Add CD pipeline for building binaries

.github/workflows/CD.yml

@@ -0,0 +1,144 @@
+# This file is autogenerated by maturin v1.11.5
+# To update, run
+#
+#    maturin generate-ci github --platform manylinux windows macos --output .github/workflows/CD.yml
+#
+name: CD
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  workflow_dispatch:
+permissions:
+  contents: read
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: x86
+          - runner: ubuntu-22.04
+            target: aarch64
+          - runner: ubuntu-22.04
+            target: armv7
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.13
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist -i python3.10 -i python3.11 -i python3.12 -i python3.13 -i python3.14
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v5
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+            python_arch: x64
+          - runner: windows-latest
+            target: x86
+            python_arch: x86
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.13
+          architecture: ${{ matrix.platform.python_arch }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v5
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-15-intel
+            target: x86_64
+          - runner: macos-latest
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.13
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v5
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v5
+        with:
+          name: wheels-sdist
+          path: dist
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
+    needs:
+      - linux
+      - windows
+      - macos
+      - sdist
+    permissions:
+      # Use to sign the release artifacts
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v6
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v3
+        with:
+          subject-path: wheels-*/*
+      - name: Install uv
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        uses: astral-sh/setup-uv@v7
+      - name: Publish to PyPI
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        run: uv publish 'wheels-*/*'

CHANGELOG.md

@@ -5,11 +5,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased](https://github.com/BattModels/smirk)
+## [v0.2.0](https://github.com/BattModels/smirk)
+
+Paper published in ACS JCIM: [*Tokenization for Molecular Foundation Models*](https://doi.org/10.1021/acs.jcim.5c01856)
 
 ### Added
 
 - Started a changelog ([#2](https://github.com/BattModels/smirk/pull/2))
+- Added a release pipeline ([#6](https://github.com/BattModels/smirk/pull/6))
 
 ### Changed
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "smirk"
-version = "0.2.0-dev"
+version = "0.2.0"
 edition = "2021"
 license = "Apache-2.0"
 description = "A chemically complete tokenizer for OpenSMILES"
@@ -25,7 +25,7 @@ either = "1.13.0"
 macro_rules_attribute = "0.2.0"
 once_cell = "1.19.0"
 paste = "1.0.14"
-pyo3 = { version = "^0.23", features = ["extension-module"] }
+pyo3 = { version = "^0.27", features = ["extension-module"] }
 regex = "1.10.3"
 serde = "1.0.197"
 serde_json = "1.0.114"

README.md

@@ -3,6 +3,8 @@
 <div align="center" display="flex" >
 
 ![GitHub License](https://img.shields.io/github/license/BattModels/smirk)
+<a href="https://doi.org/10.1021/acs.jcim.5c01856">![paper](https://img.shields.io/badge/paper-10.1021%2Facs.jcim.5c01856-blue)</a>
+<a href="https://doi.org/10.5281/zenodo.13761262">![data](https://img.shields.io/badge/data-10.5281%2Fzenodo.13761262-blue)</a>
 <a href="https://arxiv.org/abs/2409.15370">![arXiv:2409.15370](https://img.shields.io/badge/cs.LG-2409.15370-b31b1b?style=flat&amp;logo=arxiv&amp;logoColor=red)</a>
 
 </div>
@@ -11,7 +13,7 @@ Smirk is a chemistry-specific tokenizer that provides complete coverage of the [
 specification, that is built using Rust 🦀 and [HuggingFace's tokenizers](https://huggingface.co/docs/tokenizers) 🤗.
 Installation is easy, and Smirk works out-of-the-box with the [HuggingFace](https://huggingface.co/docs) ecosystem.
 
-Check our [documentation](https://eeg.engin.umich.edu/smirk) to see `smirk` in action, or [read the paper](https://arxiv.org/abs/2409.15370) to learn
+Check our [documentation](https://eeg.engin.umich.edu/smirk) to see `smirk` in action, or [read the paper](https://doi.org/10.1021/acs.jcim.5c01856) to learn
 about tokenization for molecular foundation models.
 
 ## Installation

docs/conf.py

@@ -43,6 +43,7 @@
 # -- MyST-NB -----------------------------------------------------------------
 nb_execution_in_temp = True
 nb_execution_mode = "cache"
+nb_execution_timeout = 300
 nb_render_markdown_format = "myst"
 myst_enable_extensions = [
     "fieldlist",

docs/index.md

@@ -3,6 +3,8 @@
 <div align="center" display="flex" >
 
 ![GitHub License](https://img.shields.io/github/license/BattModels/smirk)
+<a href="https://doi.org/10.1021/acs.jcim.5c01856">![paper](https://img.shields.io/badge/paper-10.1021%2Facs.jcim.5c01856-blue)</a>
+<a href="https://doi.org/10.5281/zenodo.13761262">![data](https://img.shields.io/badge/data-10.5281%2Fzenodo.13761262-blue)</a>
 <a href="https://arxiv.org/abs/2409.15370">![arXiv:2409.15370](https://img.shields.io/badge/cs.LG-2409.15370-b31b1b?style=flat&amp;logo=arxiv&amp;logoColor=red)</a>
 
 </div>
@@ -22,7 +24,7 @@ that fail to represent *all* of chemistry, inherently limiting their performance
 Enabling complete coverage of [OpenSMILES] with a vocabulary of 167 tokens.
 
 [OpenSMILES]: http://opensmiles.org/
-[paper]: https://arxiv.org/abs/2409.15370
+[paper]: https://doi.org/10.1021/acs.jcim.5c01856
 [HuggingFace]: https://huggingface.co/docs
 [Tokenizers]: https://huggingface.co/docs/tokenizers
 

docs/smirk_demo.ipynb

@@ -29,7 +29,7 @@
     "Check out the [paper] for all the details; otherwise, let's see it in action!\n",
     "\n",
     "[OpenSMILES]: http://opensmiles.org/\n",
-    "[paper]: https://doi.org/10.48550/arXiv.2409.15370\n",
+    "[paper]: https://doi.org/10.1021/acs.jcim.5c01856\n",
     "[Atom-wise]: https://doi.org/10.1039/C8SC02339E\n",
     "[bracketed atom]: https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Line_Entry_System#Atoms\n",
     "\n",