CI TESTING

.github/workflows/build_and_test.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.config.name }} (Python ${{ matrix.python-version}})
+    name: ${{ matrix.config.name }} (Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.config.os }}
     strategy:
       fail-fast: false
@@ -65,15 +65,24 @@ jobs:
         conda install -y --override-channels -c conda-forge --file tomviz/tests/python/requirements-dev.txt
         pip install --no-build-isolation --no-deps -U tomviz/tomviz/python
         pip install --no-build-isolation --no-deps -U tomviz/acquisition
+        # These do not have to be in the same environment as Tomviz, but the dependencies
+        # are so far compatible and we'll just let it go for the tests.
+        conda install -y --override-channels -c conda-forge --file tomviz/.github/workflows/pyxrf_requirements.txt
+        pip install --no-build-isolation --no-deps -U tomviz/tomviz/python/tomviz/pyxrf/pyxrf-utils
 
     - name: Run Tests
+      env:
+          # Make sure the Qt tests run offscreen
+          QT_QPA_PLATFORM: offscreen
+          TOMVIZ_REQUIRE_PYXRF: true
       run: |
         cd tomviz-build
-        TOMVIZ_TEST_PYTHON_EXECUTABLE=$(which python3) ctest --output-on-failure
+        export TOMVIZ_TEST_PYTHON_EXECUTABLE=$(which python3)
+        ctest --output-on-failure
 
     - name: Upload CTest Log (On Failure Only)
       if: ${{ failure() }}
       uses: actions/upload-artifact@v4
       with:
-        name: TomvizCTestLog.log
+        name: TomvizCTestLog_${{ matrix.config.name }}_Py${{ matrix.python-version }}.log
         path: tomviz-build/Testing/Temporary/LastTest.log

.github/workflows/build_requirements.txt

@@ -6,3 +6,5 @@ vtk
 libxml2-devel=2.14*
 # This is needed for building the tests
 gtest
+# This is needed for installing stuff on Python3.13
+setuptools

.github/workflows/pyxrf_requirements.txt

@@ -0,0 +1,9 @@
+# These are PyXRF workflow dependencies
+hxntools
+pyxrf
+xrf-tomo
+xraylib
+scikit-beam
+tomopy
+# These are required for installing the pyxrf-utils environment
+hatchling

.github/workflows/runtime_requirements.txt

@@ -7,10 +7,4 @@ jsonpointer
 pyfftw
 pygments
 pystackreg
-# These are PyXRF workflow dependencies
 h5py
-pyxrf
-xrf-tomo
-xraylib
-scikit-beam
-tomopy

BUILDING.md

@@ -1,8 +1,8 @@
 Building Tomviz
 ===============
 
-Building Tomviz is an advanced process that requires compiling ParaView,
-as well as ensuring all necessary dependencies are in place. Most users
+Building Tomviz can be an advanced process that requires
+ensuring that all necessary dependencies are in place. Most users
 ought to install Tomviz from the conda-forge packages rather than
 building it. These instructions are primarily for developers who wish
 to make contributions.
@@ -16,14 +16,10 @@ conda create -n tomviz -y
 conda activate tomviz
 ```
 
-First, we need to ensure that ParaView and tomviz are cloned into the
-current repository. Run the following bash code to do so:
+First, we need to ensure that tomviz is cloned into the current repository.
+Run the following bash code to do so:
 
 ```bash
-if ! [ -e "paraview" ]; then
-  git clone -b v6.0.1 --recursive https://gitlab.kitware.com/paraview/paraview
-fi
-
 if ! [ -e "tomviz" ]; then
   git clone --recursive https://github.com/NSLS2/tomviz
 fi
@@ -36,12 +32,6 @@ conda-forge. Thus we will use those lists for installation.
 conda install -y --override-channels -c conda-forge --file tomviz/.github/workflows/build_requirements.txt
 ```
 
-Next, build ParaView. This may take some time.
-
-```bash
-bash tomviz/.github/workflows/scripts/build_paraview.sh
-```
-
 Now, build Tomviz.
 
 ```bash
@@ -65,19 +55,14 @@ Tomviz may then be ran as follows:
 All of the build instructions above put into a single script are as follows:
 
 ```bash
-if ! [ -e "paraview" ]; then
-  git clone -b v6.0.1 --recursive https://gitlab.kitware.com/paraview/paraview
-fi
-
 if ! [ -e "tomviz" ]; then
   git clone --recursive https://github.com/NSLS2/tomviz
 fi
 
 # Install build requirements
 conda install -y --override-channels -c conda-forge --file tomviz/.github/workflows/build_requirements.txt
 
-# Build ParaView and Tomviz
-bash tomviz/.github/workflows/scripts/build_paraview.sh
+# Build Tomviz
 bash tomviz/.github/workflows/scripts/build_tomviz.sh
 
 # Install runtime dependencies

CMakeLists.txt

@@ -89,7 +89,7 @@ file(RELATIVE_PATH
 set(CMAKE_MODULE_PATH "${tomviz_SOURCE_DIR}/cmake")
 
 # Request C++11 standard, using new CMake variables.
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_CXX_EXTENSIONS False)
 
@@ -146,7 +146,7 @@ endif()
 
 find_package(ITK 4.9)
 
-set(PYBIND11_CPP_STANDARD "-std=c++11" CACHE STRING "")
+set(PYBIND11_CPP_STANDARD "-std=c++17" CACHE STRING "")
 add_subdirectory(${PROJECT_SOURCE_DIR}/thirdparty/pybind11)
 
 option(tomviz_ENABLE_LOOKING_GLASS "Enable the looking glass plugin" OFF)

acquisition/requirements-dev.txt

@@ -1,9 +1,10 @@
-pytest==3.0.6
-requests==2.20.0
-Pillow==8.3.2
+pytest>=8.3
+requests>=2.32.4
+Pillow==10.3.0
 # Need this for testing so we can stop there server, change when the required
 # get into a release.
-https://github.com/bottlepy/bottle/archive/41ed6965.zip
+# https://github.com/bottlepy/bottle/archive/41ed6965.zip
+bottle>=0.13.2
 mock==2.0.0
 diskcache==3.0.1
 -e git+https://[email protected]/cjh1/pydm3reader.git@filelike#egg=dm3_lib

acquisition/setup.py

@@ -30,7 +30,7 @@
     },
     entry_points={
         'console_scripts': [
-            'tomviz-acquisition = tomviz.acquisition.cli:main',
+            'tomviz-acquisition = tomviz_acquisition.acquisition.cli:main',
             'tomviz-tiltseries-writer = tests.mock.tiltseries.writer:main'
         ]
     }

acquisition/tests/conftest.py

@@ -4,7 +4,7 @@
 from threading import Thread
 from bottle import default_app, WSGIRefServer
 
-from tomviz.acquisition import server
+from tomviz_acquisition.acquisition import server
 from .mock.tiltseries import TIFFWriter, DM3Writer
 
 

acquisition/tests/fei_test.py

@@ -4,17 +4,17 @@
 import sys
 import os
 
-from tomviz.jsonrpc import jsonrpc_message
+from tomviz_acquisition.jsonrpc import jsonrpc_message
 
 # Add mock modules to path
-mock_dir = os.path.join(os.path.dirname(__file__), '..', 'tomviz',
+mock_dir = os.path.join(os.path.dirname(__file__), '..', 'tomviz_acquisition',
                         'acquisition', 'vendors', 'fei', 'mock')
 sys.path.append(mock_dir)
 
 
 @pytest.fixture(scope="module")
 def fei_acquisition_server(acquisition_server):
-    acquisition_server.setup('tomviz.acquisition.vendors.fei.FeiAdapter')
+    acquisition_server.setup('tomviz_acquisition.acquisition.vendors.fei.FeiAdapter')
     yield acquisition_server
 
 

acquisition/tests/fixtures/source1.py

@@ -1,6 +1,6 @@
 import tempfile
 import os
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import AbstractSource
 
 
 class ApiAdapter1(AbstractSource):

acquisition/tests/fixtures/source2.py

@@ -1,6 +1,6 @@
 import tempfile
 import os
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import AbstractSource
 
 
 class ApiAdapter2(AbstractSource):

acquisition/tests/jsonrpc_test.py

@@ -1,6 +1,6 @@
 import pytest
 
-from tomviz.jsonrpc import JsonRpcHandler, jsonrpc_message
+from tomviz_acquisition.jsonrpc import JsonRpcHandler, jsonrpc_message
 
 
 @pytest.fixture

acquisition/tests/mock/mock_api.py

@@ -1,7 +1,7 @@
 import time
 from PIL import Image
 from . import test_image, test_black_image, angle_to_page
-from tomviz.acquisition.utility import tobytes
+from tomviz_acquisition.acquisition.utility import tobytes
 
 img = Image.open(test_image())
 black = test_black_image().read()

acquisition/tests/mock/source.py

@@ -1,6 +1,6 @@
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import AbstractSource
 from . import mock_api
-from tomviz.acquisition import describe
+from tomviz_acquisition.acquisition import describe
 
 
 class ApiAdapter(AbstractSource):

acquisition/tests/passive_test.py

@@ -7,9 +7,9 @@
 from PIL import Image
 import dm3_lib as dm3
 
-from tomviz.jsonrpc import jsonrpc_message
+from tomviz_acquisition.jsonrpc import jsonrpc_message
 from .mock import test_image, test_dm3_tilt_series
-from tomviz.acquisition.utility import tobytes
+from tomviz_acquisition.acquisition.utility import tobytes
 
 # Add mock modules to path
 mock_dir = os.path.join(os.path.dirname(__file__), '..', 'tomviz',
@@ -19,7 +19,7 @@
 
 @pytest.fixture(scope="module")
 def passive_acquisition_server(acquisition_server):
-    source = 'tomviz.acquisition.vendors.passive.PassiveWatchSource'
+    source = 'tomviz_acquisition.acquisition.vendors.passive.PassiveWatchSource'
     acquisition_server.setup(source)
     yield acquisition_server
 

acquisition/tests/server_test.py

@@ -5,7 +5,7 @@
 import pytest
 import inspect
 
-from tomviz.jsonrpc import jsonrpc_message
+from tomviz_acquisition.jsonrpc import jsonrpc_message
 from tests.mock.source import ApiAdapter
 
 

acquisition/tomviz/acquisition/cli/__init__.py → acquisition/tomviz_acquisition/acquisition/cli/__init__.py

@@ -1,5 +1,5 @@
 import argparse
-from tomviz.utility import logging
+from tomviz_acquisition.utility import logging
 
 
 def main():
@@ -23,7 +23,7 @@ def main():
     if args.redirect:
         logging.setup_std_loggers()
 
-    from tomviz.acquisition import server
+    from tomviz_acquisition.acquisition import server
 
     logging.setup_loggers(args.debug, args.redirect)
     server_params = vars(args)

acquisition/tomviz/acquisition/server.py → acquisition/tomviz_acquisition/acquisition/server.py

@@ -8,10 +8,9 @@
 import bottle
 from bottle import run, route, request, HTTPResponse, Bottle
 
-import tomviz
-from tomviz import jsonrpc
-from tomviz.utility import inject
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition import jsonrpc
+from tomviz_acquisition.utility import inject
+from tomviz_acquisition.acquisition import AbstractSource
 import shutil
 
 # For python 3
@@ -26,7 +25,7 @@
 PORT = 8080
 LOG_BUF_SIZE = 65536
 
-logger = logging.getLogger('tomviz')
+logger = logging.getLogger('tomviz_acquisition')
 app = Bottle()
 
 

acquisition/tomviz/acquisition/vendors/passive/__init__.py → acquisition/tomviz_acquisition/acquisition/vendors/passive/__init__.py

@@ -5,9 +5,9 @@
 import os
 import dm3_lib as dm3
 
-from tomviz.acquisition import AbstractSource
-from tomviz.acquisition import describe
-from tomviz.acquisition.utility import tobytes
+from tomviz_acquisition.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import describe
+from tomviz_acquisition.acquisition.utility import tobytes
 from .filesystem import Monitor
 
 try:

acquisition/tomviz/utility/logging.py → acquisition/tomviz_acquisition/utility/logging.py

@@ -60,7 +60,7 @@ def setup_std_loggers():
 
 
 def setup_loggers(debug=False, redirect=False):
-    logger = logging.getLogger('tomviz')
+    logger = logging.getLogger('tomviz_acquisition')
     logger.setLevel(logging.DEBUG if debug else logging.INFO)
 
     file_handler = logging.handlers.RotatingFileHandler(