Restore stdin

MANIFEST.in

@@ -3,6 +3,7 @@ include LICENSE
 include ChangeLog.md
 include Makefile
 include pyproject.toml
+include cli_test.sh
 
 graft micov
 graft ci

Makefile

@@ -2,7 +2,7 @@
 
 test:
 	pytest micov
-
+	bash cli_test.sh
 lint:
 	ruff check micov setup.py
 	check-manifest

cli_test.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+xzcat micov/tests/test_data/test.sam.xz | micov compress > from_stdin
+micov compress --data micov/tests/test_data/test.sam.xz > from_args
+cmp --silent <(sort from_stdin) <(sort from_args)
+if [[ $? -ne 0 ]]; then
+    echo "Files are different"
+    exit 1
+fi

micov/cli.py

@@ -6,7 +6,6 @@
 import os
 import io
 import sys
-import tqdm
 from glob import glob
 from ._io import (parse_genome_lengths, parse_taxonomy, set_taxonomy_as_id,
                   parse_qiita_coverages, parse_sam_to_df, write_qiita_cov,
@@ -105,7 +104,7 @@ def compress(data, output, disable_compression, lengths, taxonomy):
         if taxonomy is not None:
             taxonomy = parse_taxonomy(taxonomy)
 
-    if os.path.isdir(data):
+    if data is not None and os.path.isdir(data):
         file_list = (glob(data + "/*.sam")
                     + glob(data + '/*.sam.xz')
                     + glob(data + '/*.sam.gz'))

micov/tests/test_cov.py

@@ -1,7 +1,7 @@
 import unittest
 from micov._cov import compress, coverage_percent
 from micov._constants import (BED_COV_SCHEMA, COLUMN_GENOME_ID,
-                              GENOME_LENGTH_SCHEMA,
+                              GENOME_LENGTH_SCHEMA, COLUMN_START,
                               GENOME_COVERAGE_SCHEMA)
 import polars as pl
 import polars.testing as plt
@@ -28,7 +28,7 @@ def test_compress(self):
                              ['G456', 400, 500]],
                             orient='row',
                             schema=BED_COV_SCHEMA.dtypes_flat)
-        obs = compress(data).sort(COLUMN_GENOME_ID)
+        obs = compress(data).sort(COLUMN_GENOME_ID).sort(COLUMN_START)
         plt.assert_frame_equal(obs, exp)
 
     def test_coverage_percent(self):