In 1.5.0, solver from config is ignored

[Anastasiabum]

Hello, thank you for the update!

I ran into an issue with the solver configuration. When I use a configuration file that contains solver=cbc, this setting seems to be ignored, and OptiType tries to use glpsol instead. Since glpsol is not installed on my system, the run fails:

root@3c76f309505c:/outputs# /usr/local/bin/optitype run -c /soft/OptiType-1.5.0/test/test_config.ini -i /input/input_1.fastq.gz -i /input/input_1.fastq.gz  --dna -p test1 -o /output/optitype_test1_no_config  2>&1 | tee /output/test1_no_config.log
WARNING: Initializing ordered Set R with a fundamentally unordered data source
(type: set).  This WILL potentially lead to nondeterministic behavior in Pyomo
WARNING: Could not locate the 'glpsol' executable, which is required for
solver 'glpk'
Solver does not support multi-threading. Falling back to single-threading.
WARNING: Could not locate the 'glpsol' executable, which is required for
solver 'glpk'
Error: No executable found for solver 'glpk'

I'm using the test configuration file from the repository, which does contain solver=cbc:

root@3c76f309505c:/outputs# grep "solver=cbc" /soft/OptiType-1.5.0/test/test_config.ini
solver=cbc

However, when I explicitly add --solver cbc to the command line, everything works as expected:

root@3c76f309505c:/outputs# /usr/local/bin/optitype run --solver cbc -i /input/input_1.fastq.gz -i /input/input_1.fastq.gz --dna -p test1 -o /output/optitype_test1_solver
WARNING: Initializing ordered Set R with a fundamentally unordered data source
(type: set).  This WILL potentially lead to nondeterministic behavior in Pyomo

============================================================
HLA Typing Results
============================================================
  HLA-A: A*01:01 (homozygous)
  HLA-B: B*08:01, B*57:01
  HLA-C: C*06:02, C*07:01

Reads: 1306
Objective: 1282.49

Results written to: /output/optitype_test1_solver/test1_result.tsv
Coverage plot: /output/optitype_test1_solver/test1_coverage_plot.pdf

If --solver is not provided on the command line, OptiType should use the value from config.ini (or the built-in default if the configuration file does not specify one). This is the expected behavior and matches how it worked in v1.3.5

I suspect the issue is related to the following:

• In cli.py, the --solver option has a hardcoded default value of glpk (link)
• Later in the same file, this value is unconditionally assigned to pipeline_config.solver = solver (link), overriding any solver setting that was loaded from the configuration file

It's also possible that the same issue affects other configuration options that have command-line defaults.

Thank you for your time and effort!