hpc-maths · gouarin · Nov 6, 2023 · Nov 6, 2023 · Nov 6, 2023 · Nov 6, 2023
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -173,13 +173,13 @@ jobs:
         run: |
           export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"
           cd build
-          ./test/test_samurai_lib
+          ./tests/test_samurai_lib
 
       - name: Test with pytest
         shell: bash -l {0}
         run: |
           export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"
-          cd test
+          cd tests
           pytest -v -s --h5diff
 
   macos-mamba:
@@ -224,5 +224,5 @@ jobs:
       - name: Run tests
         shell: bash -l {0}
         run: |
-          ./build/test/test_samurai_lib
-          cd test; pytest --h5diff
+          ./build/tests/test_samurai_lib
+          cd tests; pytest --h5diff
diff --git a/.github/workflows/schedule.yml b/.github/workflows/schedule.yml
@@ -156,13 +156,13 @@ jobs:
       - name: Unix test
         if: runner.os != 'Windows'
         run: |
-          ./build/test/Release/test_samurai_lib
-          cd test; pytest --h5diff
+          ./build/tests/Release/test_samurai_lib
+          cd tests; pytest --h5diff
       - name: Windows test
         if: runner.os == 'Windows'
         run: |
-          .\build\test\Release\test_samurai_lib
-          # cd test; pytest -s --h5diff
+          .\build\tests\Release\test_samurai_lib
+          # cd tests; pytest -s --h5diff
 
   #
   # Check vcpkg build
@@ -258,13 +258,13 @@ jobs:
       - name: Unix test
         if: runner.os != 'Windows'
         run: |
-          ./build/test/Release/test_samurai_lib
-          cd test; pytest --h5diff
+          ./build/tests/Release/test_samurai_lib
+          cd tests; pytest --h5diff
       - name: Windows test
         if: runner.os == 'Windows'
         run: |
-          .\build\test\Release\test_samurai_lib
-          cd test; pytest -s --h5diff
+          .\build\tests\Release\test_samurai_lib
+          cd tests; pytest -s --h5diff
 
   #
   # Check windows build using mamba
@@ -308,5 +308,5 @@ jobs:
       - name: Windows test
         shell: bash -l {0}
         run: |
-          ./build/test/Release/test_samurai_lib
-          cd test; pytest -s --h5diff
+          ./build/tests/Release/test_samurai_lib
+          cd tests; pytest -s --h5diff
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-      - id: check-added-large-files
+      # - id: check-added-large-files
       - id: check-case-conflict
       - id: end-of-file-fixer
       - id: trailing-whitespace

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,2 +1,12 @@
+version: 2
+
+build:
+    os: "ubuntu-20.04"
+    tools:
+        python: "mambaforge-22.9"
+
+sphinx:
+    configuration: docs/source/conf.py
+
 conda:
-    file: doc/environment.yml
+    environment: docs/environment.yml
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -128,7 +128,7 @@ if(BUILD_BENCHMARKS)
 endif()
 
 if(BUILD_TESTS)
-  add_subdirectory(test)
+  add_subdirectory(tests)
 endif()
 
 if(BUILD_DEMOS)

diff --git a/doc/CODE_OF_CONDUCT.md → docs/CODE_OF_CONDUCT.md b/doc/CODE_OF_CONDUCT.md → docs/CODE_OF_CONDUCT.md
diff --git a/doc/CONTRIBUTING.md → docs/CONTRIBUTING.md b/doc/CONTRIBUTING.md → docs/CONTRIBUTING.md
diff --git a/doc/Doxyfile → docs/Doxyfile b/doc/Doxyfile → docs/Doxyfile
diff --git a/doc/Makefile → docs/Makefile b/doc/Makefile → docs/Makefile
diff --git a/doc/environment.yml → docs/environment.yml b/doc/environment.yml → docs/environment.yml
@@ -5,3 +5,4 @@ channels:
 
 dependencies:
   - breathe
+  - sphinx_rtd_theme
diff --git a/doc/make.bat → docs/make.bat b/doc/make.bat → docs/make.bat
diff --git a/doc/source/LBM/figures/D1Q2.pdf → docs/source/LBM/figures/D1Q2.pdf b/doc/source/LBM/figures/D1Q2.pdf → docs/source/LBM/figures/D1Q2.pdf
diff --git a/doc/source/LBM/figures/D1Q2.png → docs/source/LBM/figures/D1Q2.png b/doc/source/LBM/figures/D1Q2.png → docs/source/LBM/figures/D1Q2.png
diff --git a/doc/source/LBM/figures/D1Q222.pdf → docs/source/LBM/figures/D1Q222.pdf b/doc/source/LBM/figures/D1Q222.pdf → docs/source/LBM/figures/D1Q222.pdf
diff --git a/doc/source/LBM/figures/D1Q222.png → docs/source/LBM/figures/D1Q222.png b/doc/source/LBM/figures/D1Q222.png → docs/source/LBM/figures/D1Q222.png
diff --git a/doc/source/LBM/figures/D1Q5.pdf → docs/source/LBM/figures/D1Q5.pdf b/doc/source/LBM/figures/D1Q5.pdf → docs/source/LBM/figures/D1Q5.pdf
diff --git a/doc/source/LBM/figures/D1Q5.png → docs/source/LBM/figures/D1Q5.png b/doc/source/LBM/figures/D1Q5.png → docs/source/LBM/figures/D1Q5.png
diff --git a/doc/source/LBM/figures/D2Q4444.png → docs/source/LBM/figures/D2Q4444.png b/doc/source/LBM/figures/D2Q4444.png → docs/source/LBM/figures/D2Q4444.png
diff --git a/...e/LBM/figures/D2Q5444_Rayleigh_Taylor.png → ...e/LBM/figures/D2Q5444_Rayleigh_Taylor.png b/...e/LBM/figures/D2Q5444_Rayleigh_Taylor.png → ...e/LBM/figures/D2Q5444_Rayleigh_Taylor.png
diff --git a/...gures/D2Q5444_Rayleigh_Taylor_cropped.png → ...gures/D2Q5444_Rayleigh_Taylor_cropped.png b/...gures/D2Q5444_Rayleigh_Taylor_cropped.png → ...gures/D2Q5444_Rayleigh_Taylor_cropped.png
diff --git a/doc/source/LBM/figures/D2Q9.png → docs/source/LBM/figures/D2Q9.png b/doc/source/LBM/figures/D2Q9.png → docs/source/LBM/figures/D2Q9.png
diff --git a/doc/source/LBM/test_cases.rst → docs/source/LBM/test_cases.rst b/doc/source/LBM/test_cases.rst → docs/source/LBM/test_cases.rst
diff --git a/doc/source/_static/css/custom.css → docs/source/_static/css/custom.css b/doc/source/_static/css/custom.css → docs/source/_static/css/custom.css
diff --git a/doc/source/api/algorithm.rst → docs/source/api/algorithm.rst b/doc/source/api/algorithm.rst → docs/source/api/algorithm.rst
diff --git a/doc/source/api/box.rst → docs/source/api/box.rst b/doc/source/api/box.rst → docs/source/api/box.rst
diff --git a/doc/source/api/cell.rst → docs/source/api/cell.rst b/doc/source/api/cell.rst → docs/source/api/cell.rst
diff --git a/doc/source/api/interval.rst → docs/source/api/interval.rst b/doc/source/api/interval.rst → docs/source/api/interval.rst
diff --git a/doc/source/api/subset.rst → docs/source/api/subset.rst b/doc/source/api/subset.rst → docs/source/api/subset.rst
diff --git a/doc/source/conf.py → docs/source/conf.py b/doc/source/conf.py → docs/source/conf.py
diff --git a/doc/source/index.rst → docs/source/index.rst b/doc/source/index.rst → docs/source/index.rst
@@ -1,8 +1,8 @@
 .. _topics-index:
 
-===============================
-Samurai |version| documentation
-===============================
+========================
+ |project| documentation
+========================
 
 The main goal of |project| is to provide a new data structure based on intervals and algebra of sets to handle efficiently adaptive mesh refinement methods based on a cartesian grid. Such an approach has to be versatile enough to handle both AMR and multi-resolution methods.
 
@@ -20,25 +20,10 @@ In order to improve the efficiency of the tree / space-filling curve, the propos
 
 SAMURAI: Structured Adaptive mesh and MUlti-Resolution based on Algebra of Intervals.
 
-.. toctree::
-   :caption: Table of contents
-   :hidden:
-
-Test cases
-========
-.. toctree::
-   :caption: Test cases
-   :hidden:
-
-   LBM/test_cases
-
-
-Tutorial
-========
 
 .. toctree::
    :caption: Tutorial
-   :hidden:
+   :maxdepth: 1
 
    tutorial/interval
    tutorial/field
@@ -60,23 +45,23 @@ Tutorial
 
 .. :doc:`tutorial/1d_burgers_amr`
 
-Reference
-=========
+.. toctree::
+   :caption: Test cases
+   :maxdepth: 1
+
+   LBM/test_cases
 
 .. toctree::
    :caption: Reference
-   :hidden:
+   :maxdepth: 2
 
    reference/subset
 
 .. :doc:`reference/subset`
 
-API reference
-=============
-
 .. toctree::
    :caption: API reference
-   :hidden:
+   :maxdepth: 2
 
    api/algorithm
    api/interval

diff --git a/doc/source/logo/dark_logo.png → docs/source/logo/dark_logo.png b/doc/source/logo/dark_logo.png → docs/source/logo/dark_logo.png
diff --git a/doc/source/logo/light_logo.png → docs/source/logo/light_logo.png b/doc/source/logo/light_logo.png → docs/source/logo/light_logo.png
diff --git a/doc/source/logo/logo.svg → docs/source/logo/logo.svg b/doc/source/logo/logo.svg → docs/source/logo/logo.svg
diff --git a/doc/source/logo/samurai_logo.png → docs/source/logo/samurai_logo.png b/doc/source/logo/samurai_logo.png → docs/source/logo/samurai_logo.png
diff --git a/doc/source/philosophy.rst → docs/source/philosophy.rst b/doc/source/philosophy.rst → docs/source/philosophy.rst
diff --git a/doc/source/reference/figures/interval.svg → docs/source/reference/figures/interval.svg b/doc/source/reference/figures/interval.svg → docs/source/reference/figures/interval.svg
diff --git a/...reference/figures/interval_example_1D.jpg → ...reference/figures/interval_example_1D.jpg b/...reference/figures/interval_example_1D.jpg → ...reference/figures/interval_example_1D.jpg
diff --git a/...reference/figures/interval_example_1D.svg → ...reference/figures/interval_example_1D.svg b/...reference/figures/interval_example_1D.svg → ...reference/figures/interval_example_1D.svg
diff --git a/...nce/figures/interval_example_1D_field.svg → ...nce/figures/interval_example_1D_field.svg b/...nce/figures/interval_example_1D_field.svg → ...nce/figures/interval_example_1D_field.svg
diff --git a/...source/reference/figures/subset_1d.drawio → ...source/reference/figures/subset_1d.drawio b/...source/reference/figures/subset_1d.drawio → ...source/reference/figures/subset_1d.drawio
diff --git a/doc/source/reference/figures/subset_1d.png → docs/source/reference/figures/subset_1d.png b/doc/source/reference/figures/subset_1d.png → docs/source/reference/figures/subset_1d.png
diff --git a/...urce/reference/figures/subset_1d_proj.png → ...urce/reference/figures/subset_1d_proj.png b/...urce/reference/figures/subset_1d_proj.png → ...urce/reference/figures/subset_1d_proj.png
diff --git a/...source/reference/figures/subset_algorithm → ...source/reference/figures/subset_algorithm b/...source/reference/figures/subset_algorithm → ...source/reference/figures/subset_algorithm
diff --git a/...ference/figures/subset_algorithm-init.png → ...ference/figures/subset_algorithm-init.png b/...ference/figures/subset_algorithm-init.png → ...ference/figures/subset_algorithm-init.png
diff --git a/...erence/figures/subset_algorithm-step1.png → ...erence/figures/subset_algorithm-step1.png b/...erence/figures/subset_algorithm-step1.png → ...erence/figures/subset_algorithm-step1.png
diff --git a/...erence/figures/subset_algorithm-step2.png → ...erence/figures/subset_algorithm-step2.png b/...erence/figures/subset_algorithm-step2.png → ...erence/figures/subset_algorithm-step2.png
diff --git a/...erence/figures/subset_algorithm-step3.png → ...erence/figures/subset_algorithm-step3.png b/...erence/figures/subset_algorithm-step3.png → ...erence/figures/subset_algorithm-step3.png
diff --git a/...erence/figures/subset_algorithm-step4.png → ...erence/figures/subset_algorithm-step4.png b/...erence/figures/subset_algorithm-step4.png → ...erence/figures/subset_algorithm-step4.png
diff --git a/...rce/reference/figures/subset_level.drawio → ...rce/reference/figures/subset_level.drawio b/...rce/reference/figures/subset_level.drawio → ...rce/reference/figures/subset_level.drawio
diff --git a/...source/reference/figures/subset_level.png → ...source/reference/figures/subset_level.png b/...source/reference/figures/subset_level.png → ...source/reference/figures/subset_level.png
diff --git a/doc/source/reference/snippet/subset_1d.cpp → docs/source/reference/snippet/subset_1d.cpp b/doc/source/reference/snippet/subset_1d.cpp → docs/source/reference/snippet/subset_1d.cpp
diff --git a/...ce/reference/snippet/subset_1d_output.txt → ...ce/reference/snippet/subset_1d_output.txt b/...ce/reference/snippet/subset_1d_output.txt → ...ce/reference/snippet/subset_1d_output.txt
diff --git a/doc/source/reference/subset.rst → docs/source/reference/subset.rst b/doc/source/reference/subset.rst → docs/source/reference/subset.rst
diff --git a/doc/source/tutorial/1d_burgers_amr.rst → docs/source/tutorial/1d_burgers_amr.rst b/doc/source/tutorial/1d_burgers_amr.rst → docs/source/tutorial/1d_burgers_amr.rst
diff --git a/doc/source/tutorial/algorithm.rst → docs/source/tutorial/algorithm.rst b/doc/source/tutorial/algorithm.rst → docs/source/tutorial/algorithm.rst
diff --git a/doc/source/tutorial/field.rst → docs/source/tutorial/field.rst b/doc/source/tutorial/field.rst → docs/source/tutorial/field.rst
diff --git a/doc/source/tutorial/figures/2D_mesh.png → docs/source/tutorial/figures/2D_mesh.png b/doc/source/tutorial/figures/2D_mesh.png → docs/source/tutorial/figures/2D_mesh.png
diff --git a/doc/source/tutorial/figures/2D_mesh_box.png → docs/source/tutorial/figures/2D_mesh_box.png b/doc/source/tutorial/figures/2D_mesh_box.png → docs/source/tutorial/figures/2D_mesh_box.png
diff --git a/...ce/tutorial/figures/2D_mesh_numbering.png → ...ce/tutorial/figures/2D_mesh_numbering.png b/...ce/tutorial/figures/2D_mesh_numbering.png → ...ce/tutorial/figures/2D_mesh_numbering.png
diff --git a/...orial/figures/graduation_case_1_after.png → ...orial/figures/graduation_case_1_after.png b/...orial/figures/graduation_case_1_after.png → ...orial/figures/graduation_case_1_after.png
diff --git a/...rial/figures/graduation_case_1_before.png → ...rial/figures/graduation_case_1_before.png b/...rial/figures/graduation_case_1_before.png → ...rial/figures/graduation_case_1_before.png
diff --git a/...orial/figures/graduation_case_2_after.png → ...orial/figures/graduation_case_2_after.png b/...orial/figures/graduation_case_2_after.png → ...orial/figures/graduation_case_2_after.png
diff --git a/...res/graduation_case_2_after_graduated.png → ...res/graduation_case_2_after_graduated.png b/...res/graduation_case_2_after_graduated.png → ...res/graduation_case_2_after_graduated.png
diff --git a/...rial/figures/graduation_case_2_before.png → ...rial/figures/graduation_case_2_before.png b/...rial/figures/graduation_case_2_before.png → ...rial/figures/graduation_case_2_before.png
diff --git a/...res/graduation_case_3_with_graduation.png → ...res/graduation_case_3_with_graduation.png b/...res/graduation_case_3_with_graduation.png → ...res/graduation_case_3_with_graduation.png
diff --git a/.../graduation_case_3_without_graduation.png → .../graduation_case_3_without_graduation.png b/.../graduation_case_3_without_graduation.png → .../graduation_case_3_without_graduation.png
diff --git a/doc/source/tutorial/figures/interval-2.png → docs/source/tutorial/figures/interval-2.png b/doc/source/tutorial/figures/interval-2.png → docs/source/tutorial/figures/interval-2.png
diff --git a/doc/source/tutorial/figures/interval-3.png → docs/source/tutorial/figures/interval-3.png b/doc/source/tutorial/figures/interval-3.png → docs/source/tutorial/figures/interval-3.png
diff --git a/doc/source/tutorial/figures/interval.drawio → docs/source/tutorial/figures/interval.drawio b/doc/source/tutorial/figures/interval.drawio → docs/source/tutorial/figures/interval.drawio
diff --git a/doc/source/tutorial/figures/interval.png → docs/source/tutorial/figures/interval.png b/doc/source/tutorial/figures/interval.png → docs/source/tutorial/figures/interval.png
diff --git a/...torial/figures/interval_example_1D.drawio → ...torial/figures/interval_example_1D.drawio b/...torial/figures/interval_example_1D.drawio → ...torial/figures/interval_example_1D.drawio
diff --git a/.../tutorial/figures/interval_example_1D.png → .../tutorial/figures/interval_example_1D.png b/.../tutorial/figures/interval_example_1D.png → .../tutorial/figures/interval_example_1D.png
diff --git a/.../figures/interval_example_1D_field.drawio → .../figures/interval_example_1D_field.drawio b/.../figures/interval_example_1D_field.drawio → .../figures/interval_example_1D_field.drawio
diff --git a/...ial/figures/interval_example_1D_field.png → ...ial/figures/interval_example_1D_field.png b/...ial/figures/interval_example_1D_field.png → ...ial/figures/interval_example_1D_field.png
diff --git a/doc/source/tutorial/figures/level_set.png → docs/source/tutorial/figures/level_set.png b/doc/source/tutorial/figures/level_set.png → docs/source/tutorial/figures/level_set.png
diff --git a/...l/figures/segments-resolution-overlap.png → ...l/figures/segments-resolution-overlap.png b/...l/figures/segments-resolution-overlap.png → ...l/figures/segments-resolution-overlap.png
diff --git a/.../tutorial/figures/segments-resolution.png → .../tutorial/figures/segments-resolution.png b/.../tutorial/figures/segments-resolution.png → .../tutorial/figures/segments-resolution.png
diff --git a/doc/source/tutorial/figures/segments.drawio → docs/source/tutorial/figures/segments.drawio b/doc/source/tutorial/figures/segments.drawio → docs/source/tutorial/figures/segments.drawio
diff --git a/doc/source/tutorial/figures/segments.png → docs/source/tutorial/figures/segments.png b/doc/source/tutorial/figures/segments.png → docs/source/tutorial/figures/segments.png
diff --git a/doc/source/tutorial/figures/subset_op.drawio → .../source/tutorial/figures/subset_op.drawio b/doc/source/tutorial/figures/subset_op.drawio → .../source/tutorial/figures/subset_op.drawio
diff --git a/doc/source/tutorial/figures/subset_op.png → docs/source/tutorial/figures/subset_op.png b/doc/source/tutorial/figures/subset_op.png → docs/source/tutorial/figures/subset_op.png
diff --git a/...ource/tutorial/figures/subset_op_proj.png → ...ource/tutorial/figures/subset_op_proj.png b/...ource/tutorial/figures/subset_op_proj.png → ...ource/tutorial/figures/subset_op_proj.png
diff --git a/doc/source/tutorial/graduation.rst → docs/source/tutorial/graduation.rst b/doc/source/tutorial/graduation.rst → docs/source/tutorial/graduation.rst
diff --git a/doc/source/tutorial/graduation_case_1.rst → docs/source/tutorial/graduation_case_1.rst b/doc/source/tutorial/graduation_case_1.rst → docs/source/tutorial/graduation_case_1.rst
diff --git a/doc/source/tutorial/graduation_case_2.rst → docs/source/tutorial/graduation_case_2.rst b/doc/source/tutorial/graduation_case_2.rst → docs/source/tutorial/graduation_case_2.rst
diff --git a/doc/source/tutorial/graduation_case_3.rst → docs/source/tutorial/graduation_case_3.rst b/doc/source/tutorial/graduation_case_3.rst → docs/source/tutorial/graduation_case_3.rst
diff --git a/doc/source/tutorial/interval.rst → docs/source/tutorial/interval.rst b/doc/source/tutorial/interval.rst → docs/source/tutorial/interval.rst
diff --git a/doc/source/tutorial/level_set.rst → docs/source/tutorial/level_set.rst b/doc/source/tutorial/level_set.rst → docs/source/tutorial/level_set.rst
diff --git a/doc/source/tutorial/operator_on_subset.rst → docs/source/tutorial/operator_on_subset.rst b/doc/source/tutorial/operator_on_subset.rst → docs/source/tutorial/operator_on_subset.rst
diff --git a/doc/source/tutorial/snippet/2d_mesh_box.cpp → docs/source/tutorial/snippet/2d_mesh_box.cpp b/doc/source/tutorial/snippet/2d_mesh_box.cpp → docs/source/tutorial/snippet/2d_mesh_box.cpp
diff --git a/...e/tutorial/snippet/2d_mesh_box_output.txt → ...e/tutorial/snippet/2d_mesh_box_output.txt b/...e/tutorial/snippet/2d_mesh_box_output.txt → ...e/tutorial/snippet/2d_mesh_box_output.txt
diff --git a/...torial/snippet/2d_mesh_representation.cpp → ...torial/snippet/2d_mesh_representation.cpp b/...torial/snippet/2d_mesh_representation.cpp → ...torial/snippet/2d_mesh_representation.cpp
diff --git a/...snippet/2d_mesh_representation_output.txt → ...snippet/2d_mesh_representation_output.txt b/...snippet/2d_mesh_representation_output.txt → ...snippet/2d_mesh_representation_output.txt
diff --git a/doc/source/tutorial/snippet/interval.cpp → docs/source/tutorial/snippet/interval.cpp b/doc/source/tutorial/snippet/interval.cpp → docs/source/tutorial/snippet/interval.cpp
diff --git a/...urce/tutorial/snippet/interval_output.txt → ...urce/tutorial/snippet/interval_output.txt b/...urce/tutorial/snippet/interval_output.txt → ...urce/tutorial/snippet/interval_output.txt
diff --git a/test/CMakeLists.txt → tests/CMakeLists.txt b/test/CMakeLists.txt → tests/CMakeLists.txt
diff --git a/test/conftest.py → tests/conftest.py b/test/conftest.py → tests/conftest.py
diff --git a/test/copyGTest.cmake.in → tests/copyGTest.cmake.in b/test/copyGTest.cmake.in → tests/copyGTest.cmake.in
diff --git a/test/downloadGTest.cmake.in → tests/downloadGTest.cmake.in b/test/downloadGTest.cmake.in → tests/downloadGTest.cmake.in
diff --git a/test/main.cpp → tests/main.cpp b/test/main.cpp → tests/main.cpp
diff --git a/test/pytest.ini → tests/pytest.ini b/test/pytest.ini → tests/pytest.ini
diff --git a/...volume/test_finite_volume_demo_burgers.h5 → ...volume/test_finite_volume_demo_burgers.h5 b/...volume/test_finite_volume_demo_burgers.h5 → ...volume/test_finite_volume_demo_burgers.h5
diff --git a/...me_demo_finite-volume-advection-1d-0.1.h5 → ...me_demo_finite-volume-advection-1d-0.1.h5 b/...me_demo_finite-volume-advection-1d-0.1.h5 → ...me_demo_finite-volume-advection-1d-0.1.h5
diff --git a/...mo_finite-volume-advection-1d-0.1_init.h5 → ...mo_finite-volume-advection-1d-0.1_init.h5 b/...mo_finite-volume-advection-1d-0.1_init.h5 → ...mo_finite-volume-advection-1d-0.1_init.h5
diff --git a/...e_demo_finite-volume-advection-2d-0.01.h5 → ...e_demo_finite-volume-advection-2d-0.01.h5 b/...e_demo_finite-volume-advection-2d-0.01.h5 → ...e_demo_finite-volume-advection-2d-0.01.h5
diff --git a/...o_finite-volume-advection-2d-0.01_init.h5 → ...o_finite-volume-advection-2d-0.01_init.h5 b/...o_finite-volume-advection-2d-0.01_init.h5 → ...o_finite-volume-advection-2d-0.01_init.h5
diff --git a/...e_demo_finite-volume-amr-burgers-hat-1.h5 → ...e_demo_finite-volume-amr-burgers-hat-1.h5 b/...e_demo_finite-volume-amr-burgers-hat-1.h5 → ...e_demo_finite-volume-amr-burgers-hat-1.h5
diff --git a/...olume_demo_finite-volume-level-set-0.1.h5 → ...olume_demo_finite-volume-level-set-0.1.h5 b/...olume_demo_finite-volume-level-set-0.1.h5 → ...olume_demo_finite-volume-level-set-0.1.h5
diff --git a/...nite-volume-level-set-from-scratch-0.1.h5 → ...nite-volume-level-set-from-scratch-0.1.h5 b/...nite-volume-level-set-from-scratch-0.1.h5 → ...nite-volume-level-set-from-scratch-0.1.h5
diff --git a/..._finite-volume-scalar-burgers-2d-0.001.h5 → ..._finite-volume-scalar-burgers-2d-0.001.h5 b/..._finite-volume-scalar-burgers-2d-0.001.h5 → ..._finite-volume-scalar-burgers-2d-0.001.h5
diff --git a/...te-volume-scalar-burgers-2d-0.001_init.h5 → ...te-volume-scalar-burgers-2d-0.001_init.h5 b/...te-volume-scalar-burgers-2d-0.001_init.h5 → ...te-volume-scalar-burgers-2d-0.001_init.h5
diff --git a/.../test_finite_volume_demo_heat_explicit.h5 → .../test_finite_volume_demo_heat_explicit.h5 b/.../test_finite_volume_demo_heat_explicit.h5 → .../test_finite_volume_demo_heat_explicit.h5
diff --git a/...olume_demo_heat_heterogeneous_explicit.h5 → ...olume_demo_heat_heterogeneous_explicit.h5 b/...olume_demo_heat_heterogeneous_explicit.h5 → ...olume_demo_heat_heterogeneous_explicit.h5
diff --git a/...olume_demo_heat_heterogeneous_implicit.h5 → ...olume_demo_heat_heterogeneous_implicit.h5 b/...olume_demo_heat_heterogeneous_implicit.h5 → ...olume_demo_heat_heterogeneous_implicit.h5
diff --git a/.../test_finite_volume_demo_heat_implicit.h5 → .../test_finite_volume_demo_heat_implicit.h5 b/.../test_finite_volume_demo_heat_implicit.h5 → .../test_finite_volume_demo_heat_implicit.h5
diff --git a/...inite_volume_demo_stokes_nonstationary.h5 → ...inite_volume_demo_stokes_nonstationary.h5 b/...inite_volume_demo_stokes_nonstationary.h5 → ...inite_volume_demo_stokes_nonstationary.h5
diff --git a/...t_finite_volume_demo_stokes_stationary.h5 → ...t_finite_volume_demo_stokes_stationary.h5 b/...t_finite_volume_demo_stokes_stationary.h5 → ...t_finite_volume_demo_stokes_stationary.h5
diff --git a/test/reference/p4est/test_simple_2d.h5 → tests/reference/p4est/test_simple_2d.h5 b/test/reference/p4est/test_simple_2d.h5 → tests/reference/p4est/test_simple_2d.h5
diff --git a/test/reference/pablo/test_2d_bubbles.h5 → tests/reference/pablo/test_2d_bubbles.h5 b/test/reference/pablo/test_2d_bubbles.h5 → tests/reference/pablo/test_2d_bubbles.h5
diff --git a/test/reference/tutorial/test_2d_mesh.h5 → tests/reference/tutorial/test_2d_mesh.h5 b/test/reference/tutorial/test_2d_mesh.h5 → tests/reference/tutorial/test_2d_mesh.h5
diff --git a/test/reference/tutorial/test_burgers_0.h5 → tests/reference/tutorial/test_burgers_0.h5 b/test/reference/tutorial/test_burgers_0.h5 → tests/reference/tutorial/test_burgers_0.h5
diff --git a/test/reference/tutorial/test_burgers_1.h5 → tests/reference/tutorial/test_burgers_1.h5 b/test/reference/tutorial/test_burgers_1.h5 → tests/reference/tutorial/test_burgers_1.h5
diff --git a/test/reference/tutorial/test_burgers_2.h5 → tests/reference/tutorial/test_burgers_2.h5 b/test/reference/tutorial/test_burgers_2.h5 → tests/reference/tutorial/test_burgers_2.h5
diff --git a/test/reference/tutorial/test_burgers_3.h5 → tests/reference/tutorial/test_burgers_3.h5 b/test/reference/tutorial/test_burgers_3.h5 → tests/reference/tutorial/test_burgers_3.h5
diff --git a/test/reference/tutorial/test_burgers_4.h5 → tests/reference/tutorial/test_burgers_4.h5 b/test/reference/tutorial/test_burgers_4.h5 → tests/reference/tutorial/test_burgers_4.h5
diff --git a/...ce/tutorial/test_burgers_4_criterion-0.h5 → ...ce/tutorial/test_burgers_4_criterion-0.h5 b/...ce/tutorial/test_burgers_4_criterion-0.h5 → ...ce/tutorial/test_burgers_4_criterion-0.h5
diff --git a/...ce/tutorial/test_burgers_4_criterion-1.h5 → ...ce/tutorial/test_burgers_4_criterion-1.h5 b/...ce/tutorial/test_burgers_4_criterion-1.h5 → ...ce/tutorial/test_burgers_4_criterion-1.h5
diff --git a/...ce/tutorial/test_burgers_4_criterion-2.h5 → ...ce/tutorial/test_burgers_4_criterion-2.h5 b/...ce/tutorial/test_burgers_4_criterion-2.h5 → ...ce/tutorial/test_burgers_4_criterion-2.h5
diff --git a/...ce/tutorial/test_burgers_4_criterion-3.h5 → ...ce/tutorial/test_burgers_4_criterion-3.h5 b/...ce/tutorial/test_burgers_4_criterion-3.h5 → ...ce/tutorial/test_burgers_4_criterion-3.h5
diff --git a/...ce/tutorial/test_burgers_4_criterion-4.h5 → ...ce/tutorial/test_burgers_4_criterion-4.h5 b/...ce/tutorial/test_burgers_4_criterion-4.h5 → ...ce/tutorial/test_burgers_4_criterion-4.h5
diff --git a/...ce/tutorial/test_burgers_4_criterion-5.h5 → ...ce/tutorial/test_burgers_4_criterion-5.h5 b/...ce/tutorial/test_burgers_4_criterion-5.h5 → ...ce/tutorial/test_burgers_4_criterion-5.h5
diff --git a/...ce/tutorial/test_burgers_4_criterion-6.h5 → ...ce/tutorial/test_burgers_4_criterion-6.h5 b/...ce/tutorial/test_burgers_4_criterion-6.h5 → ...ce/tutorial/test_burgers_4_criterion-6.h5
diff --git a/test/reference/tutorial/test_burgers_5.h5 → tests/reference/tutorial/test_burgers_5.h5 b/test/reference/tutorial/test_burgers_5.h5 → tests/reference/tutorial/test_burgers_5.h5
diff --git a/...ce/tutorial/test_burgers_5_criterion-0.h5 → ...ce/tutorial/test_burgers_5_criterion-0.h5 b/...ce/tutorial/test_burgers_5_criterion-0.h5 → ...ce/tutorial/test_burgers_5_criterion-0.h5
diff --git a/...ce/tutorial/test_burgers_5_criterion-1.h5 → ...ce/tutorial/test_burgers_5_criterion-1.h5 b/...ce/tutorial/test_burgers_5_criterion-1.h5 → ...ce/tutorial/test_burgers_5_criterion-1.h5
diff --git a/...ce/tutorial/test_burgers_5_criterion-2.h5 → ...ce/tutorial/test_burgers_5_criterion-2.h5 b/...ce/tutorial/test_burgers_5_criterion-2.h5 → ...ce/tutorial/test_burgers_5_criterion-2.h5
diff --git a/...ce/tutorial/test_burgers_5_criterion-3.h5 → ...ce/tutorial/test_burgers_5_criterion-3.h5 b/...ce/tutorial/test_burgers_5_criterion-3.h5 → ...ce/tutorial/test_burgers_5_criterion-3.h5
diff --git a/...ce/tutorial/test_burgers_5_criterion-4.h5 → ...ce/tutorial/test_burgers_5_criterion-4.h5 b/...ce/tutorial/test_burgers_5_criterion-4.h5 → ...ce/tutorial/test_burgers_5_criterion-4.h5
diff --git a/...ce/tutorial/test_burgers_5_criterion-5.h5 → ...ce/tutorial/test_burgers_5_criterion-5.h5 b/...ce/tutorial/test_burgers_5_criterion-5.h5 → ...ce/tutorial/test_burgers_5_criterion-5.h5
diff --git a/...ce/tutorial/test_burgers_5_criterion-6.h5 → ...ce/tutorial/test_burgers_5_criterion-6.h5 b/...ce/tutorial/test_burgers_5_criterion-6.h5 → ...ce/tutorial/test_burgers_5_criterion-6.h5
diff --git a/test/reference/tutorial/test_burgers_6.h5 → tests/reference/tutorial/test_burgers_6.h5 b/test/reference/tutorial/test_burgers_6.h5 → tests/reference/tutorial/test_burgers_6.h5
diff --git a/...ence/tutorial/test_graduation_3_extra0.h5 → ...ence/tutorial/test_graduation_3_extra0.h5 b/...ence/tutorial/test_graduation_3_extra0.h5 → ...ence/tutorial/test_graduation_3_extra0.h5
diff --git a/...ence/tutorial/test_graduation_3_extra1.h5 → ...ence/tutorial/test_graduation_3_extra1.h5 b/...ence/tutorial/test_graduation_3_extra1.h5 → ...ence/tutorial/test_graduation_3_extra1.h5
diff --git a/...tion_extra0-tutorial-reconstruction-1d.h5 → ...tion_extra0-tutorial-reconstruction-1d.h5 b/...tion_extra0-tutorial-reconstruction-1d.h5 → ...tion_extra0-tutorial-reconstruction-1d.h5
diff --git a/...tion_extra0-tutorial-reconstruction-2d.h5 → ...tion_extra0-tutorial-reconstruction-2d.h5 b/...tion_extra0-tutorial-reconstruction-2d.h5 → ...tion_extra0-tutorial-reconstruction-2d.h5
diff --git a/...tion_extra0-tutorial-reconstruction-3d.h5 → ...tion_extra0-tutorial-reconstruction-3d.h5 b/...tion_extra0-tutorial-reconstruction-3d.h5 → ...tion_extra0-tutorial-reconstruction-3d.h5
diff --git a/...tion_extra1-tutorial-reconstruction-1d.h5 → ...tion_extra1-tutorial-reconstruction-1d.h5 b/...tion_extra1-tutorial-reconstruction-1d.h5 → ...tion_extra1-tutorial-reconstruction-1d.h5
diff --git a/...tion_extra1-tutorial-reconstruction-2d.h5 → ...tion_extra1-tutorial-reconstruction-2d.h5 b/...tion_extra1-tutorial-reconstruction-2d.h5 → ...tion_extra1-tutorial-reconstruction-2d.h5
diff --git a/...tion_extra1-tutorial-reconstruction-3d.h5 → ...tion_extra1-tutorial-reconstruction-3d.h5 b/...tion_extra1-tutorial-reconstruction-3d.h5 → ...tion_extra1-tutorial-reconstruction-3d.h5
diff --git a/...tion_extra2-tutorial-reconstruction-1d.h5 → ...tion_extra2-tutorial-reconstruction-1d.h5 b/...tion_extra2-tutorial-reconstruction-1d.h5 → ...tion_extra2-tutorial-reconstruction-1d.h5
diff --git a/...tion_extra2-tutorial-reconstruction-2d.h5 → ...tion_extra2-tutorial-reconstruction-2d.h5 b/...tion_extra2-tutorial-reconstruction-2d.h5 → ...tion_extra2-tutorial-reconstruction-2d.h5
diff --git a/...tion_extra2-tutorial-reconstruction-3d.h5 → ...tion_extra2-tutorial-reconstruction-3d.h5 b/...tion_extra2-tutorial-reconstruction-3d.h5 → ...tion_extra2-tutorial-reconstruction-3d.h5
diff --git a/test/test_bc.cpp → tests/test_bc.cpp b/test/test_bc.cpp → tests/test_bc.cpp
diff --git a/test/test_box.cpp → tests/test_box.cpp b/test/test_box.cpp → tests/test_box.cpp
diff --git a/test/test_cell.cpp → tests/test_cell.cpp b/test/test_cell.cpp → tests/test_cell.cpp
diff --git a/test/test_cell_array.cpp → tests/test_cell_array.cpp b/test/test_cell_array.cpp → tests/test_cell_array.cpp
diff --git a/test/test_cell_list.cpp → tests/test_cell_list.cpp b/test/test_cell_list.cpp → tests/test_cell_list.cpp
diff --git a/test/test_common.hpp → tests/test_common.hpp b/test/test_common.hpp → tests/test_common.hpp
diff --git a/test/test_demo_finite_volume.py → tests/test_demo_finite_volume.py b/test/test_demo_finite_volume.py → tests/test_demo_finite_volume.py
diff --git a/test/test_demo_p4est.py → tests/test_demo_p4est.py b/test/test_demo_p4est.py → tests/test_demo_p4est.py
diff --git a/test/test_demo_pablo.py → tests/test_demo_pablo.py b/test/test_demo_pablo.py → tests/test_demo_pablo.py
diff --git a/test/test_demo_tutorial.py → tests/test_demo_tutorial.py b/test/test_demo_tutorial.py → tests/test_demo_tutorial.py
diff --git a/test/test_field.cpp → tests/test_field.cpp b/test/test_field.cpp → tests/test_field.cpp
diff --git a/test/test_for_each.cpp → tests/test_for_each.cpp b/test/test_for_each.cpp → tests/test_for_each.cpp
diff --git a/test/test_graduation.cpp → tests/test_graduation.cpp b/test/test_graduation.cpp → tests/test_graduation.cpp
diff --git a/test/test_interval.cpp → tests/test_interval.cpp b/test/test_interval.cpp → tests/test_interval.cpp
diff --git a/test/test_level_cell_list.cpp → tests/test_level_cell_list.cpp b/test/test_level_cell_list.cpp → tests/test_level_cell_list.cpp
diff --git a/test/test_list_of_intervals.cpp → tests/test_list_of_intervals.cpp b/test/test_list_of_intervals.cpp → tests/test_list_of_intervals.cpp
diff --git a/test/test_operator_set.cpp → tests/test_operator_set.cpp b/test/test_operator_set.cpp → tests/test_operator_set.cpp
diff --git a/test/test_periodic.cpp → tests/test_periodic.cpp b/test/test_periodic.cpp → tests/test_periodic.cpp
diff --git a/test/test_portion.cpp → tests/test_portion.cpp b/test/test_portion.cpp → tests/test_portion.cpp
diff --git a/test/test_utils.cpp → tests/test_utils.cpp b/test/test_utils.cpp → tests/test_utils.cpp
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,3 +5,4 @@ channels:

		dependencies:
		- breathe
		- sphinx_rtd_theme