The problem

I tried to compare the performance results between different Python versions and implementations. While the comparison between CPython 3.6 and CPython 2.7 works as expected, I get an exception when comparing the results obtained with CPython 2.7.13 and PyP 2.7.13.

Exact versions:

CPython:

 Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:05:08) 
 [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin

PyPy:

 (Python 2.7.13 (c925e7381036, Jun 05 2017, 20:53:58) 
 [PyPy 5.8.0 with GCC 4.2.1 Compatible  Apple LLVM 5.1 (clang-503.0.40)]

How to reproduce the issue

Run from CPython 2 environment:

 python -m  performance run  -o py27.json

Run from PyPy environment:

pypy -m performance run -o pypy27.json

Compare:

pyperformance compare -O table py27.json pypy27.json 

What you expected to happen

I expected table like this:
+-------------------------+-----------+-------------+-----------------+-------------------------+
| Benchmark | py27.json | pypy27.json | Change | Significance |
+=========================+===========+=============+=================+=========================+
| 2to3 | 767 ms | 1.63 sec | 2.13x slower | Significant (t=-142.45) |
+-------------------------+-----------+-------------+-----------------+-------------------------+
| chaos | 215 ms | 5.58 ms | 38.62x faster | Significant (t=204.35) |
+-------------------------+-----------+-------------+-----------------+-------------------------+

What actually happens

I get this exception:

compare.py", line 212, in __init__
    raise RuntimeError("base and changed don't have "
 RuntimeError: base and changed don't have the same number of values

Note: The line number my have change do to my debug prints.

Cause

The number of values for the benchmarks python_startup and python_startup_no_site are different, i.e. 200 for CPython and 60 for PyPy (same numbers for both benchmarks)

My work around

I just skipped python_startup and python_startup_no_site with:

        if name in ('python_startup', 'python_startup_no_site'):
            continue

in compare.compare_results:

def compare_results(options):
   base_label, changed_label = get_labels(options.baseline_filename,
                                           options.changed_filename)

    base_suite = perf.BenchmarkSuite.load(options.baseline_filename)
    changed_suite = perf.BenchmarkSuite.load(options.changed_filename)

    results = []
    common = set(base_suite.get_benchmark_names()) & set(
        changed_suite.get_benchmark_names())
    for name in sorted(common):
        print(name)
        if name in ('python_startup', 'python_startup_no_site'):
            continue
        base_bench = base_suite.get_benchmark(name)
        changed_bench = changed_suite.get_benchmark(name)
        result = BenchmarkResult(base_bench, changed_bench)
        results.append(result)

Suggested better solution

Either:

1. Allow command line argument to explicitly skip comparison of tests.
2. Skip non-comparable tests automatically and just list them at the end. Make this optional via a command line switch.