From b1acdfa1e05f12df71400feb51f420e105030963 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Wed, 19 Feb 2020 12:19:29 +0000
Subject: [PATCH] doc update.
---
phasecalculator/io/phasecsvconverter.py | 64 ++++-----
.../runners/phasexmlcreatorrunner.py | 135 ++++++++++--------
2 files changed, 108 insertions(+), 91 deletions(-)
diff --git a/phasecalculator/io/phasecsvconverter.py b/phasecalculator/io/phasecsvconverter.py
index 991ad35..c041517 100755
--- a/phasecalculator/io/phasecsvconverter.py
+++ b/phasecalculator/io/phasecsvconverter.py
@@ -37,34 +37,34 @@ NAME_INCHIKEY_MAP = pureinf.get_name_inchikey_mapping()
INCHIKEY_SSIP_FILE_DICT = pureinf.get_ssip_file_dict()
def convert_csv_file_to_phases(csv_filename):
- """
+ """Read CSV file and convert contents to Phases.
Parameters
----------
- csv_filename : TYPE
- DESCRIPTION.
+ csv_filename : str
+ CSV filename.
Returns
-------
- TYPE
- DESCRIPTION.
+ Phases
+ Phases object.
"""
csv_file_contents = read_csv_file(csv_filename)
return create_phases(csv_file_contents)
def read_csv_file(csv_filename):
- """
+ """Read CSV file to list of rows.
Parameters
----------
- csv_filename : TYPE
- DESCRIPTION.
+ csv_filename : str
+ CSV filename.
Returns
-------
list
- DESCRIPTION.
+ list of rows.
"""
with open(csv_filename, "r") as csv_file:
@@ -72,17 +72,17 @@ def read_csv_file(csv_filename):
return [row for row in csv_reader]
def create_phases(csv_file_contents):
- """
+ """Create Phases for csv file contents
Parameters
----------
- csv_file_contents : TYPE
- DESCRIPTION.
+ csv_file_contents : list of lists
+ List of CSV file lines.
Returns
-------
- TYPE
- DESCRIPTION.
+ Phases
+ Phases object.
"""
phase_list = []
@@ -93,18 +93,18 @@ def create_phases(csv_file_contents):
def create_phase(csv_file_line):
- """
+ """Create Phase from information list.
Parameters
----------
- csv_file_line : TYPE
- DESCRIPTION.
+ csv_file_line : list of str
+ line from CSV file.
Returns
-------
- TYPE
- DESCRIPTION.
+ Phase
+ Phase object.
"""
temperature = create_temperature(float(csv_file_line[0]))
@@ -116,24 +116,24 @@ def create_phase(csv_file_line):
return Phase(molecule_list, temperature)
def create_molecule(name, molefraction):
- """
+ """Create Molecule.
Parameters
----------
- name : TYPE
- DESCRIPTION.
- molefraction : TYPE
- DESCRIPTION.
+ name : str
+ Molecule name.
+ molefraction : float
+ mole fraction of molecule in phase.
Raises
------
keyerr
- DESCRIPTION.
+ Name does not match.
Returns
-------
- TYPE
- DESCRIPTION.
+ Molecule
+ Molecule object.
"""
try:
@@ -145,17 +145,17 @@ def create_molecule(name, molefraction):
raise keyerr
def create_temperature(temperature_value):
- """
+ """Create Temperature.
Parameters
----------
- temperature_value : TYPE
- DESCRIPTION.
+ temperature_value : float
+ value in Kelvin.
Returns
-------
- TYPE
- DESCRIPTION.
+ Temperature
+ Temperature object.
"""
return Temperature(temperature_value, "KELVIN")
\ No newline at end of file
diff --git a/phasecalculator/runners/phasexmlcreatorrunner.py b/phasecalculator/runners/phasexmlcreatorrunner.py
index 776fcb9..ebc1aaf 100755
--- a/phasecalculator/runners/phasexmlcreatorrunner.py
+++ b/phasecalculator/runners/phasexmlcreatorrunner.py
@@ -31,23 +31,28 @@ LOGGER.setLevel(logging.WARN)
def create_phase_and_solvent_files(system_info, filestem="system", **kwargs):
- """
+ """Create solvent and phase files for given system.
Parameters
----------
- system_info : TYPE
- DESCRIPTION.
- filestem : TYPE, optional
- DESCRIPTION. The default is "system".
- **kwargs : TYPE
- DESCRIPTION.
+ system_info : System
+ System object.
+ filestem : str, optional
+ filename stem. The default is "system".
+ solvent_info_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
+
Returns
-------
- phase_file : TYPE
- DESCRIPTION.
- solvent_list : TYPE
- DESCRIPTION.
+ phase_file : str
+ Phase filename.
+ solvent_list : list of dict
+ List of dictionaries containing solvent filename and temperature information.
"""
create_scratch_dir(system_info)
@@ -60,21 +65,25 @@ def create_phase_and_solvent_files(system_info, filestem="system", **kwargs):
return phase_file, solvent_list
def create_phase_file(system_info, filestem, **kwargs):
- """
+ """Create phase file for input information.
Parameters
----------
- system_info : TYPE
- DESCRIPTION.
- filestem : TYPE
- DESCRIPTION.
- **kwargs : TYPE
- DESCRIPTION.
+ system_info : System
+ System object.
+ filestem : str
+ filename stem.
+ solvent_info_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
Returns
-------
- phase_filename : TYPE
- DESCRIPTION.
+ phase_filename : str
+ phase filename.
"""
phase_filename = create_phase_filename(system_info.runtime_information.scratch_dir, filestem)
@@ -83,21 +92,25 @@ def create_phase_file(system_info, filestem, **kwargs):
phasexmlcreate.create_phase_file(mole_fractions_by_temp_dict, phase_filename, ssip_filename_list=ssip_filename_list, **kwargs)
return phase_filename
def create_solvent_files(system_info, filestem, **kwargs):
- """
+ """Create solvent files for input information.
Parameters
----------
- system_info : TYPE
- DESCRIPTION.
- filestem : TYPE
- DESCRIPTION.
- **kwargs : TYPE
- DESCRIPTION.
+ system_info : System
+ System object.
+ filestem : str
+ filename stem.
+ solvent_info_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
Returns
-------
- solvent_list : TYPE
- DESCRIPTION.
+ solvent_list : list of dict
+ List of dictionaries containing solvent filename and temperature information.
"""
mole_fractions_by_temp_dict = system_info.get_phase_compositions_by_temperature()
@@ -113,27 +126,31 @@ def create_solvent_files(system_info, filestem, **kwargs):
def create_solvent_file(mole_fraction_dict_list, ssip_filename_list, temp_info, filestem, scratch_dir, **kwargs):
- """
+ """Create solvent file for input information.
Parameters
----------
- mole_fraction_dict_list : TYPE
- DESCRIPTION.
- ssip_filename_list : TYPE
- DESCRIPTION.
- temp_info : TYPE
- DESCRIPTION.
- filestem : TYPE
- DESCRIPTION.
- scratch_dir : TYPE
- DESCRIPTION.
- **kwargs : TYPE
- DESCRIPTION.
+ mole_fraction_dict_list : list of dict
+ Solvent compositions.
+ ssip_filename_list : list of str
+ SSIP filenames for molecules.
+ temp_info : Temperature
+ Temperature object.
+ filestem : str
+ filename stem.
+ scratch_dir : str
+ scratch directory name.
+ solvent_info_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
Returns
-------
- solvent_filename : TYPE
- DESCRIPTION.
+ solvent_filename : str
+ filename path including scratch directory.
"""
solvent_filename = create_solvent_filename(scratch_dir, temp_info, filestem)
@@ -157,21 +174,21 @@ def create_scratch_dir(system_info):
scratch_path.mkdir(parents=True,exist_ok=True)
def create_solvent_filename(scratch_dir, temp_info, filestem):
- """
+ """Create solvent filename.
Parameters
----------
- scratch_dir : TYPE
- DESCRIPTION.
- temp_info : TYPE
- DESCRIPTION.
- filestem : TYPE
- DESCRIPTION.
+ scratch_dir : str
+ scratch directory name.
+ temp_info : Temperature
+ Temperature object.
+ filestem : str
+ filename stem.
Returns
-------
- path : TYPE
- DESCRIPTION.
+ path : str
+ filename path including scratch directory.
"""
temp_string = create_temperaturestring(temp_info.temperature, temp_info.temperature_unit)
@@ -184,15 +201,15 @@ def create_phase_filename(scratch_dir, filestem):
Parameters
----------
- scratch_dir : TYPE
- DESCRIPTION.
- filestem : TYPE
- DESCRIPTION.
+ scratch_dir : str
+ scratch directory name.
+ filestem : str
+ filename stem.
Returns
-------
- path : TYPE
- DESCRIPTION.
+ path : str
+ filename path including scratch directory.
"""
filename = filestem + ".xml"
--
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