diffbio 0.1.1__tar.gz → 0.1.3__tar.gz

{diffbio-0.1.1 → diffbio-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: diffbio
-Version: 0.1.1
+Version: 0.1.3
 Summary: DiffBio: End-to-end differentiable bioinformatics pipelines built on Datarax, Artifex, Opifex, and Calibrax
 Project-URL: Bug Tracker, https://github.com/avitai/DiffBio/issues
 Project-URL: Documentation, https://diffbio.readthedocs.io
@@ -36,30 +36,31 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.12
+Requires-Python: <3.14,>=3.12
 Requires-Dist: anndata>=0.9.1
-Requires-Dist: avitai-artifex>=0.1.4
+Requires-Dist: avitai-artifex>=0.1.5
 Requires-Dist: beartype>=0.14.1
 Requires-Dist: biopython>=1.81
-Requires-Dist: calibrax>=0.1.2
+Requires-Dist: calibrax>=0.1.5
 Requires-Dist: chex>=0.1.7
-Requires-Dist: datarax>=0.1.5
-Requires-Dist: flax>=0.12.1
+Requires-Dist: datarax>=0.1.7
+Requires-Dist: flax>=0.12.9
 Requires-Dist: h5py>=3.7
 Requires-Dist: jax-md>=0.2.27
-Requires-Dist: jax>=0.6.1
+Requires-Dist: jax>=0.11.1
 Requires-Dist: jaxtyping>=0.2.20
 Requires-Dist: numpy>=1.24
-Requires-Dist: opifex>=0.2.1
+Requires-Dist: opifex>=0.2.2
 Requires-Dist: optax>=0.2.8
-Requires-Dist: orbax-checkpoint>=0.11.10
 Requires-Dist: scipy>=1.10
+Requires-Dist: substrax>=0.1.5
 Provides-Extra: all
 Requires-Dist: bandit[toml]>=1.8.6; extra == 'all'
 Requires-Dist: beartype>=0.14.1; extra == 'all'
@@ -73,7 +74,7 @@ Requires-Dist: griffe>=1.7.3; extra == 'all'
 Requires-Dist: import-linter>=2.5; extra == 'all'
 Requires-Dist: interrogate>=1.7.0; extra == 'all'
 Requires-Dist: ipykernel>=6.29.5; extra == 'all'
-Requires-Dist: jax[cuda12]>=0.6.1; extra == 'all'
+Requires-Dist: jax[cuda12]>=0.11.1; extra == 'all'
 Requires-Dist: lineax>=0.0.8; extra == 'all'
 Requires-Dist: matplotlib>=3.7; extra == 'all'
 Requires-Dist: mkdocs-include-exclude-files>=0.1; extra == 'all'
@@ -129,7 +130,7 @@ Requires-Dist: flake8>=7.0; extra == 'cuda-dev'
 Requires-Dist: import-linter>=2.5; extra == 'cuda-dev'
 Requires-Dist: interrogate>=1.7.0; extra == 'cuda-dev'
 Requires-Dist: ipykernel>=6.29.5; extra == 'cuda-dev'
-Requires-Dist: jax[cuda12]>=0.6.1; extra == 'cuda-dev'
+Requires-Dist: jax[cuda12]>=0.11.1; extra == 'cuda-dev'
 Requires-Dist: pylint>=3.3.8; extra == 'cuda-dev'
 Requires-Dist: pyright>=1.1.336; extra == 'cuda-dev'
 Requires-Dist: pytest-asyncio>=0.23; extra == 'cuda-dev'
@@ -147,7 +148,7 @@ Requires-Dist: ruff>=0.1.5; extra == 'cuda-dev'
 Requires-Dist: shellcheck-py>=0.10.0.1; extra == 'cuda-dev'
 Requires-Dist: wemake-python-styleguide>=1.0; extra == 'cuda-dev'
 Provides-Extra: cuda12
-Requires-Dist: jax[cuda12]>=0.6.1; extra == 'cuda12'
+Requires-Dist: jax[cuda12]>=0.11.1; extra == 'cuda12'
 Provides-Extra: dev
 Requires-Dist: bandit[toml]>=1.8.6; extra == 'dev'
 Requires-Dist: build>=1.0.3; extra == 'dev'
@@ -278,12 +279,13 @@ For complete operator and pipeline listings, see the [Operators Overview](https:
 ## Installation
 
 ```bash
-# Clone the repository
+# From PyPI
+uv add diffbio          # or: pip install diffbio
+
+# From source
 git clone https://github.com/avitai/DiffBio.git
 cd DiffBio
-
-# Install with uv
-uv sync
+./setup.sh              # detects the backend and syncs the extras
 ```
 
 ## Quick Start
@@ -506,7 +508,7 @@ DiffBio/
 - Flax 0.12+
 - Optax 0.1.4+
 - jaxtyping 0.2.20+
-- Datarax, Artifex, Opifex, and Calibrax (installed automatically from PyPI)
+- Datarax, Artifex, Opifex, Calibrax and Substrax (installed automatically from PyPI)
 
 ## License
 

{diffbio-0.1.1 → diffbio-0.1.3}/README.md

@@ -70,12 +70,13 @@ For complete operator and pipeline listings, see the [Operators Overview](https:
 ## Installation
 
 ```bash
-# Clone the repository
+# From PyPI
+uv add diffbio          # or: pip install diffbio
+
+# From source
 git clone https://github.com/avitai/DiffBio.git
 cd DiffBio
-
-# Install with uv
-uv sync
+./setup.sh              # detects the backend and syncs the extras
 ```
 
 ## Quick Start
@@ -298,7 +299,7 @@ DiffBio/
 - Flax 0.12+
 - Optax 0.1.4+
 - jaxtyping 0.2.20+
-- Datarax, Artifex, Opifex, and Calibrax (installed automatically from PyPI)
+- Datarax, Artifex, Opifex, Calibrax and Substrax (installed automatically from PyPI)
 
 ## License
 

{diffbio-0.1.1 → diffbio-0.1.3}/pyproject.toml

@@ -5,6 +5,7 @@ requires = ["hatchling>=1.18"]
 [dependency-groups]
 dev = [
   "bandit[toml]>=1.8.6",
+  "pre-commit>=4.6",
   "hypothesis>=6.156.6",
   "import-linter>=2.5",
   "interrogate>=1.7.0",
@@ -31,28 +32,29 @@ classifiers = [
   "Topic :: Software Development :: Libraries :: Python Modules",
   "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "License :: OSI Approved :: MIT License"
 ]
 dependencies = [
   # Datarax - operator, source, and pipeline contracts
-  "datarax>=0.1.5",
+  "datarax>=0.1.7",
   # Artifex - modeling, modality, and transformer substrate
-  "avitai-artifex>=0.1.4",
+  "avitai-artifex>=0.1.5",
   # Opifex - scientific ML, operator learning, and advanced optimization
-  "opifex>=0.2.1",
+  "opifex>=0.2.2",
   # Calibrax - benchmarking, comparison, profiling, and regression control
-  "calibrax>=0.1.2",
+  "calibrax>=0.1.5",
+  # Substrax - device identity, meshes and checkpoint store shared by the siblings
+  "substrax>=0.1.5",
   # JAX ecosystem
   "beartype>=0.14.1",
   "chex>=0.1.7",
-  # 0.12.1 is where nnx Variable gained set_value / get_value.
-  "flax>=0.12.1",
-  "jax>=0.6.1",
+  "flax>=0.12.9",
+  "jax>=0.11.1",
   "jaxtyping>=0.2.20",
   # 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",
   "scipy>=1.10",
@@ -67,8 +69,8 @@ keywords = ["jax", "flax", "bioinformatics", "differentiable", "variant-calling"
 license = {file = "LICENSE"}
 name = "diffbio"
 readme = "README.md"
-requires-python = ">=3.12"
-version = "0.1.1"
+requires-python = ">=3.12,<3.14"
+version = "0.1.3"
 
 [project.optional-dependencies]
 all = ["diffbio[benchmark,chem,cuda12,dev,docs,genomics,soft-ops-advanced,soft-ops-ot,test,torch-io]"]
@@ -92,7 +94,7 @@ 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"]
+cuda12 = ["jax[cuda12]>=0.11.1"]
 dev = [
   "bandit[toml]>=1.8.6",
   "build>=1.0.3",
@@ -264,6 +266,7 @@ match-dir = "^(?!tests|examples).*"
 exclude = ["docs", "examples", "scripts", ".deprecated", "**/__pycache__", "**/.venv", "memory-bank"]
 extraPaths = ["."]
 include = ["src", "tests"]
+pythonVersion = "3.12"
 reportAbstractUsage = false
 reportArgumentType = "warning"
 reportAssignmentType = false

{diffbio-0.1.1 → diffbio-0.1.3}/src/diffbio/__init__.py

@@ -1,7 +1,7 @@
 """DiffBio: End-to-end differentiable bioinformatics pipelines built on the wider JAX/NNX ecosystem.
 
 This package provides differentiable bioinformatics pipeline components that
-integrate with Datarax, Artifex, Opifex, and Calibrax for gradient-based
+integrate with Datarax, Artifex, Opifex, Calibrax and Substrax for gradient-based
 optimization of genomics workflows.
 
 Key components:
@@ -13,6 +13,8 @@ Key components:
 - constants: Centralized constants for the library
 """
 
+import importlib.metadata
+
 from diffbio import (
     configs,
     constants,
@@ -24,7 +26,7 @@ from diffbio import (
     utils,
 )
 
-__version__ = "0.1.0"
+__version__ = importlib.metadata.version("diffbio")
 
 __all__ = [
     "__version__",

{diffbio-0.1.1 → diffbio-0.1.3}/src/diffbio/operators/protein/secondary_structure.py

@@ -458,7 +458,7 @@ def _compute_backbone_constraints(
         BondAngleExtension,
         BondLengthExtension,
     )
-    from artifex.generative_models.extensions.protein.backbone import (  # noqa: PLC0415
+    from artifex.generative_models.core.configuration import (  # noqa: PLC0415
         ProteinExtensionConfig,
     )
 

{diffbio-0.1.1 → diffbio-0.1.3}/src/diffbio/sources/anndata_source.py

@@ -34,7 +34,7 @@ from flax import nnx
 
 from datarax.core.config import StructuralConfig
 from datarax.core.data_source import DataSourceModule
-from datarax.sources._eager_source_ops import eager_get_batch, eager_iter, eager_reset
+from datarax.sources import eager_get_batch, eager_iter, eager_reset
 
 from diffbio.sources._anndata_shared import (
     build_anndata_data,

{diffbio-0.1.1 → diffbio-0.1.3}/src/diffbio/sources/bam.py

@@ -114,10 +114,12 @@ class BAMSource(IndexedBatchSourceMixin, DataSourceModule):
         super().__init__(config, rngs=rngs, name=name)
 
         # Import pysam lazily to allow installation without it
+        # pysam builds its package ``__all__`` at import time, so the typed name is the
+        # defining module's.
         try:
-            import pysam
+            from pysam.libcalignmentfile import AlignmentFile
 
-            self._pysam = pysam
+            self._alignment_file = AlignmentFile
         except ImportError as err:
             raise ImportError(
                 "pysam is required for BAMSource. Install with: pip install pysam"
@@ -147,9 +149,7 @@ class BAMSource(IndexedBatchSourceMixin, DataSourceModule):
         mode = "rb" if str(config.file_path).endswith(".bam") else "rc"
         reference = str(config.reference_path) if config.reference_path else None
 
-        with self._pysam.AlignmentFile(
-            str(config.file_path), mode, reference_filename=reference
-        ) as bam:
+        with self._alignment_file(str(config.file_path), mode, reference_filename=reference) as bam:
             for read in self._iter_reads(bam):
                 if self._should_skip_read(read):
                     continue

{diffbio-0.1.1 → diffbio-0.1.3}/src/diffbio/splitters/random.py

@@ -82,7 +82,8 @@ class RandomSplitter(SplitterModule):
         if self.config.seed is not None:
             key = jax.random.key(self.config.seed)
         elif self.rngs is not None and "split" in self.rngs:
-            key = self.rngs.split()
+            # Subscript, not attribute: ``Rngs.split`` is also a method that takes a count.
+            key = self.rngs["split"]()
         else:
             key = jax.random.key(0)
 

{diffbio-0.1.1 → diffbio-0.1.3}/src/diffbio/utils/dependency_runtime.py

@@ -10,7 +10,7 @@ from pathlib import Path
 import site
 from types import ModuleType
 
-ECOSYSTEM_PACKAGES: tuple[str, ...] = ("datarax", "artifex", "opifex", "calibrax")
+ECOSYSTEM_PACKAGES: tuple[str, ...] = ("datarax", "artifex", "opifex", "calibrax", "substrax")
 
 
 @dataclass(frozen=True)