Skip to content

Fix/update packages to address security alert #89

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
woodsh17 wants to merge 5 commits into
base: production
Choose a base branch
from
Open

Fix/update packages to address security alert #89

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
8769ecd
Update urllib3 package based on security alert
Jun 8, 2026
358c4dc
Update tornado due to security risk
Jun 8, 2026
36fae05
Update packages to address security risks
Jun 8, 2026
4ce3a8b
Update formatting
Jun 8, 2026
7ba1b58
Revert torch dependency version back to 2.2.0 in pyproject.toml
woodsh17 Jun 9, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions docs/conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,5 +97,5 @@
}

html_js_files = [
('https://scripts.simpleanalyticscdn.com/latest.js', {'async': 'async', 'defer': 'defer'}),
]
("https://scripts.simpleanalyticscdn.com/latest.js", {"async": "async", "defer": "defer"}),
]
13 changes: 11 additions & 2 deletions pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ dependencies = [
"scipy>=1.13.1",
# ... data tools
"pandas>=2.2", # Data manipulation and analysis
"pyarrow>=17.0.0", # Columnar data format for efficient data storage and processing # TODO: Test later versions
"pyarrow>=23.0.1", # Columnar data format for efficient data storage and processing # TODO: Test later versions
# ... compression
"zstandard>=0.21.0", # Zstandard compression for MSA files and other data
# ... bioinformatics
Expand All @@ -43,6 +43,10 @@ dependencies = [
"hydride>=1.2.3", # Biotite-supported tool for hydrogen addition
# ... small molecule libraries
"rdkit>=2024.3.5",
"urllib3>=2.7.0",
"pillow>=12.2.0",
"idna>=3.15",
"requests>=2.33.0",
]

[project.optional-dependencies]
Expand All @@ -52,13 +56,15 @@ ml = [
"einops>=0.7.0",
"jaxtyping>=0.2.17",
"beartype>=0.18.0",
"filelock>=3.20.3"
]

ase = [
# ASE (Atomic Simulation Environment) dataset support
"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)
"cryptography>=46.0.7",
]

openbabel = [
Expand All @@ -70,21 +76,24 @@ dev = [
# Linters & formatters
"ruff==0.8.3",
# Testing tools
"pytest>=8.2.0", # testing framework
"pytest>=9.0.3", # 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
"tornado>6.5.5",
"python-dotenv>=1.2.2",
]

docs = [
"sphinx>=8.0.0",
"sphinx-gallery>=0.19.0",
"pydata-sphinx-theme>=0.16.1",
"matplotlib>=3.10.0",
"Pygments>=2.20.0",
]

[dependency-groups]
Expand Down
Loading