Merge pull request #25 from psavery/update-paraview

celiafish · web-flow · commit ff9dd5b76d6c · 2026-04-16T19:20:37.000-04:00
Update paraview to 6.1.0
diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -19,6 +19,14 @@ jobs:
             name: Linux,
             os: ubuntu-latest
           }
+        - {
+            name: macOS,
+            os: macos-latest
+          }
+        - {
+            name: Windows,
+            os: windows-latest
+          }
 
     defaults:
       run:
@@ -52,9 +60,15 @@ jobs:
         echo "build_env.yml file contents is:"
         cat build_env.yml
 
-    - name: Build Tomviz
+    - name: Build Tomviz (Unix)
+      if: runner.os != 'Windows'
       run: bash tomviz/.github/workflows/scripts/build_tomviz.sh
 
+    - name: Build Tomviz (Windows)
+      if: runner.os == 'Windows'
+      shell: cmd /C CALL {0}
+      run: tomviz\.github\workflows\scripts\build_tomviz.bat
+
     - name: Install Runtime Requirements
       # I can't get the defaults channel fully removed, so we have to
       # --override-channels here.
diff --git a/.github/workflows/build_requirements.txt b/.github/workflows/build_requirements.txt
@@ -1,7 +1,7 @@
 cxx-compiler
 cmake
 ninja
-paraview==6.0.1
+paraview==6.1.0
 vtk
 libxml2-devel=2.14*
 # This is needed for building the tests
diff --git a/.github/workflows/pyxrf_requirements.txt b/.github/workflows/pyxrf_requirements.txt
@@ -4,7 +4,8 @@ pyxrf
 xrf-tomo
 xraylib
 scikit-beam
-tomopy
+# 1.15.3 is required for NumPy 2.x compatibility
+tomopy>=1.15.3
 # These are required for installing the pyxrf-utils environment
 hatchling
 # Pandas needs to be pinned to prevent a bug in xrf-tomo, until
diff --git a/.github/workflows/runtime_requirements.txt b/.github/workflows/runtime_requirements.txt
@@ -8,3 +8,5 @@ pyfftw
 pygments
 pystackreg
 h5py
+click
+scikit-image
diff --git a/.github/workflows/scripts/build_tomviz.bat b/.github/workflows/scripts/build_tomviz.bat
@@ -0,0 +1,20 @@
+@echo off
+
+mkdir tomviz-build
+cd tomviz-build
+
+REM FIXME: setting the zlib paths manually shouldn't be necessary forever.
+REM Try removing it sometime
+cmake -G"Ninja" ^
+  -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo ^
+  -DCMAKE_INSTALL_LIBDIR:STRING=lib ^
+  -DTOMVIZ_USE_EXTERNAL_VTK:BOOL=ON ^
+  -DENABLE_TESTING:BOOL=ON ^
+  -DPython3_FIND_STRATEGY:STRING=LOCATION ^
+  -DZLIB_LIBRARY=%CONDA_PREFIX%\Library\lib\zlib.lib ^
+  -DZLIB_INCLUDE_DIR=%CONDA_PREFIX%\Library\include ^
+  ..\tomviz
+if %errorlevel% neq 0 exit /b %errorlevel%
+
+ninja
+if %errorlevel% neq 0 exit /b %errorlevel%
diff --git a/.github/workflows/scripts/build_tomviz.sh b/.github/workflows/scripts/build_tomviz.sh
@@ -2,14 +2,37 @@
 
 mkdir -p tomviz-build && cd tomviz-build
 
+CMAKE_ARGS=(
+  -G"Ninja"
+  -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo
+  -DCMAKE_INSTALL_LIBDIR:STRING=lib
+  -DTOMVIZ_USE_EXTERNAL_VTK:BOOL=ON
+  -DENABLE_TESTING:BOOL=ON
+  -DPython3_FIND_STRATEGY:STRING=LOCATION
+)
+
 # FIXME: setting the zlib paths manually shouldn't be necessary forever.
 # Try removing it sometime
-cmake -G"Ninja" -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo \
-  -DCMAKE_INSTALL_LIBDIR:STRING=lib \
-  -DTOMVIZ_USE_EXTERNAL_VTK:BOOL=ON \
-  -DENABLE_TESTING:BOOL=ON \
-  -DPython3_FIND_STRATEGY:STRING=LOCATION \
-  -DZLIB_LIBRARY=$CONDA_PREFIX/lib/libz.so.1 \
-  -DZLIB_INCLUDE_DIR=$CONDA_PREFIX/include \
-  ../tomviz
+case "$(uname -s)" in
+  Linux*)
+    CMAKE_ARGS+=(
+      -DZLIB_LIBRARY=$CONDA_PREFIX/lib/libz.so.1
+      -DZLIB_INCLUDE_DIR=$CONDA_PREFIX/include
+    )
+    ;;
+  Darwin*)
+    CMAKE_ARGS+=(
+      -DZLIB_LIBRARY=$CONDA_PREFIX/lib/libz.dylib
+      -DZLIB_INCLUDE_DIR=$CONDA_PREFIX/include
+    )
+    ;;
+  MINGW*|MSYS*)
+    CMAKE_ARGS+=(
+      -DZLIB_LIBRARY=$CONDA_PREFIX/Library/lib/zlib.lib
+      -DZLIB_INCLUDE_DIR=$CONDA_PREFIX/Library/include
+    )
+    ;;
+esac
+
+cmake "${CMAKE_ARGS[@]}" ../tomviz
 ninja
diff --git a/README.md b/README.md
@@ -22,8 +22,19 @@ Installing
 ----------
 <img align="right" src="https://github.com/OpenChemistry/tomviz/blob/master/docs/images/animation_nponcarbon1_small.gif">
 
-We recommend downloading the current [stable release](../../releases),
-but also provide nightly binaries built by our [dashboards][Dashboard] for
+Tomviz is currently undergoing major upgrades. Updated packages are available
+on [conda-forge](https://anaconda.org/conda-forge/tomviz) for Linux:
+
+    conda install -c conda-forge tomviz
+
+Within the next 6 months, we plan to provide conda-forge packages for all
+other operating systems (Windows, macOS), as well as installable binary
+packages (MSI, DMG, etc.).
+
+### Older releases
+
+For older releases, we recommend downloading the [stable release](../../releases).
+Nightly binaries were also previously built by our [dashboards][Dashboard] for
 Windows, macOS, and Linux.
 
 __Windows__: Follow the installation instructions, double-click on the Tomviz
diff --git a/cmake/CompilerFlags.cmake b/cmake/CompilerFlags.cmake
@@ -2,12 +2,8 @@ if (UNIX)
   include(CheckCXXCompilerFlag)
 
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pedantic -Wshadow -Wextra")
-elseif (WIN32)
-  if (MSVC AND MSVC14)
-    set(CMAKE_CXX_FLAGS_STD_CPP)
-  else()
-    message(FATAL_ERROR "Only the MSVC 2015 compiler is supported on windows.")
-  endif()
+elseif (WIN32 AND MSVC)
+  set(CMAKE_CXX_FLAGS_STD_CPP)
 endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
diff --git a/tests/cxx/CMakeLists.txt b/tests/cxx/CMakeLists.txt
@@ -59,10 +59,16 @@ add_cxx_qtest(ModulePlot)
 add_cxx_qtest(Tvh5Data)
 add_cxx_qtest(InterfaceBuilder)
 add_cxx_qtest(PipelineExecution PYTHONPATH ${_pythonpath})
-add_cxx_qtest(DockerUtilities)
-add_cxx_qtest(AcquisitionClient PYTHONPATH "${CMAKE_SOURCE_DIR}/acquisition")
+if(UNIX AND NOT APPLE)
+  add_cxx_qtest(DockerUtilities)
+endif()
+if(NOT WIN32)
+  add_cxx_qtest(AcquisitionClient PYTHONPATH "${CMAKE_SOURCE_DIR}/acquisition")
+endif()
 add_cxx_qtest(PtychoWorkflow PYTHONPATH ${_pythonpath})
+set_tests_properties(PtychoWorkflow PROPERTIES TIMEOUT 1800)
 add_cxx_qtest(PyXRFWorkflow PYTHONPATH ${_pythonpath})
+set_tests_properties(PyXRFWorkflow PROPERTIES TIMEOUT 1800)
 
 # Generate the executable
 create_test_executable(tomvizTests)
diff --git a/tests/cxx/PyXRFWorkflowTest.cxx b/tests/cxx/PyXRFWorkflowTest.cxx
@@ -150,13 +150,16 @@ private slots:
     // Keep processing events until all dialogs have
     // been found and accepted/rejected.
     int timeElapsed = 0;
-    int maxTime = 30;
+    int maxTime = 120;
     while (!found && timeElapsed < maxTime) {
       QThread::sleep(1);
       QApplication::processEvents();
       timeElapsed += 1;
     }
 
+    // Clean up the runner (terminates any running processes)
+    delete runner;
+
     // Verify everything was found
     QVERIFY(found);
 
diff --git a/tests/cxx/Tvh5DataTest.cxx b/tests/cxx/Tvh5DataTest.cxx
@@ -52,7 +52,9 @@ class Tvh5DataTest : public QObject
   {
     QTemporaryFile tmpFile(QDir::tempPath() + "/tomviz_test_XXXXXX.tvh5");
     tmpFile.setAutoRemove(false);
-    tmpFile.open();
+    if (!tmpFile.open()) {
+      return {};
+    }
     auto path = tmpFile.fileName();
     tmpFile.close();
     m_tempFiles.push_back(path);
diff --git a/tests/python/external_operator_test.py b/tests/python/external_operator_test.py
@@ -1,4 +1,5 @@
 import json
+import os
 import sys
 
 import numpy as np
@@ -43,14 +44,21 @@ def test_transform_single_external_operator():
     # Find the environment that has tomviz-pipeline installed.
     # Use sys.prefix for the current environment, but also check
     # the conda env path since tests may run from a different prefix.
+    if sys.platform == 'win32':
+        scripts_dir = 'Scripts'
+        exec_name = 'tomviz-pipeline.exe'
+    else:
+        scripts_dir = 'bin'
+        exec_name = 'tomviz-pipeline'
+
     tomviz_pipeline_env = sys.prefix
-    exec_path = Path(tomviz_pipeline_env) / 'bin' / 'tomviz-pipeline'
+    exec_path = Path(tomviz_pipeline_env) / scripts_dir / exec_name
     if not exec_path.exists():
         # Try the conda env path
-        conda_prefix = sys.environ.get('CONDA_PREFIX')
+        conda_prefix = os.environ.get('CONDA_PREFIX')
         if conda_prefix:
             tomviz_pipeline_env = conda_prefix
-            exec_path = Path(tomviz_pipeline_env) / 'bin' / 'tomviz-pipeline'
+            exec_path = Path(tomviz_pipeline_env) / scripts_dir / exec_name
 
     if not exec_path.exists():
         pytest.skip('tomviz-pipeline not found')
diff --git a/tests/python/pystackreg_test.py b/tests/python/pystackreg_test.py
@@ -41,9 +41,12 @@ def test_pystackreg(hxn_xrf_example_dataset: Dataset,
     # Verify the keys match
     assert list(sorted(pystackreg_reference_output)) == list(sorted(dataset.arrays))
 
-    # Arrays should now match
+    # Arrays should now match (use atol for cross-platform tolerance since
+    # pystackreg's C extension can produce slightly different results on
+    # different architectures, e.g. x86 vs ARM)
     assert all(
-        np.allclose(pystackreg_reference_output[key], dataset.arrays[key])
+        np.allclose(pystackreg_reference_output[key], dataset.arrays[key],
+                    atol=1e-2)
         for key in pystackreg_reference_output
     )
 
diff --git a/tomviz/CMakeLists.txt b/tomviz/CMakeLists.txt
@@ -245,7 +245,6 @@ set(SOURCES
   Tvh5Format.h
   Utilities.cxx
   Utilities.h
-  core/Variant.cxx
   core/Variant.h
   ViewFrameActions.cxx
   ViewFrameActions.h
@@ -765,7 +764,9 @@ configure_file(tomvizConfig.h.in tomvizConfig.h @ONLY)
 configure_file(tomvizPythonConfig.h.in tomvizPythonConfig.h @ONLY)
 
 add_library(tomvizlib STATIC ${SOURCES} ${accel_srcs})
-set_target_properties(tomvizlib PROPERTIES OUTPUT_NAME tomviz)
+if(NOT WIN32)
+  set_target_properties(tomvizlib PROPERTIES OUTPUT_NAME tomviz)
+endif()
 
 # Need to set this property so that in stack traces, tomviz symbols
 # can be resolved.
diff --git a/tomviz/DataSource.cxx b/tomviz/DataSource.cxx
@@ -18,6 +18,8 @@
 #include "TimeSeriesStep.h"
 #include "Utilities.h"
 
+#include <iostream>
+
 #include <vtkDataObject.h>
 #include <vtkDoubleArray.h>
 #include <vtkFieldData.h>
@@ -243,14 +245,14 @@ bool DataSource::appendSlice(vtkImageData* slice)
     if (data) {
       int extents[6];
       data->GetExtent(extents);
-      cout << "The data is ";
+      std::cout << "The data is ";
       for (int i = 0; i < 6; ++i)
-        cout << extents[i] << ", ";
-      cout << endl;
+        std::cout << extents[i] << ", ";
+      std::cout << std::endl;
       for (int i = 0; i < 4; ++i) {
         if (extents[i] != sliceExtents[i]) {
-          cout << "Mismatch: " << extents[i] << " != " << sliceExtents[i]
-               << endl;
+          std::cout << "Mismatch: " << extents[i] << " != " << sliceExtents[i]
+               << std::endl;
           return false;
         }
       }
@@ -1088,7 +1090,7 @@ bool DataSource::removeOperator(Operator* op)
     op->deleteLater();
 
     foreach (Operator* opPtr, this->Internals->Operators) {
-      cout << "Operator: " << opPtr->label().toLatin1().data() << endl;
+      std::cout << "Operator: " << opPtr->label().toLatin1().data() << std::endl;
     }
 
     return true;
diff --git a/tomviz/DataSource.h b/tomviz/DataSource.h
@@ -29,7 +29,7 @@ namespace tomviz {
 class DataSourceBase;
 class Operator;
 class Pipeline;
-class TimeSeriesStep;
+struct TimeSeriesStep;
 
 using MetadataType = std::map<std::string, Variant>;
 
diff --git a/tomviz/HistogramManager.cxx b/tomviz/HistogramManager.cxx
@@ -11,6 +11,8 @@
 
 #include "ComputeHistogram.h"
 
+#include <iostream>
+
 #include <QCoreApplication>
 #include <QThread>
 
@@ -76,7 +78,7 @@ void PopulateHistogram(vtkImageData* input, vtkTable* output)
       arrayPtr->GetNumberOfTuples(), arrayPtr->GetNumberOfComponents(),
       minmax[0], minmax[1], pops, 1.0 / inc, invalid));
     default:
-      cout << "UpdateFromFile: Unknown data type" << endl;
+      std::cout << "UpdateFromFile: Unknown data type" << std::endl;
   }
 
 #ifndef NDEBUG
@@ -86,7 +88,7 @@ void PopulateHistogram(vtkImageData* input, vtkTable* output)
   assert(total == arrayPtr->GetNumberOfTuples());
 #endif
   if (invalid) {
-    cout << "Warning: NaN or infinite value in dataset" << endl;
+    std::cout << "Warning: NaN or infinite value in dataset" << std::endl;
   }
 
   output->AddColumn(extents);
@@ -132,7 +134,7 @@ void Populate2DHistogram(vtkImageData* input, vtkImageData* output)
       reinterpret_cast<VTK_TT*>(arrayPtr->GetVoidPointer(0)), dim, numComp,
       minmax, output, spacing));
     default:
-      cout << "UpdateFromFile: Unknown data type" << endl;
+      std::cout << "UpdateFromFile: Unknown data type" << std::endl;
   }
 }
 
diff --git a/tomviz/PyXRFRunner.cxx b/tomviz/PyXRFRunner.cxx
@@ -722,7 +722,23 @@ PyXRFRunner::PyXRFRunner(QObject* parent)
 {
 }
 
-PyXRFRunner::~PyXRFRunner() = default;
+PyXRFRunner::~PyXRFRunner()
+{
+  // Terminate any running processes to avoid SEGFAULT from QProcess
+  // being destroyed while still running.
+  QProcess* processes[] = { &m_internal->makeHDF5Process,
+                            &m_internal->remakeCsvFileProcess,
+                            &m_internal->processProjectionsProcess };
+  for (auto* p : processes) {
+    if (p->state() != QProcess::NotRunning) {
+      p->terminate();
+      if (!p->waitForFinished(5000)) {
+        p->kill();
+        p->waitForFinished(3000);
+      }
+    }
+  }
+}
 
 bool PyXRFRunner::isInstalled()
 {
diff --git a/tomviz/ScaleActorBehavior.cxx b/tomviz/ScaleActorBehavior.cxx
@@ -14,7 +14,6 @@
 #include <vtkNew.h>
 #include <vtkRenderer.h>
 #include <vtkVector.h>
-#include <vtkVectorOperators.h>
 
 namespace tomviz {
 
diff --git a/tomviz/acquisition/AcquisitionWidget.cxx b/tomviz/acquisition/AcquisitionWidget.cxx
diff --git a/tomviz/acquisition/PassiveAcquisitionWidget.cxx b/tomviz/acquisition/PassiveAcquisitionWidget.cxx
diff --git a/tomviz/operators/ArrayWranglerOperator.cxx b/tomviz/operators/ArrayWranglerOperator.cxx
diff --git a/tomviz/pybind11/ctvlib/eigenConversion.h b/tomviz/pybind11/ctvlib/eigenConversion.h
diff --git a/tomviz/python/tomviz/_internal.py b/tomviz/python/tomviz/_internal.py
diff --git a/tomviz/vtkOMETiffReader.cxx b/tomviz/vtkOMETiffReader.cxx
diff --git a/tomviz/vtkTransferFunctionBoxItem.cxx b/tomviz/vtkTransferFunctionBoxItem.cxx
