Merge pull request #26 from rekomodo/tagging

Implementation of tagging using sphinx-tags

.gitignore

@@ -1,5 +1,6 @@
 # Build Files
 report/_build
+report/_tags
 
 # Jupyter Notebooks
 *.ipynb

report/_config.yml

@@ -40,4 +40,27 @@ parse:
     # don't forget to list any other extensions you want enabled,
     # including those that are enabled by default!
     - amsmath
-    - dollarmath
+    - dollarmath
+
+# add sphinx configuration
+sphinx:
+  extra_extensions:
+    - sphinx_tags
+  config:
+    tags_create_tags : True
+    tags_create_badges: True
+    tags_extension : ["md"]
+    tags_page_title : "All Tags"
+    suppress_warnings: ["etoc.toctree"]
+    tags_badge_colors: {
+      "MMS": "success",
+      "MES": "success",
+      "*D": "secondary",
+    }
+    tags_index_head: "Cases categorised by tag"
+    tags_intro_text: "🏷 Tags:"
+    tags_overview_title: "🏷 Tags"
+    tags_page_header: "Cases with this tag"
+    tags_page_title: "🏷 Tag"
+
+

report/_toc.yml

@@ -25,6 +25,7 @@ parts:
     chapters:
       - file: validation/plasma-driven-permeation/plasma-driven-permeation
       - file: validation/thermodesorption_spectra/ogorodnikova/ogorodnikova-tds
-  - caption: Bibliography
+  - caption: Appendices
     chapters:
-    - file: bibliography
+    - file: bibliography
+    - file: _tags/tagsindex.md

report/environment.yml

@@ -7,6 +7,7 @@ channels:
 dependencies:
   - python
   - jupyter-book
+  - sphinx-tags
   - numpy
   - matplotlib
   - sphinx

report/validation/plasma-driven-permeation/plasma-driven-permeation.md

@@ -12,8 +12,12 @@ kernelspec:
   name: python3
 ---
 
+
 # Plasma-driven permeation
 
+```{tags} 1D
+```
+
 This validation case is a plasma-driven permeation performed at INL in 1985 {cite}`anderl_tritium_1986`.
 Deuterium ions at 3 keV was implanted in a 0.5 mm thick sample of 316 stainless steel variant called primary candidate alloy (PCA).
 

report/validation/thermodesorption_spectra/ogorodnikova/ogorodnikova-tds.md

@@ -14,6 +14,9 @@ kernelspec:
 
 # Thermo-desorption spectrum
 
+```{tags} 1D, TDS
+```
+
 This validation case is a thermo-desorption spectrum measurement perfomed by Ogorodnikova et al. {cite}`ogorodnikova_deuterium_2003`.
 
 Deuterium ions at 200 eV were implanted in a 0.5 mm thick sample of high purity tungsten foil (PCW).

report/verification/depleting_source.md

@@ -12,8 +12,12 @@ kernelspec:
   name: python3
 ---
 
+
 # Diffusion from a Depleting Source
 
+```{tags} 2D, MES
+```
+
 This verification case {cite}`ambrosek_verification_2008` consists of an enclosure containing an initial quantity of hydrogen gas (at an initial pressure $P_0$).
 The hydrogen can dissociate on the inner surface of the enclosure and then permeate through the walls.
 As hydrogen particles escape the enclosure, the pressure decreases and as a result, so does the surface concentration on the inner walls.

report/verification/mes_radioactive_decay.md

@@ -14,6 +14,9 @@ kernelspec:
 
 # Radioactive decay 1D
 
+```{tags} 1D, MES, RadioactiveDecay
+```
+
 This example is a radioactive decay (`RadioactiveDecay`) problem on simple unit interval with a uniform mobile concentration and no boundary condition.
 
 

report/verification/mms/discontinuity.md

@@ -10,6 +10,9 @@ jupytext:
 
 # Diffusion multi-material
 
+```{tags} 2D, MMS
+```
+
 The first MMS problem has two materials (denoted, respectively, by left and right).
 In material left, the solubility is $K_{S,\mathrm{left}} = 3$ and the diffusivity is $D_\mathrm{left} = 2$.
 In material right, the solubility is $K_{S,\mathrm{right}} = 6$ and the diffusivity is $D_\mathrm{right} = 5$.

report/verification/mms/fluxes.md

@@ -12,8 +12,12 @@ kernelspec:
   name: python3
 ---
 
+
 # Diffusion with dissociation flux
 
+```{tags} 2D, MMS, DissociationFlux
+```
+
 This example is a diffusion problem with one boundary under a dissociation flux (`DissociationFlux`).
 
 The problem is:

report/verification/mms/heat_transfer.md

@@ -8,8 +8,12 @@ jupytext:
     jupytext_version: 1.16.2
 ---
 
+
 # Heat transfer multi-material
 
+```{tags} 2D, MMS, HeatTransferProblem, Multi-material
+```
+
 This case verifies the implementation of the heat transfer solver in FESTIM.
 Two materials with different thermal conductivities are defined: $\lambda_\mathrm{left} = 2$ and $\lambda_\mathrm{right} = 5$.
 

report/verification/mms/radioactive_decay.md

@@ -14,6 +14,9 @@ kernelspec:
 
 # Radioactive decay 2D
 
+```{tags} 2D, MMS, RadioactiveDecay
+```
+
 This MMS case verifies the implementation of radioactive decay in FESTIM.
 We will only consider diffusion of hydrogen in a unit square domain $\Omega$ at steady state with a homogeneous diffusion coefficient $D$.
 We will impose a radioactive decay (`RadioactiveDecay`) source over the whole domain

report/verification/mms/simple.md

@@ -12,8 +12,12 @@ kernelspec:
   name: python3
 ---
 
+
 # Simple diffusion case
 
+```{tags} 2D, MMS
+```
+
 This is a simple MMS example.
 We will only consider diffusion of hydrogen in a unit square domain $\Omega$ at steady state with an homogeneous diffusion coefficient $D$.
 Moreover, a Dirichlet boundary condition will be assumed on the boundaries $\partial \Omega $.

report/verification/mms/trapping.md

@@ -10,6 +10,9 @@ jupytext:
 
 # Single trap
 
+```{tags} 2D, MMS, Trapping, Multi-material
+```
+
 The MMS case verifies the implementation of trapping in FESTIM.
 Only one trap is considered for simplicity, but the same principle applies for more traps.
 Exact solutions are defined for both the mobile concentration and the trapped concentration.