Merge pull request #189 from open2c/Phlya-patch-1

Update readthedocs.yml

doc/conf.py

@@ -19,7 +19,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-# sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('..'))
 
 # -- General configuration ------------------------------------------------
 
@@ -38,7 +38,6 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.mathjax",
     "sphinx_click.ext",
-    "recommonmark",
     "nbsphinx",
     "sphinx_rtd_theme",
 ]
@@ -100,7 +99,7 @@ def get_version():
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

pairtools/lib/__init__.py

@@ -1,6 +1,5 @@
 from . import fileio
 from . import dedup
-from . import dedup_cython
 from . import filterbycov
 from . import headerops
 from . import pairsam_format

pairtools/lib/dedup.py

@@ -338,7 +338,7 @@ def streaming_dedup_cython(
     Returns
     -------
 
-    """
+    """    
     maxind = max(c1ind, c2ind, p1ind, p2ind, s1ind, s2ind)
     if bool(extra_cols1) and bool(extra_cols2):
         maxind = max(maxind, max(extra_cols1), max(extra_cols2))

readthedocs.yml

@@ -1,12 +1,17 @@
 
 # .readthedocs.yml
+version: 2
 
 build:
-  image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
 
-python:
-  version: 3.8
-  pip_install: true
-
-requirements_file: requirements_doc.txt
+sphinx:
+  configuration: doc/conf.py
 
+python:
+  install:
+    - requirements: requirements_doc.txt
+    - method: pip
+      path: .

requirements_doc.txt

@@ -6,9 +6,10 @@ pandas
 pysam
 bioframe
 click>=7.0
-git+https://github.com/golobor/sphinx-click
+sphinx-click
 ipython
 nbsphinx
-Sphinx
+Sphinx>=7.0
 sphinx_rtd_theme
-docutils>0.16
+docutils>0.16
+-e .