diff --git a/.github/workflows/build-verification.yml b/.github/workflows/build-verification.yml index 9dfaa55..65202bd 100644 --- a/.github/workflows/build-verification.yml +++ b/.github/workflows/build-verification.yml @@ -15,7 +15,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-14] - python-version: ["3.11", "3.12"] + python-version: ["3.12", "3.13"] steps: - uses: actions/checkout@v4 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4148a57..8677632 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -25,7 +25,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: quality linux-editable-target: ".[dev]" @@ -120,7 +120,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: unit-${{ matrix.shard.id }} # Install genomics extra so pyfaidx / pysam are present for the # error-path tests in tests/sources/test_{fasta,bam}.py. @@ -180,7 +180,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: integration linux-editable-target: ".[dev,test]" @@ -226,7 +226,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: e2e linux-editable-target: ".[dev,test]" @@ -287,7 +287,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: perf # chem carries rdkit, needed by tests/benchmarks/test_bench_dti.py and # test_bench_molnet.py. @@ -338,7 +338,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: coverage # chem carries rdkit, which the drug-discovery, molnet and molecular-splitter # tests exercise. It is an extra so that installing the package does not pull a diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 72bb011..5857004 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -27,8 +27,8 @@ jobs: - name: Set up DiffBio docs environment uses: ./.github/actions/setup-diffbio with: - python-version: '3.11' - cache-suffix: docs-py311 + python-version: '3.12' + cache-suffix: docs-py312 linux-editable-target: ".[docs]" - name: Build documentation diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index d8bc2a1..5973f22 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -41,7 +41,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v6 with: - python-version: "3.11" + python-version: "3.12" - name: Install build dependencies run: | diff --git a/.github/workflows/quality-checks.yml b/.github/workflows/quality-checks.yml index 323ddce..d84d0c9 100644 --- a/.github/workflows/quality-checks.yml +++ b/.github/workflows/quality-checks.yml @@ -14,7 +14,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: quality-report linux-editable-target: ".[dev]" diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml index 8f3094c..4031303 100644 --- a/.github/workflows/security.yml +++ b/.github/workflows/security.yml @@ -20,7 +20,7 @@ jobs: - name: Set up DiffBio uses: ./.github/actions/setup-diffbio with: - python-version: "3.11" + python-version: "3.12" cache-suffix: security linux-editable-target: ".[dev]" diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f2db9ee..855f468 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,7 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.11" + python: "3.12" jobs: post_install: - pip install mkdocs-material diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 9d7376b..49b9a77 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -20,7 +20,7 @@ source ./activate.sh ### Prerequisites -- Python 3.11+ +- Python 3.12+ - uv package manager - Git diff --git a/README.md b/README.md index 3a6d3d0..6fc78cf 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # DiffBio

- Python 3.11+ + Python 3.12+ JAX Flax License @@ -293,7 +293,7 @@ DiffBio/ ## Requirements -- Python 3.11+ +- Python 3.12+ - JAX 0.6.1+ - Flax 0.12+ - Optax 0.1.4+ diff --git a/benchmarks/_optimizers.py b/benchmarks/_optimizers.py index c041f71..7d12656 100644 --- a/benchmarks/_optimizers.py +++ b/benchmarks/_optimizers.py @@ -16,12 +16,19 @@ def create_benchmark_optimizer( learning_rate: float, optimizer_type: str = "adam", gradient_clip: float | None = None, + weight_decay: float = 0.0, ) -> optax.GradientTransformation: - """Create the benchmark optimizer through the Opifex training substrate.""" + """Create the benchmark optimizer through the Opifex training substrate. + + ``weight_decay`` is exposed because ``OptimizerConfig`` defaults it to 0.0 while + ``optax.adamw`` defaults it to 1e-4; a caller moving off a direct ``optax.adamw`` + call needs to be able to say which of the two it meant. + """ return create_optimizer( OptimizerConfig( optimizer_type=optimizer_type, learning_rate=learning_rate, gradient_clip=gradient_clip, + weight_decay=weight_decay, ) ) diff --git a/benchmarks/singlecell/compute_cost.py b/benchmarks/singlecell/compute_cost.py index f3890fd..6af7adf 100644 --- a/benchmarks/singlecell/compute_cost.py +++ b/benchmarks/singlecell/compute_cost.py @@ -24,9 +24,9 @@ import jax import jax.numpy as jnp import numpy as np -import optax from flax import nnx +from benchmarks._optimizers import create_benchmark_optimizer from benchmarks.singlecell._gate2_arms import ( _ProjectionProbe, _embedding_probe, @@ -91,7 +91,14 @@ def measure( ) labels = jax.device_put(rng.integers(0, n_classes, size=effective_batch).astype(np.int32)) model, forward = _build(arm, n_features, n_components, n_classes, seed) - optimizer = nnx.Optimizer(model, optax.adamw(1e-3), wrt=nnx.Param) + # Routed through the shared Opifex boundary (benchmarks/_optimizers.py) rather than + # optax directly. weight_decay=1e-4 is optax.adamw's own default, restated here + # because OptimizerConfig defaults it to 0.0 -- this keeps the optimizer identical. + optimizer = nnx.Optimizer( + model, + create_benchmark_optimizer(learning_rate=1e-3, optimizer_type="adamw", weight_decay=1e-4), + wrt=nnx.Param, + ) # donate_argnames lets XLA reuse the model/optimizer buffers in place (Flax NNX # best practice), so peak memory reflects realistic in-place training, not double diff --git a/docs/getting-started/installation.md b/docs/getting-started/installation.md index 7117b5d..401336a 100644 --- a/docs/getting-started/installation.md +++ b/docs/getting-started/installation.md @@ -1,6 +1,6 @@ # Installation -DiffBio requires Python 3.11+ and works on Linux, macOS, and Windows (via WSL). +DiffBio requires Python 3.12+ and works on Linux, macOS, and Windows (via WSL). ## Quick Install diff --git a/pyproject.toml b/pyproject.toml index 4b8d050..e5122bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,6 @@ classifiers = [ "Topic :: Software Development :: Libraries", "Topic :: Software Development :: Libraries :: Python Modules", "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "License :: OSI Approved :: MIT License" ] @@ -46,10 +45,13 @@ dependencies = [ # JAX ecosystem "beartype>=0.14.1", "chex>=0.1.7", - "flax>=0.12.0", + # 0.12.1 is where nnx Variable gained set_value / get_value. + "flax>=0.12.1", "jax>=0.6.1", "jaxtyping>=0.2.20", - "optax>=0.1.4", + # 0.2.8 stopped setting jax_pmap_shmap_merge, which jax removed in 0.10; below it, + # importing flax raises AttributeError and collection dies for the whole suite. + "optax>=0.2.8", "orbax-checkpoint>=0.11.10", # Scientific computing "numpy>=1.24", @@ -65,11 +67,11 @@ keywords = ["jax", "flax", "bioinformatics", "differentiable", "variant-calling" license = {file = "LICENSE"} name = "diffbio" readme = "README.md" -requires-python = ">=3.11" +requires-python = ">=3.12" version = "0.1.0" [project.optional-dependencies] -all = ["diffbio[benchmark,chem,dev,docs,genomics,gpu,soft-ops-advanced,soft-ops-ot,test,torch-io]"] +all = ["diffbio[benchmark,chem,cuda12,dev,docs,genomics,soft-ops-advanced,soft-ops-ot,test,torch-io]"] benchmark = [ "scib-metrics>=0.5", "pynndescent>=0.5", @@ -79,7 +81,14 @@ benchmark = [ "pandas>=2.0", "matplotlib>=3.7" ] -cuda-dev = ["diffbio[dev,gpu]"] +# RDKit, for the molecular-graph and fingerprint operators. Every call site imports it +# lazily, so the rest of diffbio installs and runs without it. +chem = ["rdkit>=2025.9.3"] +cuda-dev = ["diffbio[cuda12,dev]"] +# Named for the CUDA major version, as JAX names its own extras (cuda12, cuda12-local, +# cuda13); JAX publishes no `gpu` extra. No jaxlib line: every jax cuda extra already +# requires jaxlib<=X,>=X at its own version, so restating it only lets the two disagree. +cuda12 = ["jax[cuda12]>=0.6.1"] dev = [ "bandit[toml]>=1.8.6", "build>=1.0.3", @@ -115,11 +124,7 @@ docs = [ "mkdocstrings-python>=1.1.2", "pymdown-extensions>=10.14.3" ] -# RDKit, for the molecular-graph and fingerprint operators. Every call site imports it -# lazily, so the rest of diffbio installs and runs without it. -chem = ["rdkit>=2025.9.3"] genomics = ["pysam>=0.22.0", "pyfaidx>=0.8.0"] -gpu = ["jax[cuda12]>=0.6.1", "jaxlib>=0.6.1"] soft-ops-advanced = ["optimistix>=0.0.9", "lineax>=0.0.8"] soft-ops-ot = ["diffbio[soft-ops-advanced]", "ott-jax>=0.5.0"] test = [ @@ -341,7 +346,7 @@ exclude = ["memory-bank", ".deprecated", "examples", ".venv"] extend-include = ["*.ipynb"] line-length = 100 src = ["src"] -target-version = "py311" +target-version = "py312" [tool.ruff.format] indent-style = "space" @@ -365,6 +370,15 @@ ignore = [ "UP015", "UP024", "UP035", + # PEP 695 generic syntax (`def f[T]`, `class C[T]`). Enabled by target-version py312, but + # the docstring gate is pydocstyle 6.3.0, whose parser predates PEP 695: it reports D101 / + # D103 "missing docstring" for generic functions, and for generic classes with a bound, on + # definitions whose docstring is plainly present. 6.3.0 is its final release (2023-01-17), + # so no version of it reads this syntax. Re-enable these together with replacing pydocstyle + # with ruff's own D rules, which parse it correctly. + "UP046", # Generic class uses Generic subclass instead of type parameters + "UP047", # Generic function should use type parameters + "UP049", # Private type parameter name "RUF005" ] select = ["E", "F", "UP"] @@ -384,6 +398,11 @@ convention = "google" # setuptools arrives through torch, tensorflow and tensorboard, which require it at # runtime; it is not this project's build backend, which is hatchling. constraint-dependencies = [ + # dm-haiku arrives through jax-md. Up to 0.0.16 it does + # `DropVar: TypeAlias = jax.core.DropVar` at import time, and jax removed jax.core.DropVar + # in 0.11.0, so importing diffbio.operators.molecular_dynamics dies with AttributeError. + # 0.0.17 guards it with a try/except onto jax.extend.core. + "dm-haiku>=0.0.17", "setuptools>=83.0.0" # PYSEC-2026-3447 ] python-preference = "only-managed" diff --git a/setup.sh b/setup.sh index cec312e..be675b0 100755 --- a/setup.sh +++ b/setup.sh @@ -120,7 +120,7 @@ SYNC_ARGS=(sync --extra dev --extra test) case "$BACKEND" in cpu) ;; cuda12) - SYNC_ARGS+=(--extra gpu) + SYNC_ARGS+=(--extra cuda12) ;; metal) SYNC_ARGS+=(--extra metal) diff --git a/src/diffbio/core/soft_ops/sorting.py b/src/diffbio/core/soft_ops/sorting.py index 424317c..398f7ac 100644 --- a/src/diffbio/core/soft_ops/sorting.py +++ b/src/diffbio/core/soft_ops/sorting.py @@ -990,4 +990,11 @@ def top_k_mask( pattern = jnp.concatenate([jnp.ones(k, x.dtype), jnp.zeros(n - k, x.dtype)]) weights = jnp.broadcast_to(pattern, x_last.shape) mask = proj_permutahedron(x_last, weights, softness=softness, mode="c0") + # The projection lands in {m : 0 <= m <= 1, sum(m) = k}, so the bound holds in exact + # arithmetic. The isotonic solver averages pooled blocks in float32 and can finish one + # ULP outside it: for ``n=4`` with scores from seed 202 the largest entry comes back as + # 1.0000001. Saturate the forward value onto the documented bound, but leave the backward + # pass on the projection's own gradient -- a plain clip would zero the gradient of + # precisely the saturated entries, which are the ones the mask selects. + mask = mask + jax.lax.stop_gradient(jnp.clip(mask, 0.0, 1.0) - mask) return jnp.moveaxis(mask, -1, axis) diff --git a/src/diffbio/sources/perturbation/_types.py b/src/diffbio/sources/perturbation/_types.py index 27cc303..133d8a5 100644 --- a/src/diffbio/sources/perturbation/_types.py +++ b/src/diffbio/sources/perturbation/_types.py @@ -8,16 +8,15 @@ from __future__ import annotations from enum import StrEnum -from typing import TypeAlias # --------------------------------------------------------------------------- # Type aliases # --------------------------------------------------------------------------- -CellIndex: TypeAlias = int -PerturbationLabel: TypeAlias = str -CellTypeLabel: TypeAlias = str -BatchLabel: TypeAlias = str +type CellIndex = int +type PerturbationLabel = str +type CellTypeLabel = str +type BatchLabel = str # --------------------------------------------------------------------------- diff --git a/uv.lock b/uv.lock index e838688..8e5c6e9 100644 --- a/uv.lock +++ b/uv.lock @@ -1,19 +1,20 @@ version = 1 revision = 3 -requires-python = ">=3.11" +requires-python = ">=3.12" resolution-markers = [ "python_full_version >= '3.14' and sys_platform == 'win32'", "python_full_version >= '3.14' and sys_platform != 'win32'", "python_full_version == '3.13.*' and sys_platform == 'win32'", "python_full_version == '3.13.*' and sys_platform != 'win32'", - "python_full_version == '3.12.*' and sys_platform == 'win32'", - "python_full_version == '3.12.*' and sys_platform != 'win32'", - "python_full_version < '3.12' and sys_platform == 'win32'", - "python_full_version < '3.12' and sys_platform != 'win32'", + "python_full_version < '3.13' and sys_platform == 'win32'", + "python_full_version < '3.13' and sys_platform != 'win32'", ] 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