"""
Module for setting up species in the working folder.
"""
import os
import json
import configparser
import urllib.request
import h5py
import species
[docs]class SpeciesInit:
"""
Class for initiating species by creating the database and configuration file in case they are
not present in the working folder, and creating the data folder for storage of input data.
"""
def __init__(self):
"""
Returns
-------
NoneType
None
"""
print(f'Initiating species v{species.__version__}...', end='', flush=True)
working_folder = os.path.abspath(os.getcwd())
config_file = os.path.join(working_folder, 'species_config.ini')
print(' [DONE]')
try:
contents = urllib.request.urlopen('https://pypi.org/pypi/species/json').read()
data = json.loads(contents)
latest_version = data['info']['version']
except urllib.error.URLError:
latest_version = None
if latest_version is not None and species.__version__ != latest_version:
print(f'A new version ({latest_version}) is available!')
if not os.path.isfile(config_file):
print('Creating species_config.ini...', end='', flush=True)
with open(config_file, 'w') as file_obj:
file_obj.write('[species]\n')
file_obj.write('database = species_database.hdf5\n')
file_obj.write('data_folder = ./data/\n')
print(' [DONE]')
config = configparser.ConfigParser()
config.read_file(open(config_file))
database_file = os.path.abspath(config['species']['database'])
data_folder = os.path.abspath(config['species']['data_folder'])
print(f'Database: {database_file}')
print(f'Data folder: {data_folder}')
print(f'Working folder: {working_folder}')
if not os.path.isfile(database_file):
print('Creating species_database.hdf5...', end='', flush=True)
h5_file = h5py.File(database_file, 'w')
h5_file.close()
print(' [DONE]')
if not os.path.exists(data_folder):
print('Creating data folder...', end='', flush=True)
os.makedirs(data_folder)
print(' [DONE]')