Improve tests

tests/test_class.py

@@ -1,4 +1,4 @@
-from subprocess import CalledProcessError
+from pathlib import Path
 
 import pandas as pd
 import pytest
@@ -7,6 +7,8 @@
 
 
 class TestCDHIT:
+    cdhit_installed = Path("~/cd-hit/cd-hit-est").expanduser().exists()
+
     @pytest.fixture(autouse=True)
     def init_cdhit(self):
         self.cdhit = _class.CDHIT(prog="cd-hit-est", path="~/cd-hit")
@@ -15,17 +17,16 @@ def test_invalid_name(self):
         with pytest.raises(ValueError):
             _class.CDHIT(prog="")
 
+    @pytest.mark.skipif(not cdhit_installed, reason="FileNotFoundError")
     def test_help(self, capsys):
-        try:
-            self.cdhit.help()
-            assert len(capsys.readouterr().out) > 0
-        except FileNotFoundError:
-            pass
+        self.cdhit.help()
+        assert len(capsys.readouterr().out) > 0
 
     def test_set_options(self):
         self.cdhit.set_options(c=0.9, n=10)
         assert self.cdhit.options == {"c": 0.9, "n": 10}
 
+    @pytest.mark.skipif(not cdhit_installed, reason="FileNotFoundError")
     def test_cluster_return_type(self):
         assert self.cdhit.options == {}
         fasta_in = pd.DataFrame(
@@ -34,9 +35,6 @@ def test_cluster_return_type(self):
                 "sequence": ["ACGTA", "CGTC", "CCGCC"],
             }
         )
-        try:
-            fasta, clstr = self.cdhit.cluster(fasta_in)
-            assert isinstance(fasta, pd.DataFrame)
-            assert isinstance(clstr, pd.DataFrame)
-        except (CalledProcessError, FileNotFoundError):
-            pass
+        fasta, clstr = self.cdhit.cluster(fasta_in)
+        assert isinstance(fasta, pd.DataFrame)
+        assert isinstance(clstr, pd.DataFrame)

tests/test_commands.py

@@ -1,6 +1,6 @@
 import os
 from pathlib import Path
-from subprocess import CalledProcessError, CompletedProcess
+from subprocess import CompletedProcess
 
 import pytest
 
@@ -14,6 +14,9 @@
 CCGCC"""
 
 
+os.environ["CD_HIT_DIR"] = "~/cd-hit"
+
+
 @pytest.fixture
 def cdhit_temp_files():
     test_dir = Path(__file__).resolve().parent
@@ -25,23 +28,23 @@ def cdhit_temp_files():
     out_path.with_suffix(".clstr").unlink(missing_ok=True)
 
 
+@pytest.mark.skipif(
+    not Path("~/cd-hit/cd-hit-est").expanduser().exists(),
+    reason="FileNotFoundError",
+)
 def test_cd_hit(cdhit_temp_files):
-    os.environ["CD_HIT_DIR"] = "~/cd-hit"
     in_path, out_path = cdhit_temp_files
     in_path.write_text(FASTA)
-    try:
-        res = _commands.cd_hit_est(i=in_path, o=out_path)
-        assert isinstance(res, CompletedProcess)
-    except (CalledProcessError, FileNotFoundError):
-        pass
+    res = _commands.cd_hit_est(i=in_path, o=out_path)
+    assert isinstance(res, CompletedProcess)
 
 
+@pytest.mark.skipif(
+    not Path("~/cd-hit/cd-hit-div").expanduser().exists(),
+    reason="FileNotFoundError",
+)
 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
+    with pytest.warns(UserWarning, match="Warning"):
+        _commands.cd_hit_div(i=in_path, o=out_path, div=1)