0.1.5rc1

Minor feature cleanup and improvements to kekulization handling and chemical database query services

• Greatly expanded robustness of smileslib.chemdbqueries:
  • Reimplemented core via Strategy pattern and provided concrete implementations for
    • NIH CACTUS CIR
    • PubChem
  • Added capability to check is services are online prior to attempting query
  • Compiled comprehensive lists of queryable chemical properties and namespaces for each implementations
  • Added service-agnostic get_chemical_property() wrapper for convenience
    *Provided greater control over Kekulization in RDKit-derived functionality
  • Added enable_kekulized_drawing() and disble_kekulized_drawing() config methods to rdutils.rdkdraw
    -* Made rdkdraw imported at toplevel rdutils
  • Added flag to disable Kekulization in SMILES string expansion (polymers.monomers.specification.expanded_SMILES(...))
• Added procrustean_string(...) function to genutils.textual.prettyprint (related to PROCRUSTES algorithm implemented in .polymers for copolymer sequencing)

0.1.4rc1

Minor fixes to README and optional dependencies

What's changed

• Fixed issue with accidental file redirect in NAGL install command in README
• Corrected typos in README
• Added missing pubchempy requirement to "chemdb" optional dependency category

0.1.3rc1

Overhaul of README and improvements to dependency management

What's changed

• Front-facing README completely rewritten to provide:
  • Details on compatible OS and package managers
  • More specific installation instruction
    • Pip-compatible installation instructions
  • Details on installing peripheral AM1-BCC toolkits
• Simplified dependencies
  • Espaloma_charge is no longer required OR optional in pyproject.toml
  • espaloma_charge dependency in release-build.yml changed from pip-based to conda-based
  • Pre-import checks for cirpy and pubchempy added to smileslib.chemdbqueries
  • Fixed str.capitalize() call in use_case arg to MissingPrerequisitePackage, as this was causing unintended lowercasing later in the string
  • Former "jupyter" and "visuals" optional dependency categories consolidated into single "interactive" category
    • Made "rich" a required dependency

0.1.1rc1

Minor tweaks to Python build files to get documentation and package index uploads working. No changes to code, only affects:

• pyproject.toml: Added pip dependencies
• readthedocs.yaml: Added pip install directive
• devtools/conda-envs/release-build.yml: Added Sphinx theme requirement to nudge ReadTheDocs build along

0.1.0rc1

Release candidate in-transition from beta to official release

What's changed

• Added new molfiles subpackage for handling molecule file writing
• Consolidated dynamic imports and dependency checking into genutils.importutils subpackage
• Added dependency check for non-pip installable dependencies (namely OpenFF stack, mBuild, OpenBabel, and OpenEye)
• Added generic tree-like data structure interface, used to reimplement file and directory trees
• Deprecated unintuitive "DOP" keyword in polymer builder in favor of explicit number of monomers
• Added Validation, end group auto-generation, and several convencience methods to MonomerGroup
• Added robust copolymer sequence checking and fitting ("PROCRUSTEAN sequence alignment"), including support for fractional base sequence repeats
• Updated OpenFF NAGL models
• Simplified OpenFF partial charge method and toolkit registration
• Increased test coverage throughout (particularly for new features)

0.0.1 Beta version

Pre-release version of polymerist.

Intended to:

• Checkpoint this version of polymerist prior to planned 1.0.0
• Allow reversion to pre-release build for dependent code
• Enable building of documentation for ReadTheDocs
• Enable testing of pip-installable version

Full Changelog: https://github.com/timbernat/polymerist/commits/v0.0.1-beta