+#
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+
+"""Test gmxapi._gmxapi file I/O routines."""
+import os
+import tempfile
+
+import pytest
+import gmxapi
+import gmxapi.simulation.fileio
+from gmxapi import _gmxapi
+
+
+@pytest.mark.usefixtures('cleandir')
+def test_core_read_tpr(spc_water_box):
+ tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
+ parameters: _gmxapi.SimulationParameters = tpr_filehandle.params()
+ assert 'nsteps' in parameters.extract()
+ assert 'foo' not in parameters.extract()
+ assert parameters.extract()['nsteps'] == 2
+
+
+@pytest.mark.usefixtures('cleandir')
+def test_core_rewrite_tprfile(spc_water_box):
+ """Test _gmxapi.rewrite_tprfile for update of end_time.
+
+ Set a new end time that is 5000 steps later than the original. Read dt
+ from file to avoid floating point round-off errors.
+
+ Transitively test gmx.fileio.read_tpr()
+ """
+ tpr_filename = spc_water_box
+ additional_steps = 5000
+ tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
+ params = tpr_filehandle.params().extract()
+ dt = params['dt']
+ nsteps = params['nsteps']
+ init_step = params['init-step']
+ initial_endtime = (init_step + nsteps) * dt
+ new_endtime = initial_endtime + additional_steps * dt
+ _, temp_filename = tempfile.mkstemp(suffix='.tpr')
+ _gmxapi.rewrite_tprfile(source=tpr_filename, destination=temp_filename, end_time=new_endtime)
+ tprfile = gmxapi.simulation.fileio.TprFile(temp_filename, 'r')
+ with tprfile as fh:
+ params = gmxapi.simulation.fileio.read_tpr(fh).parameters.extract()
+ dt = params['dt']
+ nsteps = params['nsteps']
+ init_step = params['init-step']
+ assert (init_step + nsteps) * dt == new_endtime
+
+ os.unlink(temp_filename)
+
+
+@pytest.mark.usefixtures('cleandir')
+def test_core_read_and_write_tpr_file(spc_water_box):
+ """Test gmx.fileio.write_tpr_file() using gmx.core API.
+ """
+ additional_steps = 5000
+
+ tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
+ sim_input: _gmxapi.SimulationParameters = tpr_filehandle.params()
+ params: dict = sim_input.extract()
+ nsteps = params['nsteps']
+ init_step = params['init-step']
+
+ # Choose a new nsteps to check integer parameter setting.
+ new_nsteps = init_step + additional_steps
+ # Choose a new dt to check floating point parameter setting
+ new_dt = params['dt'] * 2.
+
+ sim_input.set('nsteps', new_nsteps)
+ sim_input.set('dt', new_dt)
+
+ _, temp_filename = tempfile.mkstemp(suffix='.tpr')
+ _gmxapi.write_tprfile(temp_filename, sim_input)
+
+ tprfile = gmxapi.simulation.fileio.TprFile(temp_filename, 'r')
+ with tprfile as fh:
+ params = gmxapi.simulation.fileio.read_tpr(fh).parameters.extract()
+ # Note that we have chosen an exactly representable dt for spc_water_box.
+ # Otherwise, we would have to use pytest.approx with a suitable tolerance.
+ assert params['dt'] == new_dt
+ assert params['nsteps'] != nsteps
+ assert params['nsteps'] == new_nsteps
+
+ os.unlink(temp_filename)