Improve code coverage

pytximport/_cli.py

@@ -144,7 +144,22 @@
 def cli(  # type: ignore
     **kwargs,
 ) -> None:
-    """Convert transcript-level expression to gene-level expression."""
+    """Call the tximport function via the command line.
+
+    You can view the available options by running `pytximport --help`.
+
+    .. code-block:: bash
+
+        pytximport --help
+
+    For detailed information on pytximport's functionality, please refer to the README and online documentation.
+
+    Args:
+        **kwargs: The keyword arguments to pass to the tximport function.
+
+    Returns:
+        None
+    """
     # Add return_data to the kwargs with a default value of False
     kwargs["return_data"] = False
     kwargs["output_type"] = "anndata"

test/test_anndata_replicates.py

@@ -0,0 +1,39 @@
+"""Test importing salmon quantification files."""
+
+from pathlib import Path
+from typing import List
+
+import anndata as ad
+
+from pytximport import tximport
+
+
+def test_anndata_replicates(
+    fabry_disease_files: List[Path],
+) -> None:
+    """Test importing quantification files with inferential replicates with AnnData output.
+
+    Args:
+        fabry_disease_files (List[Path]): The paths to the quantification files.
+    """
+    fabry_directory = fabry_disease_files[0].parent
+
+    result = tximport(
+        fabry_disease_files,
+        "salmon",
+        fabry_directory / "transcript_gene_mapping_human.tsv",
+        ignore_transcript_version=True,
+        ignore_after_bar=True,
+        output_type="anndata",
+        inferential_replicates=True,
+        inferential_replicate_variance=True,
+        inferential_replicate_transformer=None,  # Do not recalculate counts but include the inferential replicates
+    )
+
+    assert isinstance(result, ad.AnnData), "The result is not an AnnData object."
+
+    # Check that variance is in the obsm
+    assert "variance" in result.obsm.keys()
+
+    # Check that inferential replicates is in the uns
+    assert "inferential_replicates" in result.uns.keys()