v0.1.0a16

What's Changed

• feat(random): unify and expose random interface by @jnooree in #513
• feat(fmt/pdb): add pdb-native alternative output format by @jnooree in #514
• feat(fmt/pdb): add more attributes to PDBAtom and fix formal charge handling by @jnooree in #515
• perf(python/fmt/pdb): bind with custom iterator by @jnooree in #516
• feat(python/fmt/pdb): add as_dict() interface for faster lib-agnostic integration by @jnooree in #517
• ci: fix ctest args by @jnooree in #520
• fix(python/fmt/pdb): avoid nurikit-specific type in native format by @jnooree in #519
• fix(core/geom): update functions for generic types and rework eigen aliases by @jnooree in #523
• ci(rtd): update environment by @jnooree in #524
• ci(gha): rename commit message checks by @jnooree in #525
• feat(fmt/pdb): don't strip first space by @jnooree in #529
• build: cleanup test discovery by @jnooree in #531
• feat(core/geom): support neighbor query between octrees and allow scaling/translation on existing octree by @jnooree in #532
• feat(desc/sasa): implement Shrake-Rupley SASA algorithm by @jnooree in #533
• perf(core/geometry/octree): optimize octree by supporting bucket size > 8 by @jnooree in #534
• perf(core/geometry/octree): save begin and all index of current node by @jnooree in #536

Full Changelog: v0.1.0a15...v0.1.0a16

v0.1.0a15

What's Changed

• build: enable free-threading build (cp313t) by @jnooree in #485
• fix(fmt/mmcif): avoid insert() function by @jnooree in #486
• build: refactor for conda integration by @jnooree in #487
• feat(algo/pcharge/gasteiger): implement Gasteiger partial charge by @jnooree in #489
• fix: handle abseil nullability deprecation gracefully by @jnooree in #490
• feat(fmt/mol2): handle charge type by @jnooree in #491
• fix(utils): ignore deprecation warning by @jnooree in #492
• feat(core/graph): implement BGL compatibility layer by @jnooree in #493
• refactor: reorganize headers and implementations by @jnooree in #494
• ci: download more dependencies by @jnooree in #495
• feat(algo/optim/nm): implement Nelder-Mead minimizer by @jnooree in #496
• fix(core/graph/adaptor): implement out/in edge correctly by @jnooree in #497
• feat(core/container): implement a fixed-size linear queue and refactor headers by @jnooree in #498
• feat(fmt/pdb): guess element from atom name if element cols are missing by @jnooree in #504
• feat(fmt/mmcif): save record type indicator (ATOM/HETATM) by @jnooree in #506
• fix(fmt/pdb): handle models without any header correctly by @jnooree in #508
• fix: fix build on eigen 3.4.1 by @jnooree in #510
• feat(tools/galign): implement galign algorithm by @jnooree in #512

Full Changelog: v0.1.0a14.post1...v0.1.0a15

v0.1.0a14.post1

What's Changed

• chore: lint commit messages with gitlint by @jnooree in #477
• build: overhaul build system by @jnooree in #479
• ci(rtd): export compile commands by @jnooree in #480
• build: package stub files in sdist by @jnooree in #481
• build: relax requirement of scikit-build-core for python 3.7 by @jnooree in #482
• build/ci: add deps min version, bump clang tools version, fix version emulation by @jnooree in #483
• docs(python): fix rst syntax by @jnooree in #484

Full Changelog: v0.1.0a14.post0...v0.1.0a14.post1

v0.1.0a14.post0

What's Changed

• build: build sdist by @jnooree in #476

Full Changelog: v0.1.0a14...v0.1.0a14.post0

v0.1.0a14

What's Changed

• ci(rtd): remove abseil from documentation build env by @jnooree in #453
• feat(fmt/mmcif): save entity_id property to residues and chains by @jnooree in #454
• fix(python/numpy): fix handling of numpy array conversion by @jnooree in #458
• build: fix CI build by @jnooree in #459
• feat(fmt/pdb): implement pdb writer by @jnooree in #463
• test(fmt/pdb): add pdb write fuzzing by @jnooree in #464
• feat(core/mol): support adding implicit hydrogens by @jnooree in #456
• refactor: use boost flat_{set,map} by @jnooree in #466
• feat(fmt/mmcif): support loading CifFrame directly by @jnooree in #470
• Cleanup implementations and documentations by @jnooree in #471
• ci(gha): disable codecov coverage search by @jnooree in #474
• feat(algo/optim/lbfgs): implement L-BFGS algorithm by @jnooree in #475

Full Changelog: v0.1.0a13...v0.1.0a14

v0.1.0a13

What's Changed

• feat(python/tools/tm): assume full alignment when no user-alignment provided by @jnooree in #423
• feat(fmt/mol2): add option to omit substructure writing by @jnooree in #424
• build: cleanup stale coverage data before linking by @jnooree in #425
• refactor: split implementation files by @jnooree in #426
• build: cleanup more stale coverage data by @jnooree in #427
• build: switch to abseil lts version to use prebuilt abseil binaries if available by @jnooree in #429
• ci(gha): fix codeql build by @jnooree in #430
• build: enable downloading prebuilt absl binaries by @jnooree in #431
• feat(core/graph/vf2++): implement VF2++ algorithm by @jnooree in #432
• feat(python): log file/line in python by @jnooree in #436
• feat(fmt/pdb): don't guess in reader by @jnooree in #437
• feat(fmt/cif): implement CIF 1.1 parser by @jnooree in #438
• test(fmt): add fuzz test and fix various bugs by @jnooree in #441
• feat(scripts/fuzz): make fuzzer script configurable by @jnooree in #442
• feat(fmt/mmcif): implement mmCif parser by @jnooree in #444
• feat(python/fmt): add cif/mmcif interfaces by @jnooree in #445
• feat(python/fmt/cif): add utility function to convert DDL2 CIF to dict by @jnooree in #446
• fix(python/fmt/cif): pass internal reference to subobject and support inconsistent CIF files by @jnooree in #447

Full Changelog: v0.1.0a12...v0.1.0a13

v0.1.0a12

What's Changed

• chore(python): cleanup config files by @jnooree in #417
• build: build on macOS x86_64 by @jnooree in #419
• ci(gha): fix build on x86_64 by @jnooree in #420
• ci(gha): enable test on macos by @jnooree in #421
• chore: update project metadata by @jnooree in #422

Full Changelog: v0.1.0a11...v0.1.0a12

v0.1.0a11

What's Changed

• feat(tools/tm): implement TM-align algorithm by @jnooree in #414
• docs(tools/tm): fix documentation by @jnooree in #415
• feat(python/tools/tm): provide TM-align interface by @jnooree in #416

Full Changelog: v0.1.0a10...v0.1.0a11

v0.1.0a10

What's Changed

• feat(fmt/pdb): handle non-conforming PDB files better by @jnooree in #403
• fix(fmt/smiles): handle smiles chirality correctly by @jnooree in #406
• Revert "chore(deps): bump codecov/codecov-action from 4 to 5 in the ci-deps group" by @jnooree in #408
• feat(algo/crdgen): handle stereogenic centers correctly by @jnooree in #407
• feat(algo/crdgen): enforce planar geometry by @jnooree in #409
• build: set C++ standard with cmake by @jnooree in #410

Full Changelog: v0.1.0a9...v0.1.0a10

v0.1.0a9

What's Changed

• feat(core/geometry): align < 2 points gracefully by @jnooree in #398
• feat(core): rework stereochemistry interface by @jnooree in #399

Full Changelog: v0.1.0a8...v0.1.0a9