#59 workaround for logo and changed file structure

README.md

@@ -68,12 +68,12 @@ You are now ready to build the documentation...
 1. You can build the documentation by __triggering every build manually__: To trigger the build, run [`sphinx-build`](https://www.sphinx-doc.org/en/master/man/sphinx-build.html) from the repository root directory:
 
 ```
-sphinx-build sphinx _build/html -b singlehtml -a
+sphinx-build source _build/html -b singlehtml -a
 ```
 
 | option | value | description |
 | ---------------------------- | ----- | ----------- |
-| sourcedir | `./sphinx` | N/A |
+| sourcedir | `./source` | N/A |
 | outdir | `./_build/html` | N/A |
 | -b | `singlehtml` | create only a single html page |
 | -a | N/A | always write all output files |
@@ -89,12 +89,12 @@ _build/html/homepage.html
 2. You can also build the documentation by automatically triggering a build after every change to the source files, providing a "live" preview of changes. To trigger the automated builds, run [`sphinx-autobuild`](https://github.com/executablebooks/sphinx-autobuild) from the repository root directory:
 
 ```
-sphinx-autobuild sphinx _build/html -a -j auto --open-browser
+sphinx-autobuild source _build/html -a -j auto --open-browser
 ```
 
 | positional argument or option| value | description |
 | ---------------------------- | ----- | ----------- |
-| sourcedir | `./sphinx` | N/A |
+| sourcedir | `./source` | N/A |
 | outdir | `./_build/html` | N/A |
 | `-a` | N/A | always write all output files |
 | `-j` | `auto` | [speed up build by using multiple processes](https://www.sphinx-doc.org/en/master/man/sphinx-build.html#cmdoption-sphinx-build-j) |

environment.yml

@@ -7,15 +7,15 @@ dependencies:
   - python=3.11
   - ipython
   # sphinx
-  - sphinx=6.2.1 # sphinx-design currently requires sphinx[version>=2,<5] # https://github.com/sphinx-doc/sphinx/releases
+  - sphinx=6.2.1
   # theme and extensions
   - pydata-sphinx-theme=0.13.3 # website theme # https://github.com/pydata/pydata-sphinx-theme/releases
   - myst-parser=2.0.0 # Markdown support # https://github.com/executablebooks/MyST-Parser/releases
   - nbsphinx=0.9.2 # Jupyter notebook support # https://github.com/spatialaudio/nbsphinx/releases
-  - sphinx-autoapi=2.1.0 # to build docs from source code instead of package import # https://github.com/readthedocs/sphinx-autoapi/tags
+  - sphinx-autoapi=2.1.1 # to build docs from source code instead of package import # https://github.com/readthedocs/sphinx-autoapi/tags
   - sphinx-design=0.4.1 # responsive web component support # https://github.com/executablebooks/sphinx-design/releases
   - sphinx-notfound-page=0.8.3 # custom 404 page # https://github.com/readthedocs/sphinx-notfound-page/tags
-  - graphviz=8.0.5 # for plotting dependency diagrams with sphinx-autoapi # https://anaconda.org/conda-forge/graphviz/files
+  - graphviz=8.1.0 # for plotting dependency diagrams with sphinx-autoapi # https://anaconda.org/conda-forge/graphviz/files
   - sphinx-favicon=1.0.1 # for custom favicons # https://github.com/tcmetzger/sphinx-favicon/releases
   - sphinx-copybutton=0.5.2 # for copy button in code blocks # https://github.com/executablebooks/sphinx-copybutton/releases
   # build process