Skip to content

Issue 2232 psf bz2#2284

Merged
orbeckst merged 3 commits intodevelopfrom
issue-2232-psf_bz2
Jul 3, 2019
Merged

Issue 2232 psf bz2#2284
orbeckst merged 3 commits intodevelopfrom
issue-2232-psf_bz2

Conversation

@richardjgowers
Copy link
Member

@richardjgowers richardjgowers commented Jul 3, 2019

Fixes #2232

Changes made in this Pull Request:

  • use self.filename rather than the .name attribute of the thing we open to workaround the bug with bz2files

I used a fixture to not have to add another file to the testsuite

PR Checklist

  • Tests?
  • Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?

can now read bz2 compressed psf files
@codecov
Copy link

codecov bot commented Jul 3, 2019

Codecov Report

Merging #2284 into develop will increase coverage by 0.09%.
The diff coverage is 0%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2284      +/-   ##
===========================================
+ Coverage    89.55%   89.64%   +0.09%     
===========================================
  Files          156      172      +16     
  Lines        19410    21398    +1988     
  Branches      2785     2785              
===========================================
+ Hits         17382    19183    +1801     
- Misses        1432     1620     +188     
+ Partials       596      595       -1
Impacted Files Coverage Δ
package/MDAnalysis/topology/PSFParser.py 87.82% <0%> (ø) ⬆️
package/MDAnalysis/analysis/psa.py 82.91% <0%> (-0.58%) ⬇️
core/util.py 100% <0%> (ø)
transformations/__init__.py 100% <0%> (ø)
auxiliary/base.py 89% <0%> (ø)
util.py 88.15% <0%> (ø)
topology/base.py 97.67% <0%> (ø)
__init__.py 91.89% <0%> (ø)
topology/__init__.py 100% <0%> (ø)
visualization/__init__.py 100% <0%> (ø)
... and 8 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 b0c70cd...3e84e81. Read the comment docs.

@richardjgowers
Copy link
Member Author

@MDAnalysis/coredevs this is good to go

Copy link
Member

@orbeckst orbeckst left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm – thanks!!

@orbeckst orbeckst merged commit 66038c7 into develop Jul 3, 2019
@orbeckst orbeckst deleted the issue-2232-psf_bz2 branch July 3, 2019 15:22
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Reading a bz2 compressed PSF file fails

2 participants