Resolve merge conflict

.github/workflows/build_documentation_devel.yml

@@ -0,0 +1,61 @@
+# Simple workflow for generating and deploying static content with Doxygen to GitHub Pages
+name: Deploy Doxygen-generated content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job for generating and deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      # Step 1: Checkout the repository
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      # Step 2: Install Doxygen and required packages
+      - name: Install Doxygen and dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y doxygen graphviz # For call graphs
+          sudo apt-get install -y texlive-latex-base texlive-pictures texlive-latex-extra # TikZ package for call graphs
+
+      # Step 3: Generate documentation using Doxygen
+      - name: Generate Doxygen documentation
+        run: |
+          cd docs
+          doxygen Doxyfile
+
+      # Step 4: Setup Pages
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      # Step 5: Upload the generated documentation (public folder)
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Path to the folder with the generated HTML files
+          path: 'docs/developers/html'
+
+      # Step 6: Deploy to GitHub Pages
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

README.md

@@ -1,6 +1,6 @@
 ![Logo](https://github.com/filippi-claudia/champ/blob/main//docs/logo_small.jpg?raw=true)
 
-[![GitHub-hosted Intel OneAPI build](https://github.com/filippi-claudia/champ/actions/workflows/github_hosted_build_champ.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/github_hosted_build_champ.yml) [![DEBUG build and testing](https://github.com/filippi-claudia/champ/actions/workflows/build_champ_debug.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/build_champ_debug.yml) [![Unit Tests](https://github.com/filippi-claudia/champ/actions/workflows/champ_unit_test.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/champ_unit_test.yml) [![TREXIO python interface](https://github.com/filippi-claudia/champ/actions/workflows/test_python.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/test_python.yml)
+[![CHAMP release build with Intel](https://github.com/filippi-claudia/champ/actions/workflows/build_champ_intel.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/build_champ_intel.yml) [![CHAMP debug build with Intel and GNU](https://github.com/filippi-claudia/champ/actions/workflows/debug_champ_intel_and_gnu.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/debug_champ_intel_and_gnu.yml) [![CHAMP with QMCkl and TREXIO build with Intel](https://github.com/filippi-claudia/champ/actions/workflows/build_champ_trexio_qmckl.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/build_champ_trexio_qmckl.yml) [![Build Docker Image](https://github.com/filippi-claudia/champ/actions/workflows/docker-image.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/docker-image.yml) [![Publish Docker image](https://github.com/filippi-claudia/champ/actions/workflows/docker-publish.yml/badge.svg?branch=main)](https://github.com/filippi-claudia/champ/actions/workflows/docker-publish.yml) [![TREXIO python interface](https://github.com/filippi-claudia/champ/actions/workflows/test_python.yml/badge.svg)](https://github.com/filippi-claudia/champ/actions/workflows/test_python.yml)
 
 
 ![Github Issues](https://img.shields.io/github/issues/filippi-claudia/champ) ![Github Pull Requests](https://img.shields.io/github/issues-pr/filippi-claudia/champ) ![Github Last Commit](https://img.shields.io/github/last-commit/filippi-claudia/champ) [![Commit Activity](https://img.shields.io/github/commit-activity/w/filippi-claudia/champ)](https://img.shields.io/github/commit-activity/t/filippi-claudia/champ
@@ -140,7 +140,7 @@ Here are a couple of recipes for commonly used computing facilities, which can b
 		```bash
 		module purge
 		module load 2022
-		module load intel/2022a               
+		module load intel/2022a
 		module load HDF5/1.12.2-iimpi-2022a
 		```
 		then set-up the build:
@@ -189,13 +189,13 @@ Here are a couple of recipes for commonly used computing facilities, which can b
 	- To build with mpiifort, load the required modules of the Intel Compiler and MPI:
 
 		```bash
- 		module load cmake/latest 
+ 		module load cmake/latest
  		module load compiler-rt/latest
  		module load debugger/latest
  		module load compiler/latest
  		module load icc/latest
  		module load mpi/latest
- 		module load hdf5/latest   
+ 		module load hdf5/latest
  		module load tbb/latest
  		module load dpl/latest
  		module load dev-utilities/latest
@@ -211,7 +211,7 @@ Here are a couple of recipes for commonly used computing facilities, which can b
 		cmake -H. -Bbuild  \
   			-DCMAKE_Fortran_COMPILER=mpiifort -DENABLE_TREXIO=ON  \
   			-DTREXIO_LIBRARY=/software/libraries/trexio/latest/lib/libtrexio.so  \
-			-DTREXIO_INCLUDE_DIR=/software/libraries/trexio/latest/include/ 
+			-DTREXIO_INCLUDE_DIR=/software/libraries/trexio/latest/include/
 		```
 	- To disable vectorization of the code:
 		```
@@ -239,13 +239,13 @@ Here are a couple of recipes for commonly used computing facilities, which can b
  		module load compiler/latest
  		module load icc/latest
  		module load mpi/latest
- 		module load hdf5/latest   
+ 		module load hdf5/latest
  		module load tbb/latest
  		module load dpl/latest
  		module load dev-utilities/latest
  		module load mkl/latest
  		module load trexio/latest
-        	
+
 	 	cd $PWD
 		mpirun -np 64 champ/bin/vmc.mov1 -i input.inp -o output.out -e error
 		```

docs/Doxyfile

@@ -471,7 +471,7 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = NO
+EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -833,7 +833,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = "README.md" "../src/vmc"  "../src/dmc" "../src/include"
+INPUT                  = "README.md" "../src/vmc"  "../src/dmc" "../src/module" "../src/parser"
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1202,15 +1202,15 @@ HTML_EXTRA_FILES       =
 # Minimum value: 0, maximum value: 359, default value: 220.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_HUE    = 220
+HTML_COLORSTYLE_HUE    = 0
 
 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
 # in the HTML output. For a value of 0 the output will use grayscales only. A
 # value of 255 will produce the most vivid colors.
 # Minimum value: 0, maximum value: 255, default value: 100.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_SAT    = 100
+HTML_COLORSTYLE_SAT    = 0
 
 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
 # luminance component of the colors in the HTML output. Values below 100
@@ -1221,7 +1221,7 @@ HTML_COLORSTYLE_SAT    = 100
 # Minimum value: 40, maximum value: 240, default value: 80.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_GAMMA  = 80
+HTML_COLORSTYLE_GAMMA  = 100
 
 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
 # page will contain the date and time when the page was generated. Setting this
@@ -1230,7 +1230,7 @@ HTML_COLORSTYLE_GAMMA  = 80
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_TIMESTAMP         = NO
+HTML_TIMESTAMP         = YES
 
 # If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
 # documentation will contain a main index with vertical navigation menus that
@@ -1241,15 +1241,15 @@ HTML_TIMESTAMP         = NO
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_DYNAMIC_MENUS     = NO
+HTML_DYNAMIC_MENUS     = YES
 
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_DYNAMIC_SECTIONS  = NO
+HTML_DYNAMIC_SECTIONS  = YES
 
 # With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
 # shown in the various tree structured indices initially; the user can expand
@@ -1262,7 +1262,7 @@ HTML_DYNAMIC_SECTIONS  = NO
 # Minimum value: 0, maximum value: 9999, default value: 100.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_INDEX_NUM_ENTRIES = 100
+HTML_INDEX_NUM_ENTRIES = 1000
 
 # If the GENERATE_DOCSET tag is set to YES, additional index files will be
 # generated that can be used as input for Apple's Xcode 3 integrated development
@@ -1478,7 +1478,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
@@ -1666,7 +1666,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -2315,7 +2315,7 @@ UML_LIMIT_NUM_FIELDS   = 10
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-TEMPLATE_RELATIONS     = NO
+TEMPLATE_RELATIONS     = YES
 
 # If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
 # YES then doxygen will generate a graph for each documented file showing the
@@ -2357,7 +2357,7 @@ CALL_GRAPH             = YES
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALLER_GRAPH           = NO
+CALLER_GRAPH           = YES
 
 # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
 # hierarchy of all classes instead of a textual one.
@@ -2388,7 +2388,7 @@ DIRECTORY_GRAPH        = YES
 # The default value is: png.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_IMAGE_FORMAT       = png
+DOT_IMAGE_FORMAT       = svg
 
 # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
 # enable generation of interactive SVG images that allow zooming and panning.