diff --git a/acmc/__init__.py b/acmc/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/acmc/__main__.py b/acmc/__main__.py new file mode 100644 index 0000000000000000000000000000000000000000..6dc525cf7b30589b5905da70238331078ae90005 --- /dev/null +++ b/acmc/__main__.py @@ -0,0 +1,4 @@ +from acmc.main import main + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/base.py b/acmc/base.py similarity index 92% rename from base.py rename to acmc/base.py index 63e1ad4b20b158ad6c15b6354d0e28f6ba1c9d17..ea14fd04ea9af9d5306798ff945de3a09727d3cb 100644 --- a/base.py +++ b/acmc/base.py @@ -1,6 +1,9 @@ import pandas as pd import os +from acmc import logging_config +logger = logging_config.setup_logger() + class bcolors: #for printing coloured text HEADER = '\033[95m' OKBLUE = '\033[94m' diff --git a/logging_config.py b/acmc/logging_config.py similarity index 100% rename from logging_config.py rename to acmc/logging_config.py diff --git a/main.py b/acmc/main.py similarity index 98% rename from main.py rename to acmc/main.py index 94b449e7181476b05f769f252eb3c12e9596be97..a78180cefcef618a18e71ae54980685121c91261 100644 --- a/main.py +++ b/acmc/main.py @@ -3,13 +3,10 @@ import logging from pathlib import Path # acmc imports -import trud -import omop -import phen +from acmc import trud, omop, phen, logging_config as lc # setup logging -import logging_config -logger = logging_config.setup_logger() +logger = lc.setup_logger() BUILD_PATH = Path('build') diff --git a/omop.py b/acmc/omop.py similarity index 99% rename from omop.py rename to acmc/omop.py index 3ad79f2005e879db86d6c9a3683ee43a36ea983c..7f109bc76295bef3bf28f0a20e494ad1f4df88f9 100644 --- a/omop.py +++ b/acmc/omop.py @@ -6,9 +6,8 @@ import json import logging from pathlib import Path -# setup logging -from logging_config import setup_logger -logger = setup_logger() +from acmc import logging_config +logger = logging_config.setup_logger() OMOP_DB_DIR = Path('./build/omop') OMOP_DB_PATH = OMOP_DB_DIR / 'omop_54.sqlite' diff --git a/parse.py b/acmc/parse.py similarity index 98% rename from parse.py rename to acmc/parse.py index ed68066355c838718fd5c61a774c932890b48e71..b5fc34a31f7e6d6583d0c33c080aa83ca7a9cba5 100644 --- a/parse.py +++ b/acmc/parse.py @@ -1,16 +1,13 @@ import pandas as pd import numpy as np import os -import trud -# setup logging -import logging_config -logger = logging_config.setup_logger() +# acmc imports +from acmc import trud, logging_config as lc +from acmc.base import log_invalid_code, bcolors, raise_ + +logger = lc.setup_logger() -from base import log_invalid_code -from base import bcolors -from base import raise_ - def in_database(codes, db, col): return codes.isin(db[col]) diff --git a/phen.py b/acmc/phen.py similarity index 99% rename from phen.py rename to acmc/phen.py index e13ad4636090d1de42577a564cbd2f4b5fabcb0b..8204c75f48302567172e19853161fd5fcae79060 100644 --- a/phen.py +++ b/acmc/phen.py @@ -14,15 +14,14 @@ from pathlib import Path from urllib.parse import urlparse, urlunparse # acmc imports -import trud -import omop -from base import log_invalid_code, bcolors, raise_ -from parse import Read2, Read3, Icd10, Snomed, Opcs4, Atc, code_types, vocab_types -from omop import publish_concept_sets, setup +from acmc import trud, omop +from acmc.base import log_invalid_code, bcolors, raise_ +from acmc.parse import Read2, Read3, Icd10, Snomed, Opcs4, Atc, code_types, vocab_types +from acmc.omop import publish_concept_sets, setup # setup logging -from logging_config import setup_logger -logger = setup_logger() +import acmc.logging_config as lc +logger = lc.setup_logger() pd.set_option("mode.chained_assignment", None) diff --git a/trud.py b/acmc/trud.py similarity index 99% rename from trud.py rename to acmc/trud.py index 74bd856ca82ddab845b2d692ed9ee48b0410668b..82c30735c1ad1e6d927bd85d84807b05095c9b6a 100644 --- a/trud.py +++ b/acmc/trud.py @@ -10,11 +10,11 @@ import pandas as pd import simpledbf from pathlib import Path -# setup logging -import logging_config -logger = logging_config.setup_logger() +from acmc.base import bcolors -from base import bcolors +# setup logging +import acmc.logging_config as lc +logger = lc.setup_logger() # Constants FQDN = "isd.digital.nhs.uk" diff --git a/tests/test_acmc.py b/tests/test_acmc.py index bc7c035797fce5853358cb6ec2cc43ceba55651d..81756246d99d8d6837f23da59d362f803d4c2667 100644 --- a/tests/test_acmc.py +++ b/tests/test_acmc.py @@ -5,14 +5,10 @@ import shutil import logging from pathlib import Path -import trud -import omop -import phen -import main +from acmc import trud, omop, main, logging_config as lc # setup logging -from logging_config import setup_logger -logger = setup_logger() +logger = lc.setup_logger() @pytest.fixture def tmp_dir():