Merge pull request #415 from daler/add-link-to-docs

Update docs
daler · Nov 5, 2024 · 9d99d2e · 9d99d2e
2 parents 332c82c + df144d1
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diff --git a/README.rst b/README.rst
@@ -2,22 +2,21 @@
 Overview
 --------
 
-.. image:: https://travis-ci.org/daler/pybedtools.png?branch=master
-    :target: https://travis-ci.org/daler/pybedtools
-
 .. image:: https://badge.fury.io/py/pybedtools.svg?style=flat
-    :target: http://badge.fury.io/py/pybedtools
+    :target: https://badge.fury.io/py/pybedtools
 
 .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
-    :target: http://bioconda.github.io
+    :target: https://bioconda.github.io
 
 The `BEDTools suite of programs <http://bedtools.readthedocs.org/>`_ is widely
 used for genomic interval manipulation or "genome algebra".  `pybedtools` wraps
 and extends BEDTools and offers feature-level manipulations from within
 Python.
 
 See full online documentation, including installation instructions, at
-http://daler.github.io/pybedtools/.
+https://daler.github.io/pybedtools/.
+
+The GitHub repo is at https://github.com/daler/pybedtools.
 
 Why `pybedtools`?
 -----------------

diff --git a/docs/source/autodocs/pybedtools.contrib.plotting.Track.rst b/docs/source/autodocs/pybedtools.contrib.plotting.Track.rst
@@ -1,4 +1,4 @@
-pybedtools.contrib.plotting.Track
+pybedtools.contrib.plotting.Track
 =================================
 
 .. currentmodule:: pybedtools.contrib.plotting
@@ -41,20 +41,25 @@ pybedtools.contrib.plotting.Track
       ~Track.get_cursor_data
       ~Track.get_dashes
       ~Track.get_datalim
+      ~Track.get_ec
       ~Track.get_edgecolor
       ~Track.get_edgecolors
       ~Track.get_facecolor
       ~Track.get_facecolors
+      ~Track.get_fc
       ~Track.get_figure
       ~Track.get_fill
       ~Track.get_gid
       ~Track.get_hatch
+      ~Track.get_in_layout
       ~Track.get_joinstyle
       ~Track.get_label
       ~Track.get_linestyle
       ~Track.get_linestyles
       ~Track.get_linewidth
       ~Track.get_linewidths
+      ~Track.get_ls
+      ~Track.get_lw
       ~Track.get_offset_position
       ~Track.get_offset_transform
       ~Track.get_offsets
@@ -66,6 +71,7 @@ pybedtools.contrib.plotting.Track
       ~Track.get_sizes
       ~Track.get_sketch_params
       ~Track.get_snap
+      ~Track.get_tightbbox
       ~Track.get_transform
       ~Track.get_transformed_clip_path_and_affine
       ~Track.get_transforms
@@ -76,8 +82,6 @@ pybedtools.contrib.plotting.Track
       ~Track.get_xlims
       ~Track.get_zorder
       ~Track.have_units
-      ~Track.hitlist
-      ~Track.is_figure_set
       ~Track.is_transform_set
       ~Track.pchanged
       ~Track.pick
@@ -86,6 +90,7 @@ pybedtools.contrib.plotting.Track
       ~Track.remove
       ~Track.remove_callback
       ~Track.set
+      ~Track.set_aa
       ~Track.set_agg_filter
       ~Track.set_alpha
       ~Track.set_animated
@@ -101,19 +106,23 @@ pybedtools.contrib.plotting.Track
       ~Track.set_color
       ~Track.set_contains
       ~Track.set_dashes
+      ~Track.set_ec
       ~Track.set_edgecolor
       ~Track.set_edgecolors
       ~Track.set_facecolor
       ~Track.set_facecolors
+      ~Track.set_fc
       ~Track.set_figure
       ~Track.set_gid
       ~Track.set_hatch
+      ~Track.set_in_layout
       ~Track.set_joinstyle
       ~Track.set_label
       ~Track.set_linestyle
       ~Track.set_linestyles
       ~Track.set_linewidth
       ~Track.set_linewidths
+      ~Track.set_ls
       ~Track.set_lw
       ~Track.set_norm
       ~Track.set_offset_position
@@ -146,12 +155,12 @@ pybedtools.contrib.plotting.Track
 
    .. autosummary::
 
-      ~Track.aname
       ~Track.axes
       ~Track.midpoint
       ~Track.mouseover
       ~Track.stale
       ~Track.sticky_edges
+      ~Track.update_dict
       ~Track.zorder
 
 
diff --git a/docs/source/pybedtools.featurefuncs.add_color.rst b/docs/source/pybedtools.featurefuncs.add_color.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.add_color
-=================================
+pybedtools.featurefuncs.add\_color
+==================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst b/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.bedgraph_scale
-======================================
+pybedtools.featurefuncs.bedgraph\_scale
+=======================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/docs/source/pybedtools.featurefuncs.extend_fields.rst b/docs/source/pybedtools.featurefuncs.extend_fields.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.extend_fields
-=====================================
+pybedtools.featurefuncs.extend\_fields
+======================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/docs/source/pybedtools.featurefuncs.five_prime.rst b/docs/source/pybedtools.featurefuncs.five_prime.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.five_prime
-==================================
+pybedtools.featurefuncs.five\_prime
+===================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/docs/source/pybedtools.featurefuncs.greater_than.rst b/docs/source/pybedtools.featurefuncs.greater_than.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.greater_than
-====================================
+pybedtools.featurefuncs.greater\_than
+=====================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/docs/source/pybedtools.featurefuncs.less_than.rst b/docs/source/pybedtools.featurefuncs.less_than.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.less_than
-=================================
+pybedtools.featurefuncs.less\_than
+==================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/docs/source/pybedtools.featurefuncs.normalized_to_length.rst b/docs/source/pybedtools.featurefuncs.normalized_to_length.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.normalized_to_length
-============================================
+pybedtools.featurefuncs.normalized\_to\_length
+==============================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/docs/source/pybedtools.featurefuncs.three_prime.rst b/docs/source/pybedtools.featurefuncs.three_prime.rst
@@ -1,5 +1,5 @@
-pybedtools.featurefuncs.three_prime
-===================================
+pybedtools.featurefuncs.three\_prime
+====================================
 
 .. currentmodule:: pybedtools.featurefuncs
 

diff --git a/pybedtools/contrib/long_range_interaction.py b/pybedtools/contrib/long_range_interaction.py
@@ -120,7 +120,7 @@ def tag_bedpe(bedpe, queries, verbose=False):
     >>> queries = OrderedDict()
     >>> queries['tss'] = tsses
     >>> queries['pk'] = peaks
-    >>> iterator, n, extra = tag_bedpe(bedpe, queries)
+    >>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, queries)
     >>> print(n)
     2
     >>> print(extra)
@@ -280,7 +280,7 @@ def cis_trans_interactions(iterator, n, extra, verbose=True):
     >>> queries = OrderedDict()
     >>> queries['tss'] = tsses
     >>> queries['pk'] = peaks
-    >>> iterator, n, extra = tag_bedpe(bedpe, queries)
+    >>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, queries)
     >>> for (label, group1, group2) in iterator:
     ...    group1 = sorted(group1, key=lambda x: str(x))
     ...    group2 = sorted(group2, key=lambda x: str(x))
@@ -303,8 +303,8 @@ def cis_trans_interactions(iterator, n, extra, verbose=True):
     and that they are also connected to gene3:
 
     >>> import pandas; pandas.set_option('display.max_columns', 10)
-    >>> iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks})
-    >>> df =  cis_trans_interactions(iterator, n, extra)
+    >>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks})
+    >>> df =  pybedtools.contrib.long_range_interaction.cis_trans_interactions(iterator, n, extra)
     >>> print(df.sort_values(list(df.columns)).reset_index(drop=True))
       target_label target_name cis_label cis_name distal_label distal_name  label
     0           pk       peak1       tss    gene1            .           .  pair2