Fix download-structures entry point (crashes for every user)

[paxcalpt]

Problem

The download-structures console script (declared in pyproject.toml as vlab4mic.download:download_suggested_structures) crashes for every user.

Fixes — src/vlab4mic/download.py

1. Wrong YAML keys. The function read data["id"] / data["title"], but the structure YAMLs nest these under a model: mapping with a capital ID (e.g. 7R5K.yaml). This raised KeyError on every file. Now reads data["model"]["ID"] / data["model"]["title"], consistent with experiments.py.

2. Wrong default path. Default data_path="data" resolved to ./data/structures, which doesn't exist. Now defaults to the installed package configs dir derived from vlab4mic.__file__, so the command works out of the box. A custom data_path is still honoured.

3. Template not skipped. The skip used filename.stem == "_template", but the file is _template_.yaml (stem _template_), so it slipped through and crashed (it has lowercase empty id: and no title:). Now uses startswith("_template").

Other

• makefile: stale help text supramolsim.download:... → vlab4mic.download:....
• tests/test_download.py: covers the default path resolution, the model: nesting (and absence of the old flat keys), and a network-mocked end-to-end run that skips existing .cifs without error.

Verification

• New tests pass (3 passed).
• Direct run against the package's bundled configs: all titles parse, 0 network calls when .cifs exist, and a missing .cif produces the correct https://files.rcsb.org/download/<ID>.cif URL.

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Fixes the download-structures console script which crashed for all users due to three bugs: wrong YAML key paths, an invalid default data path, and a faulty template-skip check. Also corrects stale help text in the makefile and adds tests covering the fixes.

Changes:

• Read structure metadata from the nested model.ID/model.title keys and default data_path to the installed package's configs directory.
• Skip the _template_.yaml file via startswith("_template") instead of an exact stem match.
• Add tests for path resolution, YAML schema expectations, and a network-mocked end-to-end run.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
src/vlab4mic/download.py	Fix YAML key access, default path resolution, and template skip predicate.
tests/test_download.py	New tests validating default path, nested-key schema, and skip-existing behavior without network.
makefile	Update stale help text from supramolsim.download to vlab4mic.download.

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[codecov-commenter]

Codecov Report

❌ Patch coverage is 87.50000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 67.96%. Comparing base (5a57c8c) to head (77dd281).

Files with missing lines	Patch %	Lines
src/vlab4mic/download.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #111      +/-   ##
==========================================
+ Coverage   67.72%   67.96%   +0.24%     
==========================================
  Files          28       28              
  Lines        5084     5088       +4     
==========================================
+ Hits         3443     3458      +15     
+ Misses       1641     1630      -11     

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