Allow any pytest version take 2

carsus/conftest.py

@@ -66,12 +66,38 @@ def pytest_configure(config):
 
 
 def pytest_addoption(parser):
-    parser.addoption("--runslow", action="store_true",
-                     help="include running slow tests during run")
-    parser.addoption("--test-db", dest='test-db', default=None,
-                     help="filename for the testing database")
-    parser.addoption("--refdata", dest='refdata', default=None,
-                     help="carsus-refdata folder location")
+    parser.addoption(
+        "--runslow", 
+        action="store_true", 
+        default=False,
+        help="include running slow tests during run"
+    )
+    parser.addoption(
+        "--test-db",
+        dest="test-db",
+        default=None,
+        help="filename for the testing database",
+    )
+    parser.addoption(
+        "--refdata", dest="refdata", default=None, help="carsus-refdata folder location"
+    )
+
+
+def pytest_collection_modifyitems(config, items):
+    skip_slow = pytest.mark.skip(reason="need --runslow option to run")
+    skip_not_with_refdata = pytest.mark.skip(
+        reason="carsus-refdata folder location not specified"
+    )
+    skip_not_with_testdb = pytest.mark.skip(
+        reason="filename for the testing database not specified"
+    )
+    for item in items:
+        if "slow" in item.keywords and not config.getoption("--runslow"):
+            item.add_marker(skip_slow)
+        if "with_refdata" in item.keywords and not config.getoption("--refdata"):
+            item.add_marker(skip_not_with_refdata)
+        if "with_test_db" in item.keywords and not config.getoption("--test-db"):
+            item.add_marker(skip_not_with_testdb)
 
 
 @pytest.fixture

carsus/io/tests/test_chianti.py

@@ -5,10 +5,6 @@
 from carsus.model import Level, Ion, Line, ECollision
 
 
-slow = pytest.mark.skipif(
-    not pytest.config.getoption("--runslow"), reason="need --runslow option to run"
-)
-
 
 @pytest.fixture
 def ch_ingester(memory_session):
@@ -45,7 +41,7 @@ def test_chianti_reader_read_collisions(self, ch_ion_reader):
         return ch_ion_reader.collisions
 
 
-@slow
+@pytest.mark.slow
 @pytest.mark.parametrize(
     "atomic_number, ion_charge, levels_count", [(10, 1, 138), (17, 3, 5)]
 )
@@ -59,7 +55,7 @@ def test_chianti_ingest_levels_count(
     assert len(ion.levels) == levels_count
 
 
-@slow
+@pytest.mark.slow
 @pytest.mark.parametrize("atomic_number, ion_charge, lines_count", [(10, 1, 1999)])
 def test_chianti_ingest_lines_count(
     memory_session, ch_ingester, atomic_number, ion_charge, lines_count
@@ -77,7 +73,7 @@ def test_chianti_ingest_lines_count(
     assert cnt == lines_count
 
 
-@slow
+@pytest.mark.slow
 @pytest.mark.parametrize("atomic_number, ion_charge, e_col_count", [(10, 1, 9453)])
 def test_chianti_ingest_e_col_count(
     memory_session, ch_ingester, atomic_number, ion_charge, e_col_count

carsus/io/tests/test_cmfgen.py

@@ -14,13 +14,10 @@
 
 from carsus.io.cmfgen.util import *
 
-with_refdata = pytest.mark.skipif(
-    not pytest.config.getoption("--refdata"), reason="--refdata folder not specified"
-)
 data_dir = os.path.join(os.path.dirname(__file__), "data")
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.fixture()
 def si1_reader():
     return CMFGENReader.from_config(
@@ -40,7 +37,7 @@ def cmfgen_refdata_fname(refdata_path, path):
     return os.path.join(refdata_path, "cmfgen", subdirectory, fname)
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 @pytest.mark.parametrize(
     "path",
@@ -55,7 +52,7 @@ def test_CMFGENEnergyLevelsParser(cmfgen_refdata_fname):
     return parser.base
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 @pytest.mark.parametrize(
     "path",
@@ -72,7 +69,7 @@ def test_CMFGENOscillatorStrengthsParser(cmfgen_refdata_fname):
     return parser.base
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 @pytest.mark.parametrize(
     "path",
@@ -86,7 +83,7 @@ def test_CMFGENCollisionalStrengthsParser(cmfgen_refdata_fname):
     return parser.base
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.parametrize(
     "path",
     [
@@ -102,7 +99,7 @@ def test_CMFGENPhoCrossSectionsParser(cmfgen_refdata_fname):
     return parser.base[0]
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 @pytest.mark.parametrize(
     "path",
@@ -116,7 +113,7 @@ def test_CMFGENHydLParser(cmfgen_refdata_fname):
     return parser.base
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 @pytest.mark.parametrize(
     "path",
@@ -130,31 +127,31 @@ def test_CMFGENHydGauntBfParser(cmfgen_refdata_fname):
     return parser.base
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 def test_reader_lines(si1_reader):
     return si1_reader.lines
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 def test_reader_levels(si1_reader):
     return si1_reader.levels
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 def test_reader_collisions(si1_reader):
     return si1_reader.collisions
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 def test_reader_cross_sections_squeeze(si1_reader):
     return si1_reader.cross_sections
 
 
-@with_refdata
+@pytest.mark.with_refdata
 @pytest.mark.array_compare(file_format="pd_hdf")
 def test_reader_ionization_energies(si1_reader):
     return si1_reader.ionization_energies.to_frame()

carsus/io/tests/test_output_tardis.py

@@ -9,10 +9,7 @@
 from carsus.io.output.tardis_ import AtomData
 from carsus.model import DataSource, Ion
 
-with_test_db = pytest.mark.skipif(
-    not pytest.config.getoption("--test-db"),
-    reason="--testing database was not specified"
-)
+
 
 @pytest.fixture
 def atom_data(test_session, chianti_short_name):
@@ -115,13 +112,13 @@ def test_atom_data_chianti_ions_subset(memory_session):
                              chianti_ions="He 1; N 5; Si 1")
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_atom_data_wo_chianti_ions_attributes(atom_data_be, test_session):
     assert atom_data_be.chianti_ions == list()
     assert test_session.query(atom_data_be.chianti_ions_table).count() == 0
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_atom_data_only_be(atom_data_be):
     assert all([atomic_number == 4 for atomic_number in
                 atom_data_be.atom_masses["atomic_number"].values.tolist()])
@@ -133,7 +130,7 @@ def test_atom_data_only_be(atom_data_be):
                 atom_data_be.lines["atomic_number"].values.tolist()])
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_atom_data_join_on_chianti_ions_table(test_session, atom_data):
 
     # This join operation leads to an empty chianti_ions list
@@ -148,7 +145,7 @@ def test_atom_data_join_on_chianti_ions_table(test_session, atom_data):
     assert set(chianti_ions) == set([(2,1), (7,5)])
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_atom_data_two_instances_same_session(
         test_session,
         chianti_short_name):
@@ -167,7 +164,7 @@ def test_atom_data_two_instances_same_session(
     atom_data2.chianti_ions_table
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, exp_mass", [
     (2, 4.002602 * u.u),
     (4, 9.0121831 * u.u),
@@ -184,7 +181,7 @@ def test_create_atom_masses(atom_masses, atomic_number, exp_mass):
     )
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, ion_number, exp_ioniz_energy", [
     (2, 1,  54.41776311 * u.eV),
     (4, 2, 153.896198 * u.eV),
@@ -201,7 +198,7 @@ def test_create_ionizatinon_energies(ionization_energies, atomic_number, ion_num
     )
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, ion_number, ionization_energy",[
     (2, 1, 54.41776311 * u.eV),
     (4, 2, 153.896198 * u.eV),
@@ -216,7 +213,7 @@ def test_create_levels_filter_auto_ionizing_levels(levels, atomic_number, ion_nu
     assert all(levels_energies < ionization_energy)
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, ion_number, level_number, exp_energy, exp_g, exp_metastable_flag",[
     # Kurucz levels
     (4, 2, 0, 0.0 * u.Unit("cm-1"), 1, True),
@@ -248,7 +245,7 @@ def test_create_levels(levels, atomic_number, ion_number, level_number,
     assert metastable_flag == exp_metastable_flag
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, ion_number, level_number_lower, level_number_upper, exp_wavelength, exp_loggf",[
     # Kurucz lines
     (14, 1, 0, 57, 81.8575 * u.Unit("nm"), -1.92),
@@ -270,7 +267,7 @@ def test_create_lines(lines, atomic_number, ion_number, level_number_lower, leve
     assert_almost_equal(loggf, exp_loggf)
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, ion_number, level_number_lower, level_number_upper, exp_wavelength, exp_loggf",[
     # Kurucz lines with wavelength above 2000 Angstrom
     (14, 1, 8, 83, 2015.574293 * u.Unit("angstrom"), -0.120),
@@ -287,7 +284,7 @@ def test_create_lines_convert_air2vacuum(lines, atomic_number, ion_number, level
     assert_quantity_allclose(wavelength, exp_wavelength)
     assert_almost_equal(loggf, exp_loggf)
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, ion_number, level_number_lower, level_number_upper", [
     # Default loggf_threshold = -3
     # Kurucz lines
@@ -304,7 +301,7 @@ def test_create_lines_loggf_treshold(lines, atomic_number, ion_number, level_num
         assert lines.loc[(atomic_number, ion_number, level_number_lower, level_number_upper)]
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number", [2, 14, 30])
 def test_levels_create_artificial_fully_ionized(levels, atomic_number):
     levels = levels.set_index(["atomic_number", "ion_number", "level_number"])
@@ -314,22 +311,22 @@ def test_levels_create_artificial_fully_ionized(levels, atomic_number):
     assert metastable
 
 # ToDo: Implement real tests
-@with_test_db
+@pytest.mark.with_test_db
 def test_create_collisions(collisions):
     assert True
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_create_macro_atom(macro_atom):
     assert True
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_create_macro_atom_ref(macro_atom_references):
     assert True
 
 
-@with_test_db
+@pytest.mark.with_test_db
 @pytest.mark.parametrize("atomic_number, ion_number, source_level_number", [
     (2, 2, 0),
     (5, 5, 0),
@@ -347,12 +344,12 @@ def test_create_macro_atom_references_levels_wo_lines(macro_atom_references, ato
     assert all([count == 0 for count in [count_up, count_down, count_total]])
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_create_zeta_data(zeta_data):
     assert True
 
 
-@with_test_db
+@pytest.mark.with_test_db
 def test_atom_data_to_hdf(atom_data, hdf5_path):
     atom_data.to_hdf(hdf5_path, store_atom_masses=True, store_ionization_energies=True,
                      store_levels=True, store_lines=True, store_macro_atom=True,

carsus_env3.yml

@@ -49,7 +49,7 @@ dependencies:
   - pandoc
 
   # Test/Coverage
-  - pytest =4
+  - pytest
   - pytest-cov
   - pytest-astropy
   - epassaro::pytest-arraydiff

pytest.ini

@@ -0,0 +1,5 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')
+    with_refdata: mark tests as needing refdata path to run
+    with_test_db: mark tests as needing test_db path to run