Cleanup: Fix linting and typing errors and update docs.

3 files changed, 24 insertions, 28 deletions

diff --git a/README.org b/README.org
index a0202dc..d0ccbf5 100644
--- a/README.org
+++ b/README.org
@@ -65,14 +65,14 @@ flask run
 
 *** Checks
 
-Run tests with:
+Run unit tests with:
 #+BEGIN_SRC shell
-  pytest
+  pytest -k unit_test
 #+END_SRC
 
 To run the linter over the code base, run:
 #+BEGIN_SRC shell
-  pylint *.py tests quality_control qc_app scripts
+  pylint *.py tests quality_control qc_app r_qtl scripts
 #+END_SRC
 
 To check for correct type usage in the application, run:
diff --git a/r_qtl/errors.py b/r_qtl/errors.py
index 648611e..20c5ced 100644
--- a/r_qtl/errors.py
+++ b/r_qtl/errors.py
@@ -1,5 +1,4 @@
 """R/qtl and R/qtl2 error types."""
-from collections import namedtuple
 
 class RQTLError(Exception):
     """Base class for R/qtl and R/qtl2 errors."""
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index ec7a954..22cf62c 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -2,16 +2,16 @@
 import io
 import csv
 import json
-import yaml
-from pathlib import Path
+from zipfile import ZipFile
 from functools import reduce
-from zipfile import ZipFile, ZipInfo, is_zipfile
-from typing import Any, List, Union, Iterator, Iterable
+from typing import Iterator, Iterable, Callable
 
-from r_qtl.errors import InvalidFormat
+import yaml
 
 from quality_control.parsing import take
 
+from r_qtl.errors import InvalidFormat
+
 def thread_op(value, *functions):
     """Thread the `value` through the sequence of `functions`."""
     return reduce(lambda result, func: func(result), functions, value)
@@ -80,19 +80,22 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
             lines = (line.strip().split(cdata.get("sep", ","))
                      for line in filter(lambda line: not line.startswith("#"),
                                          io.TextIOWrapper(genofile)))
-            id_line = next(lines)
-            id_key, samples = id_line[0], id_line[1:]
-            def __organise_by_id__(acc, item):
-                row = acc.get(item[id_key], {})
-                return {**acc, item[id_key]: {**row, **item}}
-            for _key, row in reduce(# type: ignore[var-annotated]
-                    __organise_by_id__,
-                    (row
-                     for batch in __n_batch__(lines, 300)
-                     for line in batch
-                     for row in __merge__(id_key, samples, line)),
-                    {}).items():
-                yield row
+            try:
+                id_line = next(lines)
+                id_key, samples = id_line[0], id_line[1:]
+                def __organise_by_id__(acc, item):
+                    row = acc.get(item[id_key], {})
+                    return {**acc, item[id_key]: {**row, **item}}
+                for _key, row in reduce(# type: ignore[var-annotated]
+                        __organise_by_id__,
+                        (row
+                         for batch in __n_batch__(lines, 300)
+                         for line in batch
+                         for row in __merge__(id_key, samples, line)),
+                        {}).items():
+                    yield row
+            except StopIteration:
+                return None
 
 def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> tuple[dict, ...]:
     """Read gmap files to get the genome mapping data"""
@@ -125,9 +128,3 @@ def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> tuple[dict, ...]:
         lambda gmap, row: gmap + (dict(zip(headers, row)),),
         zip(*(line[1:] for line in lines)),
         tuple())
-
-def read_r_qtl2_files(filepath: Path):
-    """Read R/qtl2 format zip files."""
-    with ZipFile(filepath, "r") as zfile:
-        cf = control_data(zfile)
-        raise NotImplementedError("Implementation is incomplete.")