Merge pull request #1 from yuanx749/warning

Issue warnings

pycdhit/__init__.py

@@ -4,7 +4,7 @@
 from ._commands import *  # noqa: F403
 from ._io import *  # noqa: F403
 
-VERSION = "1.0.0"
+VERSION = "1.1.0"
 
 __all__ = [  # noqa: F405
     "CommandBase",

pycdhit/_commands.py

@@ -2,6 +2,7 @@
 
 import os
 import subprocess
+import warnings
 from itertools import chain
 from pathlib import Path
 
@@ -40,7 +41,7 @@ def _format_program(name: str, path: str = None):
 
 def _run(command):
     try:
-        return subprocess.run(
+        completed_process = subprocess.run(
             command,
             capture_output=True,
             check=True,
@@ -53,6 +54,9 @@ def _run(command):
     except FileNotFoundError:
         print(command)
         raise
+    if "Warning" in completed_process.stdout:
+        warnings.warn(completed_process.stdout)
+    return completed_process
 
 
 def _create_function(name: str, func_name: str, env_var: str):

tests/test_commands.py

@@ -34,3 +34,14 @@ def test_cd_hit(cdhit_temp_files):
         assert isinstance(res, CompletedProcess)
     except (CalledProcessError, FileNotFoundError):
         pass
+
+
+def test_warning(cdhit_temp_files):
+    os.environ["CD_HIT_DIR"] = "~/cd-hit"
+    in_path, out_path = cdhit_temp_files
+    in_path.write_text(FASTA)
+    try:
+        with pytest.warns(UserWarning, match="Warning"):
+            _commands.cd_hit_div(i=in_path, o=out_path, div=1)
+    except (CalledProcessError, FileNotFoundError):
+        pass