Documentation fixes

README.md

@@ -5,6 +5,7 @@
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 [![Python Version Required](https://img.shields.io/pypi/pyversions/pytximport)](https://pypi.org/project/pytximport/)
 [![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport)
+[![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.readthedocs.io/en/latest/?badge=latest)
 
 `pytximport` is a Python package for fast gene count estimation based on transcript abundance, inspired by the `tximport` R package.
 

pytximport/__init__.py

@@ -1,10 +1,16 @@
 """pytximport: Convert transcript-level expression to gene-level expression.
 
 The `pytximport` package provides a Python implementation of the `tximport` R package, which converts transcript-level
-expression to gene-level expression. The package currently only supports `kallisto` quantification files.
+expression to gene-level count estimates.
 
-Please also cite the original `tximport` R package when using `pytximport`.
-DOI: https://doi.org/10.12688/f1000research.7563.1
+.. note::
+    Please also cite the original `tximport` R package when using `pytximport`.
+    DOI: https://doi.org/10.12688/f1000research.7563.1
+
+.. warning::
+    The `pytximport` package is still in development and currently does not make use of the inferential replicates,
+    unlike the `tximport` R package. Default parameters, argument names and return types may also differ between the
+    implementations.
 """
 
 from . import definitions, importers, utils

pytximport/core/_tximport.py

@@ -43,20 +43,8 @@ def tximport(
     return_data: bool = True,
     biotype_filter: Optional[List[str]] = None,
 ) -> Union[xr.Dataset, ad.AnnData, None]:
-    """Import transcript-level quantification files and convert them to gene-level expression.
-
-    An alternative to the `tximport` R package. `pytximport` is a Python package that imports transcript-level
-    quantification files and converts them to gene-level expression. Currently, only `kallisto` quantification files are
-    supported.
-
-    .. note::
-        Please also cite the original `tximport` R package when using `pytximport`.
-        DOI: https://doi.org/10.12688/f1000research.7563.1
-
-    .. warning::
-        The `pytximport` package is still in development and currently does not make use of the inferential replicates,
-        unlike the `tximport` R package. Default parameters, argument names and return types may also differ between the
-        implementations.
+    """Import transcript-level quantification files and convert them to gene-level expression estimates, correcting
+    for transcript length differences.
 
     Args:
         file_paths (List[Union[str, Path]]): The paths to the quantification files.

pytximport/utils/_replace_missing_average_transcript_length.py

@@ -1,7 +1,4 @@
-from logging import log, warning
-
 import numpy as np
-import pandas as pd
 import xarray as xr