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Fix memory leak in `MinHash.intersection`. #687

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merged 1 commit into from Jun 6, 2019

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commented Jun 6, 2019

The intersection function uses the new operator to construct
a KmerMinHash or KmerMinAbundance. Although this is Cython,
new still heap-allocates the object, and it is not marked
for garbage collection, because it isn't a PyObject. This commit
calls delete (del) on the allocated object to prevent it from
being leaked.

Addresses #685.

  • Is it mergeable?
  • make test Did it pass the tests?
  • make coverage Is the new code covered?
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Was a spellchecker run on the source code and documentation after
    changes were made?
Fix memory leak in `MinHash.intersection`.
The intersection function uses the `new` operator to construct
a `KmerMinHash` or `KmerMinAbundance`. Although this is Cython,
`new` still heap-allocates the object, and it is *not* marked
for garbage collection, because it isn't a PyObject. This commit
calls delete (`del`) on the allocated object to prevent it from
being leaked.
@codecov

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commented Jun 6, 2019

Codecov Report

Merging #687 into master will decrease coverage by 0.14%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #687      +/-   ##
==========================================
- Coverage   89.26%   89.11%   -0.15%     
==========================================
  Files          27       27              
  Lines        4238     4237       -1     
  Branches       39       39              
==========================================
- Hits         3783     3776       -7     
- Misses        455      461       +6
Impacted Files Coverage Δ
sourmash/signature_json.py 95.62% <0%> (-1.25%) ⬇️
sourmash/lca/lca_utils.py 95.23% <0%> (-0.8%) ⬇️
sourmash/lca/command_index.py 90.3% <0%> (-0.45%) ⬇️
sourmash/sbt.py 85.32% <0%> (-0.4%) ⬇️
sourmash/sbt_storage.py 86.36% <0%> (+0.97%) ⬆️

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@camillescott camillescott added the bug label Jun 6, 2019

@camillescott camillescott requested a review from luizirber Jun 6, 2019

@luizirber luizirber merged commit 6bd362f into master Jun 6, 2019

2 of 3 checks passed

codecov/project 89.11% (-0.15%) compared to ab0279a
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Travis CI - Pull Request Build Passed
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codecov/patch Coverage not affected when comparing ab0279a...3c8c54e
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@luizirber luizirber deleted the fix_intersection_memleak branch Jun 6, 2019

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