# channel passed on the command line (in CI: the conda-bld artifact of the
+# Linux conda build job).
+# Build with:
+#   rattler-build build --recipe recipes/docs -c <channel-with-tttrlib> -c conda-forge
 context:
   version: ${{ env.get("PKG_VERSION", default="0.27.0") }}
 
@@ -18,23 +22,17 @@ build:
 
 requirements:
   build:
-    - ${{ compiler('c') }}
-    - ${{ compiler('cxx') }}
-    - cmake
-    - ninja
-    - make
-    - swig >=4.1
     - doxygen
     - pandoc
     - graphviz
   host:
     - python
-    - pip
-    - scikit-build-core
+    # The package under documentation - freshly built by the CI conda job.
+    - tttrlib ==${{ version }}
     - numpy
-    - hdf5
-    - highfive
-    - nlohmann_json
+    # Reference data download (test/download_test_data.py)
+    - pooch
+    - tqdm
     # Sphinx documentation stack (mirrors the CI docs dependencies)
     - sphinx
     - sphinx-copybutton