adapt tests

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")