From e1a2de020a701087fd6c4538a466eb9d0f2138c9 Mon Sep 17 00:00:00 2001
From: Paul Saxe <paul@thesaxes.net>
Date: Wed, 26 Oct 2022 09:37:10 -0400
Subject: [PATCH 1/2] Capturing stderr from OpenBabel and printing warnings.

---
 read_structure_step/formats/mop/obabel.py | 177 ++++++++++++++++------
 1 file changed, 133 insertions(+), 44 deletions(-)

diff --git a/read_structure_step/formats/mop/obabel.py b/read_structure_step/formats/mop/obabel.py
index 266c48c..3decefc 100644
--- a/read_structure_step/formats/mop/obabel.py
+++ b/read_structure_step/formats/mop/obabel.py
@@ -2,6 +2,11 @@
 Implementation of the reader for XYZ files using OpenBabel
 """
 
+import os
+import sys
+import threading
+import time
+
 import logging
 from pathlib import Path
 import re
@@ -47,6 +52,82 @@
 }
 
 
+class OutputGrabber(object):
+    """Class used to grab standard output or another stream.
+
+    see https://stackoverflow.com/questions/24277488/in-python-how-to-capture-the-stdout-from-a-c-shared-library-to-a-variable/29834357#29834357  # noqa: E501
+    """
+
+    escape_char = "\b"
+
+    def __init__(self, stream=None, threaded=False):
+        self.origstream = stream
+        self.threaded = threaded
+        if self.origstream is None:
+            self.origstream = sys.stdout
+        self.origstreamfd = self.origstream.fileno()
+        self.capturedtext = ""
+        # Create a pipe so the stream can be captured:
+        self.pipe_out, self.pipe_in = os.pipe()
+
+    def __enter__(self):
+        self.start()
+        return self
+
+    def __exit__(self, type, value, traceback):
+        self.stop()
+
+    def start(self):
+        """
+        Start capturing the stream data.
+        """
+        self.capturedtext = ""
+        # Save a copy of the stream:
+        self.streamfd = os.dup(self.origstreamfd)
+        # Replace the original stream with our write pipe:
+        os.dup2(self.pipe_in, self.origstreamfd)
+        if self.threaded:
+            # Start thread that will read the stream:
+            self.workerThread = threading.Thread(target=self.readOutput)
+            self.workerThread.start()
+            # Make sure that the thread is running and os.read() has executed:
+            time.sleep(0.01)
+
+    def stop(self):
+        """
+        Stop capturing the stream data and save the text in `capturedtext`.
+        """
+        # Print the escape character to make the readOutput method stop:
+        self.origstream.write(self.escape_char)
+        # Flush the stream to make sure all our data goes in before
+        # the escape character:
+        self.origstream.flush()
+        if self.threaded:
+            # wait until the thread finishes so we are sure that
+            # we have until the last character:
+            self.workerThread.join()
+        else:
+            self.readOutput()
+        # Close the pipe:
+        os.close(self.pipe_in)
+        os.close(self.pipe_out)
+        # Restore the original stream:
+        os.dup2(self.streamfd, self.origstreamfd)
+        # Close the duplicate stream:
+        os.close(self.streamfd)
+
+    def readOutput(self):
+        """
+        Read the stream data (one byte at a time)
+        and save the text in `capturedtext`.
+        """
+        while True:
+            char = os.read(self.pipe_out, 1).decode(self.origstream.encoding)
+            if not char or self.escape_char in char:
+                break
+            self.capturedtext += char
+
+
 def _find_charge(regex, input_file):
     text = re.search(regex, input_file)
     if text is not None:
@@ -303,56 +384,64 @@ def load_mop(
     logger.info(f"Input data:\n\n{input_data}\n")
 
     # Now try to convert using OpenBabel
-    obConversion = openbabel.OBConversion()
-    if internals:
-        obConversion.SetInFormat("mopin")
-    else:
-        obConversion.SetInFormat("mopcrt")
-
-    obMol = openbabel.OBMol()
-    try:
-        if run_mopac:
-            raise RuntimeError("Forcing use of MOPAC output")
-        success = obConversion.ReadString(obMol, input_data)
-        if not success:
-            raise RuntimeError("obConversion failed")
-    except Exception:
-        logger.info("**** falling back to MOPAC")
-        # Try using a MOPAC output file instead. Works for e.g. mixed coordinates
-        mopac_exe = find_mopac()
-        if mopac_exe is None:
-            raise FileNotFoundError("The MOPAC executable could not be found")
-
-        # Create an input file
-        text = ["0SCF", "title", "description"]
-        text.extend(raw_geometry_lines)
-        # An empty line denotes end of input
-        text.append(" ")
-        files = {"mopac.dat": "\n".join(text)}
-
-        logger.debug(f"MOPAC input file:\n\n{files['mopac.dat']}\n")
-
-        local = seamm.ExecLocal()
-        result = local.run(
-            cmd=[mopac_exe, "mopac.dat"], files=files, return_files=["mopac.out"]
-        )
+    out = OutputGrabber(sys.stderr)
+    with out:
+        obConversion = openbabel.OBConversion()
+        if internals:
+            obConversion.SetInFormat("mopin")
+        else:
+            obConversion.SetInFormat("mopcrt")
+
+        obMol = openbabel.OBMol()
+        try:
+            if run_mopac:
+                raise RuntimeError("Forcing use of MOPAC output")
+            success = obConversion.ReadString(obMol, input_data)
+            if not success:
+                raise RuntimeError("obConversion failed")
+        except Exception:
+            logger.info("**** falling back to MOPAC")
+            # Try using a MOPAC output file instead. Works for e.g. mixed coordinates
+            mopac_exe = find_mopac()
+            if mopac_exe is None:
+                raise FileNotFoundError("The MOPAC executable could not be found")
+
+            # Create an input file
+            text = ["0SCF", "title", "description"]
+            text.extend(raw_geometry_lines)
+            # An empty line denotes end of input
+            text.append(" ")
+            files = {"mopac.dat": "\n".join(text)}
+
+            logger.debug(f"MOPAC input file:\n\n{files['mopac.dat']}\n")
+
+            local = seamm.ExecLocal()
+            result = local.run(
+                cmd=[mopac_exe, "mopac.dat"], files=files, return_files=["mopac.out"]
+            )
+
+            if result["mopac.out"]["data"] is None:
+                raise RuntimeError("MOPAC failed: " + result["mopac.out"]["exception"])
 
-        if result["mopac.out"]["data"] is None:
-            raise RuntimeError("MOPAC failed: " + result["mopac.out"]["exception"])
+            text = result["mopac.out"]["data"]
 
-        text = result["mopac.out"]["data"]
+            logger.debug(f"MOPAC output:\n\n{text}\n")
 
-        logger.debug(f"MOPAC output:\n\n{text}\n")
+            obConversion.SetInFormat("mopout")
+            success = obConversion.ReadString(obMol, text)
 
-        obConversion.SetInFormat("mopout")
-        success = obConversion.ReadString(obMol, text)
+            if not success:
+                raise RuntimeError("Could not process MOPAC file")
 
-        if not success:
-            raise RuntimeError("Could not process MOPAC file")
+        if add_hydrogens:
+            obMol.AddHydrogens()
+        configuration.from_OBMol(obMol)
 
-    if add_hydrogens:
-        obMol.AddHydrogens()
-    configuration.from_OBMol(obMol)
+    # Check any stderr information from obabel.
+    if out.capturedtext != "":
+        tmp = out.capturedtext
+        if "Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders" not in tmp:
+            logger.warning(tmp)
 
     # Record the charge, and the spin state
     charge = 0

From 2c9c2a7fff4b47de9ccb865148a58049b1ce52cf Mon Sep 17 00:00:00 2001
From: Paul Saxe <paul@thesaxes.net>
Date: Wed, 26 Oct 2022 09:41:12 -0400
Subject: [PATCH 2/2] Updated release history.

---
 HISTORY.rst | 34 +++++++++++++---------------------
 1 file changed, 13 insertions(+), 21 deletions(-)

diff --git a/HISTORY.rst b/HISTORY.rst
index 5d48c9d..dfa21d7 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,39 +2,31 @@
 History
 =======
 
-2021.2.12 (12 February 2021)
-----------------------------
+2022.10.26 -- Handling OpenBabel error messages for MOPAC .mop files
+  Hiding messages about errors Kekulizing structures, which doesn't seem to be a serious
+  issue, and printing any other messages as warnings.
 
-* Updated the README file to give a better description.
-* Updated the short description in setup.py to work with the new installer.
-* Added keywords for better searchability.
+2021.2.12 (12 February 2021)
+  * Updated the README file to give a better description.
+  * Updated the short description in setup.py to work with the new installer.
+  * Added keywords for better searchability.
 
 2021.2.4 (4 February 2021)
---------------------------
-
-* Updated for compatibility with the new system classes in MolSystem
+  Updated for compatibility with the new system classes in MolSystem
   2021.2.2 release.
 
 2020.12.5 (5 December 2020)
----------------------------
-
-* Internal: switching CI from TravisCI to GitHub Actions, and in the
+  Internal: switching CI from TravisCI to GitHub Actions, and in the
   process moving documentation from ReadTheDocs to GitHub Pages where
   it is consolidated with the main SEAMM documentation.
 
 2020.8.1 (1 August 2020)
-------------------------
-
-* Removed leftover debug print statements.
+  Removed leftover debug print statements.
 
 0.9 (15 April 2020)
--------------------
-
-* General bug fixing and code cleanup.
-* Part of release of all modules.
+  * General bug fixing and code cleanup.
+  * Part of release of all modules.
 
 
 0.7.1 (23 November 2019)
-------------------------
-
-* First release on PyPI.
+  First release on PyPI.