Small tweaks to docs before merging

README.md

@@ -1,4 +1,5 @@
 # Vamb
+[![Read the Docs](https://readthedocs.org/projects/vamb/badge/?version=latest)](https://vamb.readthedocs.io/en/latest/)
 
 Created by Jakob Nybo Nissen and Simon Rasmussen, Technical University of Denmark and Novo Nordisk Foundation Center for Protein Research, University of Copenhagen.
 

doc/README.md

@@ -12,7 +12,7 @@ Install the docs dependencies of the package (as speciefied in toml):
 
 ```bash
 # in main folder
-pip install .[docs]
+pip install '.[docs]'
 ```
 
 ## Build docs using Sphinx command line tools
@@ -23,9 +23,9 @@ Options:
   - `--separate` to build separate pages for each (sub-)module
 
 ```bash	
-# pwd: docs
+# pwd: doc
 # apidoc
-sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../vamb
+# sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../vamb
 # build docs
 sphinx-build -n -W --keep-going -b html ./ ./_build/
-```
+```

doc/conf.py

@@ -126,22 +126,22 @@
     PROJECT_ROOT = Path(__file__).parent.parent
     PACKAGE_ROOT = PROJECT_ROOT / "vamb"
 
-    def run_apidoc(_):
-        from sphinx.ext import apidoc
-
-        apidoc.main(
-            [
-                "--force",
-                "--implicit-namespaces",
-                "--module-first",
-                "--separate",
-                "-o",
-                str(PROJECT_ROOT / "doc" / "reference"),
-                str(PACKAGE_ROOT),
-                str(PACKAGE_ROOT / "*.c"),
-                str(PACKAGE_ROOT / "*.so"),
-            ]
-        )
-
-    def setup(app):
-        app.connect("builder-inited", run_apidoc)
+#     def run_apidoc(_):
+#         from sphinx.ext import apidoc
+# 
+#         apidoc.main(
+#             [
+#                 "--force",
+#                 "--implicit-namespaces",
+#                 "--module-first",
+#                 "--separate",
+#                 "-o",
+#                 str(PROJECT_ROOT / "doc" / "reference"),
+#                 str(PACKAGE_ROOT),
+#                 str(PACKAGE_ROOT / "*.c"),
+#                 str(PACKAGE_ROOT / "*.so"),
+#             ]
+#         )
+# 
+#     def setup(app):
+#         app.connect("builder-inited", run_apidoc)

doc/index.rst

@@ -5,26 +5,12 @@ Variational Autoencoder for Metagenomic Binning (VAMB)
    :parser: myst_parser.sphinx_
    :start-line: 1
 
-
 .. toctree::
    :maxdepth: 2
    :caption: Tutorial
 
    tutorial.md
 
-
-.. toctree::
-   :hidden:
-   :caption: Comparisons
-
-   CAMI2.md
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Python Package:
-
-   reference/vamb
-
 .. toctree::
    :caption: Setup Documentation