Merge branch 'development' into doc_util

AMReX-Astro · Jan 6, 2025 · bc36128 · bc36128
2 parents 8638acc + 5aa5c4c
commit bc36128
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diff --git a/.github/workflows/docs-test.yml b/.github/workflows/docs-test.yml
@@ -35,10 +35,10 @@ jobs:
 
       - name: Build docs
         run: |
-          cd sphinx_docs/
+          cd Docs/
           make SPHINXOPTS='-v -W --keep-going' html
 
       - name: Link check
         run: |
-          cd sphinx_docs/
+          cd Docs/
           make SPHINXOPTS=-v linkcheck
diff --git a/.gitignore b/.gitignore
@@ -78,7 +78,7 @@ extern.f90
 # sphinx
 build/
 doxy_files
-sphinx_docs/source/runtime_parameters.rst
+Docs/source/runtime_parameters.rst
 
 
 # C++ parameters

diff --git a/sphinx_docs/Doxyfile → Docs/Doxyfile b/sphinx_docs/Doxyfile → Docs/Doxyfile
diff --git a/sphinx_docs/Makefile → Docs/Makefile b/sphinx_docs/Makefile → Docs/Makefile
diff --git a/sphinx_docs/converting_docs.txt → Docs/converting_docs.txt b/sphinx_docs/converting_docs.txt → Docs/converting_docs.txt
diff --git a/sphinx_docs/notes.txt → Docs/notes.txt b/sphinx_docs/notes.txt → Docs/notes.txt
diff --git a/sphinx_docs/pandoc.sh → Docs/pandoc.sh b/sphinx_docs/pandoc.sh → Docs/pandoc.sh
diff --git a/sphinx_docs/rp.py → Docs/rp.py b/sphinx_docs/rp.py → Docs/rp.py
diff --git a/sphinx_docs/source/CNO_He_burn.png → Docs/source/CNO_He_burn.png b/sphinx_docs/source/CNO_He_burn.png → Docs/source/CNO_He_burn.png
diff --git a/sphinx_docs/source/ECSN.png → Docs/source/ECSN.png b/sphinx_docs/source/ECSN.png → Docs/source/ECSN.png
diff --git a/...x_docs/source/_static/theme_overrides.css → Docs/source/_static/theme_overrides.css b/...x_docs/source/_static/theme_overrides.css → Docs/source/_static/theme_overrides.css
diff --git a/...nx_docs/source/_templates/dev_layout.html → Docs/source/_templates/dev_layout.html b/...nx_docs/source/_templates/dev_layout.html → Docs/source/_templates/dev_layout.html
diff --git a/sphinx_docs/source/_templates/layout.html → Docs/source/_templates/layout.html b/sphinx_docs/source/_templates/layout.html → Docs/source/_templates/layout.html
diff --git a/sphinx_docs/source/autodiff.rst → Docs/source/autodiff.rst b/sphinx_docs/source/autodiff.rst → Docs/source/autodiff.rst
diff --git a/sphinx_docs/source/cno_extras_hide_alpha.png → Docs/source/cno_extras_hide_alpha.png b/sphinx_docs/source/cno_extras_hide_alpha.png → Docs/source/cno_extras_hide_alpha.png
diff --git a/sphinx_docs/source/comprehensive_tests.rst → Docs/source/comprehensive_tests.rst b/sphinx_docs/source/comprehensive_tests.rst → Docs/source/comprehensive_tests.rst
diff --git a/sphinx_docs/source/conf.py → Docs/source/conf.py b/sphinx_docs/source/conf.py → Docs/source/conf.py
diff --git a/sphinx_docs/source/data_structures.rst → Docs/source/data_structures.rst b/sphinx_docs/source/data_structures.rst → Docs/source/data_structures.rst
diff --git a/sphinx_docs/source/design.rst → Docs/source/design.rst b/sphinx_docs/source/design.rst → Docs/source/design.rst
@@ -12,6 +12,8 @@ and the generic solvers:
 
 * ``constants``: fundamental constants
 
+* ``Docs``: the sphinx source for this documentation
+
 * ``EOS/``: the various equations of state
 
 * ``integration/``: the ODE integration routines used for the
@@ -34,8 +36,6 @@ and the generic solvers:
 * ``screening/``: common electron screening factors used by some of the
   reaction networks.
 
-* ``sphinx_docs``: the sphinx source for this documentation
-
 * ``unit_test/``: self-contained unit tests for Microphysics. These don’t
   need any application code to build, but will require AMReX.
 

diff --git a/sphinx_docs/source/doxygen_network.png → Docs/source/doxygen_network.png b/sphinx_docs/source/doxygen_network.png → Docs/source/doxygen_network.png
diff --git a/sphinx_docs/source/eos.rst → Docs/source/eos.rst b/sphinx_docs/source/eos.rst → Docs/source/eos.rst
diff --git a/sphinx_docs/source/getting_started.rst → Docs/source/getting_started.rst b/sphinx_docs/source/getting_started.rst → Docs/source/getting_started.rst
diff --git a/sphinx_docs/source/index.rst → Docs/source/index.rst b/sphinx_docs/source/index.rst → Docs/source/index.rst
diff --git a/sphinx_docs/source/integrators.rst → Docs/source/integrators.rst b/sphinx_docs/source/integrators.rst → Docs/source/integrators.rst
diff --git a/sphinx_docs/source/mathsymbols.tex → Docs/source/mathsymbols.tex b/sphinx_docs/source/mathsymbols.tex → Docs/source/mathsymbols.tex
diff --git a/sphinx_docs/source/networks-overview.rst → Docs/source/networks-overview.rst b/sphinx_docs/source/networks-overview.rst → Docs/source/networks-overview.rst
diff --git a/sphinx_docs/source/networks.rst → Docs/source/networks.rst b/sphinx_docs/source/networks.rst → Docs/source/networks.rst
diff --git a/sphinx_docs/source/nova.png → Docs/source/nova.png b/sphinx_docs/source/nova.png → Docs/source/nova.png
diff --git a/sphinx_docs/source/nova2.png → Docs/source/nova2.png b/sphinx_docs/source/nova2.png → Docs/source/nova2.png
diff --git a/sphinx_docs/source/nse.rst → Docs/source/nse.rst b/sphinx_docs/source/nse.rst → Docs/source/nse.rst
diff --git a/sphinx_docs/source/ode_integrators.rst → Docs/source/ode_integrators.rst b/sphinx_docs/source/ode_integrators.rst → Docs/source/ode_integrators.rst
diff --git a/sphinx_docs/source/one_zone_tests.rst → Docs/source/one_zone_tests.rst b/sphinx_docs/source/one_zone_tests.rst → Docs/source/one_zone_tests.rst
diff --git a/sphinx_docs/source/react_aprox13_logX.png → Docs/source/react_aprox13_logX.png b/sphinx_docs/source/react_aprox13_logX.png → Docs/source/react_aprox13_logX.png
diff --git a/sphinx_docs/source/refs.bib → Docs/source/refs.bib b/sphinx_docs/source/refs.bib → Docs/source/refs.bib
diff --git a/sphinx_docs/source/rp_intro.rst → Docs/source/rp_intro.rst b/sphinx_docs/source/rp_intro.rst → Docs/source/rp_intro.rst
diff --git a/Docs/source/runtime_parameters.rst b/Docs/source/runtime_parameters.rst
diff --git a/sphinx_docs/source/screening.rst → Docs/source/screening.rst b/sphinx_docs/source/screening.rst → Docs/source/screening.rst
diff --git a/sphinx_docs/source/sdc.rst → Docs/source/sdc.rst b/sphinx_docs/source/sdc.rst → Docs/source/sdc.rst
diff --git a/sphinx_docs/source/subch_base.png → Docs/source/subch_base.png b/sphinx_docs/source/subch_base.png → Docs/source/subch_base.png
diff --git a/sphinx_docs/source/subch_simple.png → Docs/source/subch_simple.png b/sphinx_docs/source/subch_simple.png → Docs/source/subch_simple.png
diff --git a/sphinx_docs/source/templated_networks.rst → Docs/source/templated_networks.rst b/sphinx_docs/source/templated_networks.rst → Docs/source/templated_networks.rst
diff --git a/sphinx_docs/source/tolerances.png → Docs/source/tolerances.png b/sphinx_docs/source/tolerances.png → Docs/source/tolerances.png
diff --git a/sphinx_docs/source/transport.rst → Docs/source/transport.rst b/sphinx_docs/source/transport.rst → Docs/source/transport.rst
diff --git a/sphinx_docs/source/unit_tests.rst → Docs/source/unit_tests.rst b/sphinx_docs/source/unit_tests.rst → Docs/source/unit_tests.rst
diff --git a/sphinx_docs/source/util.rst → Docs/source/util.rst b/sphinx_docs/source/util.rst → Docs/source/util.rst
diff --git a/sphinx_docs/source/zreferences.rst → Docs/source/zreferences.rst b/sphinx_docs/source/zreferences.rst → Docs/source/zreferences.rst
diff --git a/sphinx_docs/textsymbols.tex → Docs/textsymbols.tex b/sphinx_docs/textsymbols.tex → Docs/textsymbols.tex
diff --git a/README.md b/README.md
@@ -2,7 +2,9 @@
 
 # Microphysics
 
-*A collection of astrophysical microphysics routines for stellar explosions and interstellar medium chemistry (including primordial chemistry)*
+*A collection of astrophysical microphysics routines for stellar
+explosions and interstellar medium chemistry (including primordial
+chemistry)*
 
 There are several core types of microphysics routines hosted here:
 
@@ -87,7 +89,7 @@ system to ensure the interfaces are tested.
 A user's guide for Microphysics is available at:
 http://amrex-astro.github.io/Microphysics/docs/
 
-The sphinx source for the documentation is in `Microphysics/sphinx_docs/`
+The Sphinx source for the documentation is in `Microphysics/Docs/`
 
 ## Development Model:
 

diff --git a/deploy_docs_action.sh b/deploy_docs_action.sh
@@ -12,19 +12,19 @@ mkdir out
 # if on the dev branch, use the dev_layout.html template to get the
 # links correct
 if [ "$GITHUB_BRANCH" = "$DEV_BRANCH" ]; then
-    mv sphinx_docs/source/_templates/dev_layout.html sphinx_docs/source/_templates/layout.html
+    mv Docs/source/_templates/dev_layout.html Docs/source/_templates/layout.html
 fi
 
 # Build the Sphinx documentation
-cd sphinx_docs
+cd Docs
 make html
 cd ../
 
 mkdir -p out/docs/
 if [ "$GITHUB_BRANCH" = "$MAIN_BRANCH" ]; then
     mkdir -p out/docs
-    mv sphinx_docs/build/html/* out/docs
+    mv Docs/build/html/* out/docs
 else
     mkdir -p out/docs/dev/
-    mv sphinx_docs/build/html/* out/docs/dev
+    mv Docs/build/html/* out/docs/dev
 fi