Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix DATAWriter, CRD, PQR, and PDBQT compressed file writing #4163

Merged
merged 12 commits into from
Jun 18, 2023
Merged

Conversation

IAlibay
Copy link
Member

@IAlibay IAlibay commented Jun 6, 2023

Whislt this direclty Fixes #4159 it also opens a big can of worms...

TODO?

As far as I can tell, the following file types also misuse utils.filename leading to this problem

  • CRD
  • PQR
  • PDBQT

Changes made in this Pull Request:

PR Checklist

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

📚 Documentation preview 📚: https://mdanalysis--4163.org.readthedocs.build/en/4163/

@github-actions
Copy link

github-actions bot commented Jun 6, 2023

Linter Bot Results:

Hi @IAlibay! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location Outcome
main package ⚠️ Possible failure
testsuite ⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/5304762197/jobs/9601303663


Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

@codecov
Copy link

codecov bot commented Jun 6, 2023

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (efc51af) 93.60% compared to head (e72e05f) 93.60%.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #4163   +/-   ##
========================================
  Coverage    93.60%   93.60%           
========================================
  Files          193      193           
  Lines        25147    25147           
  Branches      4056     4056           
========================================
  Hits         23539    23539           
  Misses        1092     1092           
  Partials       516      516           
Impacted Files Coverage Δ
package/MDAnalysis/coordinates/NAMDBIN.py 100.00% <ø> (ø)
package/MDAnalysis/lib/util.py 89.65% <ø> (ø)
package/MDAnalysis/coordinates/CRD.py 90.19% <100.00%> (ø)
package/MDAnalysis/coordinates/LAMMPS.py 95.03% <100.00%> (ø)
package/MDAnalysis/coordinates/PDBQT.py 83.50% <100.00%> (ø)
package/MDAnalysis/coordinates/PQR.py 92.85% <100.00%> (ø)

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

IAlibay added 8 commits June 18, 2023 15:02
Unpopular opinion; the Foo Fighters have become a more iconic band
than Nirvana.
You know, I don't think I've ever watched Breakfast at Tiffany's.
At 20 miles a day, it would take 50 days for the Proclaimers to
get to fall down at your door. That's some shockingly poor delivery
service...
You know Billy, you might not have started the fire, but you _could_
have helped try to put it out... A little bit of water goes a long way.
We built this city on <s>Rock N Roll</s>.. poorly documented ideas of
what file types you can open. anyopen? more like maybeopen
Flying like a GZIP, like a GUNZIP?
The power of a changelog is a curious thing. Make one developer weep,
make another sing. Change existing scripts into new ones.
@IAlibay IAlibay changed the title [WIP] Fix DATAWriter compressed file writing Fix DATAWriter compressed file writing Jun 18, 2023
@IAlibay
Copy link
Member Author

IAlibay commented Jun 18, 2023

Ok this should be good to go.

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Copy link
Member

@RMeli RMeli left a comment

Choose a reason for hiding this comment

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

Small docs comments, otherwise LGTM

(That "t" key... 😉)

package/MDAnalysis/coordinates/CRD.py Outdated Show resolved Hide resolved
package/MDAnalysis/coordinates/PDBQT.py Outdated Show resolved Hide resolved
package/MDAnalysis/coordinates/PQR.py Outdated Show resolved Hide resolved
package/MDAnalysis/lib/util.py Outdated Show resolved Hide resolved
package/MDAnalysis/lib/util.py Outdated Show resolved Hide resolved
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
@IAlibay IAlibay changed the title Fix DATAWriter compressed file writing Fix DATAWriter, CRD, PQR, and PDBQT compressed file writing Jun 18, 2023
@RMeli RMeli merged commit 4f36e2a into develop Jun 18, 2023
@RMeli RMeli deleted the issue-4159 branch June 18, 2023 20:40
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

When trying to write a compressed data file, an uncompressed file is created with '.data.data' extension
2 participants