From 5e1fdfc475cee3047057d3d10f912a132cdbc8e9 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Tue, 18 Feb 2025 21:34:01 +0000
Subject: [PATCH] refactored files into the module acmc and sorted all the
imports
---
acmc/__init__.py | 0
acmc/__main__.py | 4 ++++
base.py => acmc/base.py | 3 +++
logging_config.py => acmc/logging_config.py | 0
main.py => acmc/main.py | 7 ++-----
omop.py => acmc/omop.py | 5 ++---
parse.py => acmc/parse.py | 13 +++++--------
phen.py => acmc/phen.py | 13 ++++++-------
trud.py => acmc/trud.py | 8 ++++----
tests/test_acmc.py | 8 ++------
10 files changed, 28 insertions(+), 33 deletions(-)
create mode 100644 acmc/__init__.py
create mode 100644 acmc/__main__.py
rename base.py => acmc/base.py (92%)
rename logging_config.py => acmc/logging_config.py (100%)
rename main.py => acmc/main.py (98%)
rename omop.py => acmc/omop.py (99%)
rename parse.py => acmc/parse.py (98%)
rename phen.py => acmc/phen.py (99%)
rename trud.py => acmc/trud.py (99%)
diff --git a/acmc/__init__.py b/acmc/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/acmc/__main__.py b/acmc/__main__.py
new file mode 100644
index 0000000..6dc525c
--- /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 63e1ad4..ea14fd0 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 94b449e..a78180c 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 3ad79f2..7f109bc 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 ed68066..b5fc34a 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 e13ad46..8204c75 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 74bd856..82c3073 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 bc7c035..8175624 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():
--
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