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bump pytest to read pyproject.toml #71

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bump pytest to read pyproject.toml #71

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d18ee3b
bump pytest to read pyproject.toml
ltalirz Apr 30, 2021
68da05f
remove access to low-level repo methods
ltalirz May 3, 2021
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
[![Build Status](https://travis-ci.org/yakutovicha/aiida-raspa.svg?branch=develop)](https://travis-ci.org/yakutovicha/aiida-raspa)
[![Build Status](https://github.com/yakutovicha/aiida-raspa/workflows/ci/badge.svg)](https://github.com/yakutovicha/aiida-raspa/actions)
[![Coverage Status](https://coveralls.io/repos/github/yakutovicha/aiida-raspa/badge.svg?branch=develop)](https://coveralls.io/github/yakutovicha/aiida-raspa?branch=develop)
[![PyPI version](https://badge.fury.io/py/aiida-raspa.svg)](https://badge.fury.io/py/aiida-raspa)

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25 changes: 9 additions & 16 deletions aiida_raspa/parsers/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
from aiida.engine import ExitCode
from aiida.orm import Dict, List
from aiida.parsers.parser import Parser
from aiida_raspa.utils import parse_base_output
from aiida_raspa.utils import parse_base_output_fobj

# parser
# --------------------------------------------------------------------------------------------
Expand All @@ -19,12 +19,12 @@ class RaspaParser(Parser):
def parse(self, **kwargs): # pylint: disable=too-many-locals
"""Receives in input a dictionary of retrieved nodes. Does all the logic here."""
try:
out_folder = self.retrieved
self.retrieved
except NotExistent:
return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER
output_folder_name = self.node.process_class.OUTPUT_FOLDER

if output_folder_name not in out_folder._repository.list_object_names(): # pylint: disable=protected-access
if output_folder_name not in self.retrieved.list_object_names():
return self.exit_codes.ERROR_NO_OUTPUT_FILE

output_parameters = {}
Expand All @@ -33,27 +33,20 @@ def parse(self, **kwargs): # pylint: disable=too-many-locals
for system_id, system_name in enumerate(self.node.get_extra('system_order')):
# specify the name for the system
system = "System_{}".format(system_id)
fname = out_folder._repository.list_object_names(os.path.join(output_folder_name, system))[0] # pylint: disable=protected-access
fname = self.retrieved.list_object_names(os.path.join(output_folder_name, system))[0] # pylint: disable=protected-access

# get absolute path of the output file
output_abs_path = os.path.join(
out_folder._repository._get_base_folder().abspath, # pylint: disable=protected-access
self.node.process_class.OUTPUT_FOLDER,
system,
fname)

# Check for possible errors
with open(output_abs_path) as fobj:
with self.retrieved.open(os.path.join(system, fname)) as fobj:
content = fobj.read()
if "Starting simulation" not in content:
return self.exit_codes.ERROR_SIMULATION_DID_NOT_START
if "Simulation finished" not in content:
return self.exit_codes.TIMEOUT

# parse output parameters and warnings
parsed_parameters, parsed_warnings = parse_base_output(output_abs_path, system_name, ncomponents)
output_parameters[system_name] = parsed_parameters
warnings += parsed_warnings
# parse output parameters and warnings
parsed_parameters, parsed_warnings = parse_base_output_fobj(fobj, system_name, ncomponents)
output_parameters[system_name] = parsed_parameters
warnings += parsed_warnings

self.out("output_parameters", Dict(dict=output_parameters))
self.out("warnings", List(list=warnings))
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2 changes: 1 addition & 1 deletion aiida_raspa/utils/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# -*- coding: utf-8 -*-
"""Raspa utils."""
from .base_parser import parse_base_output
from .base_parser import parse_base_output, parse_base_output_fobj
from .base_input_generator import RaspaInput
from .inspection_tools import add_write_binary_restart, modify_number_of_cycles, increase_box_lenght
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