From 57e60e6b463550160b1937f4870c0209517c6eb9 Mon Sep 17 00:00:00 2001
From: gbouras13 <george.bouras@adelaide.edu.au>
Date: Wed, 23 Aug 2023 13:31:05 +0930
Subject: [PATCH] temp not tmp - it isnt timelimit

---
 tests/test_overall.py  | 4 ++--
 tests/test_proteins.py | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/test_overall.py b/tests/test_overall.py
index a42182d..cb1389c 100755
--- a/tests/test_overall.py
+++ b/tests/test_overall.py
@@ -75,7 +75,7 @@ def test_download(tmp_dir):
 def test_overall(tmp_dir):
     """test pharokka overall"""
     input_fasta: Path = f"{standard_data}/SAOMS1.fasta"
-    cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f"
+    cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {temp_dir} -t {threads} -f"
     exec_command(cmd)
 
 
@@ -135,7 +135,7 @@ def test_overall(tmp_dir):
 #     exec_command(cmd)
 
 
-# temp_dir = Path(f"{test_data}/fake_out")
+
 
 
 # class testFails(unittest.TestCase):
diff --git a/tests/test_proteins.py b/tests/test_proteins.py
index 6fba9aa..86bd2c8 100755
--- a/tests/test_proteins.py
+++ b/tests/test_proteins.py
@@ -26,7 +26,6 @@
 
 # test data
 test_data = Path("tests/test_data")
-
 database_dir = Path(f"{test_data}/database")
 overall_data = Path(f"{test_data}/overall")
 meta_data = Path(f"{test_data}/Meta_example")
@@ -45,6 +44,7 @@ def remove_directory(dir_path):
 def tmp_dir(tmpdir_factory):
     return tmpdir_factory.mktemp("tmp")
 
+temp_dir = Path(f"{proteins_data}/fake_out")
 
 def exec_command(cmnd, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
     """executes shell command and returns stdout if completes exit code 0
@@ -72,21 +72,21 @@ def test_download(tmp_dir):
 def test_proteins(tmp_dir):
     """test pharokka proteins"""
     input_fasta: Path = f"{proteins_data}/phanotate.faa"
-    cmd = f"pharokka_proteins.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f"
+    cmd = f"pharokka_proteins.py -i {input_fasta} -d {database_dir} -o {temp_dir} -t {threads} -f"
     exec_command(cmd)
 
 
 def test_proteins_hmm_only(tmp_dir):
     """test pharokka proteins hmm_only"""
     input_fasta: Path = f"{proteins_data}/phanotate.faa"
-    cmd = f"pharokka_proteins.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f --hmm_only"
+    cmd = f"pharokka_proteins.py -i {input_fasta} -d {database_dir} -o {temp_dir} -t {threads} -f --hmm_only"
     exec_command(cmd)
 
 
 def test_proteins_mmseqs_only(tmp_dir):
     """test pharokka proteins mmseqs_only"""
     input_fasta: Path = f"{proteins_data}/phanotate.faa"
-    cmd = f"pharokka_proteins.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f --mmseqs2_only"
+    cmd = f"pharokka_proteins.py -i {input_fasta} -d {database_dir} -o {temp_dir} -t {threads} -f --mmseqs2_only"
     exec_command(cmd)