TST: Switch to pytest, simplify CI (#225)

* Switch nose to pytest (nose is deprecated) * Remove conda metachannel code path (macOS) on travis because it doesn't seem to impact performance * Switch to Xenial on all travis tests: https://docs.travis-ci.com/user/reference/xenial/#differences-from-the-trusty-images
pycalphad · Jul 19, 2019 · 74d8917 · 74d8917
1 parent 21be98a
commit 74d8917
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diff --git a/.coveragerc b/.coveragerc
diff --git a/.travis.yml b/.travis.yml
@@ -6,12 +6,16 @@ notifications:
 
 matrix:
     include:
-        - python: 2.7
-        - python: 3.6
+        - name: "Python 2.7.15 on Xenial Linux"
+          python: 2.7           # this works for Linux but is ignored on macOS or Windows
+          dist: xenial
+        - name: "Python 3.6.1 on Xenial Linux"
+          python: 3.6           # this works for Linux but is ignored on macOS or Windows
+          dist: xenial
           env: DEPLOY_ENC_LABEL=e64cfe3b4e81
         - name: "Python 3.7.1 on Xenial Linux"
           python: 3.7           # this works for Linux but is ignored on macOS or Windows
-          dist: xenial          # required for Python >= 3.7
+          dist: xenial
         - language: generic
           os: osx
           env: TRAVIS_PYTHON_VERSION=2.7
@@ -34,20 +38,8 @@ install:
       . $HOME/miniconda2/etc/profile.d/conda.sh
       conda deactivate
       conda activate condaenv
-      # Use a conda-forge metachannel for speed, including only dependencies
-      # of pycalphad. See https://github.com/regro/conda-metachannel
-      # For some reason, conda-metachannel is breaking Linux by not picking
-      # up some packages (e.g. libgfortran-ng), which I think come from
-      # defaults. Only use conda metachannel on Mac.
-      if [ "$TRAVIS_OS_NAME" == "osx" ]; then
-        echo "!!! Installing pycalphad dependencies via conda metachannel"
-        conda install  --yes --override-channels -c https://metachannel.conda-forge.org/conda-forge/nose,pycalphad,python-symengine python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib nose pandas sympy pyparsing dask dill xarray cython cyipopt symengine python-symengine
-      else
-        echo "!!! Installing pycalphad dependencies via conda the normal way"
-        # I think the problem is that libgfortran-ng from defaults is not picked up. add those to the metachannel
-        conda install --yes python=$TRAVIS_PYTHON_VERSION gxx_linux-64 numpy scipy matplotlib nose pandas sympy pyparsing dask dill python-symengine
-        conda install --yes xarray cython cyipopt
-      fi
+      echo "!!! Installing pycalphad dependencies via conda"
+      conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib pytest pytest-cov pandas sympy pyparsing dask dill python-symengine xarray cython cyipopt
       echo "!!! pip pycalphad as editable"
       pip install -e .
 
@@ -60,8 +52,8 @@ script:
       conda list
       echo "!!! matplotlib py27 fix"
       echo 'backend : Agg' > matplotlibrc
-      echo "!!! running nosetests"
-      nosetests --with-coverage
+      echo "!!! running pytest"
+      pytest --cov=pycalphad
       echo "!!! Running ci/deploy script"
       bash ci/deploy.sh
       coveralls
diff --git a/appveyor.yml b/appveyor.yml
@@ -46,11 +46,11 @@ install:
   - "conda config --add channels conda-forge"
   - "conda config --add channels pycalphad"
   # install pycalphad and dependencies
-  - "conda install --yes -n condaenv --quiet vc=14 pip setuptools nose numpy pandas scipy sympy pyparsing matplotlib xarray 'tinydb>=3.8' cython cyipopt libpython symengine python-symengine"
+  - "conda install --yes -n condaenv --quiet vc=14 pip setuptools pytest numpy pandas scipy sympy pyparsing matplotlib xarray 'tinydb>=3.8' cython cyipopt libpython symengine python-symengine"
   # Hack to force compiler: https://github.com/pypa/pip/issues/18#issuecomment-73703672
   - "pip install --global-option build_ext --global-option --compiler=msvc --editable ."
 
 build: false
 
 test_script:
-  - "python -c \"import nose ; nose.main()\" -s -v pycalphad"
+  - "python -c \"import pytest ; pytest.main()\" -s -v pycalphad"
diff --git a/conda_recipe/meta.yaml b/conda_recipe/meta.yaml
@@ -29,8 +29,7 @@ requirements:
     - setuptools
     - matplotlib
     - pandas
-    - nose
-    - mock
+    - pytest
     - xarray >=0.11.2
     - sympy ==1.4
     - pyparsing

diff --git a/pycalphad/tests/test_calculate.py b/pycalphad/tests/test_calculate.py
@@ -3,7 +3,7 @@
 Model quantities correctly.
 """
 
-import nose.tools
+import pytest
 from pycalphad import Database, calculate, Model
 import numpy as np
 try:
@@ -24,11 +24,10 @@ def test_surface():
     calculate(DBF, ['AL', 'CR', 'NI'], 'L12_FCC',
                 T=1273., mode='numpy')
 
-@nose.tools.raises(AttributeError)
 def test_unknown_model_attribute():
     "Sampling an unknown model attribute raises exception."
-    calculate(DBF, ['AL', 'CR', 'NI'], 'L12_FCC',
-                T=1400.0, output='_fail_')
+    with pytest.raises(AttributeError):
+        calculate(DBF, ['AL', 'CR', 'NI'], 'L12_FCC', T=1400.0, output='_fail_')
 
 def test_statevar_upcast():
     "Integer state variable values are cast to float."
@@ -67,31 +66,26 @@ def test_calculate_some_phases_filtered():
     calculate(ALFE_DBF, ['AL', 'VA'], ['FCC_A1', 'AL13FE4'], T=1200, P=101325)
 
 
-@nose.tools.raises(ConditionError)
 def test_calculate_raises_with_no_active_phases_passed():
     """Passing inactive phases to calculate() raises a ConditionError."""
     # Phase cannot be built without FE
-    calculate(ALFE_DBF, ['AL', 'VA'], ['AL13FE4'], T=1200, P=101325)
+    with pytest.raises(ConditionError):
+        calculate(ALFE_DBF, ['AL', 'VA'], ['AL13FE4'], T=1200, P=101325)
 
 
-@nose.tools.raises(ValueError)
 def test_incompatible_model_instance_raises():
     "Calculate raises when an incompatible Model instance built with a different phase is passed."
     comps = ['AL', 'CR', 'NI']
     phase_name = 'L12_FCC'
     mod = Model(DBF, comps, 'LIQUID')  # Model instance does not match the phase
-    calculate(DBF, comps, phase_name, T=1400.0, output='_fail_', model=mod)
+    with pytest.raises(ValueError):
+        calculate(DBF, comps, phase_name, T=1400.0, output='_fail_', model=mod)
 
 
-@nose.tools.raises(ValueError)
 def test_single_model_instance_raises():
     "Calculate raises when a single Model instance is passed with multiple phases."
     comps = ['AL', 'CR', 'NI']
     phase_name = 'L12_FCC'
     mod = Model(DBF, comps, 'L12_FCC')  # Model instance does not match the phase
-    calculate(DBF, comps, ['LIQUID', 'L12_FCC'], T=1400.0, output='_fail_', model=mod)
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run()
+    with pytest.raises(ValueError):
+        calculate(DBF, comps, ['LIQUID', 'L12_FCC'], T=1400.0, output='_fail_', model=mod)
diff --git a/pycalphad/tests/test_database.py b/pycalphad/tests/test_database.py
@@ -2,7 +2,7 @@
 The test_database module contains tests for the Database object.
 """
 from __future__ import print_function
-import warnings
+import pytest
 import hashlib
 import os
 from copy import deepcopy
@@ -14,15 +14,13 @@
 from pycalphad.io.tdb import expand_keyword
 from pycalphad.io.tdb import _apply_new_symbol_names, DatabaseExportError
 from pycalphad.tests.datasets import ALCRNI_TDB, ALFE_TDB, ALNIPT_TDB, ROSE_TDB, DIFFUSION_TDB
-import nose.tools
 try:
     # Python 2
     from StringIO import StringIO
 except ImportError:
     # Python 3
     from io import StringIO
 
-warnings.simplefilter("always", UserWarning) # so we can test warnings
 
 #
 # DATABASE LOADING TESTS
@@ -87,36 +85,28 @@ def test_export_import():
 def test_incompatible_db_warns_by_default():
     "Symbol names too long for Thermo-Calc warn and write the database as given by default."
     test_dbf = Database.from_string(INVALID_TDB_STR, fmt='tdb')
-    with warnings.catch_warnings(record=True) as w:
+    with pytest.warns(UserWarning, match='Ignoring that the following function names are beyond the 8 character TDB limit'):
         invalid_dbf = test_dbf.to_string(fmt='tdb')
-        assert len(w) >= 1
-        expected_string_fragment = 'Ignoring that the following function names are beyond the 8 character TDB limit'
-        assert any([expected_string_fragment in str(warning.message) for warning in w])
     assert test_dbf == Database.from_string(invalid_dbf, fmt='tdb')
 
-@nose.tools.raises(DatabaseExportError)
 def test_incompatible_db_raises_error_with_kwarg_raise():
     "Symbol names too long for Thermo-Calc raise error on write with kwarg raise."
     test_dbf = Database.from_string(INVALID_TDB_STR, fmt='tdb')
-    test_dbf.to_string(fmt='tdb', if_incompatible='raise')
+    with pytest.raises(DatabaseExportError):
+        test_dbf.to_string(fmt='tdb', if_incompatible='raise')
 
 def test_incompatible_db_warns_with_kwarg_warn():
     "Symbol names too long for Thermo-Calc warn and write the database as given."
     test_dbf = Database.from_string(INVALID_TDB_STR, fmt='tdb')
-    with warnings.catch_warnings(record=True) as w:
+    with pytest.warns(UserWarning, match='Ignoring that the following function names are beyond the 8 character TDB limit'):
         invalid_dbf = test_dbf.to_string(fmt='tdb', if_incompatible='warn')
-        assert len(w) >= 1
-        expected_string_fragment = 'Ignoring that the following function names are beyond the 8 character TDB limit'
-        assert any([expected_string_fragment in str(warning.message) for warning in w])
     assert test_dbf == Database.from_string(invalid_dbf, fmt='tdb')
 
+@pytest.mark.filterwarnings("error")
 def test_incompatible_db_ignores_with_kwarg_ignore():
     "Symbol names too long for Thermo-Calc are ignored the database written as given."
     test_dbf = Database.from_string(INVALID_TDB_STR, fmt='tdb')
-    with warnings.catch_warnings(record=True) as w:
-        invalid_dbf = test_dbf.to_string(fmt='tdb', if_incompatible='ignore')
-        not_expected_string_fragment = 'Ignoring that the following function names are beyond the 8 character TDB limit'
-        assert all([not_expected_string_fragment not in str(warning.message) for warning in w])
+    invalid_dbf = test_dbf.to_string(fmt='tdb', if_incompatible='ignore')
     assert test_dbf == Database.from_string(invalid_dbf, fmt='tdb')
 
 def test_incompatible_db_mangles_names_with_kwarg_fix():
@@ -158,33 +148,32 @@ def test_tdb_content_after_line_end_is_neglected():
     test_dbf = Database.from_string(tdb_line_ending_str, fmt='tdb')
     assert len(test_dbf._parameters) == 3
 
-def _remove_file_with_name_testwritedb():
+@pytest.fixture
+def _testwritetdb():
     fname = 'testwritedb.tdb'
+    yield fname  # run the test
     os.remove(fname)
 
-@nose.tools.with_setup(None, _remove_file_with_name_testwritedb)
-@nose.tools.raises(FileExistsError)
-def test_to_file_defaults_to_raise_if_exists():
+def test_to_file_defaults_to_raise_if_exists(_testwritetdb):
     "Attempting to use Database.to_file should raise by default if it exists"
-    fname = 'testwritedb.tdb'
+    fname = _testwritetdb
     test_dbf = Database(ALNIPT_TDB)
     test_dbf.to_file(fname)  # establish the initial file
-    test_dbf.to_file(fname)  # test if_exists behavior
+    with pytest.raises(FileExistsError):
+        test_dbf.to_file(fname)  # test if_exists behavior
 
-@nose.tools.with_setup(None, _remove_file_with_name_testwritedb)
-@nose.tools.raises(FileExistsError)
-def test_to_file_raises_with_bad_if_exists_argument():
+def test_to_file_raises_with_bad_if_exists_argument(_testwritetdb):
     "Database.to_file should raise if a bad behavior string is passed to if_exists"
-    fname = 'testwritedb.tdb'
+    fname = _testwritetdb
     test_dbf = Database(ALNIPT_TDB)
     test_dbf.to_file(fname)  # establish the initial file
-    test_dbf.to_file(fname, if_exists='TEST_BAD_ARGUMENT')  # test if_exists behavior
+    with pytest.raises(FileExistsError):
+        test_dbf.to_file(fname, if_exists='TEST_BAD_ARGUMENT')  # test if_exists behavior
 
-@nose.tools.with_setup(None, _remove_file_with_name_testwritedb)
-def test_to_file_overwrites_with_if_exists_argument():
-    import time
+def test_to_file_overwrites_with_if_exists_argument(_testwritetdb):
     "Database.to_file should overwrite if 'overwrite' is passed to if_exists"
-    fname = 'testwritedb.tdb'
+    import time
+    fname = _testwritetdb
     test_dbf = Database(ALNIPT_TDB)
     test_dbf.to_file(fname)  # establish the initial file
     inital_modification_time = os.path.getmtime(fname)
@@ -193,20 +182,20 @@ def test_to_file_overwrites_with_if_exists_argument():
     overwrite_modification_time = os.path.getmtime(fname)
     assert overwrite_modification_time > inital_modification_time
 
-@nose.tools.raises(ValueError)
 def test_unspecified_format_from_string():
     "from_string: Unspecified string format raises ValueError."
-    Database.from_string(ALCRNI_TDB)
+    with pytest.raises(ValueError):
+        Database.from_string(ALCRNI_TDB)
 
-@nose.tools.raises(NotImplementedError)
 def test_unknown_format_from_string():
     "from_string: Unknown import string format raises NotImplementedError."
-    Database.from_string(ALCRNI_TDB, fmt='_fail_')
+    with pytest.raises(NotImplementedError):
+        Database.from_string(ALCRNI_TDB, fmt='_fail_')
 
-@nose.tools.raises(NotImplementedError)
 def test_unknown_format_to_string():
     "to_string: Unknown export file format raises NotImplementedError."
-    REFERENCE_DBF.to_string(fmt='_fail_')
+    with pytest.raises(NotImplementedError):
+        REFERENCE_DBF.to_string(fmt='_fail_')
 
 def test_load_from_stringio():
     "Test database loading from a file-like object."
@@ -218,25 +207,25 @@ def test_load_from_stringio_from_file():
     test_tdb = Database.from_file(StringIO(ALCRNI_TDB), fmt='tdb')
     assert test_tdb == REFERENCE_DBF
 
-@nose.tools.raises(ValueError)
 def test_unspecified_format_from_file():
     "from_file: Unspecified format for file descriptor raises ValueError."
-    Database.from_file(StringIO(ALCRNI_TDB))
+    with pytest.raises(ValueError):
+        Database.from_file(StringIO(ALCRNI_TDB))
 
-@nose.tools.raises(ValueError)
 def test_unspecified_format_to_file():
     "to_file: Unspecified format for file descriptor raises ValueError."
-    REFERENCE_DBF.to_file(StringIO())
+    with pytest.raises(ValueError):
+        REFERENCE_DBF.to_file(StringIO())
 
-@nose.tools.raises(NotImplementedError)
 def test_unknown_format_from_file():
     "from_string: Unknown import file format raises NotImplementedError."
-    Database.from_string(ALCRNI_TDB, fmt='_fail_')
+    with pytest.raises(NotImplementedError):
+        Database.from_string(ALCRNI_TDB, fmt='_fail_')
 
-@nose.tools.raises(NotImplementedError)
 def test_unknown_format_to_file():
     "to_file: Unknown export file format raises NotImplementedError."
-    REFERENCE_DBF.to_file(StringIO(), fmt='_fail_')
+    with pytest.raises(NotImplementedError):
+        REFERENCE_DBF.to_file(StringIO(), fmt='_fail_')
 
 def test_expand_keyword():
     "expand_keyword expands command abbreviations."
@@ -402,12 +391,12 @@ def test_species_are_parsed_in_tdb_phases_and_parameters():
     assert test_dbf_reread.phases['T2SL'].constituents == ({Species('AL+3')}, {Species('O-2')})
     assert len(test_dbf_reread._parameters.search(where('constituent_array') == ((Species('AL+3'),),(Species('O-2'),)))) == 1
 
-@nose.tools.raises(ParseException)
 def test_tdb_missing_terminator_element():
     tdb_str = """$ Note missing '!' in next line
                ELEMENT ZR   BCT_A5
                FUNCTION EMBCCTI    298.15 -39.72; 6000 N !"""
-    Database(tdb_str)
+    with pytest.raises(ParseException):
+        Database(tdb_str)
 
 
 def test_database_parsing_of_floats_with_no_values_after_decimal():

diff --git a/pycalphad/tests/test_energy.py b/pycalphad/tests/test_energy.py
@@ -3,16 +3,15 @@
 correct abstract syntax tree for the energy.
 """
 
-import nose.tools
+import pytest
 from sympy import S
-from pycalphad import Database, Model, calculate, ReferenceState
+from pycalphad import Database, Model, ReferenceState
 from pycalphad.core.utils import make_callable
 from pycalphad.tests.datasets import ALCRNI_TDB, FEMN_TDB, ALFE_TDB, \
     CRFE_BCC_MAGNETIC_TDB, VA_INTERACTION_TDB, CUMG_TDB
 from pycalphad.core.errors import DofError
 import pycalphad.variables as v
 import numpy as np
-import warnings
 
 DBF = Database(ALCRNI_TDB)
 ALFE_DBF = Database(ALFE_TDB)
@@ -21,12 +20,12 @@
 CUMG_DBF = Database(CUMG_TDB)
 VA_INTERACTION_DBF = Database(VA_INTERACTION_TDB)
 
-@nose.tools.raises(ValueError)
 def test_sympify_safety():
     "Parsing malformed strings throws exceptions instead of executing code."
     from pycalphad.io.tdb import _sympify_string
     teststr = "().__class__.__base__.__subclasses__()[216]('ls')"
-    _sympify_string(teststr) # should throw ParseException
+    with pytest.raises(ValueError):
+        _sympify_string(teststr)
 
 
 def calculate_output(model, variables, output, mode='sympy'):
@@ -234,12 +233,12 @@ def test_reference_energy_of_unary_twostate_einstein_magnetic_is_zero():
     check_output(m, statevars, 'GMR', 0.0)
 
 
-@nose.tools.raises(DofError)
 def test_underspecified_refstate_raises():
     """A Model cannot be shifted to a new reference state unless references for all pure elements are specified."""
     m = Model(FEMN_DBF, ['FE', 'MN', 'VA'], 'LIQUID')
     refstates = [ReferenceState(v.Species('FE'), 'LIQUID')]
-    m.shift_reference_state(refstates, FEMN_DBF)
+    with pytest.raises(DofError):
+        m.shift_reference_state(refstates, FEMN_DBF)
 
 
 def test_reference_energy_of_binary_twostate_einstein_is_zero():