fix: infer optional CALYPSO inputs

[njzjz-bot]

Summary

• infer atomic numbers from name_of_atoms when omitted
• generate the required distance matrix from the maintained covalent-radius table
• preserve explicit lists and per-element radius overrides
• cover the fully omitted optional-field case through task generation

Tests

• PYTHONPATH=tests python -m unittest -v tests.exploration.test_make_task_group_from_config.TestMakeCalyTaskGroupFromConfig.test_infers_optional_atomic_numbers_and_distances tests.exploration.test_make_task_group_from_config.TestMakeCalyTaskGroupFromConfig.test_caly_task_group
• ruff format --check dpgen2/exploration/task/caly_task_group.py tests/exploration/test_make_task_group_from_config.py
• isort --check-only dpgen2/exploration/task/caly_task_group.py tests/exploration/test_make_task_group_from_config.py
• git diff --check

Closes #357

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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📥 Commits

Reviewing files that changed from the base of the PR and between 6b01f29 and 3a037c0.

📒 Files selected for processing (2)

• dpgen2/exploration/task/caly_task_group.py
• tests/exploration/test_make_task_group_from_config.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.43%. Comparing base (6b01f29) to head (3a037c0).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #383   +/-   ##
=======================================
  Coverage   84.43%   84.43%           
=======================================
  Files         104      104           
  Lines        6110     6111    +1     
=======================================
+ Hits         5159     5160    +1     
  Misses        951      951           

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