Fix: Add compatibility with anndata >= 0.10

[NatalieCao323]

This PR fixes the ImportError: cannot import name 'read' from 'anndata' that occurs when using dynamo-release with anndata >= 0.10.

Problem

The anndata.read() function was deprecated in anndata 0.8 and removed in anndata 0.10.0 (released December 2023). Dynamo-release v1.4.1 still imports this function directly, causing an ImportError for all users with modern anndata versions.

Error:

ImportError: cannot import name 'read' from 'anndata'

Location: dynamo/data_io.py, line 9

Impact

This issue affects:

• All users with anndata >= 0.10 (released Dec 2023)
• All new installations (pip installs latest anndata by default)
• All downstream packages (spateo-release, etc.)

Solution

Added a compatibility wrapper that:

1. Tries to import read from anndata (for old versions)
2. Falls back to read_h5ad if read doesn't exist (for new versions)
3. Maintains backward compatibility with anndata < 0.10
4. Ensures forward compatibility with anndata >= 0.10

Changes

File: dynamo/data_io.py

Before:

from anndata import (
    AnnData,
    read,  # ❌ This doesn't exist in anndata >= 0.10
    read_csv,
    # ... other imports
)

After:

from anndata import (
    AnnData,
    read_csv,
    # ... other imports (removed 'read' from here)
)

# Compatibility with anndata >= 0.10
# The 'read' function was deprecated and removed in anndata 0.10.0
# Use read_h5ad as a fallback for backward compatibility
try:
    from anndata import read
except ImportError:
    # anndata >= 0.10 removed 'read', use 'read_h5ad' instead
    from anndata import read_h5ad as read

Testing

Tested with:

• anndata 0.9.2 (old version) - Works
• anndata 0.10.9 (new version) - Works
• anndata 0.12.2 (latest) - Works
• Python 3.11
• macOS, Linux (expected to work on Windows too)

Verification:

# Import test
import dynamo as dyn  # ✅ No ImportError
print(dyn.__version__)  # ✅ 1.4.1

# Downstream test
import spateo as st  # ✅ Now works!
print(st.__version__)  # ✅ 1.1.1

[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 36.56%. Comparing base (9f82563) to head (746d85d).
⚠️ Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
dynamo/data_io.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #730   +/-   ##
=======================================
  Coverage   36.56%   36.56%           
=======================================
  Files         183      183           
  Lines       35352    35334   -18     
=======================================
- Hits        12925    12919    -6     
+ Misses      22427    22415   -12     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Xiaojieqiu]

looks good. I am merging it now