Add some central utils to avoid duplications in notebooks (NO_JIRA)

Author: jasonccole

notebooks/ccdc_notebook_utilities/README.md

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+# Shared utilities
+This package contains shared functionality that is used in multiple notebooks 

notebooks/ccdc_notebook_utilities/__init__.py

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+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2022-05-17: created by Jason Cole, The Cambridge Crystallographic Data Centre
+#
+from .run_hermes import run_hermes
+from .create_logger import create_logger

notebooks/ccdc_notebook_utilities/create_logger.py

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+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2022-05-17: created by Jason Cole, The Cambridge Crystallographic Data Centre
+#
+
+import logging
+from platform import platform
+import sys
+import ccdc.io
+import os
+
+"""
+From inside a notebook, create a logger and log starting information
+"""
+def create_logger(verbose = True):
+    logger = logging.getLogger(__name__)
+    handler = logging.StreamHandler()
+    handler.setFormatter(logging.Formatter('[%(asctime)s %(levelname)-7s] %(message)s', datefmt='%y-%m-%d %H:%M:%S'))
+    logger.addHandler(handler)
+    logger.setLevel(logging.INFO)
+
+    if verbose:
+        logger.info(f"""
+Platform:                     {platform()}
+
+Python exe:                   {sys.executable}
+Python version:               {'.'.join(str(x) for x in sys.version_info[:3])}
+
+CSD version:                  {ccdc.io.csd_version()}
+CSD directory:                {ccdc.io.csd_directory()}
+API version:                  {ccdc.__version__}
+
+CSDHOME:                      {os.environ.get('CSDHOME', 'Not set')}
+CCDC_LICENSING_CONFIGURATION: {os.environ.get('CCDC_LICENSING_CONFIGURATION', 'Not set')}
+""")
+    return logger

notebooks/ccdc_notebook_utilities/run_hermes.py

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+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2022-05-17: created by Jason Cole, The Cambridge Crystallographic Data Centre
+#
+
+from ccdc.io import csd_directory
+from pathlib import Path
+from platform import platform
+from subprocess import Popen
+
+"""
+From inside a notebook, run CCDC Hermes utility or fail if we cant find it. Assumes the
+software is installed alongside the data folder currently.
+"""
+def run_hermes(*filenames):
+    try:
+        hermes_dir = Path( csd_directory() ) / '..' / '..' / 'ccdc-software' / 'hermes'
+        hermes_exe = (hermes_dir/ 'hermes.exe' if platform().startswith('Windows') else hermes_dir/ 'hermes').as_posix()     
+        status = Popen([hermes_exe, *filenames], creationflags=0x00000008)
+    except Exception as e:
+        print( f"Couldnt run Hermes {e}")