changed multiprocessing test to NP data

pytest.ini

@@ -1,3 +1,3 @@
 [pytest]
-addopts = --ignore setup.py --doctest-modules --ignore=docs/plot_diffprefs_prior.py --ignore=tests/test_diffprefsbysite.py --ignore=tests/test_prepalignment.py --ignore=tests/test_phydms_modeladequacy_multiprocessing.py
+addopts = --ignore setup.py --doctest-modules --ignore=docs/plot_diffprefs_prior.py --ignore=tests/test_diffprefsbysite.py --ignore=tests/test_prepalignment.py
 # ignore script to create docs plot, requires `LaTeX`

tests/expected_modeladequacy_results/ExpCM_pvalues_seed0_mp.csv

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tests/test_phydms_modeladequacy_multiprocessing.py

@@ -30,40 +30,33 @@ class test_modeladequacy_ExpCM_mp(unittest.TestCase):
     """Runs model adequacy on an ExpCM with >1 CPU."""
     # run parameters
     MODEL = "ExpCM_{0}".format(os.path.join(os.path.abspath(os.path.dirname(__file__)),
-                               "modeladequacy_tests/HA_short_prefs_nsites10.csv"))
+                               "NP_data/NP_prefs_short.csv"))
     EXPECTED = os.path.join(os.path.abspath(os.path.dirname(__file__)),
-                            "expected_modeladequacy_results/ExpCM_pvalues_seed0_2000rep_pvalues.csv")
-    SEED = 0
+                            "expected_modeladequacy_results/ExpCM_pvalues_seed0_mp.csv")
     TREE = os.path.join(os.path.abspath(os.path.dirname(__file__)),
-                        "modeladequacy_tests/HA_short_nsites10_nseqs34_tree.newick")
-    NCPUS = 4
+                        "NP_data/NP_tree_short.newick")
+    NCPUS = 2
 
     def test_modeladequacy(self):
-        """Runs model adequacy and compares against expected results."""
         """Runs model adequacy and compares against expected results."""
         n_sim = 2000
+        seed = 0
         alignment = os.path.join(os.path.abspath(os.path.dirname(__file__)),
-                                 "modeladequacy_tests/HA_short_nsites10_nseqs34.fasta")
+                                 "NP_data/NP_alignment_short.fasta")
         outprefix = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                                  "_model_adequacy_results")
         cmd = ["phydms_modeladequacy", outprefix, alignment,
                self.MODEL, "--number_simulations", str(n_sim), "--tree",
-               self.TREE, "--seed", str(self.SEED), "--ncpus", str(self.NCPUS)]
+               self.TREE, "--seed", str(seed), "--ncpus", str(self.NCPUS)]
         subprocess.check_call(cmd)
 
-        final = (pd.read_csv("{0}_pvalues.csv".format(outprefix))
-                 .sort_values(by=["site", "metric"]))
-        expected = (pd.read_csv(self.EXPECTED)
-                    .sort_values(by=["site", "metric"]))
-
-        self.assertTrue(scipy.allclose(final["pvalue"], expected["pvalue"], atol=1e-2),
-                       " pvalue: Expected \n{0}\n \nvs.\n \n{1}.".format(
-                       expected["pvalue"].to_string(),
-                       final["pvalue"].to_string()))
-        self.assertTrue(scipy.allclose(final["qvalue"], expected["qvalue"], atol=1e-2),
-                       " qvalue: Expected \n{0}\n \nvs.\n \n{1}.".format(
-                       expected["qvalue"].to_string(),
-                       final["qvalue"].to_string()))
+        final = (pd.read_csv("{0}_pvalues.csv".format(outprefix)))
+        expected = (pd.read_csv(self.EXPECTED))
+        merged = pd.merge(final, expected, on=["site", "metric"], how='outer', suffixes=('_final', '_expected'))
+        merged = merged[["site", "metric", "pvalue_final", "pvalue_expected", "qvalue_final", "qvalue_expected"]]
+        self.assertTrue(scipy.allclose(merged["pvalue_expected"],
+                                       merged["pvalue_final"], atol=1e-3),
+                                        "Unexpected results: \n{0}".format(merged))
 
         # remove files
         for fname in glob.glob("{0}_*".format(outprefix)):