Skip slow tests unless --run-slow is specified.

docs/install.rst

@@ -5,28 +5,34 @@ Installation
 Requirements
 ^^^^^^^^^^^^
 
-`sbpy` has the following requirements that will be automatically taken
-care of with installation using pip:
+`sbpy` has the following requirements that will be automatically taken care of
+with installation using pip:
 
 * Python 3.6 or later
 * `numpy <https://numpy.org/>`__ 1.16.0 or later
 * pytest 3.1 or later
 * `astropy <https://www.astropy.org/>`__
-* `astroquery <https://astroquery.readthedocs.io/en/latest/>`__ 0.4.1.dev5892 or later: For retrieval of online data, e.g., ephemerides and orbits.
-* `scipy <https://www.scipy.org/>`__: For numerical integrations in `sbpy.activity.gas` and `sbpy.photometry`, among others.
-* `synphot <https://github.com/spacetelescope/synphot_refactor>`__ 0.1.3 or later: For calibration with respect to the Sun and Vega, filtering spectra through bandpasses.
-
-The following packages will have to be installed manually, if the user
-wants to use them:
-
-* `oorb <https://github.com/oorb/oorb/tree/master/python>`__: For
-  orbit transformations (`~sbpy.data.Orbit.oo_transform`) and
-  propagations (`~sbpy.data.Orbit.oo_propagate`), as well as
-  ephemerides calculations (`~sbpy.data.Ephem.from_oo`).
-* `pyradex <https://github.com/keflavich/pyradex>`__: For non-LTE
-  production rate calculation related to cometary activity
-  (`~sbpy.activity.gas.NonLTE`).
-* `ginga <https://ejeschke.github.io/ginga/>`__ and `photutils <https://photutils.readthedocs.io/en/stable/>`__: To interactively enhance images of comets with the `~sbpy.imageanalysis.CometaryEnhancement` Ginga plugin.
+* `astroquery <https://astroquery.readthedocs.io/en/latest/>`__ 0.4.1.dev5892 or
+  later: For retrieval of online data, e.g., ephemerides and orbits.
+* `scipy <https://www.scipy.org/>`__: For numerical integrations in
+  `sbpy.activity.gas` and `sbpy.photometry`, among others.
+* `synphot <https://github.com/spacetelescope/synphot_refactor>`__ 0.1.3 or
+  later: For calibration with respect to the Sun and Vega, filtering spectra
+  through bandpasses.
+
+The following packages will have to be installed manually, if the user wants to
+use them:
+
+* `oorb <https://github.com/oorb/oorb/tree/master/python>`__: For orbit
+  transformations (`~sbpy.data.Orbit.oo_transform`) and propagations
+  (`~sbpy.data.Orbit.oo_propagate`), as well as ephemerides calculations
+  (`~sbpy.data.Ephem.from_oo`).
+* `pyradex <https://github.com/keflavich/pyradex>`__: For non-LTE production
+  rate calculation related to cometary activity (`~sbpy.activity.gas.NonLTE`).
+* `ginga <https://ejeschke.github.io/ginga/>`__ and `photutils
+  <https://photutils.readthedocs.io/en/stable/>`__: To interactively enhance
+  images of comets with the `~sbpy.imageanalysis.CometaryEnhancement` Ginga
+  plugin.
 
 
 Using pip
@@ -49,9 +55,9 @@ The latest development version of `sbpy` can be easily installed using
 Using GitHub
 ^^^^^^^^^^^^
 
-This way of installing `sbpy` is recommended if you plan to contribute
-to the module. The current development version of `sbpy` can be
-obtained from `GitHub <https://github.com/NASA-Planetary-Science/sbpy>`__ using
+This way of installing `sbpy` is recommended if you plan to contribute to the
+module. The current development version of `sbpy` can be obtained from `GitHub
+<https://github.com/NASA-Planetary-Science/sbpy>`__ using
 
 .. code-block:: bash
 
@@ -63,9 +69,41 @@ This will create a new directory (``sbpy/``). In this directory, run
 
     $ python setup.py install --user
 
-in order to use `sbpy` in your default Python environment. If you plan to work on the code and always want to use the latest version of your code, you can install it with
+in order to use `sbpy` in your default Python environment. If you plan to work
+on the code and always want to use the latest version of your code, you can
+install it with
 
 
 .. code-block:: bash
 
     $ python setup.py develop --user
+
+
+Running tests
+^^^^^^^^^^^^^
+
+To verify your installation is properly working, run `sbpy`'s testing suite.
+
+First, install the required testing packages by using the "test" option, e.g.,
+`sbpy[test]`:
+
+.. code-block:: bash
+
+    # for testing a stable package
+    $ pip install sbpy[test]
+
+    # for testing a development packge from a GitHub
+    $ pip install sbpy[test]@git+https://github.com/NASA-Planetary-Science/sbpy.git
+
+Next, test with pytest:
+
+.. code-block:: bash
+
+    $ pytest --pyargs sbpy
+
+Add the `--remote-data` option to aslo run tests that require a network
+connection, and `-m "not slow"` to skip any tests marked as slow.
+
+It is recommended that developers use `tox` for testing in order to use
+controlled environments.  See the ``astropy` testing guidelines
+<https://docs.astropy.org/en/latest/development/testguide.html>`__ for more.

sbpy/activity/gas/tests/test_core.py

@@ -127,9 +127,11 @@ def test_column_density_small_angular_aperture(self):
         eph = dict(delta=1 * u.au)
         parent = 1e4 * u.km
         N_avg = 2 * Haser(Q, v, parent).column_density(rho, eph)
-        rho_km = (rho * eph['delta'] * 725.24 * u.km / u.arcsec / u.au).to('km')
+        rho_km = (rho * eph['delta'] * 725.24 *
+                  u.km / u.arcsec / u.au).to('km')
         ideal = Q / v / 2 / rho_km
-        assert np.isclose(N_avg.to_value('1/m2'), ideal.to_value('1/m2'), rtol=0.001)
+        assert np.isclose(N_avg.to_value('1/m2'),
+                          ideal.to_value('1/m2'), rtol=0.001)
 
     def test_column_density(self):
         """
@@ -412,12 +414,12 @@ def test_grid_count(self):
             'tau_d': 101730 * u.s,
             'v_outflow': 1 * u.km/u.s,
             'sigma': 3e-16 * u.cm**2
-            })
+        })
         # Fragment molecule is OH
         fragment = Phys.from_dict({
             'tau_T': photo_timescale('OH') * 0.93,
             'v_photo': 1.05 * u.km/u.s
-            })
+        })
 
         coma = VectorialModel(base_q=base_q,
                               parent=parent,
@@ -441,21 +443,23 @@ def test_total_number_large_aperture(self):
             'tau_d': 101730 * u.s,
             'v_outflow': 1 * u.km/u.s,
             'sigma': 3e-16 * u.cm**2
-            })
+        })
         # Fragment molecule is OH
         fragment = Phys.from_dict({
             'tau_T': photo_timescale('OH') * 0.93,
             'v_photo': 1.05 * u.km/u.s
-            })
+        })
 
         coma = VectorialModel(base_q=base_q,
                               parent=parent,
                               fragment=fragment)
 
         fragment_theory = coma.vmodel['num_fragments_theory']
-        ap = core.CircularAperture((coma.vmodel['max_grid_radius'].value) * u.m)
+        ap = core.CircularAperture(
+            (coma.vmodel['max_grid_radius'].value) * u.m)
         assert np.isclose(fragment_theory, coma.total_number(ap), rtol=0.02)
 
+    @pytest.mark.slow
     def test_model_symmetry(self):
         """
             The symmetry of the model allows the parent production to be
@@ -486,12 +490,12 @@ def test_model_symmetry(self):
             'tau_d': 101730 * u.s,
             'v_outflow': 1 * u.km/u.s,
             'sigma': 3e-16 * u.cm**2
-            })
+        })
         # Fragment molecule is OH
         fragment = Phys.from_dict({
             'tau_T': photo_timescale('OH') * 0.93,
             'v_photo': 1.05 * u.km/u.s
-            })
+        })
 
         coma = VectorialModel(base_q=base_production*(1/u.s),
                               parent=parent,
@@ -508,12 +512,12 @@ def test_model_symmetry(self):
             'tau_d': 101730 * u.s,
             'v_outflow': 1 * u.km/u.s,
             'sigma': 3e-16 * u.cm**2
-            })
+        })
         # Fragment molecule is OH
         fragment_check = Phys.from_dict({
             'tau_T': photo_timescale('OH') * 0.93,
             'v_photo': 1.05 * u.km/u.s
-            })
+        })
         coma_check = VectorialModel(base_q=calculated_q*(1/u.s),
                                     parent=parent_check,
                                     fragment=fragment_check)

sbpy/activity/gas/tests/test_prodrate_remote.py

@@ -64,6 +64,7 @@ def data_path(filename):
     return os.path.join(data_dir, filename)
 
 
+@pytest.mark.slow
 @remote_data
 def test_remote_prodrate_simple_hcn():
 
@@ -151,9 +152,7 @@ def test_remote_prodrate_simple_ch3oh():
     assert np.all(err < 0.35)
 
 
-# Issue #296
-# MSK: disabling test as CO and HCN are no longer present in LAMDA database(?)
-@pytest.mark.skip
+@pytest.mark.slow
 @remote_data
 def test_einstein():
 
@@ -184,7 +183,7 @@ def test_einstein():
 
         mol_name = mol['NAME'].data[0]
 
-        lam_search = Lamda.query(mol=mol_name.lower())
+        lam_search = Lamda().query(mol=mol_name.lower())
 
         lam_result = lam_search[1]
 

sbpy/conftest.py

@@ -9,6 +9,7 @@
 
 import os
 
+import pytest
 from astropy.version import version as astropy_version
 
 # For Astropy 3.0 and later, we can use the standalone pytest plugin
@@ -48,6 +49,11 @@ def pytest_configure(config):
         packagename = os.path.basename(os.path.dirname(__file__))
         TESTED_VERSIONS[packagename] = __version__
 
+    config.addinivalue_line(
+        "markers",
+        "slow: marks tests as slow (deselect with '-m \"not slow\"')"
+    )
+
 # Uncomment the last two lines in this block to treat all DeprecationWarnings
 # as exceptions. For Astropy v2.0 or later, there are 2 additional keywords,
 # as follow (although default should work for most cases).

sbpy/data/tests/test_obs_remote.py

@@ -14,6 +14,7 @@
 @pytest.mark.remote_data
 class TestObsfromMPC:
 
+    @pytest.mark.slow
     def test_simple(self):
         # asteroid
         data = Obs.from_mpc('12893')