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chore: upgrade structure and configuration #668

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merged 6 commits into from Jun 24, 2019

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commented Jun 21, 2019

  • fix #665
  • description of feature/fix
  • tests added/passed
  • add an entry to the next release

@Midnighter Midnighter self-assigned this Jun 21, 2019

@Midnighter Midnighter requested a review from ChristianLieven Jun 22, 2019

@Midnighter Midnighter changed the title chore: upgrade structure and configuration [WIP] chore: upgrade structure and configuration Jun 22, 2019

Midnighter added 6 commits Jun 21, 2019
chore: introduce src directory
* Upgrade configuration
chore: move coverage config back
Since memote uses subprocesses for parts of its application there needs
to be a `.coveragerc` file. Otherwise those subprocesses do not read the
configuration from the `tox.ini`.

@Midnighter Midnighter force-pushed the chore-upgrade branch from 23034b0 to a2cae10 Jun 24, 2019

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commented Jun 24, 2019

Codecov Report

Merging #668 into develop will decrease coverage by 2.42%.
The diff coverage is 100%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #668      +/-   ##
===========================================
- Coverage    85.02%   82.59%   -2.43%     
===========================================
  Files           59       49      -10     
  Lines         3258     2597     -661     
  Branches       436      424      -12     
===========================================
- Hits          2770     2145     -625     
+ Misses         401      366      -35     
+ Partials        87       86       -1
Impacted Files Coverage Δ
src/memote/suite/reporting/__init__.py 100% <ø> (ø)
src/memote/experimental/growth.py 78.78% <ø> (ø)
src/memote/support/__init__.py 100% <ø> (ø)
src/memote/support/validation.py 85.29% <ø> (ø)
src/memote/support/consistency.py 96.51% <ø> (ø)
src/memote/suite/results/__init__.py 100% <ø> (ø)
src/memote/experimental/__init__.py 100% <ø> (ø)
src/memote/experimental/essentiality.py 90.62% <ø> (ø)
src/memote/__init__.py 100% <ø> (ø)
src/memote/experimental/medium.py 100% <ø> (ø)
... and 42 more

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d81f42f...a2cae10. Read the comment docs.

1 similar comment
@codecov

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commented Jun 24, 2019

Codecov Report

Merging #668 into develop will decrease coverage by 2.42%.
The diff coverage is 100%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #668      +/-   ##
===========================================
- Coverage    85.02%   82.59%   -2.43%     
===========================================
  Files           59       49      -10     
  Lines         3258     2597     -661     
  Branches       436      424      -12     
===========================================
- Hits          2770     2145     -625     
+ Misses         401      366      -35     
+ Partials        87       86       -1
Impacted Files Coverage Δ
src/memote/suite/reporting/__init__.py 100% <ø> (ø)
src/memote/experimental/growth.py 78.78% <ø> (ø)
src/memote/support/__init__.py 100% <ø> (ø)
src/memote/support/validation.py 85.29% <ø> (ø)
src/memote/support/consistency.py 96.51% <ø> (ø)
src/memote/suite/results/__init__.py 100% <ø> (ø)
src/memote/experimental/__init__.py 100% <ø> (ø)
src/memote/experimental/essentiality.py 90.62% <ø> (ø)
src/memote/__init__.py 100% <ø> (ø)
src/memote/experimental/medium.py 100% <ø> (ø)
... and 42 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d81f42f...a2cae10. Read the comment docs.

@@ -87,7 +87,6 @@ def evaluate(self, model):
essen = single_gene_deletion(
model, gene_list=self.data["gene"], processes=1)
essen["gene"] = [list(g)[0] for g in essen.index]
essen.index = essen["gene"]

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@ChristianLieven

ChristianLieven Jun 24, 2019

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Is this change to satisfy the updated pandas?

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@Midnighter

Midnighter Jun 24, 2019

Author Member

Yes, it now complains when the index and a column have the same name. Another solution would be to just give it a different name.

@Midnighter Midnighter merged commit 709563d into develop Jun 24, 2019

4 checks passed

codecov/patch 100% of diff hit (target 85.02%)
Details
codecov/project Absolute coverage decreased by -2.42% but relative coverage increased by +14.97% compared to d81f42f
Details
continuous-integration/appveyor/pr AppVeyor build succeeded
Details
continuous-integration/travis-ci/pr The Travis CI build passed
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@Midnighter Midnighter deleted the chore-upgrade branch Jun 24, 2019

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