Lomap v3.3.0

What's Changed

• one back tick too many by @mikemhenry in #69
• Switch to setuptools_scm by @mikemhenry in #72
• Ensure PEP-639 Support by @mikemhenry in #84
• fix docs memory build error by @atravitz in #85
• Add necessary files for rever changelog by @IAlibay in #86
• update CI workflow versions by @atravitz in #87
• add CHANGELOG in index - fix docs build by @atravitz in #90
• Adapt default charge change score to allow for charge changing transformations by @hannahbaumann in #83
• switch to src/ layout by @atravitz in #81
• let setuptools auto detect pkg layout and remove deps by @mikemhenry in #91
• Change default max3d value to 1.0 by @IAlibay in #94
• Docs/fixes by @IAlibay in #95
• Update CI file by @IAlibay in #124
• Add pre-commit & ruff by @IAlibay in #126
• Fix logging message for MCS molecules by @IAlibay in #131
• Linter changes by @IAlibay in #130
• Type checking & fixing typing issues by @IAlibay in #125
• Ignore linting PR in git blame by @IAlibay in #132
• Make gufe optional by @IAlibay in #134
• Fix various typos by @IAlibay in #135
• Deprecate the fp module by @IAlibay in #136
• Remove unused test code in mcs.py by @IAlibay in #137
• Deprecate dbmol CLI by @IAlibay in #139
• Docs for installing optional dependencies and better handling of pygraphviz optional deps by @IAlibay in #141
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #143
• Small updates to py311+ by @IAlibay in #145
• Fix gufe mncar score by @IAlibay in #148
• Docstring fixes for gufe bindings methods by @IAlibay in #142
• Typing and docstring fixes to mcs.py by @IAlibay in #150
• Clean up init a little bit by @IAlibay in #152
• Change MCS seed parameter type to optional string in MCS by @IAlibay in #156
• Add dependencies back into pyproject.toml by @IAlibay in #153
• Remove legacy examples by @IAlibay in #159
• Error or warn if we have a disconnected network by @IAlibay in #154
• Typing and docstring fixes for graphgen by @IAlibay in #151
• Duecredit remaining tasks by @IAlibay in #158
• Update typing and docstrings for dbmol by @IAlibay in #160
• Add PR template by @IAlibay in #164
• Fix PR template by @IAlibay in #165
• Update authors list by @IAlibay in #166
• Migrate LomapAtomMapper testing to the gufe mixin by @IAlibay in #157
• Update README.md by @hannahbaumann in #162
• Add getting started docs by @hannahbaumann in #163
• Add main citation for Lomap by @IAlibay in #146
• v3.3 pre-release by @IAlibay in #168

Full Changelog: v3.2.1...v3.3.0

v3.2.1

3.2.1

Fixed

• Fixed bug where generate_lomap_network() would throw an error if molecules was passed in instead of ligands.

v3.2.0

Changed

• Replaced the molecules argument with ligands in generate_lomap_network(). Argument name molecules will be deprecated.

v3.1.0

Main changes

• The default lomap score's ecr_score now optionally takes a user defined minimum value to allow
  for networks with net charge changes. See #52 by @hannahbaumann

Other changes

• Change defaults to "what works" for gufe bindings by @IAlibay in #45
• Add docs badge to readme by @IAlibay in #49
• Update macos runner to macos-12 by @IAlibay in #54
• Update README.md by @mikemhenry in #55

New Contributors

• @hannahbaumann made their first contribution in #52

Full Changelog: v3.0.3...v3.1.0

v3.0.3

What's Changed

• Update CI & packaging by @IAlibay in #40
• include date in cache key by @mikemhenry in #46
• Make mapper tokenizable by @richardjgowers in #47

Full Changelog: v3.0.2...v3.0.3

v3.0.2 - generate_lomap_network fix

Fixes an issue with generate_lomap_network that would cause it to fail in systems where some mappings could not be generated

What's Changed

• Fix pkg_resources deprecation & path as context manager is a no-op by @IAlibay in #39
• add repr to LomapAtomMapper by @richardjgowers in #42
• score matrix was initially full of perfect values not worst values by @richardjgowers in #44

Full Changelog: v3.0.1...v3.0.2

3.0.1 - Hotfix - Fixes packaging

See previous release notes for changes in the 3.x series relative to 2.x

v3.0.0 - Added gufe bindings

Highlights

• The API for GraphGen has been reworked from accepting a DBMol object to instead accepting multiple parameters
• If you are programmatically using Lomap you might need to pin to the 2.x series of releases.
• Adds bindings for gufe API components. Allows interoperable use of Lomap in other free energy tooling.

What's Changed

• Add gufe Bindings to Lomap package by @richardjgowers in #29
• Improve CI by @mikemhenry in #30
• Update CI.yaml by @richardjgowers in #31
• Enforce single fragment from MCS by @richardjgowers in #33
• Switch to OFE theme and remove redundant CSS by @Yoshanuikabundi in #34
• add duecredit by @richardjgowers in #36

New Contributors

• @Yoshanuikabundi made their first contribution in #34

Full Changelog: v2.3.0...v3.0.0

v2.3.1 - whole fragments fix

Fixes issue #32 - Sometimes a disconnected structure was given as the mapping from MCS.

Full Changelog: v2.3.0...v2.3.1

v3.0.0

What's Changed

• Add gufe Bindings to Lomap package by @richardjgowers in #29
• Improve CI by @mikemhenry in #30
• Update CI.yaml by @richardjgowers in #31

Full Changelog: v2.3.0...v3.0.0a2