Merge branch 'update-ci' into 'master'

Update ci

See merge request !32

.gitlab-ci.yml

-image: docker.km3net.de/base/singularity-py3:3.5.3
+image: docker.km3net.de/base/python:3
 
 variables:
     GIT_SUBMODULE_STRATEGY: recursive
@@ -37,11 +37,11 @@ reset_test_image:
 
 .virtualenv_template: &virtualenv_definition |
   python -V
+  export SETUPTOOLS_USE_DISTUTILS=stdlib
   pip install virtualenv
   virtualenv venv
   source venv/bin/activate
   pip install -U pip setuptools yapf
-  if [ ! -f GiBUU.simg ]; then make buildremote; fi
   make install-dev
   pip list
   date
@@ -53,7 +53,7 @@ reset_test_image:
 
 
 test:
-    image: docker.km3net.de/base/singularity-py3:3.5.3
+    image: python:3
     stage: test
     tags:
         - docker
@@ -63,7 +63,7 @@ test:
     <<: *junit_definition
 
 code-style:
-    image: docker.km3net.de/base/singularity-py3:3.5.3
+    image: python:3 
     stage: test
     script:
         - *virtualenv_definition
@@ -71,7 +71,7 @@ code-style:
     allow_failure: true
 
 coverage:
-    image: docker.km3net.de/base/singularity-py3:3.5.3
+    image: python:3
     stage: coverage
     tags:
         - docker
@@ -116,7 +116,7 @@ release-image:
     - tags
 
 pages:
-    image: docker.km3net.de/base/python:3.6
+    image: docker.km3net.de/base/python:3
     stage: doc
     script:
         - make install-dev

km3buu/tests/test_config.py

@@ -32,7 +32,6 @@ path=/tmp/gseagen
 
 
 class TestConfig(unittest.TestCase):
-
     def setUp(self):
         self.cfg_tmpfile = NamedTemporaryFile(delete=False)
         self.mock_image_file = NamedTemporaryFile(delete=False)

km3buu/tests/test_ctrl.py

@@ -11,21 +11,24 @@ __email__ = "jschumann@km3net.de"
 __status__ = "Development"
 
 import csv
+import pytest
 import unittest
 import numpy as np
 from km3buu.jobcard import *
 from km3buu.ctrl import run_jobcard
 from tempfile import TemporaryDirectory, NamedTemporaryFile
-from os import listdir
+from os import listdir, environ
 from os.path import abspath, join, dirname
 from thepipe.logger import get_logger
 from km3net_testdata import data_path
 
 TESTDATA_DIR = data_path("gibuu")
 
+GIBUU_INSTALL_AVAILABLE = environ.get("CONTAINER_GIBUU_EXEC") is not None
 
-class TestCTRLbyJobcardFile(unittest.TestCase):
 
+@pytest.mark.skipif(not GIBUU_INSTALL_AVAILABLE, reason="GiBUU not installed")
+class TestCTRLbyJobcardFile(unittest.TestCase):
     def setUp(self):
         self.filename = join(TESTDATA_DIR, "km3net_testdata.job")
         self.output_dir = TemporaryDirectory()
@@ -48,8 +51,8 @@ class TestCTRLbyJobcardFile(unittest.TestCase):
         assert "EventOutput.Pert.00000001.root" in files
 
 
+@pytest.mark.skipif(not GIBUU_INSTALL_AVAILABLE, reason="GiBUU not installed")
 class TestCTRLbyJobcardObject(unittest.TestCase):
-
     def setUp(self):
         log = get_logger("ctrl.py")
         log.setLevel("INFO")

km3buu/tests/test_environment.py

@@ -19,7 +19,6 @@ from km3buu import DOCKER_URL, IMAGE_NAME
 
 
 class TestBuild(unittest.TestCase):
-
     def test_wrong_dir_path(self):
         wrong_path = "foobar"
         try:

km3buu/tests/test_geometry.py

@@ -17,14 +17,12 @@ import numpy as np
 
 
 class TestGeneralGeometry(unittest.TestCase):
-
     def test_abstract_init(self):
         with self.assertRaises(TypeError) as ctx:
             d = DetectorVolume()
 
 
 class TestSphere(unittest.TestCase):
-
     def setUp(self):
         self.detector_geometry = SphericalVolume(20, (2, 2, 2))
 
@@ -46,7 +44,6 @@ class TestSphere(unittest.TestCase):
 
 
 class TestCan(unittest.TestCase):
-
     def setUp(self):
         self.detector_geometry = CanVolume()
 

km3buu/tests/test_jobcard.py

@@ -12,15 +12,20 @@ __status__ = "Development"
 
 import unittest
 import numpy as np
+import pytest
+from os import environ
 from itertools import combinations
 from km3buu.jobcard import *
-from km3buu.ctrl import run_jobcard
 from km3buu.output import GiBUUOutput
 from tempfile import TemporaryFile, TemporaryDirectory
 
+GIBUU_INSTALL_AVAILABLE = environ.get("CONTAINER_GIBUU_EXEC") is not None
+
+if GIBUU_INSTALL_AVAILABLE:
+    from km3buu.ctrl import run_jobcard
 
-class TestJobcard(unittest.TestCase):
 
+class TestJobcard(unittest.TestCase):
     def setUp(self):
         self.test_jobcard = Jobcard()
         # Insert some test elements
@@ -50,7 +55,6 @@ class TestJobcard(unittest.TestCase):
 
 
 class TestNeutrinoEnergyRangeJobcard(unittest.TestCase):
-
     def setUp(self):
         self.test_fluxfile = TemporaryFile()
         self.test_Z = np.random.randint(1, 100)
@@ -101,7 +105,6 @@ class TestNeutrinoEnergyRangeJobcard(unittest.TestCase):
 
 
 class TestNeutrinoSingleEnergyJobcard(unittest.TestCase):
-
     def setUp(self):
         self.test_fluxfile = TemporaryFile()
         self.test_Z = np.random.randint(1, 100)
@@ -135,8 +138,8 @@ class TestNeutrinoSingleEnergyJobcard(unittest.TestCase):
                          not self.photon_propagation_flag)
 
 
+@pytest.mark.skipif(not GIBUU_INSTALL_AVAILABLE, reason="GiBUU not installed")
 class TestJobcardSeed(unittest.TestCase):
-
     def setUp(self):
         jc = generate_neutrino_jobcard(100,
                                        "CC",

km3buu/tests/test_output.py

@@ -37,7 +37,6 @@ except ModuleNotFoundError:
 
 
 class TestXSection(unittest.TestCase):
-
     def test_xsection_all(self):
         filename = join(TESTDATA_DIR, XSECTION_FILENAMES["all"])
         xsection = read_nu_abs_xsection(filename)
@@ -48,7 +47,6 @@ class TestXSection(unittest.TestCase):
 
 
 class TestGiBUUOutput(unittest.TestCase):
-
     def setup_class(self):
         self.output = GiBUUOutput(TESTDATA_DIR)
 
@@ -93,7 +91,6 @@ class TestGiBUUOutput(unittest.TestCase):
 @pytest.mark.skipif(not KM3NET_LIB_AVAILABLE,
                     reason="KM3NeT dataformat required")
 class TestOfflineFile(unittest.TestCase):
-
     def setUp(self):
         output = GiBUUOutput(TESTDATA_DIR)
         datafile = NamedTemporaryFile(suffix=".root")
@@ -148,7 +145,6 @@ class TestOfflineFile(unittest.TestCase):
 @pytest.mark.skipif(not KM3NET_LIB_AVAILABLE,
                     reason="KM3NeT dataformat required")
 class TestMultiFileOutput(unittest.TestCase):
-
     def setUp(self):
         output = GiBUUOutput(TESTDATA_DIR)
         datafile = NamedTemporaryFile(suffix=".root")

km3buu/tests/test_physics.py

@@ -28,7 +28,6 @@ MUON_TESTFILE = join(dirname(__file__), "data/muon_range_seawater.txt")
 
 
 class TestMuonRangeSeaWater(unittest.TestCase):
-
     def setUp(self):
         self.ref_values = np.loadtxt(MUON_TESTFILE).T
 
@@ -40,7 +39,6 @@ class TestMuonRangeSeaWater(unittest.TestCase):
 
 
 class TestVisEnergyParticle(unittest.TestCase):
-
     def setUp(self):
         with open(PARTICLE_TESTFILE, "r") as f:
             tmp = f.readline()
@@ -59,7 +57,6 @@ class TestVisEnergyParticle(unittest.TestCase):
 
 
 class TestVisEnergyWeightFunctions(unittest.TestCase):
-
     def setUp(self):
         self.ref_values = np.loadtxt(FUNCTIONS_TESTFILE).T
 

km3buu/tests/test_propagation.py

@@ -28,7 +28,6 @@ pp.RandomGenerator.get().set_seed(1234)
 
 @pytest.mark.skip(reason="CI boost lib problem")
 class TestTauPropagation(unittest.TestCase):
-
     def setUp(self):
         data = ak.Array({
             "lepOut_E": [