Merge pull request #8 from psavery/pyxrf-workflow

Updates to PyXRF Workflow

Author: celiafish

.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
@@ -67,13 +67,18 @@ jobs:
         pip install --no-build-isolation --no-deps -U tomviz/acquisition
 
     - 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/runtime_requirements.txt

@@ -9,6 +9,7 @@ pygments
 pystackreg
 # These are PyXRF workflow dependencies
 h5py
+hxntools
 pyxrf
 xrf-tomo
 xraylib

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/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