Repository: pckroon/pysmiles

Issue:
could you not PRINT warnings?
maybe it is better to write to stderr or at least offer an option to shut off the warnings like "I can't deal with stereo yet..."

Comments:

Patch:
diff --git a/README.md b/README.md
index c8b693c..23e7b17 100644
--- a/README.md
+++ b/README.md
@@ -53,6 +53,25 @@ element attribute.
     of 1.5. If `False`, will create a molecule using *only* the information in 
     the SMILES string.
 
+### Stereochemical information
+Currently the library cannot handle stereochemical information, neither E/Z nor
+R/S. Any stereochemical information that was in the SMILES string will be
+*discarded* upon parsing. This means there will be no difference between
+parsing *e.g.* `N[C@](Br)(O)C`, `N[C@@](Br)(O)C` and `NC(Br)(O)C`. Parsing
+these *will result in the same molecule*. The same holds for *e.g.* `F/C=C/F`
+and `FC=CF`. These will result in the same molecule.
+
+Whenever stereochemical information is being discarded a warning will be
+logged using the built-in `logging` module. If you want to disable all the
+messages logged by `pysmiles` you can add the following snippet to your code,
+without interfering with any logging by your own code:
+
+```python
+import logging
+logging.getLogger('pysmiles').setLevel(logging.CRITICAL)  # Anything higher than warning
+```
+
+
 ## Writing SMILES
 The function `write_smiles(molecule, default_element='*', start=None)` can be
 used to write SMILES strings from a molecule. The function does *not* check 
@@ -196,7 +215,6 @@ print(write_smiles(mol))
 - `correct_aromatic_rings` is fragile.
 - There is currently no way of specifying stereo chemical information. The 
     parser can deal with it, but it will be discarded.
-- It is not on PyPI
 - It only processes SMILES. This might later be extended to e.g. InChi, SLN,
     SMARTS, etc.
 
diff --git a/pysmiles/read_smiles.py b/pysmiles/read_smiles.py
index 1d55882..f4bf6e0 100644
--- a/pysmiles/read_smiles.py
+++ b/pysmiles/read_smiles.py
@@ -18,6 +18,7 @@ Exposes functionality needed for parsing SMILES strings.
 """
 
 import enum
+import logging
 
 import networkx as nx
 
@@ -25,6 +26,7 @@ from .smiles_helper import (add_explicit_hydrogens, remove_explicit_hydrogens,
                             parse_atom, fill_valence, mark_aromatic_edges,
                             mark_aromatic_atoms)
 
+LOGGER = logging.getLogger(__name__)
 
 @enum.unique
 class TokenType(enum.Enum):
@@ -175,7 +177,7 @@ def read_smiles(smiles, explicit_hydrogen=False, zero_order_bonds=True,
                 ring_nums[token] = (idx - 1, next_bond)
                 next_bond = None
         elif tokentype == TokenType.EZSTEREO:
-            print("I can't deal with stereo yet...")
+            LOGGER.warning('E/Z stereochemical information, which is specified by "%s", will be discarded', token)
     if ring_nums:
         raise KeyError('Unmatched ring indices {}'.format(list(ring_nums.keys())))
 
diff --git a/pysmiles/smiles_helper.py b/pysmiles/smiles_helper.py
index cd78eb0..fb59432 100644
--- a/pysmiles/smiles_helper.py
+++ b/pysmiles/smiles_helper.py
@@ -18,11 +18,14 @@ Contains helper functions for parsing and writing SMILES strings, as well as
 some convenience functions for adding hydrogens, and detecting aromaticity.
 """
 
+import logging
 import re
 import operator
 
 import networkx as nx
 
+LOGGER = logging.getLogger(__name__)
+
 ISOTOPE_PATTERN = r'(?P<isotope>[\d]+)?'
 ELEMENT_PATTERN = r'(?P<element>b|c|n|o|s|p|\*|[A-Z][a-z]{0,2})'
 STEREO_PATTERN = r'(?P<stereo>@|@@|@TH[1-2]|@AL[1-2]|@SP[1-3]|@OH[\d]{1,2}|'\
@@ -98,7 +101,7 @@ def parse_atom(atom):
         raise ValueError("A hydrogen atom can't have hydrogens")
 
     if 'stereo' in out:
-        print("I don't quite know how to handle stereo yet...")
+        LOGGER.warning('Atom "%s" contains stereochemical information that will be discarded.', atom)
 
     return out
 


Test patch:
diff --git a/tests/test_read_smiles.py b/tests/test_read_smiles.py
index 51390d0..d85e718 100644
--- a/tests/test_read_smiles.py
+++ b/tests/test_read_smiles.py
@@ -497,12 +497,16 @@ def test_invalid_smiles(smiles, error_type):
         read_smiles(smiles)
 
 
-def test_cis_trans():
-    smiles = r'F/C=C/F', r'C(\F)=C/F', r'F\C=C/F', r'C(/F)=C/F'
-    for smile in smiles:
-        read_smiles(smile, explicit_hydrogen=False)
-
-
-def test_extended_stereo():
-    smiles = 'NC(Br)=[C@]=C(O)C'
-    read_smiles(smiles)
+@pytest.mark.parametrize('smiles, n_records',[
+    (r'F/C=C/F', 2),
+    (r'C(\F)=C/F', 2),
+    (r'F\C=C/F', 2),
+    (r'C(/F)=C/F', 2),
+    ('NC(Br)=[C@]=C(O)C', 1),
+    ('c1ccccc1', 0)
+])
+def test_stereo_logging(caplog, smiles, n_records):
+    read_smiles(smiles, explicit_hydrogen=False)
+    assert len(caplog.records) == n_records
+    for record in caplog.records:
+        assert record.levelname == "WARNING"