Intiial commit to scaling function updates.

CI/memory_scaling/test_scaling_coefficients.py

@@ -26,12 +26,117 @@
 Module to test scaling coefficients.
 """
 import pytest
+from zinchub import DataHub
+import pandas as pd
 
 import mdsuite
+import mdsuite.transformations
+
+import sqlite3
+
+import numpy as np
+
+
+def _build_atomwise(data_scaling: int, system: bool = False):
+ """
+ Build a numpy array of atom-wise data in steps of MBs.
+
+ Parameters
+ ----------
+ data_scaling : int
+ Number of atoms in the data e.g. zeroth array of the data. 1 atom is 1/10
+ of a MB of data.
+ system : bool
+ If true, the returned array should be (n_confs, 3)
+
+ Returns
+ -------
+ data_array : np.ones
+ A numpy array of ones that matches close to 1/10 * data_scaling MBs in
+ size (~98%).
+ Notes
+ -----
+ TODO: When moved to (confs, n_atoms, dim), this will need to be updated to take the
+ first column as atoms otherwise the memory scaling will be wrong.
+
+ """
+ if system:
+ return np.ones((data_scaling * 4096, 3))
+ else:
+ return np.ones((data_scaling, 4096, 3))
+
+
+@pytest.fixture(scope="session")
+def traj_file(tmp_path_factory) -> str:
+ """Download trajectory file into a temporary directory and keep it for all tests"""
+ temporary_path = tmp_path_factory.getbasetemp()
+
+ NaCl = DataHub(url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q")
+ NaCl.get_file(path=temporary_path)
+
+ return (temporary_path / NaCl.file_raw).as_posix()
 
 
 @pytest.fixture()
 def mdsuite_project(tmp_path) -> mdsuite.Project:
+ """
+ Build an MDSuite project with all data stored in a temp directory for easier
+ cleanup after the test.
+
+ Returns
+ -------
+ project : mdsuite.Project
+ MDSuite project to be used in the tests.
+ """
  project = mdsuite.Project(storage_path=tmp_path.as_posix())
+ project.add_experiment("NaCl", simulation_data=traj_file)
+
+ scaling_sizes = [10, 100, 500, 1000]
 
  return project
+
+
+def get_memory_usage(database: str, callable_name: str) -> float:
+ """
+ Get the memory used from the dumped sql database.
+
+ Parameters
+ ----------
+ database : str
+ Path to the sqlite database that will be read.
+ callable_name : str
+ Name of the function being measured and therefore, what memory value to
+ return.
+
+ Returns
+ -------
+ memory : float
+ memory used during the calculation.
+ """
+ with sqlite3.connect(database) as db:
+ data = pd.read_sql_query("SELECT * from TEST_METRICS", db)
+
+ data = data.loc[data['ITEM'] == callable_name]
+
+ return data['MEM_USAGE']
+
+
+def test_rdf_memory(mdsuite_project):
+ """
+ Test the memory of the RDF.
+
+ Parameters
+ ----------
+ mdsuite_project : mdsuite.Project
+ An mdsuite project with stored files in a tmp directory.
+
+ Returns
+ -------
+
+ """
+ memory_array = np.zeros((2,))
+ mdsuite_project.run.RadialDistributionFunction(plot=False)
+ memory = get_memory_usage('pymon.db', test_rdf_memory.__name__)
+ memory_array[0] = memory
+
+ print(memory_array)

mdsuite/experiment/experiment.py

@@ -607,7 +607,7 @@ def _store_metadata(self, metadata: TrajectoryMetadata, update_with_pubchempy=Fa
  ----------
  metadata: TrajectoryMetadata
  update_with_pubchempy: bool
- Load data from pubchempy and add it to fill missing infomration
+ Load data from pubchempy and add it to fill missing information.
  """
  # new trajectory: store all metadata and construct a new database
  self.temperature = metadata.temperature