Prep for v0.7.0: release notes and version bump

CHANGELOG.md

@@ -1,5 +1,52 @@
 # Changelog
 
+## 0.7.0 - 2026-10-15
+
+### Summary
+
+nvMolKit 0.7.0 adds a single-precision mode for force field minimization (MMFF, UFF, BFGS, FIRE) and ETKDG conformer generation, which is roughly an order of magnitude faster on consumer GPUs. It also adds a fused 3D descriptor API, diversity selection (Leader and MaxMin), DISE clustering, an Atom-Atom Path (AAP) similarity metric, a persistent GPU `SubstructLibrary`, and various performance improvements to existing fingerprinting, substructure search, and 3D minimization code.
+
+### Contributors
+- Eva Xue (@evasnow1992)
+- Kevin Boyd (@scal444)
+- Matthew Neba (@Matthew-Neba)
+- Ohad Mosafi (@ohadmo)
+
+### Features
+- Single-precision mode (`precision=PrecisionMode.SINGLE`) for MMFF and UFF force fields, BFGS and FIRE minimizers, and ETKDG distance geometry and ETK stages, available through the MMFF, UFF, `BatchedForcefield`, and `EmbedMolecules` APIs. On consumer GPUs, single precision is roughly an order of magnitude faster than double precision. Validation against RDKit is documented in the 3D minimizers guide ([#266](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/266))
+- GPU-accelerated 3D descriptors through the new `nvmolkit.descriptors3d.Calc3DProperties`, which computes a user-selected set of properties in one fused pass over a batch of conformers: PMI, NPR, radius of gyration, shape factors, PBF, WHIM, RDF, MORSE, AUTOCORR3D, USR, USRCAT, and GETAWAY, matching RDKit's `rdMolDescriptors` ([#341](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/341))
+- Atom-Atom Path (AAP) molecule similarity via `aap_similarity`, also usable as `metric="aap"` in `fused_leader`, `fused_maxmin`, and `fused_dise` ([#303](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/303))
+- Diversity selection with `leader` and `maxmin` for distance matrices, and `fused_leader` and `fused_maxmin` for packed fingerprints or molecules, following RDKit's `LeaderPicker` and `MaxMinPicker` ([#339](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/339))
+- Directed sphere exclusion (DISE) clustering with `dise` and `fused_dise` ([#339](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/339))
+- Standardized clustering and diversity selection APIs. Butina, DISE, Leader, and MaxMin each come in a matrix form, which takes a precomputed distance matrix, and a fused form, which computes distances on the fly so memory grows linearly instead of quadratically. Every fused form accepts any similarity metric (`"tanimoto"`, `"cosine"`, or `"aap"`) and either output mode (`OutputMode.DEVICE` or `OutputMode.RDKIT`), so algorithms, forms, metrics, and output modes combine freely, except that `fused_butina` does not yet support AAP ([#339](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/339))
+- Persistent GPU `SubstructLibrary` (`nvmolkit.substruct_library.SubstructLibrary`), the GPU counterpart of RDKit's `SubstructLibrary`. Target molecules are packed and uploaded once, then searched by any number of queries, with multi-GPU storage, asynchronous concurrent queries within a GPU-memory budget, and pattern-fingerprint prescreening ([#350](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/350))
+- ETKDG now supports eigenvalue-based initial coordinate generation (`useRandomCoords=False`), matching RDKit's initialization and retry behavior ([#288](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/288))
+- Device-side conformer pruning for ETKDG, so `pruneRmsThresh` can now be combined with GPU-resident output, by @Matthew-Neba ([#160](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/160))
+- Conformer RMSD supports `alignment_mode="pairwise"` (the default, aligning every pair independently) and `alignment_mode="first-conformer"` (matching RDKit's `GetConformerRMSMatrix`) ([#281](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/281))
+
+### Performance Improvements
+- Per-molecule BFGS minimizer is 10-40% faster, applying to ETKDG, MMFF, and UFF on the per-molecule backend ([#342](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/342), [#355](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/355))
+- Morgan fingerprint generation is up to 2x faster, through reduced CPU preprocessing and Python transfer overhead ([#267](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/267))
+- Tanimoto similarity for queries with few molecules is up to 8x faster ([#284](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/284))
+- Substructure search performance has been improved for queries with repeated recursive SMARTS, since each repeated pattern is now solved only once ([#313](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/313))
+- ETKDG conformer generation is up to 2x faster for batches with a few hard-to-embed molecules, because retries now keep GPU batches full. The default retry budget is also now bounded per molecule instead of scaling with the largest molecule in the input ([#353](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/353))
+
+### Breaking Changes
+- `butina` and `fused_butina` now return a `ClusterDeviceResult` (cluster IDs, centroids, and cluster sizes) by default, or RDKit-format cluster tuples with `output=OutputMode.RDKIT`. The `return_centroids` argument is removed ([#269](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/269))
+
+### Bug Fixes
+- Fix `countSubstructMatches` ignoring `uniquify=True`, which returned raw embedding counts that disagreed with RDKit for symmetric queries ([#275](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/275))
+- Fix SMARTS hydrogen counts excluding explicit hydrogen neighbors, so queries such as `[CH3]` now match deuterated and explicit-H targets as in RDKit ([#276](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/276))
+- Fix plain query atoms (for example from `MolFromSmiles`) being packed as wildcards in substructure search, and route targets with isotopes above 255 or unsupported bond types to the RDKit fallback instead of failing ([#349](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/349))
+- Fix ETKDG exiting early on molecules that fail to embed, which previously could skip scheduled retries and fail more often than RDKit ([#300](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/300))
+- Fix float32 division in the Tanimoto similarity kernels using approximate rounding, which could order equal distances differently than RDKit in downstream clustering ([#338](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/338))
+
+### Miscellaneous
+- Improved shared benchmark tooling, including common CLI, timing, result-reporting, and dataset-loading utilities, and RDKit-side deadlines for long-running baselines
+- Drastically improved CI coverage, and added back linters and static analysis
+- Support for CUDA 13.4 and Rubin GPUs ([#304](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/304))
+
+
 ## 0.6.0 - 2026-08-13
 
 ### Summary

CMakeLists.txt

@@ -17,7 +17,7 @@ cmake_policy(SET CMP0167 NEW)
 
 project(
   nvmolkit
-  VERSION 0.6.0
+  VERSION 0.7.0
   LANGUAGES CXX CUDA)
 set(CMAKE_CUDA_STANDARD 20)
 set(CMAKE_CXX_STANDARD 20)

README.md

@@ -24,7 +24,7 @@ Conda is the recommended way to install nvMolKit, matching the recommended distr
 you have a variant of conda installed and activated, such as [Miniconda](https://docs.conda.io/en/latest/miniconda.html) 
 or [Miniforge](https://conda-forge.org/download/).
 
-nvMolKit v0.6.0 supports RDKit 2025.09.1 through 2026.03.5. To install:
+nvMolKit v0.7.0 supports RDKit 2025.09.1 through 2026.03.5. To install:
 
 ```bash
 conda install -c conda-forge nvmolkit
@@ -59,7 +59,7 @@ Replace `cu128` with another CUDA 12 backend from the PyTorch install page if th
 compatible with your driver.
 
 The wheel published to PyPI is built against a single RDKit release per
-nvMolKit version (RDKit 2026.03.5 for nvMolKit v0.6.0), due to versioning
+nvMolKit version (RDKit 2026.03.5 for nvMolKit v0.7.0), due to versioning
 limitations in PyPI's dependency management system.
 
 Use this path if you do not have a constraint on which RDKit version to use;
@@ -73,12 +73,12 @@ To install nvMolKit pinned to a particular RDKit:
 
 ```bash
 RDKIT_VERSION=2025.9.6
-NVMOLKIT_VERSION=0.6.0
+NVMOLKIT_VERSION=0.7.0
 pip install nvmolkit==${NVMOLKIT_VERSION}+rdkit${RDKIT_VERSION} \
     --extra-index-url https://nvidia-bionemo.github.io/nvMolKit/wheels/rdkit${RDKIT_VERSION}/simple/
 ```
 
-Replace `2025.9.6` with the RDKit version you want. Variants published for nvMolKit v0.6.0 include every version between 2025.09.1 and 2026.03.5.
+Replace `2025.9.6` with the RDKit version you want. Variants published for nvMolKit v0.7.0 include every version between 2025.09.1 and 2026.03.5.
 
 
 ### Installation from Source

VERSION

@@ -1 +1 @@
-0.6.0
+0.7.0

admin/distribute/test_release_tools.py

@@ -30,19 +30,19 @@ def load_module(name: str):
 
 
 def make_wheel(path: Path) -> None:
-    dist_info = "nvmolkit-0.6.0.dist-info"
-    purl = f"pkg:pypi/nvmolkit@0.6.0?file_name={path.name}"
+    dist_info = "nvmolkit-0.7.0.dist-info"
+    purl = f"pkg:pypi/nvmolkit@0.7.0?file_name={path.name}"
     entries = {
-        "nvmolkit/__init__.py": b"__version__ = '0.6.0'\n",
-        f"{dist_info}/METADATA": (b"Metadata-Version: 2.1\nName: nvmolkit\nVersion: 0.6.0\nRequires-Dist: rdkit\n"),
+        "nvmolkit/__init__.py": b"__version__ = '0.7.0'\n",
+        f"{dist_info}/METADATA": (b"Metadata-Version: 2.1\nName: nvmolkit\nVersion: 0.7.0\nRequires-Dist: rdkit\n"),
         f"{dist_info}/WHEEL": b"Wheel-Version: 1.0\nTag: cp311-cp311-manylinux_2_28_x86_64\n",
         f"{dist_info}/sboms/auditwheel.cdx.json": json.dumps(
             {
                 "metadata": {
                     "component": {
                         "bom-ref": purl,
                         "purl": purl,
-                        "version": "0.6.0",
+                        "version": "0.7.0",
                     }
                 },
                 "dependencies": [{"ref": purl}],
@@ -70,24 +70,24 @@ def assert_valid_record(path: Path) -> None:
 
 
 def test_pin_and_retag_wheel_refresh_metadata_and_record(tmp_path: Path) -> None:
-    source = tmp_path / "nvmolkit-0.6.0-cp311-cp311-manylinux_2_28_x86_64.whl"
+    source = tmp_path / "nvmolkit-0.7.0-cp311-cp311-manylinux_2_28_x86_64.whl"
     make_wheel(source)
 
     assert pin_wheel_rdkit.rewrite_wheel(source, "2026.3.5", check=False)
     assert not pin_wheel_rdkit.rewrite_wheel(source, "2026.3.5", check=True)
     assert_valid_record(source)
 
     output = Path(retag_wheel.retag(str(source), str(tmp_path / "variants"), "rdkit2026.3.5"))
-    assert output.name.startswith("nvmolkit-0.6.0+rdkit2026.3.5-")
+    assert output.name.startswith("nvmolkit-0.7.0+rdkit2026.3.5-")
     with zipfile.ZipFile(output) as wheel:
         metadata_name = next(name for name in wheel.namelist() if name.endswith(".dist-info/METADATA"))
         metadata = wheel.read(metadata_name).decode()
-        assert "Version: 0.6.0+rdkit2026.3.5\n" in metadata
+        assert "Version: 0.7.0+rdkit2026.3.5\n" in metadata
         assert "Requires-Dist: rdkit==2026.3.5\n" in metadata
         sbom_name = next(name for name in wheel.namelist() if name.endswith("auditwheel.cdx.json"))
         sbom = json.loads(wheel.read(sbom_name))
         component = sbom["metadata"]["component"]
-        assert component["version"] == "0.6.0+rdkit2026.3.5"
+        assert component["version"] == "0.7.0+rdkit2026.3.5"
         assert output.name in component["purl"]
         assert sbom["dependencies"][0]["ref"] == component["purl"]
     assert_valid_record(output)
@@ -97,22 +97,22 @@ def test_merge_index_preserves_history_and_replaces_matching_filename(tmp_path:
     generated = tmp_path / "generated/index.html"
     destination = tmp_path / "destination/index.html"
     old_name = "nvmolkit-0.5.1-cp311.whl"
-    replaced_name = "nvmolkit-0.6.0-cp311.whl"
+    replaced_name = "nvmolkit-0.7.0-cp311.whl"
     merge_simple_index.write_index(
         destination,
         [
             merge_simple_index.Link("https://old.example/0.5.1", old_name),
-            merge_simple_index.Link("https://old.example/0.6.0", replaced_name),
+            merge_simple_index.Link("https://old.example/0.7.0", replaced_name),
         ],
     )
     merge_simple_index.write_index(
         generated,
-        [merge_simple_index.Link("https://new.example/0.6.0", replaced_name)],
+        [merge_simple_index.Link("https://new.example/0.7.0", replaced_name)],
     )
 
     assert merge_simple_index.merge_index(generated, destination)
     assert merge_simple_index.read_links(destination) == [
         merge_simple_index.Link("https://old.example/0.5.1", old_name),
-        merge_simple_index.Link("https://new.example/0.6.0", replaced_name),
+        merge_simple_index.Link("https://new.example/0.7.0", replaced_name),
     ]
     assert not merge_simple_index.merge_index(generated, destination)

docs/changelog.md

@@ -1,5 +1,51 @@
 # Changelog
 
+## 0.7.0 - 2026-10-15
+
+### Summary
+
+nvMolKit 0.7.0 adds a single-precision mode for force field minimization (MMFF, UFF, BFGS, FIRE) and ETKDG conformer generation, which is roughly an order of magnitude faster on consumer GPUs. It also adds a fused 3D descriptor API, diversity selection (Leader and MaxMin), DISE clustering, an Atom-Atom Path (AAP) similarity metric, a persistent GPU `SubstructLibrary`, and various performance improvements to existing fingerprinting, substructure search, and 3D minimization code.
+
+### Contributors
+- Eva Xue (@evasnow1992)
+- Kevin Boyd (@scal444)
+- Matthew Neba (@Matthew-Neba)
+- Ohad Mosafi (@ohadmo)
+
+### Features
+- Single-precision mode (`precision=PrecisionMode.SINGLE`) for MMFF and UFF force fields, BFGS and FIRE minimizers, and ETKDG distance geometry and ETK stages, available through the MMFF, UFF, `BatchedForcefield`, and `EmbedMolecules` APIs. On consumer GPUs, single precision is roughly an order of magnitude faster than double precision. Validation against RDKit is documented in the 3D minimizers guide ([#266](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/266))
+- GPU-accelerated 3D descriptors through the new `nvmolkit.descriptors3d.Calc3DProperties`, which computes a user-selected set of properties in one fused pass over a batch of conformers: PMI, NPR, radius of gyration, shape factors, PBF, WHIM, RDF, MORSE, AUTOCORR3D, USR, USRCAT, and GETAWAY, matching RDKit's `rdMolDescriptors` ([#341](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/341))
+- Atom-Atom Path (AAP) molecule similarity via `aap_similarity`, also usable as `metric="aap"` in `fused_leader`, `fused_maxmin`, and `fused_dise` ([#303](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/303))
+- Diversity selection with `leader` and `maxmin` for distance matrices, and `fused_leader` and `fused_maxmin` for packed fingerprints or molecules, following RDKit's `LeaderPicker` and `MaxMinPicker` ([#339](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/339))
+- Directed sphere exclusion (DISE) clustering with `dise` and `fused_dise` ([#339](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/339))
+- Standardized clustering and diversity selection APIs. Butina, DISE, Leader, and MaxMin each come in a matrix form, which takes a precomputed distance matrix, and a fused form, which computes distances on the fly so memory grows linearly instead of quadratically. Every fused form accepts any similarity metric (`"tanimoto"`, `"cosine"`, or `"aap"`) and either output mode (`OutputMode.DEVICE` or `OutputMode.RDKIT`), so algorithms, forms, metrics, and output modes combine freely, except that `fused_butina` does not yet support AAP ([#339](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/339))
+- Persistent GPU `SubstructLibrary` (`nvmolkit.substruct_library.SubstructLibrary`), the GPU counterpart of RDKit's `SubstructLibrary`. Target molecules are packed and uploaded once, then searched by any number of queries, with multi-GPU storage, asynchronous concurrent queries within a GPU-memory budget, and pattern-fingerprint prescreening ([#350](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/350))
+- ETKDG now supports eigenvalue-based initial coordinate generation (`useRandomCoords=False`), matching RDKit's initialization and retry behavior ([#288](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/288))
+- Device-side conformer pruning for ETKDG, so `pruneRmsThresh` can now be combined with GPU-resident output, by @Matthew-Neba ([#160](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/160))
+- Conformer RMSD supports `alignment_mode="pairwise"` (the default, aligning every pair independently) and `alignment_mode="first-conformer"` (matching RDKit's `GetConformerRMSMatrix`) ([#281](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/281))
+
+### Performance Improvements
+- Per-molecule BFGS minimizer is 10-40% faster, applying to ETKDG, MMFF, and UFF on the per-molecule backend ([#342](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/342), [#355](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/355))
+- Morgan fingerprint generation is up to 2x faster, through reduced CPU preprocessing and Python transfer overhead ([#267](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/267))
+- Tanimoto similarity for queries with few molecules is up to 8x faster ([#284](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/284))
+- Substructure search performance has been improved for queries with repeated recursive SMARTS, since each repeated pattern is now solved only once ([#313](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/313))
+- ETKDG conformer generation is up to 2x faster for batches with a few hard-to-embed molecules, because retries now keep GPU batches full. The default retry budget is also now bounded per molecule instead of scaling with the largest molecule in the input ([#353](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/353))
+
+### Breaking Changes
+- `butina` and `fused_butina` now return a `ClusterDeviceResult` (cluster IDs, centroids, and cluster sizes) by default, or RDKit-format cluster tuples with `output=OutputMode.RDKIT`. The `return_centroids` argument is removed ([#269](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/269))
+
+### Bug Fixes
+- Fix `countSubstructMatches` ignoring `uniquify=True`, which returned raw embedding counts that disagreed with RDKit for symmetric queries ([#275](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/275))
+- Fix SMARTS hydrogen counts excluding explicit hydrogen neighbors, so queries such as `[CH3]` now match deuterated and explicit-H targets as in RDKit ([#276](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/276))
+- Fix plain query atoms (for example from `MolFromSmiles`) being packed as wildcards in substructure search, and route targets with isotopes above 255 or unsupported bond types to the RDKit fallback instead of failing ([#349](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/349))
+- Fix ETKDG exiting early on molecules that fail to embed, which previously could skip scheduled retries and fail more often than RDKit ([#300](https://github.com/NVIDIA-BioNeMo/nvMolKit/issues/300))
+- Fix float32 division in the Tanimoto similarity kernels using approximate rounding, which could order equal distances differently than RDKit in downstream clustering ([#338](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/338))
+
+### Miscellaneous
+- Improved shared benchmark tooling, including common CLI, timing, result-reporting, and dataset-loading utilities, and RDKit-side deadlines for long-running baselines
+- Drastically improved CI coverage, and added back linters and static analysis
+- Support for CUDA 13.4 and Rubin GPUs ([#304](https://github.com/NVIDIA-BioNeMo/nvMolKit/pull/304))
+
 ## 0.6.0 - 2026-08-13
 
 ### Summary