Merge pull request #241 from fusion-energy/vtk_version_pin

pinned vtk to 9.2.5

.devcontainer/base.Dockerfile

@@ -123,7 +123,7 @@ RUN pip install cmake\
  scikit-optimize \
  scikit-opt \
  adaptive \
- vtk \
+ "vtk==9.2.5"  \
  itkwidgets \
  pytest \
  holoviews \

README.md

@@ -1,22 +1,5 @@
 
-[![Task 1](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_1.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_1.yml)
-[![Task 2](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_2.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_2.yml)
-[![Task 3](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_3.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_3.yml)
-[![Task 4](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_4.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_4.yml)
-[![Task 5](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_5.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_5.yml)
-[![Task 6](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml)
-[![Task 7](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml)
-[![Task 8](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml)
-[![Task 9](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml)
-[![Task 10](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml)
-[![Task 11](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml)
-[![Task 12](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml)
-[![Task 13](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml)
-[![Task 14](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml)
-[![Task 15](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml)
-[![Task 16](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml)
-[![Task 17](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml)
-[![Task 18](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_18.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_18.yml)
+
 
 [![docker-publish-release](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/docker-publish.yml)
 
@@ -29,8 +12,10 @@ There is a
 [slide](https://slides.com/neutronics_workshop/neutronics_workshop) deck that introduces
 the workshop and show the expected outputs of each task.
 
+There is also a [Gather Town](https://gather.town/app/QnHxhg6bPf8KQdii/openmc-workshop) space which is great for working through the workshop with colleagues.
+
 These examples require specific versions of software packages and nuclear data to run correctly.
-Therefore I highly recommend making use of the containerised environment to run these example notebooks.
+Therefore **I highly recommend making use of the containerised environment** to run these example notebooks.
 
 The repository has benefited greatly from user feedback. Please feel free to
 raise Github [issues](https://github.com/fusion-energy/neutronics-workshop/issues)
@@ -42,6 +27,28 @@ The video below gives a brief explainer of what to expect in the workshop and so
 
 <p align="center"><a href="https://youtu.be/HH-poTG-FxM" target="_blank"><img src="https://user-images.githubusercontent.com/8583900/144746742-3e31e0ee-6380-4db7-b8ea-0b1c302d497b.png" height="400" /></a></p>
 
+
+| Tasks | Keywords | Video(s) | CI test status|
+|-|-|-|-|
+| [Task 1 - Cross sections](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_01_cross_sections) | Nuclear data, cross-sections, MT numbers, Doppler | [link1](https://youtu.be/eBZ2lY_2v7I) [link2](https://youtu.be/ELZNeIdSuMY) [link3](https://youtu.be/ec5BLLL6Q_g) [link4](https://youtu.be/mkl1mVnTO6g) |[![Task 1](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_1.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_1.yml)|
+| [Task 2 - Materials](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_02_making_materials) | Materials, Neutronics Material Maker, Mixed materials | [link](https://youtu.be/-NGnY-1TWCA) | [![Task 2](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_2.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_2.yml) |
+| [Task 3 - CSG geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_03_making_CSG_geometry) | CSG geometry, Geometry visualisation | [link](https://youtu.be/Ovr7oYukYRw) | [![Task 3](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_3.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_3.yml) |
+| [Task 4 - Sources](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_04_make_sources) | Neutron point sources, Gamma sources, Plasma sources, Neutron track visualisation | [link](https://youtu.be/j9dT1Viqcu4) | [![Task 4](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_4.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_4.yml) |
+| [Task 5 - TBR](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_05_CSG_cell_tally_TBR) | Tritium Breeding Ratio, Cell tallies, Simulations | [link](https://youtu.be/Vc7Qy7QW4o8) | [![Task 5](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_5.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_5.yml) |
+| [Task 6 - DPA](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_06_CSG_cell_tally_DPA) | Displacements Per Atom, Cell tallies, Simulations, Volume calculations | [link](https://youtu.be/VLn59FSc4GA) | [![Task 6](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml) |
+| [Task 7 - Neutron and photon spectra](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_07_CSG_cell_tally_spectra) | Neutron Spectra, Photon Spectra, Cell tallies, Energy group structures, Flux, Current | [link](https://youtu.be/qHqAuqMLYPA) | [![Task 7](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml) |
+| [Task 8 - Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_08_CSG_mesh_tally) | Mesh tallies, Structured meshes | [link](https://youtu.be/KYIsDjip1nQ) |[![Task 8](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml)|
+| [Task 9 - Dose](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_09_CSG_dose_tallies) | Instantaneous Dose, Cell tallies, Dose coefficients | |[![Task 9](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml)|
+| [Task 10 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) |[![Task 10](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml)|
+| [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating | |[![Task 11](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml)|
+| [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux | |[![Task 12](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml)|
+| [Task 13 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_13_variance_reduction) | Variance reduction, weight windows | |[![Task 13](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml)|
+| [Task 14 - Activation transmutation depletion](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_activation_transmutation_depletion) | Isotope build up and tally variation as a function of time | |[![Task 14](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml)|
+| [Task 15 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | |[![Task 15](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml)|
+| [Task 16 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_parameter_study_optimisation) | Data science machine learning approaches | |[![Task 16](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml)|
+| [Task 17 - Detector examples](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_17_detector_examples) | Time filter detector response time of flight | |[![Task 17](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml)|
+| [Task 18 - stochastic volume calculation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_18_stochastic_volume_calculation) | stochastic volume material atoms in cell | |[![Task 18](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_18.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_18.yml)|
+
 <!-- # Run in the cloud (low CPU count)
 
 One advantage of the containerization of the entire software stack is that it
@@ -136,29 +143,3 @@ without installing anything locally.
 - Then follow :point_right: [this link](https://github.com/codespaces/new?hide_repo_select=true&ref=main&repo=386229912) to config a compute instance :point_right: <p align="center"><a href="https://github.com/codespaces/new?hide_repo_select=true&ref=main&repo=386229912" target="_blank"><img src="https://user-images.githubusercontent.com/8583900/179179958-cc7f0700-6df5-47e9-a10f-67a9c1e556c6.png" height="150" /></a></p>
 
 - VS Code will then launch in the browser, once loaded you must select the conda python interpreter to enable the correct Python environment.
-
-
-# Workshop tasks
-
-The task videos are all available on a [Gather Town](https://gather.town/app/QnHxhg6bPf8KQdii/openmc-workshop) space which is great for working through the workshop with colleagues.
-
-| Tasks | Keywords | Video(s) |
-|-|-|-|
-| [Task 1 - Cross sections](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_01_cross_sections) | Nuclear data, cross-sections, MT numbers, Doppler | [link1](https://youtu.be/eBZ2lY_2v7I) [link2](https://youtu.be/ELZNeIdSuMY) [link3](https://youtu.be/ec5BLLL6Q_g) [link4](https://youtu.be/mkl1mVnTO6g) |
-| [Task 2 - Materials](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_02_making_materials) | Materials, Neutronics Material Maker, Mixed materials | [link](https://youtu.be/-NGnY-1TWCA) |
-| [Task 3 - CSG geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_03_making_CSG_geometry) | CSG geometry, Geometry visualisation | [link](https://youtu.be/Ovr7oYukYRw) |
-| [Task 4 - Sources](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_04_make_sources) | Neutron point sources, Gamma sources, Plasma sources, Neutron track visualisation | [link](https://youtu.be/j9dT1Viqcu4) |
-| [Task 5 - TBR](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_05_CSG_cell_tally_TBR) | Tritium Breeding Ratio, Cell tallies, Simulations | [link](https://youtu.be/Vc7Qy7QW4o8) |
-| [Task 6 - DPA](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_06_CSG_cell_tally_DPA) | Displacements Per Atom, Cell tallies, Simulations, Volume calculations | [link](https://youtu.be/VLn59FSc4GA) |
-| [Task 7 - Neutron and photon spectra](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_07_CSG_cell_tally_spectra) | Neutron Spectra, Photon Spectra, Cell tallies, Energy group structures, Flux, Current | [link](https://youtu.be/qHqAuqMLYPA) |
-| [Task 8 - Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_08_CSG_mesh_tally) | Mesh tallies, Structured meshes | [link](https://youtu.be/KYIsDjip1nQ) |
-| [Task 9 - Dose](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_09_CSG_dose_tallies) | Instantaneous Dose, Cell tallies, Dose coefficients | |
-| [Task 10 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) |
-| [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating | |
-| [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux | |
-| [Task 13 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_13_variance_reduction) | Variance reduction, weight windows | |
-| [Task 14 - Activation transmutation depletion](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_activation_transmutation_depletion) | Isotope build up and tally variation as a function of time | |
-| [Task 15 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | |
-| [Task 16 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_parameter_study_optimisation) | Data science machine learning approaches | |
-| [Task 17 - Detector examples](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_17_detector_examples) | Time filter detector response time of flight | |
-| [Task 18 - stochastic volume calculation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_18_stochastic_volume_calculation) | stochastic volume material atoms in cell | |