diff --git a/README.md b/README.md index 62fb1e66..2cf79864 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # nvMolKit ## Documentation -Please see the official [NVIDIA nvMolKit Documentation](https://nvidia-digital-bio.github.io/nvMolKit/) for an overview of features, examples, and a detailed API reference. +Please see the official [NVIDIA nvMolKit Documentation](https://nvidia-bionemo.github.io/nvMolKit/) for an overview of features, examples, and a detailed API reference. ## Cursor / agent skill @@ -59,7 +59,7 @@ To install nvMolKit pinned to a particular RDKit: RDKIT_VERSION=2025.9.6 NVMOLKIT_VERSION=0.5.0 pip install nvmolkit==${NVMOLKIT_VERSION}+rdkit${RDKIT_VERSION} \ - --extra-index-url https://nvidia-digital-bio.github.io/nvMolKit/wheels/rdkit${RDKIT_VERSION}/simple/ + --extra-index-url https://nvidia-bionemo.github.io/nvMolKit/wheels/rdkit${RDKIT_VERSION}/simple/ ``` Replace `2025.9.6` with the RDKit version you want. Variants published for nvMolKit v0.5.0 include every version between 2025.03.6 and 2026.03.1. @@ -234,7 +234,7 @@ CIBW_MANYLINUX_X86_64_IMAGE=nvmolkit-manylinux-cuda12:test \ To narrow the matrix while iterating, set `CIBW_BUILD=cp312-manylinux_x86_64` (or whichever python tag you care about) before invoking the script. Wheels land in `wheelhouse/`. -The full CI pipeline is at [`.github/workflows/pip-build.yml`](.github/workflows/pip-build.yml). It runs on demand (`workflow_dispatch` only), expands the (rdkit, python) matrix from [`admin/distribute/rdkit_build_matrix.yaml`](admin/distribute/rdkit_build_matrix.yaml), and pulls the pre-built manylinux+CUDA image from the org's GHCR (`ghcr.io/nvidia-digital-bio/nvmolkit-manylinux-cuda12`). The image is rebuilt and pushed manually when the Dockerfile changes; the build script header documents the push command. +The full CI pipeline is at [`.github/workflows/pip-build.yml`](.github/workflows/pip-build.yml). It runs on demand (`workflow_dispatch` only), expands the (rdkit, python) matrix from [`admin/distribute/rdkit_build_matrix.yaml`](admin/distribute/rdkit_build_matrix.yaml), and pulls the pre-built manylinux+CUDA image from the org's GHCR (`ghcr.io/nvidia-bionemo/nvmolkit-manylinux-cuda12`). The image is rebuilt and pushed manually when the Dockerfile changes; the build script header documents the push command. Internally, cibuildwheel's `before-build` hook (see [`admin/distribute/cibuildwheel_before_build.sh`](admin/distribute/cibuildwheel_before_build.sh)) clones rdkit-pypi at the matching tag, runs [`admin/distribute/build_rdkit_recipe.sh`](admin/distribute/build_rdkit_recipe.sh) to reproduce its build (~30-60 min on first invocation; cached afterwards), pip-installs the matching rdkit wheel for runtime SONAME-matching libs, and stages everything at stable paths under `/tmp/nvmolkit_pip_inputs/`. setup.py picks those up via `NVMOLKIT_BUILD_AGAINST_PIP_*` env vars set in pyproject.toml's `[tool.cibuildwheel.linux].environment`. diff --git a/agent-skills/nvmolkit-usage/SKILL.md b/agent-skills/nvmolkit-usage/SKILL.md index 84b6ff6b..96204dc9 100644 --- a/agent-skills/nvmolkit-usage/SKILL.md +++ b/agent-skills/nvmolkit-usage/SKILL.md @@ -264,6 +264,6 @@ All conformers of each input molecule are minimized in one batch. Constraints at ## Going deeper -- Full feature list, API reference, and guides: -- What changed in each release: +- Full feature list, API reference, and guides: +- What changed in each release: - Worked examples (Jupyter notebooks): the `examples/` directory in the GitHub repo diff --git a/docs/agent_skill.rst b/docs/agent_skill.rst index 9ed015b6..ad40733f 100644 --- a/docs/agent_skill.rst +++ b/docs/agent_skill.rst @@ -12,7 +12,7 @@ Get the skill ------------- The skill lives at -`agent-skills/nvmolkit-usage/ `_ +`agent-skills/nvmolkit-usage/ `_ in the nvMolKit GitHub repo. Copy that directory into one of: diff --git a/docs/index.rst b/docs/index.rst index 4fea4b77..cdb9b879 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -63,7 +63,7 @@ For more fully-fledged examples, check out the Jupyter notebooks in the `example Source Code ----------- -nvMolKit is open source under the Apache License, and is available on `GitHub `_. +nvMolKit is open source under the Apache License, and is available on `GitHub `_. .. _installation: @@ -115,7 +115,7 @@ To install nvMolKit pinned to a particular RDKit: RDKIT_VERSION=2025.9.6 NVMOLKIT_VERSION=0.5.0 pip install nvmolkit==${NVMOLKIT_VERSION}+rdkit${RDKIT_VERSION} \ - --extra-index-url https://nvidia-digital-bio.github.io/nvMolKit/wheels/rdkit${RDKIT_VERSION}/simple/ + --extra-index-url https://nvidia-bionemo.github.io/nvMolKit/wheels/rdkit${RDKIT_VERSION}/simple/ Replace ``2025.9.6`` with the RDKit version you want. Variants published for nvMolKit v0.5.0 include every version between 2025.03.6 and 2026.03.1. @@ -124,7 +124,7 @@ nvMolKit v0.5.0 include every version between 2025.03.6 and 2026.03.1. From Source ^^^^^^^^^^^ -nvMolKit can be installed from source using a C++ and CUDA compiler. See installation instructions in the `GitHub README `_. +nvMolKit can be installed from source using a C++ and CUDA compiler. See installation instructions in the `GitHub README `_. Features diff --git a/pyproject.toml b/pyproject.toml index 7a7817d1..80d848a6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ changes in place, consistent with RDKit. An NVIDIA GPU with compute capability 7.0 (Volta) or newer and a Linux environment with CUDA 12 are required. For installation options, API reference, and examples, see the -[project documentation](https://nvidia-digital-bio.github.io/nvMolKit/). +[project documentation](https://nvidia-bionemo.github.io/nvMolKit/). """, content-type = "text/markdown" } license = "Apache-2.0" authors = [ @@ -62,11 +62,11 @@ classifiers = [ ] [project.urls] -Homepage = "https://nvidia-digital-bio.github.io/nvMolKit/" -Documentation = "https://nvidia-digital-bio.github.io/nvMolKit/" -Repository = "https://github.com/NVIDIA-Digital-Bio/nvMolKit" -Issues = "https://github.com/NVIDIA-Digital-Bio/nvMolKit/issues" -Changelog = "https://github.com/NVIDIA-Digital-Bio/nvMolKit/releases" +Homepage = "https://nvidia-bionemo.github.io/nvMolKit/" +Documentation = "https://nvidia-bionemo.github.io/nvMolKit/" +Repository = "https://github.com/NVIDIA-BioNeMo/nvMolKit" +Issues = "https://github.com/NVIDIA-BioNeMo/nvMolKit/issues" +Changelog = "https://github.com/NVIDIA-BioNeMo/nvMolKit/releases" [project.optional-dependencies] test = [