diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8520051f..b10e3f4c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -110,13 +110,12 @@ jobs:
       - name: Build distribution
         run: uv build
 
-      - name: Install package with mypy
+      - name: Install package with test dependencies
         run: |
           uv pip install --system dist/*.whl
-          uv pip install --system mypy
           uv pip install --system -e ".[test]"
 
-      - run: mypy --install-types --non-interactive commcare_export/ tests/ migrations/
+      - run: mypy commcare_export/ tests/
 
   finish:
     needs: test
diff --git a/MANIFEST.in b/MANIFEST.in
index 073a6993..20bf2e53 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,2 @@
-recursive-include migrations *.py *.ini
+recursive-include commcare_export/migrations *.py *.ini *.mako
 include commcare_export/VERSION
diff --git a/commcare_export/__init__.py b/commcare_export/__init__.py
index a34779a0..6c36bb8f 100644
--- a/commcare_export/__init__.py
+++ b/commcare_export/__init__.py
@@ -1,48 +1,5 @@
-import logging
-import os
-import re
 from .version import __version__
 
 __all__ = [
     '__version__',
-    'get_logger',
-    'get_error_logger',
-    'logger_name_from_filepath',
-    'Logger',
-    'repo_root',
 ]
-
-repo_root = os.path.abspath(os.path.join(__file__, os.pardir, os.pardir))
-
-
-class Logger:
-    def __init__(self, logger, level):
-        self.logger = logger
-        self.level = level
-        self.linebuf = ''
-
-    def write(self, buf):
-        for line in buf.rstrip().splitlines():
-            self.logger.log(self.level, line.rstrip())
-
-
-def logger_name_from_filepath(filepath):
-    relative_path = os.path.relpath(filepath, start=repo_root)
-    cleaned_path = relative_path.replace('/', '.')
-    return re.sub(r'\.py$', '', cleaned_path)
-
-
-def get_error_logger():
-    return Logger(logging.getLogger(), logging.ERROR)
-
-
-def get_logger(filepath=None):
-    if filepath:
-        logger = logging.getLogger(
-            logger_name_from_filepath(filepath)
-        )
-    else:
-        logger = logging.getLogger()
-
-    logger.setLevel(logging.DEBUG)
-    return logger
diff --git a/commcare_export/checkpoint.py b/commcare_export/checkpoint.py
index 62c76e93..bfffbe6a 100644
--- a/commcare_export/checkpoint.py
+++ b/commcare_export/checkpoint.py
@@ -1,6 +1,7 @@
 import datetime
-import os
+import logging
 import uuid
+from importlib import resources
 from contextlib import contextmanager
 from operator import attrgetter
 
@@ -12,9 +13,8 @@
 from commcare_export.commcare_minilinq import PaginationMode
 from commcare_export.exceptions import DataExportException
 from commcare_export.writers import SqlMixin
-from commcare_export import get_logger, repo_root
 
-logger = get_logger(__file__)
+logger = logging.getLogger(__name__)
 Base = declarative_base()
 
 
@@ -85,7 +85,7 @@ def session_scope(Session):
 
 class CheckpointManager(SqlMixin):
     table_name = 'commcare_export_runs'
-    migrations_repository = os.path.join(repo_root, 'migrations')
+    migrations_repository = resources.files("commcare_export") / "migrations"
 
     def __init__(
         self,
@@ -200,13 +200,13 @@ def _set_checkpoint(
 
     def create_checkpoint_table(self, revision='head'):
         from alembic import command, config
-        cfg = config.Config(
-            os.path.join(self.migrations_repository, 'alembic.ini')
-        )
-        cfg.set_main_option('script_location', self.migrations_repository)
-        with self.engine.begin() as connection:
-            cfg.attributes['connection'] = connection
-            command.upgrade(cfg, revision)
+
+        with resources.as_file(self.migrations_repository) as migrations_path:
+            cfg = config.Config(str(migrations_path / 'alembic.ini'))
+            cfg.set_main_option('script_location', str(migrations_path))
+            with self.engine.begin() as connection:
+                cfg.attributes['connection'] = connection
+                command.upgrade(cfg, revision)
 
     def _cleanup(self):
         self._validate_tables()
diff --git a/commcare_export/cli.py b/commcare_export/cli.py
index 0a2421d0..5591d37f 100644
--- a/commcare_export/cli.py
+++ b/commcare_export/cli.py
@@ -4,7 +4,6 @@
 import json
 import os
 import sys
-import logging
 import dateutil.parser
 import requests
 import sqlalchemy
@@ -28,11 +27,11 @@
 from commcare_export.repeatable_iterator import RepeatableIterator
 from commcare_export.utils import get_checkpoint_manager
 from commcare_export.version import __version__
-from commcare_export import get_logger, get_error_logger
+import logging
 
 EXIT_STATUS_SUCCESS = 0
 EXIT_STATUS_ERROR = 1
-logger = get_logger(__file__)
+logger = logging.getLogger(__name__)
 
 commcare_hq_aliases = {
     'local': 'http://localhost:8000',
@@ -184,13 +183,13 @@ def add_to_parser(self, parser, **additional_kwargs):
 ]
 
 
-def set_up_logging(log_dir=None):
+def set_up_file_logging(log_dir=None):
     """
     Set up file-based logging.
 
     :param log_dir: Directory where the log file will be written. If
         None, uses the current working directory.
-    :returns tuple: (success, log_file_path, error_msg)
+    :returns tuple: (success, log_file_path, error_msg, file_handler)
     """
     if log_dir is None:
         log_dir = os.getcwd()
@@ -203,15 +202,38 @@ def set_up_logging(log_dir=None):
         with open(log_file, 'a'):  # Test write permissions
             pass
 
-        logging.basicConfig(
-            filename=log_file,
-            format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
-            filemode='a',
-        )
-        sys.stderr = get_error_logger()
-        return True, log_file, None
+        file_handler = logging.FileHandler(log_file, mode='a')
+        return True, log_file, None, file_handler
     except (OSError, IOError, PermissionError) as err:
-        return False, log_file, f"{type(err).__name__}: {err}"
+        return False, log_file, f"{type(err).__name__}: {err}", None
+
+
+def set_up_logging(args):
+    stream_handler = logging.StreamHandler()
+    stream_handler.setFormatter(logging.Formatter('%(message)s'))
+    handlers = [stream_handler]
+    if not args.no_logfile:
+        success, log_file, error, file_handler = set_up_file_logging(
+            args.log_dir
+        )
+        if success:
+            file_handler.setFormatter(
+                logging.Formatter(
+                    '%(asctime)s %(name)-12s %(levelname)-8s %(message)s'
+                )
+            )
+            handlers.append(file_handler)
+            print(f'Writing logs to {log_file}')
+        else:
+            print(f'Warning: Unable to write to log file {log_file}: {error}')
+            print('Logging to console only.')
+
+    log_level = logging.DEBUG if args.verbose else logging.WARN
+    root_logger = logging.getLogger()
+    root_logger.handlers.clear()
+    root_logger.setLevel(log_level)
+    for handler in handlers:
+        root_logger.addHandler(handler)
 
 
 def main(argv):
@@ -229,24 +251,7 @@ def main(argv):
         if errors:
             raise Exception(f"Could not proceed. Following issues were found: {', '.join(errors)}.")
 
-    if not args.no_logfile:
-        success, log_file, error = set_up_logging(args.log_dir)
-        if success:
-            print(f'Writing logs to {log_file}')
-        else:
-            print(f'Warning: Unable to write to log file {log_file}: {error}')
-            print('Logging to console only.')
-
-    if args.verbose:
-        logging.basicConfig(
-            level=logging.DEBUG,
-            format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s'
-        )
-    else:
-        logging.basicConfig(
-            level=logging.WARN,
-            format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s'
-        )
+    set_up_logging(args)
 
     logging.getLogger('alembic').setLevel(logging.WARN)
     logging.getLogger('backoff').setLevel(logging.FATAL)
@@ -258,13 +263,7 @@ def main(argv):
 
     if not args.project:
         error_msg = "commcare-export: error: argument --project is required"
-        # output to log file through sys.stderr
-        print(
-            error_msg,
-            file=sys.stderr
-        )
-        # Output to console for debugging
-        print(error_msg)
+        logger.error(error_msg)
         sys.exit(1)
 
     print("Running export...")
@@ -364,11 +363,9 @@ def _get_writer(output_format, output, strict_types):
     elif output_format == 'csv':
         if not output.endswith(".zip"):
             print(
-                "WARNING: csv output is a zip file, but "
-                f"will be written to {output}"
-            )
-            print(
-                "Consider appending .zip to the file name to avoid confusion."
+                'WARNING: CSV output is a zip file, but will be written to '
+                f"'{output}'.\n"
+                "Consider appending '.zip' to the file name to avoid confusion."
             )
         return writers.CsvTableWriter(output)
     elif output_format == 'json':
@@ -383,8 +380,9 @@ def _get_writer(output_format, output, strict_types):
             charset_split = output.split('charset=')
             if len(charset_split) > 1 and charset_split[1] != 'utf8mb4':
                 raise Exception(
-                    f"The charset '{charset_split[1]}' might cause problems with the export. "
-                    f"It is recommended that you use 'utf8mb4' instead."
+                    f"The charset '{charset_split[1]}' might cause problems "
+                    "with the export. It is recommended that you use "
+                    "'utf8mb4' instead."
                 )
 
         return writers.SqlTableWriter(output, strict_types)
@@ -414,8 +412,7 @@ def _get_checkpoint_manager(args):
         args.query
     ):
         logger.warning(
-            "Checkpointing disabled for non builtin, "
-            "non file-based query"
+            "Checkpointing disabled for non builtin, non file-based query"
         )
     elif args.since or args.until:
         logger.warning(
@@ -442,29 +439,30 @@ def evaluate_query(env, query):
             lazy_result = query.eval(env)
             force_lazy_result(lazy_result)
             return 0
-        except requests.exceptions.RequestException as e:
-            if e.response and e.response.status_code == 401:
-                print(
-                    "\nAuthentication failed. Please check your credentials.",
-                    file=sys.stderr
+        except requests.exceptions.RequestException as err:
+            if err.response and err.response.status_code == 401:
+                logger.error(
+                    "Authentication failed. Please check your credentials."
                 )
                 return EXIT_STATUS_ERROR
             else:
                 raise
-        except ResourceRepeatException as e:
-            print('Stopping because the export is stuck')
-            print(e.message)
-            print('Try increasing --batch-size to overcome the error')
+        except ResourceRepeatException as err:
+            logger.error(
+                'Stopping because the export is stuck.\n'
+                f'{err.message}\n'
+                f'Try increasing --batch-size to overcome the error'
+            )
             return EXIT_STATUS_ERROR
         except (
             sqlalchemy.exc.DataError,
             sqlalchemy.exc.InternalError,
             sqlalchemy.exc.ProgrammingError
-        ) as e:
-            print('Stopping because of database error:\n', e)
+        ) as err:
+            logger.error(f'Stopping because of database error:\n{err}')
             return EXIT_STATUS_ERROR
         except KeyboardInterrupt:
-            print('\nExport aborted', file=sys.stderr)
+            logger.error("Export aborted")
             return EXIT_STATUS_ERROR
 
 
@@ -473,10 +471,9 @@ def main_with_args(args):
     writer = _get_writer(args.output_format, args.output, args.strict_types)
 
     if args.query is None and args.users is False and args.locations is False:
-        print(
-            'At least one the following arguments is required: '
-            '--query, --users, --locations',
-            file=sys.stderr
+        logger.error(
+            "At least one the following arguments is required: "
+            "--query, --users, --locations"
         )
         return EXIT_STATUS_ERROR
 
@@ -500,8 +497,8 @@ def main_with_args(args):
     lp = LocationInfoProvider(api_client, page_size=args.batch_size)
     try:
         query = get_queries(args, writer, lp, column_enforcer)
-    except DataExportException as e:
-        print(e.message, file=sys.stderr)
+    except DataExportException as err:
+        logger.error(err.message)
         return EXIT_STATUS_ERROR
 
     if args.dump_query:
diff --git a/commcare_export/commcare_hq_client.py b/commcare_export/commcare_hq_client.py
index 685f8ae1..318c1129 100644
--- a/commcare_export/commcare_hq_client.py
+++ b/commcare_export/commcare_hq_client.py
@@ -11,7 +11,6 @@
 
 import commcare_export
 from commcare_export.repeatable_iterator import RepeatableIterator
-from commcare_export import get_logger
 
 AUTH_MODE_PASSWORD = 'password'
 AUTH_MODE_APIKEY = 'apikey'
@@ -20,7 +19,7 @@
 LATEST_KNOWN_VERSION = '0.5'
 RESOURCE_REPEAT_LIMIT = 10
 
-logger = get_logger(__file__)
+logger = logging.getLogger(__name__)
 
 
 def on_wait(details):
diff --git a/commcare_export/commcare_minilinq.py b/commcare_export/commcare_minilinq.py
index 72d49540..30fee2d4 100644
--- a/commcare_export/commcare_minilinq.py
+++ b/commcare_export/commcare_minilinq.py
@@ -5,6 +5,7 @@
 API directly.
 """
 import json
+import logging
 from enum import Enum
 from typing import Any
 from urllib.parse import parse_qs, urlparse
@@ -14,9 +15,8 @@
 
 from commcare_export.env import CannotBind, CannotReplace, DictEnv
 from commcare_export.misc import unwrap
-from commcare_export import get_logger
 
-logger = get_logger(__file__)
+logger = logging.getLogger(__name__)
 
 SUPPORTED_RESOURCES = {
     'form',
diff --git a/commcare_export/location_info_provider.py b/commcare_export/location_info_provider.py
index e18eb934..495f6f83 100644
--- a/commcare_export/location_info_provider.py
+++ b/commcare_export/location_info_provider.py
@@ -1,9 +1,10 @@
 
+import logging
+
 from commcare_export.commcare_minilinq import SimplePaginator
 from commcare_export.misc import unwrap_val
-from commcare_export import get_logger
 
-logger = get_logger(__file__)
+logger = logging.getLogger(__name__)
 
 # LocationInfoProvider uses the /location_type/ endpoint of the API to
 # retrieve location type data, stores that information in a dictionary
diff --git a/commcare_export/migrations/README.md b/commcare_export/migrations/README.md
new file mode 100644
index 00000000..2654fea7
--- /dev/null
+++ b/commcare_export/migrations/README.md
@@ -0,0 +1,16 @@
+## Migrations
+
+Migrations use [alembic](http://alembic.zzzcomputing.com/en/latest).
+
+**Create new migration**
+
+```
+$ alembic -c commcare_export/migrations/alembic.ini revision -m "description"
+```
+
+
+**Run migrations from command line**
+
+```
+$ alembic -c commcare_export/migrations/alembic.ini -x "url=<db url>" upgrade <version e.g. 'head'>
+```
diff --git a/migrations/__init__.py b/commcare_export/migrations/__init__.py
similarity index 100%
rename from migrations/__init__.py
rename to commcare_export/migrations/__init__.py
diff --git a/migrations/alembic.ini b/commcare_export/migrations/alembic.ini
similarity index 100%
rename from migrations/alembic.ini
rename to commcare_export/migrations/alembic.ini
diff --git a/migrations/env.py b/commcare_export/migrations/env.py
similarity index 100%
rename from migrations/env.py
rename to commcare_export/migrations/env.py
diff --git a/migrations/script.py.mako b/commcare_export/migrations/script.py.mako
similarity index 100%
rename from migrations/script.py.mako
rename to commcare_export/migrations/script.py.mako
diff --git a/migrations/versions/29c27e7e2bf6_rename_time_of_run_to_since_param.py b/commcare_export/migrations/versions/29c27e7e2bf6_rename_time_of_run_to_since_param.py
similarity index 100%
rename from migrations/versions/29c27e7e2bf6_rename_time_of_run_to_since_param.py
rename to commcare_export/migrations/versions/29c27e7e2bf6_rename_time_of_run_to_since_param.py
diff --git a/migrations/versions/3b37b3b06104_added_cursor_to_checkpoint.py b/commcare_export/migrations/versions/3b37b3b06104_added_cursor_to_checkpoint.py
similarity index 100%
rename from migrations/versions/3b37b3b06104_added_cursor_to_checkpoint.py
rename to commcare_export/migrations/versions/3b37b3b06104_added_cursor_to_checkpoint.py
diff --git a/migrations/versions/53f1aad98e33_add_args_columns.py b/commcare_export/migrations/versions/53f1aad98e33_add_args_columns.py
similarity index 100%
rename from migrations/versions/53f1aad98e33_add_args_columns.py
rename to commcare_export/migrations/versions/53f1aad98e33_add_args_columns.py
diff --git a/migrations/versions/6f158d161ab6_add_pagination_mode_to_checkpoint.py b/commcare_export/migrations/versions/6f158d161ab6_add_pagination_mode_to_checkpoint.py
similarity index 100%
rename from migrations/versions/6f158d161ab6_add_pagination_mode_to_checkpoint.py
rename to commcare_export/migrations/versions/6f158d161ab6_add_pagination_mode_to_checkpoint.py
diff --git a/migrations/versions/9945abb4ec70_add_back_time_of_run.py b/commcare_export/migrations/versions/9945abb4ec70_add_back_time_of_run.py
similarity index 100%
rename from migrations/versions/9945abb4ec70_add_back_time_of_run.py
rename to commcare_export/migrations/versions/9945abb4ec70_add_back_time_of_run.py
diff --git a/migrations/versions/__init__.py b/commcare_export/migrations/versions/__init__.py
similarity index 100%
rename from migrations/versions/__init__.py
rename to commcare_export/migrations/versions/__init__.py
diff --git a/migrations/versions/a56c82a8d02e_add_detail_to_checkpoint.py b/commcare_export/migrations/versions/a56c82a8d02e_add_detail_to_checkpoint.py
similarity index 100%
rename from migrations/versions/a56c82a8d02e_add_detail_to_checkpoint.py
rename to commcare_export/migrations/versions/a56c82a8d02e_add_detail_to_checkpoint.py
diff --git a/migrations/versions/c36489c5a628_create_commcare_export_runs.py b/commcare_export/migrations/versions/c36489c5a628_create_commcare_export_runs.py
similarity index 100%
rename from migrations/versions/c36489c5a628_create_commcare_export_runs.py
rename to commcare_export/migrations/versions/c36489c5a628_create_commcare_export_runs.py
diff --git a/migrations/versions/d3ce9dc9907a_add_final_column.py b/commcare_export/migrations/versions/d3ce9dc9907a_add_final_column.py
similarity index 100%
rename from migrations/versions/d3ce9dc9907a_add_final_column.py
rename to commcare_export/migrations/versions/d3ce9dc9907a_add_final_column.py
diff --git a/migrations/versions/d82e1d06a82c_add_key_column.py b/commcare_export/migrations/versions/d82e1d06a82c_add_key_column.py
similarity index 100%
rename from migrations/versions/d82e1d06a82c_add_key_column.py
rename to commcare_export/migrations/versions/d82e1d06a82c_add_key_column.py
diff --git a/migrations/versions/f4fd4c80f40a_add_table_name_column.py b/commcare_export/migrations/versions/f4fd4c80f40a_add_table_name_column.py
similarity index 100%
rename from migrations/versions/f4fd4c80f40a_add_table_name_column.py
rename to commcare_export/migrations/versions/f4fd4c80f40a_add_table_name_column.py
diff --git a/commcare_export/minilinq.py b/commcare_export/minilinq.py
index 794a0c0b..9c165665 100644
--- a/commcare_export/minilinq.py
+++ b/commcare_export/minilinq.py
@@ -1,3 +1,4 @@
+import logging
 from typing import Any, Dict
 from typing import List as ListType
 from typing import Optional
@@ -6,9 +7,8 @@
 from commcare_export.misc import unwrap, unwrap_val
 from commcare_export.repeatable_iterator import RepeatableIterator
 from commcare_export.specs import TableSpec
-from commcare_export import get_logger
 
-logger = get_logger(__file__)
+logger = logging.getLogger(__name__)
 
 
 class MiniLinq:
diff --git a/commcare_export/writers.py b/commcare_export/writers.py
index 4426292b..e143bbc2 100644
--- a/commcare_export/writers.py
+++ b/commcare_export/writers.py
@@ -1,5 +1,6 @@
 import csv
 import datetime
+import logging
 from tempfile import NamedTemporaryFile
 import zipfile
 from itertools import zip_longest
@@ -12,9 +13,8 @@
 from alembic.operations import Operations
 from commcare_export.data_types import UnknownDataType, get_sqlalchemy_type
 from commcare_export.specs import TableSpec
-from commcare_export import get_logger
 
-logger = get_logger(__file__)
+logger = logging.getLogger(__name__)
 MAX_COLUMN_SIZE = 2000
 
 
diff --git a/migrations/README.md b/migrations/README.md
deleted file mode 100644
index 2704817d..00000000
--- a/migrations/README.md
+++ /dev/null
@@ -1,16 +0,0 @@
-## Migrations
-
-Migrations use [alembic](http://alembic.zzzcomputing.com/en/latest).
-
-**Create new migration**
-
-```
-$ alembic -c migrations/alembic.ini revision -m "description"
-```
-
-
-**Run migrations from command line**
-
-```
-$ alembic -c migrations/alembic.ini -x "url=<db url>" upgrade <version e.g. 'head'>
-```
diff --git a/pyproject.toml b/pyproject.toml
index 15ddad47..30e6403c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,9 +49,16 @@ dependencies = [
 
 [project.optional-dependencies]
 test = [
-    "pytest",
-    "psycopg2-binary",
     "mock",
+    "mypy",
+    "psycopg2-binary",
+    "pytest",
+    "pytest-unmagic",
+    "types-mock",
+    "types-python-dateutil",
+    "types-pytz",
+    "types-requests",
+    "types-simplejson",
 ]
 base_sql = [
     "SQLAlchemy",
@@ -95,11 +102,21 @@ commcare-export = "commcare_export.cli:entry_point"
 commcare-export-utils = "commcare_export.utils_cli:entry_point"
 
 [tool.setuptools]
-packages = ["commcare_export"]
+packages = [
+    "commcare_export",
+    "commcare_export.migrations",
+    "commcare_export.migrations.versions",
+]
 include-package-data = true
 
 [tool.setuptools.package-data]
-commcare_export = ["VERSION"]
+commcare_export = [
+    "VERSION",
+    "migrations/*.ini",
+    "migrations/*.mako",
+    "migrations/*.py",
+    "migrations/versions/*.py",
+]
 
 [tool.setuptools_scm]
 version_file = "commcare_export/VERSION"
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 8931a231..8d3ff640 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,4 +1,5 @@
 import csv
+import logging
 import os
 import re
 import unittest
@@ -11,6 +12,7 @@
 from tests.utils import SqlWriterWithTearDown
 
 import pytest
+from unmagic import fixture
 from commcare_export.checkpoint import (
     Checkpoint,
     CheckpointManager,
@@ -48,6 +50,18 @@ def make_args(project='test', username='test', password='test', **kwargs):
     return namespace
 
 
+@fixture
+def restore_root_logger():
+    root_logger = logging.getLogger()
+    previous_handlers = list(root_logger.handlers)
+    previous_level = root_logger.level
+    yield
+    root_logger.handlers.clear()
+    root_logger.setLevel(previous_level)
+    for handler in previous_handlers:
+        root_logger.addHandler(handler)
+
+
 def mock_hq_client(include_parent):
     return MockCommCareHqClient({
         'form': [({
@@ -315,92 +329,109 @@ def test_cli_table_plus_locations(self, mock_client):
             + get_expected_locations_results(True)
         )
 
-    @mock.patch('logging.basicConfig')
     @mock.patch('os.getcwd', return_value='/mock/cwd')
     @mock.patch('os.makedirs')
     @mock.patch('builtins.open', new_callable=mock.mock_open)
+    @mock.patch('logging.FileHandler')
     def test_log_dir_default(
         self,
+        mock_file_handler,
         mock_open,
         mock_makedirs,
         mock_getcwd,
-        mock_basicConfig,
     ):
-        from commcare_export.cli import set_up_logging
+        from commcare_export.cli import set_up_file_logging
 
-        success, log_file, error = set_up_logging()
+        handler = mock.Mock()
+        mock_file_handler.return_value = handler
+        success, log_file, error, file_handler = set_up_file_logging()
 
         assert success is True
         assert log_file == '/mock/cwd/commcare_export.log'
         assert error is None
+        assert file_handler is handler
         mock_makedirs.assert_called_once_with('/mock/cwd', exist_ok=True)
-        mock_basicConfig.assert_called_once()
-        call_kwargs = mock_basicConfig.call_args[1]
-        assert call_kwargs['filename'] == '/mock/cwd/commcare_export.log'
-        assert call_kwargs['filemode'] == 'a'
+        mock_file_handler.assert_called_once_with(
+            '/mock/cwd/commcare_export.log',
+            mode='a'
+        )
 
-    @mock.patch('logging.basicConfig')
     @mock.patch('os.makedirs')
     @mock.patch('builtins.open', new_callable=mock.mock_open)
+    @mock.patch('logging.FileHandler')
     def test_log_dir_custom(
         self,
+        mock_file_handler,
         mock_open,
         mock_makedirs,
-        mock_basicConfig,
     ):
-        from commcare_export.cli import set_up_logging
+        from commcare_export.cli import set_up_file_logging
 
-        success, log_file, error = set_up_logging('/custom/log/path')
+        handler = mock.Mock()
+        mock_file_handler.return_value = handler
+        success, log_file, error, file_handler = set_up_file_logging(
+            '/custom/log/path'
+        )
 
         assert success is True
         assert log_file == '/custom/log/path/commcare_export.log'
         assert error is None
+        assert file_handler is handler
         mock_makedirs.assert_called_once_with('/custom/log/path', exist_ok=True)
-        mock_basicConfig.assert_called_once()
-        call_kwargs = mock_basicConfig.call_args[1]
-        assert call_kwargs['filename'] == '/custom/log/path/commcare_export.log'
+        mock_file_handler.assert_called_once_with(
+            '/custom/log/path/commcare_export.log',
+            mode='a'
+        )
 
     @mock.patch('os.makedirs', side_effect=PermissionError("Permission denied"))
     def test_log_dir_permission_error(
         self,
         mock_makedirs,
     ):
-        from commcare_export.cli import set_up_logging
+        from commcare_export.cli import set_up_file_logging
 
-        success, log_file, error = set_up_logging('/restricted/path')
+        success, log_file, error, file_handler = set_up_file_logging(
+            '/restricted/path'
+        )
 
         assert success is False
         assert log_file == '/restricted/path/commcare_export.log'
         assert error == "PermissionError: Permission denied"
+        assert file_handler is None
         mock_makedirs.assert_called_once_with('/restricted/path', exist_ok=True)
 
-    @mock.patch('logging.basicConfig')
     @mock.patch('os.getcwd', return_value='/test/dir')
     @mock.patch('os.makedirs')
     @mock.patch('builtins.open', new_callable=mock.mock_open)
+    @mock.patch('logging.FileHandler')
     def test_log_append_mode(
         self,
+        mock_file_handler,
         mock_open,
         mock_makedirs,
         mock_getcwd,
-        mock_basicConfig,
     ):
-        from commcare_export.cli import set_up_logging
+        from commcare_export.cli import set_up_file_logging
 
-        success, log_file, error = set_up_logging()
+        handler = mock.Mock()
+        mock_file_handler.return_value = handler
+        success, log_file, error, file_handler = set_up_file_logging()
 
         assert success is True
-        mock_basicConfig.assert_called_once()
-        call_kwargs = mock_basicConfig.call_args[1]
-        assert call_kwargs['filemode'] == 'a'
+        assert file_handler is handler
+        mock_file_handler.assert_called_once_with(
+            '/test/dir/commcare_export.log',
+            mode='a'
+        )
 
     @mock.patch('commcare_export.cli._get_api_client', return_value=mock_hq_client(True))
-    @mock.patch('commcare_export.cli.set_up_logging')
+    @mock.patch('commcare_export.cli.set_up_file_logging')
     @mock.patch('sys.exit')
-    def test_no_logfile_still_works(
+    @restore_root_logger
+    def test_no_logfile(
         self,
         mock_exit,
-        mock_set_up_logging,
+        mock_set_up_file_logging,
         mock_client,
     ):
         from commcare_export.cli import main
@@ -415,7 +446,23 @@ def test_no_logfile_still_works(
             '--log-dir', '/some/path'  # Should be ignored
         ])
 
-        mock_set_up_logging.assert_not_called()
+        mock_set_up_file_logging.assert_not_called()
+
+    @restore_root_logger
+    def test_set_up_logging_uses_message_only_formatter(self):
+        from commcare_export.cli import set_up_logging
+
+        args = Namespace(
+            verbose=False,
+            no_logfile=True,
+            log_dir=None,
+        )
+        root_logger = logging.getLogger()
+        set_up_logging(args)
+        assert len(root_logger.handlers) == 1
+        formatter = root_logger.handlers[0].formatter
+        assert formatter is not None
+        assert formatter._style._fmt == '%(message)s'
 
 
 @pytest.fixture(scope='function')
@@ -752,29 +799,25 @@ def _pull_mock_data(
 class TestCLIWithDatabaseErrors:
 
     def test_cli_database_error(
-        self, strict_writer, all_db_checkpoint_manager, capfd
+        self, strict_writer, all_db_checkpoint_manager, caplog
     ):
         _pull_mock_data(
             strict_writer, all_db_checkpoint_manager, CONFLICTING_TYPES_CLIENT,
             'tests/013_ConflictingTypes.xlsx'
         )
-        out, err = capfd.readouterr()
-
         expected_re = re.compile('Stopping because of database error')
-        assert re.search(expected_re, out)
+        assert re.search(expected_re, caplog.text)
 
     def test_cli_database_error_checkpoint(
-        self, strict_writer, all_db_checkpoint_manager, capfd
+        self, strict_writer, all_db_checkpoint_manager, caplog
     ):
         _pull_mock_data(
             strict_writer, all_db_checkpoint_manager,
             get_conflicting_types_checkpoint_client(),
             'tests/013_ConflictingTypes.xlsx'
         )
-        out, err = capfd.readouterr()
-
         expected_re = re.compile('Stopping because of database error')
-        assert re.search(expected_re, out), out
+        assert re.search(expected_re, caplog.text), caplog.text
 
         # expect checkpoint to have the date from the first batch and
         # not the 2nd
diff --git a/tests/test_commcare_export.py b/tests/test_commcare_export.py
deleted file mode 100644
index cd367c82..00000000
--- a/tests/test_commcare_export.py
+++ /dev/null
@@ -1,33 +0,0 @@
-import os
-from commcare_export import logger_name_from_filepath, repo_root
-
-
-class TestLoggerNameFromFilePath:
-
-    @staticmethod
-    def _file_path(rel_path):
-        return os.path.join(repo_root, rel_path)
-
-    def test_file_in_root(self):
-        path = self._file_path("file.py")
-        assert logger_name_from_filepath(path) == 'file'
-
-    def test_file_in_subdirectory(self):
-        path = self._file_path("subdir/file.py")
-        assert logger_name_from_filepath(path) == 'subdir.file'
-
-    def test_file_in_deeper_subdirectory(self):
-        path = self._file_path("subdir/another_sub/file.py")
-        assert logger_name_from_filepath(path) == 'subdir.another_sub.file'
-
-    def test_file_contains_py(self):
-        path = self._file_path("subdir/pytest.py")
-        assert logger_name_from_filepath(path) == 'subdir.pytest'
-
-    def test_file_dir_contains_periods(self):
-        path = self._file_path("sub.dir/pytest.py")
-        assert logger_name_from_filepath(path) == 'sub.dir.pytest'
-
-    def test_random_file_name(self):
-        path = self._file_path("pyppy.excel_query.py")
-        assert logger_name_from_filepath(path) == 'pyppy.excel_query'