uninstall panacota before testing installation

.gitlab-ci.yml

@@ -18,7 +18,7 @@ build-from-ubuntu:
     - install
   script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
     - py.test test/test_install/test_make_ubuntu.py -xv
 
 build-from-barrnap:
@@ -28,7 +28,7 @@ build-from-barrnap:
     - install
   script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
     - py.test test/test_install/test_make_barrnap.py -xv
 
 build-from-prokka-quicktree:
@@ -48,7 +48,7 @@ build-from-prodigal:
     - install
   script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
     - py.test test/test_install/test_make_prodigal.py -xv
 
 build-from-test-image:
@@ -57,7 +57,7 @@ build-from-test-image:
     - install
   script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
     - pip install git+https://github.com/chasemc/ncbi-genome-download@4c5c24e27aa8123c7995890046b17b815da3571b 
     - py.test test/test_install/test_make_all-installed.py -xv
 
@@ -70,7 +70,7 @@ unit-test-ubuntu:
     - install
   before_script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
     - pip install git+https://github.com/chasemc/ncbi-genome-download@4c5c24e27aa8123c7995890046b17b815da3571b 
     - ./make
   script:
@@ -103,7 +103,7 @@ func-test-ubuntu:
     - install
   before_script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
     - pip install git+https://github.com/chasemc/ncbi-genome-download@4c5c24e27aa8123c7995890046b17b815da3571b 
     - ./make
   script:
@@ -137,7 +137,7 @@ coverage:
     - func-test-ubuntu
   before_script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
   script:
     - pwd
     - coverage combine .coverage.unit .coverage.functional
@@ -157,8 +157,7 @@ sphinx-doc:
     - master
     - documentation
   before_script:
-    - pip3 install -r requirements-dev.txt
-    - ./make
+    - ./make develop
   script:
     - cd doc/source
     - make html

test/test_install/test_make_all-installed.py

@@ -37,14 +37,17 @@ def test_install_panacota():
     """
     Test that when installing from a computer containing only all dependencies, it returns a message without any warning: everything is ok
     """
-    cmd = "python3 make"
-    error = "Error trying to install PanACoTA from base"
+    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("barrnap")
     assert utils.check_installed("prokka")
     assert utils.check_installed("mash")
     assert utils.check_installed("FastTreeMP")
     # Install panacota
+    cmd = "python3 make"
+    error = "Error trying to install PanACoTA from base"
     utils.run_cmd(cmd, error)
     assert utils.check_installed("PanACoTA")
     assert utils.check_installed("barrnap")
@@ -115,6 +118,9 @@ def test_upgrade_notinstalled():
     Test upgrading PanACoTA when dependencies are not installed (only barrnap),
     and PanACoTA is not installed. It just installs PanACoTA, without prokka dep
     """
+    cmd = "python3 make uninstall"
+    error = "Error trying to uninstall PanACoTa"
+    utils.run_cmd(cmd, error)
     assert utils.check_installed("barrnap")
     assert utils.check_installed("prokka")
     assert utils.check_installed("FastTreeMP")
@@ -167,6 +173,9 @@ def test_develop():
     """
     Test installing PanACoTA in developer mode, when prokka and barrnap are 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("barrnap")
     assert utils.check_installed("prokka")
@@ -220,6 +229,9 @@ def test_install_user():
     Test that when installing from a computer in user mode, it really installs
     PanACoTA in user mode (pip showing PanACoTA when asking for user installed packages)
     """
+    cmd = "python3 make uninstall"
+    error = "Error trying to uninstall PanACoTa"
+    utils.run_cmd(cmd, error)
     cmd = "python3 make --user"
     error = "Error trying to install PanACoTA from base"
     assert utils.check_installed("barrnap")