Overlap methods revised

docs/_templates/custom_method_summary.rst

@@ -0,0 +1,5 @@
+{{ fullname | escape | underline }}
+
+.. currentmodule:: {{ module }}
+
+.. automethod:: {{ objname }}

docs/conf.py

@@ -60,7 +60,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = ['_generated_hidden*']
 
 master_doc = "index"
 

docs/developer_guide.rst

@@ -99,7 +99,7 @@ Task sequence
 ~~~~~~~~~~~~~
 
 1. Create and download your own Pyranges fork
-------------------------------------------
+---------------------------------------------
 
 The easiest way to do this is through github. Login into the github website if you aren't already,
 then visit the Pyranges page on github, click "Fork" on the top right. 
@@ -295,7 +295,7 @@ case, google how to set up a github token that you can use.
 
 
 10. Open a pull request
-----------------------
+-----------------------
 
 The easiest way to open a pull request is through the github website. Go to **your**
 Pyranges fork on github, then find the "Contribute" button (near the **<> Code** button). Click
@@ -315,7 +315,7 @@ Pyranges administrators will inspect the pull request, comment it if necessary,
 
 
 11. Core team only: upload to PyPI
----------------------------------
+----------------------------------
 
 Every now and then, the core development team considers that a new pyranges version should be
 released. To do so:
@@ -347,5 +347,7 @@ property-based tests):
 
     pytest -n 4 tests/property_based
 
+Other useful tools:
+
 * [rg](https://github.com/BurntSushi/ripgrep): ripgrep recursively searches directories for a regex pattern while respecting your gitignore
 * [fd](https://github.com/sharkdp/fd): A simple, fast and user-friendly alternative to 'find'

docs/how_to_pages.rst

@@ -4,12 +4,13 @@ How-to pages
 These pages explain pyranges functionalities grouped by topic:
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
 
    how_to_create
    how_to_write
    how_to_inspect
    how_to_rows
    how_to_columns
    how_to_sequences
-   how_to_genomic_ops
+   how_to_genomic_ops
+   how_to_overlap

docs/index.rst

@@ -50,9 +50,8 @@ Documentation outline
    developer_guide
 
 
-Indices and tables
-==================
+Indices
+=======
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`

docs/installation.rst

@@ -12,10 +12,10 @@ The preferred way to install pyranges is via pip::
 
     pip install pyranges1
 
-The command above will install a minimal version of pyranges.
+The command above will install a **minimal version** of pyranges.
 Pyranges has several optional dependencies, required for certain functionalities.
 
-To install all optional dependencies, use::
+To **install all optional dependencies**, use::
 
     pip install pyranges1[all]
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyranges1"
-version = "1.0.0"
+version = "1.0.1"
 description = "GenomicRanges for Python."
 requires-python = ">=3.12.0"
 readme = "README.md"

pyranges/core/pyranges_helpers.py

@@ -11,7 +11,6 @@
     STRAND_BEHAVIOR_SAME,
     STRAND_COL,
     STRICT_STRAND_BEHAVIOR_TYPE,
-    TEMP_STRAND_COL,
     USE_STRAND_AUTO,
     VALID_BY_OPTIONS,
     VALID_STRAND_BEHAVIOR_OPTIONS,
@@ -119,17 +118,17 @@ def group_keys_from_validated_strand_behavior(
     """Return group keys based on strand behavior.
 
     If strand_behavior is 'same', return [CHROM_COL, STRAND_COL].
-    If strand_behavior is 'opposite', return [CHROM_COL, TEMP_STRAND_COL].
+    If strand_behavior is 'opposite', return [CHROM_COL, STRAND_COL].
     If strand_behavior is 'ignore', return [CHROM_COL].
 
     In each case, if a by argument is provided, it is appended/extended to the list of group keys.
 
     """
-    strand_cols = (
-        [STRAND_COL]
-        if strand_behavior == STRAND_BEHAVIOR_SAME
-        else ([TEMP_STRAND_COL] if strand_behavior == STRAND_BEHAVIOR_OPPOSITE else [])
-    )
+    if strand_behavior == STRAND_BEHAVIOR_AUTO:
+        msg = "this function must be called with a validated strand_behavior"
+        raise ValueError(msg)
+
+    strand_cols = [STRAND_COL] if strand_behavior in [STRAND_BEHAVIOR_SAME, STRAND_BEHAVIOR_OPPOSITE] else []
 
     return [CHROM_COL, *strand_cols, *arg_to_list(by)]