From d07a166aa87d712afa0b4bc0de0c3ac552f5b0e8 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 7 Sep 2023 19:13:26 +0200
Subject: [PATCH] adapt tests
---
test/test_install/test_make_prodigal.py | 22 +++++++++-------------
1 file changed, 9 insertions(+), 13 deletions(-)
diff --git a/test/test_install/test_make_prodigal.py b/test/test_install/test_make_prodigal.py
index 7bd47bf2..0dc32b6e 100644
--- a/test/test_install/test_make_prodigal.py
+++ b/test/test_install/test_make_prodigal.py
@@ -20,7 +20,6 @@ def install_panacota():
error = "Error installing"
utils.run_cmd(cmd, error)
-
def teardown_function(function):
"""
Uninstall PanACoTA and installed dependencies at the end of each test
@@ -32,13 +31,15 @@ def teardown_function(function):
os.remove("install.log")
print("cleaning repo")
-
def test_install_panacota():
"""
Test that when installing from a computer containing only prodigal,it installs
PanACoTA, and returns the list of missing dependencies
"""
# check installed softs before installing panacota
+ cmd = "python3 make uninstall"
+ error = "Error trying to uninstall PanACoTa"
+ utils.run_cmd(cmd, error)
cmd = "python3 make"
error = "Error trying to install PanACoTA from base"
assert not utils.check_installed("barrnap")
@@ -141,6 +142,9 @@ def test_develop():
"""
Test installing PanACoTA in developer mode, when prodigal is already installed
"""
+ cmd = "python3 make uninstall"
+ error = "Error trying to uninstall PanACoTa"
+ utils.run_cmd(cmd, error)
assert not utils.check_installed("PanACoTA")
assert utils.check_installed("prodigal")
assert not utils.check_installed("prokka")
@@ -152,17 +156,6 @@ def test_develop():
assert utils.check_installed("prodigal")
assert not utils.check_installed("prokka")
assert not utils.check_installed("barrnap")
- cmd = "pip3 show PanACoTA"
- err = "error pip3"
- stdout = "stdout_pip3show.out"
- with open(stdout, "w") as stdof:
- utils.run_cmd(cmd, err, stdout=stdof, stderr=stdof)
- with open(stdout, "r") as stdof:
- for line in stdof:
- if line.startswith("Location"):
- loc = line.split()[-1]
- assert glob.glob(os.path.join(loc, r'PanACoTA*egg-info'))
- os.remove(stdout)
logfile = "install.log"
content = ["Installing developer packages needed for PanACoTA",
"- mash (for prepare subcommand, to filter genomes)",
@@ -199,6 +192,9 @@ def test_install_user():
Test that when installing from a computer in user mode, it really installs
PanACoTA in user mode
"""
+ cmd = "python3 make uninstall"
+ error = "Error trying to uninstall PanACoTa"
+ utils.run_cmd(cmd, error)
assert utils.check_installed("prodigal")
assert not utils.check_installed("barrnap")
assert not utils.check_installed("prokka")
--
GitLab