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commit b77a165 Author: Parashar <[email protected]> Date: Fri Jul 26 18:58:50 2024 +0200 docs update
parashardhapola · Jul 26, 2024 · c906e0f · c906e0f
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commit c906e0f
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,20 +1,19 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: "ubuntu-22.04"
   tools:
     python: "3.11"
 
-sphinx:
-  configuration: docs/source/conf.py
-  builder: html
-  fail_on_warning: false
-
-
 python:
   install:
     - requirements: requirements.txt
     - requirements: requirements_extra.txt
     - requirements: docs/source/requirements.txt
     - method: pip
       path: .
+
+sphinx:
+  configuration: docs/source/conf.py
+  builder: html
+  fail_on_warning: false
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -21,7 +21,6 @@
 ]
 
 templates_path = ["_templates"]
-source_suffix = [".rst"]
 master_doc = "index"
 exclude_patterns = [
     "_build",
@@ -39,9 +38,9 @@
     "colon_fence",
 ]
 
+html_static_path = ["_static"]
 html_css_files = ["styles.css"]
 html_theme = "sphinx_book_theme"
-html_static_path = ["_static"]
 html_favicon = "favicon.ico"
 html_logo = "logo.png"
 html_title = "Scarf documentation"
@@ -54,13 +53,18 @@
     "use_download_button": True,
     "use_fullscreen_button": True,
     "home_page_in_toc": True,
-    "extra_navbar": "",
-    "logo_only": True,
     "show_navbar_depth": 2,
     "toc_title": "Sections",
 }
+htmlhelp_basename = "Scarf Documentation"
+html_sidebars = {
+    "**": [
+        "globaltoc.html",
+        "searchbox.html",
+    ],
+    'using/windows': ['windows-sidebar.html', 'searchbox.html'],
+}
 
-htmlhelp_basename = "ScarfDoc"
 man_pages = [(master_doc, "scarf", "Scarf Documentation", [author], 1)]
 
 nb_execution_allow_errors = True

diff --git a/docs/source/contributions.md b/docs/source/contributions.md
@@ -25,17 +25,17 @@ extension.
 ## Contributors
 Contributors to the Scarf repository. Thank you everyone!
 
-:::{eval-rst}
+```{eval-rst}
 .. include:: contributors.rst
-:::
+```
 
 ## Open-source stack
 A diverse number of open-source packages in Python scientific stack are being used to build Scarf.
 Here we acknowledge some of them (atleast those with pretty logos..)
 
-:::{eval-rst}
+```{eval-rst}
 .. include:: logos.rst
-:::
+```
 
 [guideline]: https://www.dataschool.io/how-to-contribute-on-github
 [discussion page]: https://www.dataschool.io/how-to-contribute-on-github

diff --git a/docs/source/install.md b/docs/source/install.md
@@ -28,7 +28,7 @@ To use Scarf you need the Python programming language, version 3.10 or upwards,
 First, check whether you already have Python installed. To do so, you need to open a terminal
 window (aka command prompt).
 
-:::{eval-rst}
+```{eval-rst}
 .. tabs::
 
   .. tab:: Linux
@@ -46,7 +46,7 @@ window (aka command prompt).
 
      Press `CMD+Space` to open spotlight search, and type `terminal` and hit `RETURN`.
 
-:::
+```
 
 **Step 2:**
 

diff --git a/scarf/datastore/datastore.py b/scarf/datastore/datastore.py
@@ -730,11 +730,9 @@ def run_cell_cycle_scoring(
 
         - Average expression of all the genes in across `cell_key` cells is calculated
         - The log average expression is divided in `n_bins` bins
-        - A control set of genes is identified by sampling genes from same expression bins where phase's genes are
-        present.
+        - A control set of genes is identified by sampling genes from same expression bins where phase's genes are present.
         - The average expression of phase genes (Ep) and control genes (Ec) is calculated per cell.
-        - A phase score is calculated as: Ep-Ec
-        Cell cycle phase is assigned to each cell based on following rule set:
+        - A phase score is calculated as: Ep-Ec Cell cycle phase is assigned to each cell based on following rule set:
         - G1 phase: S score < -1 > G2M sore
         - S phase: S score > G2M score
         - G2M phase: G2M score > S score