fix(deps): remove upper bounds on direct dependencies (#88)

Author: kierandidi

pyproject.toml

@@ -23,68 +23,68 @@ classifiers = [
 
 dependencies = [
     # ... generic tools
-    "cython>=3.0.0,<4", # Cython compiler for C extensions
-    "cytoolz>=0.12.3,<1", # Cython-optimized tools for itertools and functional programming
-    "tqdm>=4.65.0,<5", # Fast, extensible progress bar for loops and more
+    "cython>=3.0.0", # Cython compiler for C extensions
+    "cytoolz>=0.12.3", # Cython-optimized tools for itertools and functional programming
+    "tqdm>=4.65.0", # Fast, extensible progress bar for loops and more
     # ... CLI & config management
-    "typer>=0.12.5,<1", # Modern CLI framework
+    "typer>=0.12.5", # Modern CLI framework
     # ... linear algebra, maths & ml
-    "numpy>=1.25.0,<3",
-    "scipy>=1.13.1,<2",
+    "numpy>=1.25.0",
+    "scipy>=1.13.1",
     # ... data tools
-    "pandas>=2.2,<2.4", # Data manipulation and analysis
-    "pyarrow==17.0.0", # Columnar data format for efficient data storage and processing  # TODO: Test later versions
+    "pandas>=2.2", # Data manipulation and analysis
+    "pyarrow>=17.0.0", # Columnar data format for efficient data storage and processing  # TODO: Test later versions
     # ... compression
-    "zstandard>=0.21.0,<1", # Zstandard compression for MSA files and other data
+    "zstandard>=0.21.0", # Zstandard compression for MSA files and other data
     # ... bioinformatics
-    "py3Dmol>=2.2.1,<3", # Python wrapper for 3Dmol.js
+    "py3Dmol>=2.2.1", # Python wrapper for 3Dmol.js
     "pymol-remote>=0.0.5", # Remote access to PyMOL from Python (has no dependencies)
-    "biotite==1.4.0", # Biotite is a Python library for bioinformatics  # TODO: Test newer versions
-    "hydride>=1.2.3,<2", # Biotite-supported tool for hydrogen addition
+    "biotite==1.4.0", # Pinned — biotite upgrades have broken atomworks in the past
+    "hydride>=1.2.3", # Biotite-supported tool for hydrogen addition
     # ... small molecule libraries
-    "rdkit>=2024.3.5,<2025.9",
+    "rdkit>=2024.3.5",
 ]
 
 [project.optional-dependencies]
 ml = [
     # atomworks-ml dependencies
-    "torch>=2.2.0,<2.8",
-    "einops>=0.7.0,<1",
-    "jaxtyping>=0.2.17,<1",
-    "beartype>=0.18.0,<1",
+    "torch>=2.2.0",
+    "einops>=0.7.0",
+    "jaxtyping>=0.2.17",
+    "beartype>=0.18.0",
 ]
 
 ase = [
     # ASE (Atomic Simulation Environment) dataset support
-    "ase>=3.22.0,<4",  # Atomic Simulation Environment
-    "ase-db-backends>=0.10.0,<1",  # Database backends for ASE (PostgreSQL, MySQL, LMDB)
-    "lmdb>=1.5.0,<2",  # LMDB backend for ASE database support (required for .aselmdb files)
+    "ase>=3.22.0",  # Atomic Simulation Environment
+    "ase-db-backends>=0.10.0",  # Database backends for ASE (PostgreSQL, MySQL, LMDB)
+    "lmdb>=1.5.0",  # LMDB backend for ASE database support (required for .aselmdb files)
 ]
 
 openbabel = [
     # Optional openbabel dependency
-    "openbabel-wheel==3.1.1.22",
+    "openbabel-wheel>=3.1.1.22",
 ]
 
 dev = [
     # Linters & formatters
     "ruff==0.8.3",
     # Testing tools
-    "pytest>=8.2.0,<9", # testing framework
-    "pytest-testmon>=2.1.1,<3", # run only tests related to changed code
-    "pytest-xdist>=3.6.1,<4", # run tests in parallel
-    "pytest-dotenv>=0.5.2,<1", # load environment variables from .env file
-    "pytest-cov>=4.1.0,<5", # generate coverage report
-    "pytest-benchmark>=5.0.0,<6", # benchmark tests for speed
+    "pytest>=8.2.0", # testing framework
+    "pytest-testmon>=2.1.1", # run only tests related to changed code
+    "pytest-xdist>=3.6.1", # run tests in parallel
+    "pytest-dotenv>=0.5.2", # load environment variables from .env file
+    "pytest-cov>=4.1.0", # generate coverage report
+    "pytest-benchmark>=5.0.0", # benchmark tests for speed
     # Jupyter notebooks
     "ipykernel>=6.28.0", # IPython kernel for Jupyter
 ]
 
 docs = [
-    "sphinx>=8.0.0,<9",
-    "sphinx-gallery>=0.19.0,<1",
-    "pydata-sphinx-theme>=0.16.1,<1",
-    "matplotlib>=3.10.0,<4",
+    "sphinx>=8.0.0",
+    "sphinx-gallery>=0.19.0",
+    "pydata-sphinx-theme>=0.16.1",
+    "matplotlib>=3.10.0",
 ]
 
 [dependency-groups]