From 726628cc4c953e5cfb2aaefd9aa6f461fba27fd6 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.ai>
Date: Sun, 11 Dec 2022 00:21:46 +0000
Subject: [PATCH] enable full logging with -v (PR #26)

* fix #25
* enable full logging at INFO when -v (verbose) is requested
* Update CHANGES
---
 CHANGES                     | 11 ++++++++++-
 flamel/flamel.py            |  5 ++++-
 flamel/tests/test_flamel.py | 12 ++++++++++++
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/CHANGES b/CHANGES
index 5d2116f..9a4c648 100644
--- a/CHANGES
+++ b/CHANGES
@@ -13,15 +13,24 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" https://semver.org
 
 ------------------------------------------------------------------------------
+2022-??-??  xiki-tempula
+
+  * 0.3.2
+  
+Fixes
+
+- enable logger output for -v (issue #25)
+
 
 2022-12-06  xiki-tempula, hejamu
 
   * 0.3.1
 
- Fixes
+Fixes
 
 - Handle 0 as input to the forwrev (Issue #18/ PR #20).
 
+
 2022-11-09  xiki-tempula, orbeckst
 
   * 0.3.0
diff --git a/flamel/flamel.py b/flamel/flamel.py
index d4b1d66..8709566 100644
--- a/flamel/flamel.py
+++ b/flamel/flamel.py
@@ -173,7 +173,10 @@ def main():
 
     # Print the logging to the console
     if args.verbose:
-        logging.getLogger().addHandler(logging.StreamHandler())
+        logging.basicConfig(
+            level=logging.INFO,
+            handlers=[logging.StreamHandler()],
+        )
 
     if args.output_directory == "":
         out = args.datafile_directory
diff --git a/flamel/tests/test_flamel.py b/flamel/tests/test_flamel.py
index 28f0012..361d0b1 100644
--- a/flamel/tests/test_flamel.py
+++ b/flamel/tests/test_flamel.py
@@ -6,6 +6,7 @@
 import sys
 import pathlib
 import pickle
+import subprocess
 
 import pytest
 from numpy.testing import assert_approx_equal
@@ -47,6 +48,17 @@ def test_dhdl_TI(self, setup):
         assert (setup / "dhdl_TI.pdf").exists()
 
 
+def test_verbose():
+    p = subprocess.Popen(
+        ["flamel", "-v"], stdout=subprocess.PIPE, stderr=subprocess.PIPE
+    )
+    out, err = p.communicate()
+    assert (
+        "INFO:alchemlyb.workflows.ABFE:Initialise Alchemlyb ABFE Workflow"
+        in err.decode()
+    )
+
+
 class TestFlamelOptions(TestFlamel):
     @staticmethod
     @pytest.fixture(scope="session")