Reformat files to match new sphinx build system for doc

mkdocks no longer used

.gitlab-ci.yml

@@ -191,9 +191,10 @@ pages:
   stage: doc_builds
   script:
     - source cpp_sisso_env/bin/activate
-    - pip install mkdocs mkdocs-material pymdown-extensions mkdocs-minify-plugin
-    - mkdocs build
-    - mv site public
+    - pip install sphinx sphinx-rtd-theme breathe sphinx-sitemap
+    - cd docs/
+    - make html
+    - mv _build ../public
   artifacts:
     paths:
     - public

Doxyfile

@@ -52,7 +52,7 @@ PROJECT_LOGO           =
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = docs
+OUTPUT_DIRECTORY       = doc/
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -885,7 +885,7 @@ GENERATE_HTML          = YES
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `html' will be used as the default path.
 
-HTML_OUTPUT            = C++_API
+HTML_OUTPUT            = html
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for
 # each generated HTML page (for example: .htm,.php,.asp). If it is left blank
@@ -1293,7 +1293,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
 # generate Latex output.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = ON
 
 # 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

mkdocs.yml

-site_name: SISSO++
-
-repo_url: https://gitlab.com/sissopp-developers/sissopp
-
-copyright: 'Copyright © 2021 Thomas A.R. Purcell'
-
-theme:
-    name: 'readthedocs'
-nav:
-    - Home:
-        - Welcome!: README.md
-        - Installation.md
-        - Credits.md
-        - References.md
-        - CONTRIBUTING.md
-        - License: license.md
-    - Tutorial:
-        - Overview: Tutorial/0_intro.md
-        - Using the command line interface: Tutorial/1_combined.md
-        - Using the python interface: Tutorial/2_python.md
-        - Classification problems: Tutorial/3_classification.md
-plugins:
-  - search
-  - minify:
-      minify_html: true
-  - search
-
-markdown_extensions:
-    - toc:
-        permalink: "#"
-        toc_depth: 3
-    - pymdownx.arithmatex
-    - pymdownx.details
-    - pymdownx.superfences
-    - footnotes
-    - admonition
-
-extra_javascript:
-  - 'javascripts/mathjax.js'
-  - 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-MML-AM_CHTML'
-
-
-extra:
-  social:
-    - type: gitlab
-      link: https://gitlab.com/sissopp-developers/sissopp