Added unwrap and wrap transformations#2020
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davidercruz wants to merge 22 commits intoMDAnalysis:developfrom
Closed
Added unwrap and wrap transformations#2020davidercruz wants to merge 22 commits intoMDAnalysis:developfrom
davidercruz wants to merge 22 commits intoMDAnalysis:developfrom
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* removed use of pytest.approx * removed mock decorator, playing badly with pytest fixtures
Using consistently np.int64 for the indices used in pkdtree avoids type errors when using unique_int_1d. This should reduce the number of failing tests on windows.
* Fixes Issue MDAnalysis#2021 with Windows xdr large file offset handling * on the Windows platform xdr file offsets are now forced to use a 64-bit storage type so that, for example, file seeks beyond 4 GB are correctly reported
corrected rotateby transformation calculation
* added an option to check for pairs within coordinate array using bruteforce_capped_self, pkdtree_capped_self + tests * Modified guess bonds to use capped function * seperated the self_capped_function, added tests, modified the guess_bonds function * modified CHANGELOG, and minor modifications * modified test for increased coverage, minor modifications to the self_capped_distance
…lysis#2022) * kdtree now works with pbc, modified _apply_kdtree method in pointselections * CHANGELOG
MDAnalysis#2011) * fixes Issue MDAnalysis#2001 - support for Tinker periodic boundary box
Contributor
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Could you rebase against develop? (not merge) The test failure has been fixed in an other pr. |
…e_bytes BUG: Force 64-bit storage for xdr file offsets
Codecov Report
@@ Coverage Diff @@
## develop #2020 +/- ##
===========================================
- Coverage 88.45% 88.31% -0.14%
===========================================
Files 143 144 +1
Lines 17223 17241 +18
Branches 2637 2638 +1
===========================================
- Hits 15234 15227 -7
- Misses 1389 1407 +18
- Partials 600 607 +7
Continue to review full report at Codecov.
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Contributor
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Can you tell me what git command you used? It would help me understand what went wrong and how to fix it. |
Contributor
Author
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Here's what I did:
git remote add upstream https://github.com/MDAnalysis/mdanalysis.git
git pull --rebase upstream develop
And then solved some conflicts and:
git rebase --continue
…On Tue, Aug 7, 2018 at 6:18 PM Jonathan Barnoud ***@***.***> wrote:
Can you tell me what git command you used? It would help me understand
what went wrong and how to fix it.
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| @pytest.mark.parametrize('weights', ( | ||
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Member
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@davidercruz that should have worked, but I guess it hasn't. Might be best to start a new branch and cherry-pick the commits you made so far. |
Contributor
Author
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@richardjgowers So I should create a new PR and close this one? |
Contributor
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It may be the easiest solution. Do not forget to reference this pr in the next one. Le 9 août 2018 11:36 PM, Davide Cruz <notifications@github.com> a écrit :@richardjgowers So I should create a new PR and close this one?
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Adds a wrap transformation based on
atoms.wrapand a unwrap transformation based on @richardjgowers 's_cutil.make_wholeThis is the last transformation in my GSOC project :D
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