update docs configuration files

README.md

@@ -48,9 +48,8 @@ Besides basic scientific and plotting libraries, the current version requires
 
 ### Installation
 
-<!--- tapir releases can be easily installed through the python standard package manager  
-`pip install tapir`.
---->
+tapir releases can be easily installed through the python standard package manager  
+`pip install tapir-rna`
 
 To install the latest (unreleased) version you can download it from this repository by running 
 
@@ -71,8 +70,8 @@ significance.
 
 ### Contact us
 
-- federico.comitani@sickkids.ca
-- josh.nash@sickkids.ca
+- federico.comitani at sickkids.ca
+- josh.nash at sickkids.ca
 
 <!--
 ### Citation

docs/conf.py

@@ -12,13 +12,14 @@
 #
 import os
 import sys
+sys.path.insert(0, os.path.abspath('../'))
 sys.path.insert(0, os.path.abspath('../tapir'))
 
 # -- Project information -----------------------------------------------------
 
 project = 'tapir'
-copyright = '2021-2022, Federico Comitani, Josh Oren Nash'
-author = 'Federico Comitani, Josh Oren Nash'
+copyright = '2022, Federico Comitani and Josh Oren NAsh'
+author = 'Federico Comitani'
 
 # The full version, including alpha/beta/rc tags
 release = '0.1.0'
@@ -30,9 +31,9 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.napoleon',
     'sphinx.ext.autodoc',
     'sphinx.ext.coverage',
-    'sphinx.ext.napoleon',
     'sphinx.ext.autosectionlabel',
 ]
 
@@ -46,7 +47,6 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
-
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -58,7 +58,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = []
 
 def skip(app, what, name, obj, would_skip, options):
     if name == "__init__":

docs/installation.rst

@@ -10,7 +10,7 @@ Installation
 
    .. code-block:: bash
 
-      pip install tapir
+      pip install tapir-rna
 
 To install the latest (unreleased) version 
 you can download it from our GitHub repository by running 

environment.yml

@@ -1,7 +1,9 @@
 channels:
   - conda-forge
+  - defaults
 dependencies:
-  - python=3.7.6
+  - python=3.8
+  - pip=22.2.2
   - numpy>=1.20.2
   - pandas>=1.1.3
   - gseapy>=0.9.5

requirements.txt

@@ -7,8 +7,3 @@ seaborn >= 0.11.1
 scikit-learn >= 0.4.6
 statsmodels >= 0.11.1
 umap-learn >= 0.3.9
-
-#documentation
-sphinx==3.5.4
-sphinx_rtd_theme==0.5.1
-readthedocs-sphinx-search==0.1.0

setup.py

@@ -11,7 +11,7 @@
 
 setup(
 
-    name='tapir',
+    name='tapir-rna',
 
     version=version,