Merge remote-tracking branch 'origin/master' into section-change-error

.github/workflows/publish-sdist-wheels.yml

@@ -6,7 +6,7 @@ env:
 
   CIBW_BUILD_VERBOSITY: 1
   CIBW_BUILD: 'cp*'
-  CIBW_SKIP: 'cp35-* cp36-* cp37-* cp313-* *-manylinux_i686 *-musllinux_* *-win32'
+  CIBW_SKIP: 'cp35-* cp36-* cp37-* cp38-* *-manylinux_i686 *-musllinux_* *-win32'
   CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
   CIBW_TEST_COMMAND: pytest -s -v {project}/tests
   UNIXY_HDF5_VERSION: 1.14.3
@@ -21,7 +21,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-12, windows-2022]
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-20.04, windows-2022, macos-13, macos-14]
 
     steps:
       - uses: actions/checkout@v4
@@ -39,7 +40,7 @@ jobs:
 
       - name: Cache HDF5 On Linux/macOS
         if: runner.os == 'Linux' || runner.os == 'macOS'
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache-hdf5-posix
         env:
           cache-name: cache-hdf5-posix
@@ -69,7 +70,7 @@ jobs:
       - name: Build wheels Mac OS
         if: runner.os == 'macOS'
         env:
-          CIBW_ENVIRONMENT_PASS: "STATIC_HDF5 CMAKE_PREFIX_PATH CMAKE_OSX_ARCHITECTURES MACOSX_DEPLOYMENT_TARGET"
+          CIBW_ENVIRONMENT_PASS: "STATIC_HDF5 CMAKE_PREFIX_PATH"
           CIBW_BEFORE_BUILD: |
             # CMake complains if the dependencies come from within the same tree
             # as the source, so we'll just pretend they are elsewhere
@@ -80,25 +81,13 @@ jobs:
           # used by setup.py to decide if to set `FindHDF5` to use static hdf5 libraries
           export STATIC_HDF5=True
 
-          # x86_64 macOS allows for cross compilation; first we do arm64,
-          # only for the 11.0 target; and store in the cache the compiled code...
-          export CIBW_ARCHS_MACOS="arm64"
-          export CMAKE_OSX_ARCHITECTURES="arm64"
-          export MACOSX_DEPLOYMENT_TARGET="11.0"
-          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
-          python -m cibuildwheel --output-dir dist
-
-          # ...and now we do both targets for x86_64
-          export CIBW_ARCHS_MACOS="x86_64"
-          export CMAKE_OSX_ARCHITECTURES="x86_64"
-          unset MACOSX_DEPLOYMENT_TARGET
-          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
+          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-`uname -m`/install
           python -m cibuildwheel --output-dir dist
 
       - name: Cache HDF5 On Windows
         if: runner.os == 'Windows'
         id: cache-hdf5-windows
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-name: cache-hdf5-windows
         with:
@@ -122,7 +111,7 @@ jobs:
         # this has a partial table:
         # https://devblogs.microsoft.com/cppblog/side-by-side-minor-version-msvc-toolsets-in-visual-studio-2017/
         run: |
-          # vc141 was removed, add it back here: https://github.com/actions/runner-images/issues/9701 
+          # vc141 was removed, add it back here: https://github.com/actions/runner-images/issues/9701
           Set-Location "C:\Program Files (x86)\Microsoft Visual Studio\Installer\"
           $InstallPath = "C:\Program Files\Microsoft Visual Studio\2022\Enterprise"
           $componentsToAdd= @(
@@ -198,7 +187,7 @@ jobs:
       - name: Download artifacts produced during the build_wheels and build_sdist jobs
         uses: actions/download-artifact@v4
         with:
-          name: dist-*
+          pattern: dist-*
           path: dist/
           merge-multiple: true
 

CHANGELOG.md

@@ -4,7 +4,29 @@ Improvements:
 * New SWC parser:
     * handles `locale` correctly, so decimal numbers using comma are allowed
     * ~800 line SWC parse time goes from 0.976 to 0.699
-    * Doesn't create changes to bifurcations at the root nodes of SWC fils
+    * Doesn't create changes to bifurcations at the root nodes of SWC files
+    * More strict Neuromorpho 3 point soma checks
+    * disallow repeated Sample IDs
+    * Follow https://swc-specification.readthedocs.io/en/latest/swc.html more closely
+    * Allow only positive integer Sample IDs 
+    * Allow for the type of neurite to change at bifurcation points
+    * Allow Window style `End of Lines`
+    * allow trailing spaces on sample lines
+
+* Since this is a large change to the SWC parser, the minor release was increased 
+
+v3.3.10
+=======
+* This is primarily so that 3.13 wheels exist before the new SWC parser is put into production.
+* try to work around removal of older MSVC tools
+* Remove Errorlevel::Info; it's not an error if it's only informative
+* Update upload/download actions to v4.
+* update HDF5 url
+* Update HighFive to 2.10.0
+
+v3.3.9
+======
+* remove embarrassing debug print; Hat-tip SarahM
 
 v3.3.8
 ======

ci/hdf5-build.sh

@@ -13,7 +13,7 @@ function download_unpack_hdf5 {
     local name=CMake-hdf5-$UNIXY_HDF5_VERSION.tar.gz
     if [[ ! -e $name ]]; then
         echo "Downloading & unpacking HDF5 ${UNIXY_HDF5_VERSION}"
-        curl -fsSLO "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${UNIXY_HDF5_VERSION%.*}/hdf5-$UNIXY_HDF5_VERSION/src/$name"
+        curl -fsSLO "https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_${UNIXY_HDF5_VERSION//\./_}/src/$name"
     fi
     tar xzf "$name"
     popd

src/readers/morphologySWC.cpp

@@ -318,7 +318,7 @@ class SWCBuilder
             if (children_.count(s.id) > 0 && children_.at(s.id).size() > 1) {
                 std::vector<SWCSample> soma_bifurcations;
                 for (auto id : children_.at(s.id)) {
-                    if (samples_[id].type == SECTION_SOMA) {
+                    if (samples_[id].type == SECTION_SOMA && s.parentId != SWC_ROOT) {
                         soma_bifurcations.push_back(samples_[id]);
                     }
                 }
@@ -528,7 +528,6 @@ class SWCBuilder
     WarningHandler* warning_handler_;
     unsigned int options_;
 };
-
 }  // namespace details
 
 namespace readers {

src/readers/utils.cpp

@@ -21,11 +21,14 @@ namespace morphio {
 
 #endif
 
+// Only create the `locale` to facilitate number handling once
 StringToNumber::StringToNumber()
 #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+    // On windows, use their locale handling for their runtime
     : locale(_create_locale(LC_ALL, "C")) {
 }
 #else
+    // On other platforms, use the POSIX version
     : locale(newlocale(LC_NUMERIC_MASK, "POSIX", nullptr)) {
 }
 #endif