feat: get smiles from pubchem

[Kohulan]

No description provided.

[codecov]

Codecov Report

Attention: Patch coverage is 94.98607% with 18 lines in your changes missing coverage. Please review.

Project coverage is 92.00%. Comparing base (2cbd16c) to head (ec40b6c).
Report is 8 commits behind head on development.

Files with missing lines	Patch %	Lines
app/routers/chem.py	21.73%	18 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development     #546      +/-   ##
===============================================
+ Coverage        91.61%   92.00%   +0.39%     
===============================================
  Files               47       50       +3     
  Lines             2792     3141     +349     
===============================================
+ Hits              2558     2890     +332     
- Misses             234      251      +17     

Flag	Coverage Δ
service	92.00% <94.98%> (+0.39%)	⬆️

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[Copilot]

Pull Request Overview

This PR introduces a new feature for retrieving canonical SMILES from PubChem based on a flexible chemical identifier input. Key changes include the addition of comprehensive tests for the PubChemClient, updates to the FastAPI router to incorporate a new endpoint, and modifications to schema definitions and utility functions to support PubChem retrieval.

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_pubchem_client.py	New test suite for various PubChem retrieval scenarios
tests/test_chem.py	Update to test parameters for chemical input validation
app/schemas/pubchem_schema.py	New Pydantic model for PubChem response
app/schemas/coconut.py	Minor formatting adjustments in field names
app/routers/chem.py	Addition of a new endpoint to retrieve SMILES from PubChem
app/modules/toolkits/cdk_wrapper.py	Format adjustments in the Murcko framework helper function
app/modules/pubchem_retrieve.py	Implementation of PubChemClient with multiple query methods
app/modules/coconut/preprocess.py	Update to use consistent naming for Murcko framework fields
app/modules/coconut/descriptors.py	Consistent use of Murcko framework retrieval in descriptors
app/main.py	Metadata update and OpenAPI tag restructuring
CHANGELOG.md	Changelog updated to reflect the new feature changes

Comments suppressed due to low confidence (2)

app/modules/pubchem_retrieve.py:250

• The SMILES detection logic uses a length cutoff of 10 characters, which might inadvertently exclude valid SMILES strings. Consider revising the condition or adding additional checks to better differentiate SMILES inputs.

and len(user_input) <= 10

app/routers/chem.py:1226

• The logic for detecting InChIKey identifiers is brittle due to explicit index and format checks. Consider using a regular expression matching the standard InChIKey format for improved robustness.

elif (len(identifier) == 27 and identifier.count("-") == 2 and all(c.isupper() or c.isdigit() or c == "-" for c in identifier) and identifier[14] == "-" and identifier[25] == "-"):