some file clean up.

phasecalculator/classes/phase.py

@@ -15,14 +15,13 @@
 #    You should have received a copy of the GNU Affero General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
-Created on Tue Jan  7 16:34:17 2020
+Class for representing Phase.
 
 @author: Mark
 """
 
 import logging
 from lxml import etree
-import functools
 from phasecalculator.classes.xmlnamespacing import (
     PHASE_CALCULATOR,
     PHASE_CALC_NAMESPACE_DICT,

phasecalculator/phasecalculatorcli.py

@@ -23,13 +23,13 @@ Script with CLI for phasecalculator.
 import logging
 import argparse
 import textwrap
+import puresolventinformation.information as pureinf
 import phasecalculator.runners.phasecalculatorrunner as phasecrun
 import phasecalculator.io.systemcollectionprocessor as sysproc
 import phasecalculator.io.phasecsvconverter as csvconv
 from phasecalculator.classes.runtimeinformation import RuntimeInformation
 from phasecalculator.classes.outputinformation import OutputInformation
 from phasecalculator.classes.system import System, SystemCollection
-import puresolventinformation.information as pureinf
 
 logging.basicConfig()
 LOGGER = logging.getLogger(__name__)
@@ -38,12 +38,6 @@ LOGGER.setLevel(logging.INFO)
 INFO_LOGGER = logging.getLogger(__name__)
 INFO_LOGGER.setLevel(logging.INFO)
 
-phasecrun.LOGGER.setLevel(logging.INFO)
-phasecrun.phasexmlrun.LOGGER.setLevel(logging.DEBUG)
-phasecrun.fgiprun.phaserun.LOGGER.setLevel(logging.INFO)
-# phasecrun.fgiprun.fgipanalysis.solvmapgen.LOGGER.setLevel(logging.DEBUG)
-# phasecrun.fgiprun.fgipanalysis.solvmapgen.fractionaloccupancycalculator.LOGGER.setLevel(logging.DEBUG)
-
 
 def main():
     """Run function when program called.

phasecalculator/runners/phasetransferrunner.py

@@ -60,10 +60,10 @@ def run_vle_calculation(jar_path, phase_filename, output_filename, **kwargs):
         vle_args = generate_vle_calc_args(
             jar_path, phase_filename, output_filename, **kwargs
         )
-        LOGGER.info("phasetransfer args: %s", vle_args)
+        LOGGER.info(f"phasetransfer args: {vle_args}")
         return run_calculation(vle_args)
     else:
-        raise FileNotFoundError("File does not exist: %s", jar_path)
+        raise FileNotFoundError(f"File does not exist: {jar_path}")
 
 
 def run_phasetransfer_binding_energy(
@@ -109,7 +109,7 @@ def run_phasetransfer_binding_energy(
         LOGGER.info("phasetransfer args: %s", phase_binding_args)
         return run_calculation(phase_binding_args)
     else:
-        raise FileNotFoundError("File does not exist: %s", jar_path)
+        raise FileNotFoundError(f"File does not exist: {jar_path}")
 
 
 def run_phasetransfer_free_energy(
@@ -152,7 +152,7 @@ def run_phasetransfer_free_energy(
         LOGGER.info("phasetransfer args: %s", phase_free_args)
         return run_calculation(phase_free_args)
     else:
-        raise FileNotFoundError("File does not exist: %s", jar_path)
+        raise FileNotFoundError(f"File does not exist: {jar_path}")
 
 
 def run_calculation(arg_list):
@@ -342,7 +342,7 @@ def generate_solvent_calc_args(
         "--temperatureUnit",
         temperature_unit,
         "-t",
-        "{:.1f}".format(temperature),
+        f"{temperature:.1f}",
     ]
 
 
@@ -364,7 +364,7 @@ def make_java_arguments(jar_path, memory_req=None):
     """
     mem_options = []
     if memory_req is not None:
-        mem_options = ["-Xms{}".format(memory_req), "-Xmx{}".format(memory_req)]
+        mem_options = [f"-Xms{memory_req}", f"-Xmx{memory_req}"]
     return ["java"] + mem_options + ["-jar", jar_path]
 
 

phasecalculator/test/phasecalculatortests.py

@@ -25,31 +25,31 @@ This can also be used to run tests on the installed instance of the library.
 import logging
 import unittest
 import sys
-from phasecalculator.test.iotest.phasetransferxmlcreatortest import (
+from phasecalculator.test.iotest.phasetransferxmlcreator_test import (
     PhasetransferXMLCreatorTestCase,
 )
-from phasecalculator.test.iotest.solventextractortest import SolventExtractorTestCase
-from phasecalculator.test.runnerstest.phasetransferrunnertest import (
+from phasecalculator.test.iotest.solventextractor_test import SolventExtractorTestCase
+from phasecalculator.test.runnerstest.phasetransferrunner_test import (
     PhasetransferRunnerTestCase,
 )
-from phasecalculator.test.runnerstest.fgipanalysisrunnertest import (
+from phasecalculator.test.runnerstest.fgipanalysisrunner_test import (
     FGIPAnalysisRunnerTestCase,
 )
-from phasecalculator.test.runnerstest.vleanalysisrunnertest import (
+from phasecalculator.test.runnerstest.vleanalysisrunner_test import (
     VLEAnalysisRunnerTestCase,
 )
-from phasecalculator.test.analysistest.fgipanalysistest import FGIPAnalysisTestCase
-from phasecalculator.test.classestest.moleculetest import MoleculeTestCase
-from phasecalculator.test.classestest.outputinformationtest import (
+from phasecalculator.test.analysistest.fgipanalysis_test import FGIPAnalysisTestCase
+from phasecalculator.test.classestest.molecule_test import MoleculeTestCase
+from phasecalculator.test.classestest.outputinformation_test import (
     OutputInformationTestCase,
 )
-from phasecalculator.test.classestest.phasestest import PhasesTestCase
-from phasecalculator.test.classestest.phasetest import PhaseTestCase
-from phasecalculator.test.classestest.runtimeinformationtest import (
+from phasecalculator.test.classestest.phases_test import PhasesTestCase
+from phasecalculator.test.classestest.phase_test import PhaseTestCase
+from phasecalculator.test.classestest.runtimeinformation_test import (
     RuntimeInformationTestCase,
 )
-from phasecalculator.test.classestest.systemtest import SystemTestCase
-from phasecalculator.test.classestest.temperaturetest import TemperatureTestCase
+from phasecalculator.test.classestest.system_test import SystemTestCase
+from phasecalculator.test.classestest.temperature_test import TemperatureTestCase
 
 logging.basicConfig()
 LOGGER = logging.getLogger(__name__)