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refactored unit_test data access
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@ChiCheng45
ChiCheng45 committed Jan 16, 2024
1 parent 9f2bf7c commit 3c2d3ba
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Showing 15 changed files with 27 additions and 76 deletions.
15 changes: 3 additions & 12 deletions MDANSE/Tests/UnitTests/Analysis/test_dynamics.py
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Expand Up @@ -2,26 +2,17 @@
import tempfile
import os
from os import path

import pytest
from icecream import ic
import numpy as np

from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
from MDANSE.Framework.Jobs.IJob import IJob
from MDANSE.Framework.UserDefinitionStore import UD_STORE

from ..Data.data import short_traj

sys.setrecursionlimit(100000)
ic.disable()

_, just_filename = path.split(short_traj)

# now we have the following variables related to the trajectory:
# 1. short_traj (str) - full path to the trajectory
# 2. just_filename (str) - filename of the trajectory
# 3. trajectory (pytest.fixture) - returns an instance of HDFTrajectoryInputData
short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "Data",
"short_trajectory_after_changes.h5")


@pytest.fixture(scope="module")
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25 changes: 6 additions & 19 deletions MDANSE/Tests/UnitTests/Analysis/test_meansquare.py
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Expand Up @@ -2,24 +2,18 @@
import tempfile
import os
from os import path
import pytest
from icecream import ic
import numpy as np
import h5py
from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
from MDANSE.Framework.Jobs.IJob import IJob
from ..Data.data import short_traj


sys.setrecursionlimit(100000)
ic.disable()
short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "Data",
"short_trajectory_after_changes.h5")

_, just_filename = path.split(short_traj)

# now we have the following variables related to the trajectory:
# 1. short_traj (str) - full path to the trajectory
# 2. just_filename (str) - filename of the trajectory
# 3. trajectory (pytest.fixture) - returns an instance of HDFTrajectoryInputData

# Mean Square Displacements can accept many parameters, most of them optional
# settings['trajectory']=('hdf_trajectory',{})
Expand All @@ -33,14 +27,7 @@
# settings['running_mode']=('running_mode',{})


@pytest.fixture(scope="module")
def trajectory():
trajectory = HDFTrajectoryInputData(short_traj)
trajectory = short_traj
yield trajectory


def test_basic_meansquare(trajectory):
def test_basic_meansquare():
temp_name = tempfile.mktemp()
parameters = {}
parameters["frames"] = (0, 10, 1)
Expand All @@ -54,7 +41,7 @@ def test_basic_meansquare(trajectory):
os.remove(temp_name + ".h5")


def test_parallel_meansquare(trajectory):
def test_parallel_meansquare():
temp_name = tempfile.mktemp()
parameters = {}
parameters["frames"] = (0, 10, 1)
Expand All @@ -79,7 +66,7 @@ def test_parallel_meansquare(trajectory):
os.remove(temp_name2 + ".h5")


def test_atom_selection(trajectory):
def test_atom_selection():
temp_name = tempfile.mktemp()
parameters = {}
parameters["frames"] = (0, 10, 1)
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15 changes: 3 additions & 12 deletions MDANSE/Tests/UnitTests/Analysis/test_qvectors.py
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Expand Up @@ -2,27 +2,18 @@
import tempfile
import os
from os import path

import pytest
from icecream import ic
import numpy as np

from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
from MDANSE.Framework.QVectors.IQVectors import IQVectors
from MDANSE.Framework.Jobs.IJob import IJob
from MDANSE.Framework.UserDefinitionStore import UD_STORE

from ..Data.data import mol_traj as short_traj

sys.setrecursionlimit(100000)
ic.disable()

_, just_filename = path.split(short_traj)

# now we have the following variables related to the trajectory:
# 1. short_traj (str) - full path to the trajectory
# 2. just_filename (str) - filename of the trajectory
# 3. trajectory (pytest.fixture) - returns an instance of HDFTrajectoryInputData
short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "Data",
"short_trajectory_after_changes.h5")


@pytest.fixture(scope="module")
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12 changes: 4 additions & 8 deletions MDANSE/Tests/UnitTests/Analysis/test_resolutions.py
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Expand Up @@ -9,17 +9,13 @@
IInstrumentResolution,
)
from MDANSE.Framework.Jobs.IJob import IJob
from ..Data.data import mol_traj as short_traj


sys.setrecursionlimit(100000)
ic.disable()

_, just_filename = path.split(short_traj)

# now we have the following variables related to the trajectory:
# 1. short_traj (str) - full path to the trajectory
# 2. just_filename (str) - filename of the trajectory
# 3. trajectory (pytest.fixture) - returns an instance of HDFTrajectoryInputData
short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "Data",
"short_trajectory_after_changes.h5")


@pytest.fixture(scope="module")
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12 changes: 4 additions & 8 deletions MDANSE/Tests/UnitTests/Analysis/test_scattering.py
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Expand Up @@ -6,17 +6,13 @@
from icecream import ic
from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
from MDANSE.Framework.Jobs.IJob import IJob
from ..Data.data import mol_traj as short_traj


sys.setrecursionlimit(100000)
ic.disable()

_, just_filename = path.split(short_traj)

# now we have the following variables related to the trajectory:
# 1. short_traj (str) - full path to the trajectory
# 2. just_filename (str) - filename of the trajectory
# 3. trajectory (pytest.fixture) - returns an instance of HDFTrajectoryInputData
short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "Data",
"short_trajectory_after_changes.h5")


@pytest.fixture(scope="module")
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11 changes: 3 additions & 8 deletions MDANSE/Tests/UnitTests/Analysis/test_thermodynamics.py
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Expand Up @@ -8,18 +8,13 @@
import h5py
from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
from MDANSE.Framework.Jobs.IJob import IJob
from ..Data.data import short_traj


sys.setrecursionlimit(100000)
ic.disable()

_, just_filename = path.split(short_traj)

# now we have the following variables related to the trajectory:
# 1. short_traj (str) - full path to the trajectory
# 2. just_filename (str) - filename of the trajectory
# 3. trajectory (pytest.fixture) - returns an instance of HDFTrajectoryInputData
short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "Data",
"short_trajectory_after_changes.h5")


@pytest.fixture(scope="module")
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0 ...sts/UnitTests/molecules/CO2GAS-dump-1.pdb → ...SE/Tests/UnitTests/Data/CO2GAS-dump-1.pdb
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Empty file removed MDANSE/Tests/UnitTests/Data/__init__.py
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0 ...E/Tests/UnitTests/molecules/co2gas_md3.h5 → MDANSE/Tests/UnitTests/Data/co2gas_md3.h5
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6 changes: 0 additions & 6 deletions MDANSE/Tests/UnitTests/Data/data.py
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2 changes: 1 addition & 1 deletion MDANSE/Tests/UnitTests/molecules/test_chemistry.py
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Expand Up @@ -8,7 +8,7 @@


short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "co2gas_md3.h5")
os.path.dirname(os.path.realpath(__file__)), "..", "Data", "co2gas_md3.h5")


@pytest.fixture(scope="module")
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2 changes: 1 addition & 1 deletion MDANSE/Tests/UnitTests/molecules/test_connectivity.py
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Expand Up @@ -7,7 +7,7 @@


short_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "co2gas_md3.h5")
os.path.dirname(os.path.realpath(__file__)), "..", "Data", "co2gas_md3.h5")


@pytest.fixture(scope="module")
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3 changes: 2 additions & 1 deletion MDANSE/Tests/UnitTests/molecules/test_rdkit.py
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Expand Up @@ -10,7 +10,8 @@


fname = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "CO2GAS-dump-1.pdb")
os.path.dirname(os.path.realpath(__file__)), "..", "Data",
"CO2GAS-dump-1.pdb")


@pytest.fixture()
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