cosym fix np.random.seed #1621
Merged
cosym fix np.random.seed #1621
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Fix occassional test failure by also setting np.random.seed
Codecov Report
@@ Coverage Diff @@
## main #1621 +/- ##
=======================================
Coverage 66.60% 66.60%
=======================================
Files 614 614
Lines 68748 68750 +2
Branches 9571 9571
=======================================
+ Hits 45789 45791 +2
+ Misses 21029 21028 -1
- Partials 1930 1931 +1 |
dagewa
approved these changes
Mar 5, 2021
graeme-winter
approved these changes
Mar 5, 2021
| if seed is not None: | ||
| flex.set_random_seed(seed) | ||
| random.seed(seed) | ||
| np.random.seed(seed) |
Yes - by definition the cosym procedure is dependent on a random number generator as it is used to generate random starting coordinates for the procedure: dials/algorithms/symmetry/cosym/__init__.py Line 295 in c9cdceb In the command line script all the potentially relevant random seeds (random, flex.random, np.random) are set. Setting |
rjgildea
added a commit
to xia2/xia2
that referenced
this pull request
Mar 23, 2021
This meant that the post-scaling cos-angle clustering would vary between runs. See also dials/dials#1621
rjgildea
added a commit
to xia2/xia2
that referenced
this pull request
Mar 24, 2021
* Fix np.random.seed for xia2.multiplex This meant that the post-scaling cos-angle clustering would vary between runs. See also dials/dials#1621 * Use d_min cutoff from scaling for cluster analysis This probably gives more meaningful results than using all data to the edges of the data, and also makes the reported cluster completeness comparable to that reported after scaling. * Use proteinase_k fixture Gets the lists of experiment and reflection files, and removes any .refl files after a test has completed.
ndevenish
pushed a commit
to xia2/xia2
that referenced
this pull request
Mar 24, 2021
* Fix np.random.seed for xia2.multiplex This meant that the post-scaling cos-angle clustering would vary between runs. See also dials/dials#1621 * Use d_min cutoff from scaling for cluster analysis This probably gives more meaningful results than using all data to the edges of the data, and also makes the reported cluster completeness comparable to that reported after scaling. * Use proteinase_k fixture Gets the lists of experiment and reflection files, and removes any .refl files after a test has completed.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fix occassional test failure by also setting np.random.seed