Perf tweaks #1

mortonjt · 2016-08-04T18:40:09Z

Adding in two more test cases to help debugging.

Basically, your code is failing to create an orthogonal basis. I have a really small example put together

          /-O0
         |
         |          /-O1
-y0------|         |
         |         |                                        /-O8
         |         |                              /y7------|
         |         |                             |          \-O9
          \y1------|                    /y5------|
                   |                   |         |          /-O6
                   |                   |          \y8------|
                   |          /y3------|                    \-O7
                   |         |         |
                   |         |         |          /-O4
                    \y2------|          \y6------|
                             |                    \-O5
                             |
                             |          /-O2
                              \y4------|
                                        \-O3

Will lead to the following basis

          O0        O1        O2        O3        O4        O5        O8        O9        O6        O7  
y0  0.037280  0.106969  0.106969  0.106969  0.106969  0.106969  0.106969  0.106969  0.106969  0.106969   
y1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000   
y2  0.096245  0.037491  0.108283  0.108283  0.108283  0.108283  0.108283  0.108283  0.108283  0.108283   
y3  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000   
y4  0.094502  0.094502  0.077053  0.077053  0.077053  0.077053  0.077053  0.077053  0.174338  0.174338   
y5  0.094700  0.094700  0.070955  0.070955  0.070955  0.070955  0.168691  0.168691  0.094700  0.094700   
y6  0.095046  0.095046  0.095046  0.095046  0.095046  0.095046  0.095046  0.095046  0.046864  0.192765   
y7  0.095143  0.095143  0.057707  0.057707  0.156864  0.156864  0.095143  0.095143  0.095143  0.095143   
y8  0.095046  0.095046  0.095046  0.095046  0.095046  0.095046  0.046864  0.192765  0.095046  0.095046

So y1 and y4 are exactly identical.

Will do some more digging into the code. Thanks for putting together!

Adding license

Last touches before release

Correcting documentation in setup.py

Adding tests for duplicate ids, updating documentation. Adding headers for copyright

GPL license

Adding some mutability tests Adding warning about replacing internal node names

Util

…sort

Nichesort

Adding in link

Updating changelog

…tweaks

wasade · 2016-08-04T19:05:15Z

Against my repo?

On Aug 4, 2016 21:40, "Jamie Morton" notifications@github.com wrote:

Adding in two more test cases to help debugging.

Basically, your code is failing to create an orthogonal basis. I have a
really small example put together
      /-O0
     |
     |          /-O1
-y0------| |
| | /-O8
| | /y7------|
| | | -O9
\y1------| /y5------|
| | | /-O6
| | \y8------|
| /y3------| -O7
| | |
| | | /-O4
\y2------| \y6------|
| -O5
|
| /-O2
\y4------|
-O3

Will lead to the following
      O0        O1        O2        O3        O4        O5        O8        O9        O6        O7
y0 0.037280 0.106969 0.106969 0.106969 0.106969 0.106969 0.106969 0.106969 0.106969 0.106969
y1 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000
y2 0.096245 0.037491 0.108283 0.108283 0.108283 0.108283 0.108283 0.108283 0.108283 0.108283
y3 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000
y4 0.094502 0.094502 0.077053 0.077053 0.077053 0.077053 0.077053 0.077053 0.174338 0.174338
y5 0.094700 0.094700 0.070955 0.070955 0.070955 0.070955 0.168691 0.168691 0.094700 0.094700
y6 0.095046 0.095046 0.095046 0.095046 0.095046 0.095046 0.095046 0.095046 0.046864 0.192765
y7 0.095143 0.095143 0.057707 0.057707 0.156864 0.156864 0.095143 0.095143 0.095143 0.095143
y8 0.095046 0.095046 0.095046 0.095046 0.095046 0.095046 0.046864 0.192765 0.095046 0.095046

You can view, comment on, or merge this pull request online at:

#1
Commit Summary

PERF: more direct use of numpy

Adding license

Merge pull request Adding license biocore/gneiss#9 from mortonjt/license.txt

Last touches before release

Merge pull request Last touches before release biocore/gneiss#10 from mortonjt/license.txt

ENH: Adding util functions

STY: pep8

STY: Flake8 to the rescue

STY: Addressing @antgonza and @josenavas comments

STY: pep8 flake8

GPL license

Adding changelog

Merge pull request GPL license biocore/gneiss#13 from mortonjt/license.txt

DOC: Changing method name

STY: clean up pep8/flake8

Merge branch 'master' of https://github.com/biocore/gneiss into util

DOC: Updating changelog

ENH: Adding in niche sorting algorithm

TST: Adding in length and nan tests

DOC: typo

ENH: Adding inplace option

STY: Code dereplication

DOC: cleaning up docstrings

pep8

Merge pull request Util biocore/gneiss#12 from mortonjt/util

Merge branch 'master' of https://github.com/biocore/gneiss into
nichesort

FIX: Fixing ordering

pep8

Adding @josenavas and @antgonza comments

TST: Adding callable error

DOC: Adding raises section

DOC: Clarifying formulat in mean_niche_estimator

DOC: Correcting formula

Merge pull request Nichesort biocore/gneiss#16 from mortonjt/nichesort

Updating changelog

Merge pull request Updating changelog biocore/gneiss#19 from mortonjt/nichesort

Typo in ipython notebook

Fixing typo in ipython notebook

Adding another test

Merge branch 'master' of https://github.com/biocore/gneiss into
perf_tweaks

Adding additional test cases

File Changes

A CHANGELOG.md
https://github.com/wasade/gneiss/pull/1/files#diff-0 (10)

A COPYING.txt
https://github.com/wasade/gneiss/pull/1/files#diff-1 (674)

M gneiss/init.py
https://github.com/wasade/gneiss/pull/1/files#diff-2 (4)

M gneiss/balances.py
https://github.com/wasade/gneiss/pull/1/files#diff-3 (134)

M gneiss/layouts.py
https://github.com/wasade/gneiss/pull/1/files#diff-4 (8)

A gneiss/sort.py
https://github.com/wasade/gneiss/pull/1/files#diff-5 (116)

A gneiss/tests/data/large_tree2.nwk
https://github.com/wasade/gneiss/pull/1/files#diff-6 (1)

A gneiss/tests/data/small_tree.nwk
https://github.com/wasade/gneiss/pull/1/files#diff-7 (1)

M gneiss/tests/test_balances.py
https://github.com/wasade/gneiss/pull/1/files#diff-8 (64)

A gneiss/tests/test_sort.py
https://github.com/wasade/gneiss/pull/1/files#diff-9 (178)

A gneiss/tests/test_util.py
https://github.com/wasade/gneiss/pull/1/files#diff-10 (313)

A gneiss/util.py
https://github.com/wasade/gneiss/pull/1/files#diff-11 (162)

M ipynb/balance_trees.ipynb
https://github.com/wasade/gneiss/pull/1/files#diff-12 (2)

M setup.py https://github.com/wasade/gneiss/pull/1/files#diff-13
(6)

Patch Links:

https://github.com/wasade/gneiss/pull/1.patch

https://github.com/wasade/gneiss/pull/1.diff

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#1, or mute the thread
https://github.com/notifications/unsubscribe-auth/AAc8spwrBjh1D09ZZ0in9J7SjRjV9E5kks5qcjIJgaJpZM4Jc_1R
.

mortonjt · 2016-08-04T19:07:00Z

Meant to do it against your fork ...

wasade and others added 30 commits July 10, 2016 20:48

PERF: more direct use of numpy

23ad7ae

Adding license

2a5d4fe

Merge pull request #9 from mortonjt/license.txt

2721bf4

Adding license

Last touches before release

b979d41

Merge pull request #10 from mortonjt/license.txt

1be0fe7

Last touches before release

ENH: Adding util functions

362fe9e

Correcting documentation in setup.py

STY: pep8

a1b9cef

STY: Flake8 to the rescue

2908c93

STY: Addressing @antgonza and @josenavas comments

e2e2e63

Adding tests for duplicate ids, updating documentation. Adding headers for copyright

STY: pep8 flake8

d6a037b

GPL license

38b64c8

Adding changelog

1cbc6ad

Merge pull request biocore#13 from mortonjt/license.txt

f79d9a6

GPL license

DOC: Changing method name

d197605

Adding some mutability tests Adding warning about replacing internal node names

STY: clean up pep8/flake8

2ded931

Merge branch 'master' of https://github.com/biocore/gneiss into util

a54d051

DOC: Updating changelog

477d196

ENH: Adding in niche sorting algorithm

e0c7505

TST: Adding in length and nan tests

3d9ded6

DOC: typo

4c8d41d

ENH: Adding inplace option

371cc16

STY: Code dereplication

6d70cf9

DOC: cleaning up docstrings

9003db8

pep8

b049ced

Merge pull request biocore#12 from mortonjt/util

ff3df22

Util

Merge branch 'master' of https://github.com/biocore/gneiss into niche…

0ed7267

…sort

FIX: Fixing ordering

ac1832d

pep8

42221f5

Adding @josenavas and @antgonza comments

23acedf

TST: Adding callable error

940d7e8

mortonjt and others added 11 commits July 27, 2016 14:10

DOC: Adding raises section

7ee169c

DOC: Clarifying formulat in mean_niche_estimator

0168b42

DOC: Correcting formula

c9e2373

Merge pull request biocore#16 from mortonjt/nichesort

8f2d1a7

Nichesort

Updating changelog

c51b215

Adding in link

Merge pull request biocore#19 from mortonjt/nichesort

22cbcc3

Updating changelog

Typo in ipython notebook

6a247a7

Fixing typo in ipython notebook

f13954d

Adding another test

452d62c

Merge branch 'master' of https://github.com/biocore/gneiss into perf_…

ecc88d2

…tweaks

Adding additional test cases

475b96f

mortonjt closed this Aug 4, 2016

mortonjt mentioned this pull request Aug 4, 2016

Perf tweaks #2

Closed

mortonjt deleted the perf_tweaks branch April 6, 2017 11:43

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Perf tweaks #1

Perf tweaks #1

mortonjt commented Aug 4, 2016 •

edited

Loading

wasade commented Aug 4, 2016

mortonjt commented Aug 4, 2016

Perf tweaks #1

Perf tweaks #1

Conversation

mortonjt commented Aug 4, 2016 • edited Loading

wasade commented Aug 4, 2016

mortonjt commented Aug 4, 2016

mortonjt commented Aug 4, 2016 •

edited

Loading