removed .py script examples and replaced with .ipynb

.circleci/config.yml

@@ -73,7 +73,7 @@ jobs:
       - run:
           name: run example reactor tests
           command: 
-            pytest tests/test_example_reactors.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+            pytest --capture=tee-sys tests/test_example_reactors.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
 
       - store_test_results:
           path: test-reports

docs/source/example_neutronics_simulations.rst

@@ -1,53 +1,62 @@
 Examples - Neutronics Simulations
 =================================
 
-There are minimal examples of neutronics simulations that just make a single
-and there are slightly more involved examples that make more complex models or
-a series of models.
+These are minimal examples of neutronics simulations that demonstrate the core
+functionality of the neutronics features. In general it easy to export geomtry
+in h5m format for use in DAGMC enabled simulations. There are two options for
+this export. The Trelis method of converting geometry imprints and merges
+surfaces while the PyMoab converts the geoemtry without imprinting and merging
+surfaces.
 
-OpenMC logo simulation
-^^^^^^^^^^^^^^^^^^^^^^
+The resulting h5m files can be used in DAGMC enabled neutronics codes such as
+OpenMC and MCNP. There is also a class (NeutronicsModel) that facilitates
+adding tallies, materials and a source to the geoemtry to create a complete
+OpenMC neutronics model which can be simulated. The simulated results are also
+extracted from the statepoint.h5 file that OpenMC produces and converted to
+vtk, png and JSON files depending on the tally.
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_neutronics_simulations/openmc_logo_example.ipynb>`_
 
-.. raw:: html
+ball_reactor.ipynb
+^^^^^^^^^^^^^^^^^^
 
-   <iframe width="560" height="315" src="https://www.youtube.com/embed/40VARwD44FA" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+`Link to notebook <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/ball_reactor.py>`_
+
+
+ball_reactor_minimal.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+`Link to notebook <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/ball_reactor_minimal.py>`_
 
 
-ball_reactor_minimal
-^^^^^^^^^^^^^^^^^^^^
+ball_reactor_source_plot.ipynb 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: examples.example_neutronics_simulations.ball_reactor_minimal
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_neutronics_simulations/ball_reactor_source_plot.ipynb>`_
 
-`Link to script <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/ball_reactor_minimal.py>`_
 
+center_column_study_reactor.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-center_column_study_reactor_minimal
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+`Link to notebook <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/center_column_study_reactor.ipynb>`_
 
-.. automodule:: examples.example_neutronics_simulations.center_column_study_reactor_minimal
-   :members:
-   :show-inheritance:
 
-`Link to script <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/center_column_study_reactor_minimal.py>`_
+center_column_study_reactor_minimal.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-ball_reactor
-^^^^^^^^^^^^
+`Link to notebook <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/center_column_study_reactor_minimal.ipynb>`_
 
-.. automodule:: examples.example_neutronics_simulations.ball_reactor
-   :members:
-   :show-inheritance:
 
-`Link to script <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/ball_reactor.py>`_
+OpenMC logo simulation
+^^^^^^^^^^^^^^^^^^^^^^
+
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_neutronics_simulations/openmc_logo_example.ipynb>`_
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/40VARwD44FA" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
-center_column_study_reactor
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: examples.example_neutronics_simulations.center_column_study_reactor
-   :members:
-   :show-inheritance:
+text_example.ipynb 
+^^^^^^^^^^^^^^^^^^
 
-`Link to script <https://github.com/ukaea/paramak/blob/main/examples/example_neutronics_simulations/center_column_study_reactor.py>`_
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_neutronics_simulations/text_example.ipynb>`_

docs/source/example_parametric_components.rst

@@ -1,70 +1,78 @@
 Examples - Parametric Components
 ================================
 
-make_all_parametric_components.py
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+make_components_blankets.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. image:: https://user-images.githubusercontent.com/8583900/98823600-387eea00-242a-11eb-9fe3-df65aaa3dd21.png
-   :width: 713
-   :align: center
-
-.. automodule:: examples.example_parametric_components.make_all_parametric_components
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_components_blankets.ipynb>`_
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_all_parametric_components.py>`_
 
-make_plasmas.py
-^^^^^^^^^^^^^^^
+make_components_center_column.ipynb 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. image:: https://user-images.githubusercontent.com/8583900/93624384-2e1b1380-f9d8-11ea-99d1-9bf9e4e5b838.png
-   :width: 1050
-   :height: 700
-   :align: center
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_components_center_column.ipynb>`_
 
-.. automodule:: examples.example_parametric_components.make_plasmas
-   :members:
-   :show-inheritance:
+make_components_magnets.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_plasmas.py>`_
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_components_center_column.ipynb>`_
 
-make_demo_style_blankets.py
+make_components_other.ipynb
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_components_other.ipynb>`_
+
+
+make_demo_style_blankets.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 .. image:: https://user-images.githubusercontent.com/8583900/93619812-02e0f600-f9d1-11ea-903c-913c8bcb0f1b.png
    :width: 1050
    :height: 350
    :align: center
 
-.. automodule:: examples.example_parametric_components.make_demo_style_blankets
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_demo_style_blankets.ipynb>`_
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_demo_style_blankets.py>`_
 
-make_firstwall_for_neutron_wall_loading.py
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+make_firstwall_for_neutron_wall_loading.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. image:: https://user-images.githubusercontent.com/8583900/93807581-bc92cd80-fc42-11ea-8522-7fe14287b3c4.png
    :width: 437
    :height: 807
    :align: center
 
-.. automodule:: examples.example_parametric_components.make_firstwall_for_neutron_wall_loading
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_firstwall_for_neutron_wall_loading.ipynb>`_
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_firstwall_for_neutron_wall_loading.py>`_
 
-make_magnet_set
-^^^^^^^^^^^^^^^
+make_magnet_set.ipynb
+^^^^^^^^^^^^^^^^^^^^^
 
 .. image:: https://user-images.githubusercontent.com/8583900/99276201-5088ac00-2824-11eb-9927-a7ea1094b1e5.png
    :width: 500
    :align: center
 
-.. automodule:: examples.example_parametric_components.make_magnet_set
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_magnet_set.ipynb>`_
+
+
+make_plasmas.ipynb
+^^^^^^^^^^^^^^^^^^
+
+.. image:: https://user-images.githubusercontent.com/8583900/93624384-2e1b1380-f9d8-11ea-99d1-9bf9e4e5b838.png
+   :width: 1050
+   :height: 700
+   :align: center
+
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_plasmas.ipynb>`_
+
+
+make_vacuum_vessel_with_ports.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_vacuum_vessel_with_ports.ipynb>`_
+
+
+make_varible_offset_firstwall.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_magnet_set.py>`_
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_components/make_varible_offset_firstwall.ipynb>`_

docs/source/example_parametric_reactors.rst

@@ -1,72 +1,61 @@
 Examples - Parametric Reactors
 ==============================
 
-ball_reactor.py
-^^^^^^^^^^^^^^^
+ball_reactor.ipynb
+^^^^^^^^^^^^^^^^^^
 
-.. automodule:: examples.example_parametric_reactors.ball_reactor
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/ball_reactor.ipynb>`_
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/ball_reactor.py>`_
 
-ball_reactor_single_null.py
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ball_reactor_single_null.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: examples.example_parametric_reactors.ball_reactor_single_null
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/ball_reactor_single_null.ipynb>`_
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/ball_reactor_single_null.py>`_
 
-segmented_blanket_ball_reactor.py
+center_column_study_reactor.ipynb
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: examples.example_parametric_reactors.segmented_blanket_ball_reactor
-   :members:
-   :show-inheritance:
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/center_column_study_reactor.ipynb>`_
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/segmented_blanket_ball_reactor.py>`_
+eu_demo_from_2015_paper.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-submersion_reactor.py
-^^^^^^^^^^^^^^^^^^^^^
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/eu_demo_from_2015_paper.ipynb>`_
 
-.. automodule:: examples.example_parametric_reactors.submersion_reactor
-   :members:
-   :show-inheritance:
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/submersion_reactor.py>`_
+make_animation.ipynb
+^^^^^^^^^^^^^^^^^^^^
 
-submersion_reactor_single_null.py
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: examples.example_parametric_reactors.submersion_reactor_single_null
-   :members:
-   :show-inheritance:
+|animation1| |animation2|
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/submersion_reactor_single_null.py>`_
+.. |animation1| image:: https://user-images.githubusercontent.com/8583900/107040396-155ca000-67b7-11eb-8b99-4aa9bf8a8655.gif
+   :width: 300
+.. |animation2| image:: https://user-images.githubusercontent.com/8583900/107030664-e2131480-67a8-11eb-84bb-59656e9e7722.gif
+   :width: 300
 
-center_column_study_reactor.py
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/submersion_reactor.ipynb>`_
 
-.. automodule:: examples.example_parametric_reactors.center_column_study_reactor
-   :members:
-   :show-inheritance:
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/center_column_study_reactor.py>`_
+segmented_blanket_ball_reactor.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-make_animation.py
-^^^^^^^^^^^^^^^^^
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/segmented_blanket_ball_reactor.ipynb>`_
 
-.. automodule:: examples.example_parametric_reactors.make_animation
-   :members:
-   :show-inheritance:
+sparc_from_2020_paper.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-|animation1| |animation2|
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/sparc_from_2020_paper.ipynb>`_
 
-.. |animation1| image:: https://user-images.githubusercontent.com/8583900/107040396-155ca000-67b7-11eb-8b99-4aa9bf8a8655.gif
-   :width: 300
-.. |animation2| image:: https://user-images.githubusercontent.com/8583900/107030664-e2131480-67a8-11eb-84bb-59656e9e7722.gif
-   :width: 300
 
-`Link to script <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/make_animation.py>`_
+submersion_reactor.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/submersion_reactor.ipynb>`_
+
+
+submersion_reactor_single_null.ipynb
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+`Link to notebook <https://github.com/ukaea/paramak/blob/develop/examples/example_parametric_reactors/submersion_reactor_single_null.ipynb>`_