From 51a1e7931f82126e3c767b1ae19e6cfdb98e478a Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Sun, 16 Jun 2024 23:43:36 -0700
Subject: [PATCH] improved warning management

- ignore some warnings in pytest
- check for some gromacs.UsageWarning explicitly
---
 pyproject.toml      | 11 +++++++++--
 tests/test_setup.py | 46 ++++++++++++++++++++++++++-------------------
 2 files changed, 36 insertions(+), 21 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0a07a2df..13e99342 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -84,6 +84,13 @@ rmprefix = "release-"
 file = "gromacs/_version.py"
 
 
-
 [tool.black]
-extend-exclude = "tests/(test_core|fileformats/test_convert)\\.py"
\ No newline at end of file
+extend-exclude = "tests/(test_core|fileformats/test_convert)\\.py"
+
+
+[tool.pytest.ini_options]
+filterwarnings = [
+	       "ignore::gromacs.AutoCorrectionWarning",
+	       "ignore::gromacs.LowAccuracyWarning",
+	       "ignore::numkit.LowAccuracyWarning",
+	       ]
diff --git a/tests/test_setup.py b/tests/test_setup.py
index ba2cfbd6..dbf3828b 100644
--- a/tests/test_setup.py
+++ b/tests/test_setup.py
@@ -61,13 +61,17 @@ def energy_minimize(solvate, low_performance):
     TMPDIR, solvate_args = solvate
     nt = 2 if low_performance else 0
     with TMPDIR.as_cwd():
-        em_args = gromacs.setup.energy_minimize(
-            mdrun_args={"nt": nt},
-            integrator="steep",
-            emtol=5000,
-            maxwarn=1,
-            **solvate_args,
-        )
+        with pytest.warns(
+            gromacs.UsageWarning,
+            match="Unprocessed mdp option are interpreted as options for grompp",
+        ):
+            em_args = gromacs.setup.energy_minimize(
+                mdrun_args={"nt": nt},
+                integrator="steep",
+                emtol=5000,
+                maxwarn=1,
+                **solvate_args,
+            )
     return TMPDIR, em_args
 
 
@@ -106,18 +110,22 @@ def test_energy_minimize_custom_mdp(
     TMPDIR, solvate_args = solvate
     nt = 2 if low_performance else 0
     with TMPDIR.as_cwd():
-        try:
-            em_args = gromacs.setup.energy_minimize(
-                mdrun_args={"nt": nt}, mdp=mdp, emtol=5000, **solvate_args
-            )
-        except gromacs.exceptions.GromacsError as err:
-            # sometimes the em does not converge at all, e.g. 5.02988e+04 on atom 3277;
-            # (happens on Travis Linux with Gromacs 4.6.5 but not locally or on Travis OSX) so we
-            # re-run with a ridiculous tolerance so that we can at least test that the whole
-            # function can run to completion
-            em_args = gromacs.setup.energy_minimize(
-                mdrun_args={"nt": nt}, mdp=mdp, emtol=6e4, **solvate_args
-            )
+        with pytest.warns(
+            gromacs.UsageWarning,
+            match="Unprocessed mdp option are interpreted as options for grompp",
+        ):
+            try:
+                em_args = gromacs.setup.energy_minimize(
+                    mdrun_args={"nt": nt}, mdp=mdp, emtol=5000, **solvate_args
+                )
+            except gromacs.exceptions.GromacsError as err:
+                # sometimes the em does not converge at all, e.g. 5.02988e+04 on atom 3277;
+                # (happens on Travis Linux with Gromacs 4.6.5 but not locally or on Travis OSX) so we
+                # re-run with a ridiculous tolerance so that we can at least test that the whole
+                # function can run to completion
+                em_args = gromacs.setup.energy_minimize(
+                    mdrun_args={"nt": nt}, mdp=mdp, emtol=6e4, **solvate_args
+                )
     assert os.path.exists(em_args["struct"])
     assert os.path.exists(em_args["top"])
     assert em_args["mainselection"] == '"Protein"'