v3.0.1: Add JI method to test similarity of outputs; Sphinx documentations; Dependencies adjustment #619

taoliu · 2024-02-16T17:54:32Z

Add JI method to test similarity of outputs
Sphinx documentations
Dependencies adjustment

…acluate jaccard index of two peak files; use the new jaccard.py script to check if two peak files are similar

Doc/macs3/sphinx migration -> test_peak_overlap

…s3-project/MACS into feat/macs3/test_peak_overlap

…phinx rtd theme.

… create archive of hmmratac results through github actions

…ck of the scipy version

philippadoherty

code looks good, per our discussion we'll update workflows for releases to pypi and conda in the future

… because it took too long to finish. we only keep aarch64 or arm v8 in the standard non-x86 test

taoliu and others added 30 commits February 12, 2024 15:50

add function in Region.py to find intersection;made a jaccard.py to c…

fca1328

…acluate jaccard index of two peak files; use the new jaccard.py script to check if two peak files are similar

now can check empty files

285ac07

fix a bug in jaccard.py; update ChangeLog

261997f

test numpy==1.24

1d09e70

test numpy==1.25

0df3274

test numpy 1.25 w/o py 3.12

c94311f

numpy 1.25 py 3.11

0828ba4

numpy 1.24 w/o py 3.12

1cd6f00

numpy 1.25 w/o py 3.12

1ba9ad0

change non x64 py version to 3.11, numpy 1.24

1d1e7bd

test non x64, numpy 1.25

523246e

test nonx64 with py 3.11, numpy 1.24

1d7468b

test nonx64

c2979e8

try debian bookworm

4e8f5ce

try ubuntu-22.04

77d51e3

try again ubuntu22.04

859ec85

try again ubuntu22.04

7baa3b9

update docs to work with Sphinx

593e22a

update build-and-test website workflow with Sphinx

ef04fb3

Merge pull request #618 from macs3-project/doc/macs3/sphinx_migration

261408e

Doc/macs3/sphinx migration -> test_peak_overlap

try simpler pip install via requirements.txt

338b81c

Merge branch 'feat/macs3/test_peak_overlap' of https://github.com/mac…

6053b13

…s3-project/MACS into feat/macs3/test_peak_overlap

try alt pip install

5b04181

try pip install

ceb375c

define venv w/o py version, pip install

97b1c52

retry

1f6f34a

retry

e984754

limit scikit-learn version so numpy won't be upgraded too high. Add s…

d7c044d

…phinx rtd theme.

update pyproject

5bf482e

add sphinx rtd theme

e01ee2f

taoliu added 25 commits February 14, 2024 23:17

mac os13 only

08bb626

do not archive testing results

b7a06d2

let numpy>=1.24

43c1f60

add ninja/meson to non-x64 tests. upgrade versions of github actions.

66b7958

we will run hmmratac on non-x86 but not check the results;and we will…

82a3d23

… create archive of hmmratac results through github actions

correct archive filenames

d2008c1

correct the numbering of testing steps in cmdlinetest

5477cc3

add tests for python3.12; update INSTALL.md

2900b79

fix build-test-website action

f269770

correct hmmratc commandlines in cmdlinetest-nohmmratac

29e2b68

update github actions;fix macosx tests to use different python versions

6585154

update md

ab61c70

fix version of upload-pages-artifact action

ce2c8b0

fix version of upload-pages-artifact action

caa7119

fix cmdlinetest-nohmmratac script

f9761e5

add scipy as dependency -- hmmlearn needs it, so that we can keep tra…

735007a

…ck of the scipy version

apt install cmake

18ba351

apt install libopenblas-dev

583b5df

apt install pkg-config

fe64372

return to pip default behavior to see if the results can be reproduced

e0bae57

return to pip default behavior to see if the results can be reproduced

0649575

let require scikit-learn >=1.2.

4613cf6

Merge branch 'master' into feat/macs3/test_peak_overlap

5007f06

turn back on non-x86 test for hmmratac results

46b9a2f

update documentations

014e996

taoliu requested a review from philippadoherty February 16, 2024 18:01

adjust the triggers for publish-to-* actions

2a4df94

philippadoherty reviewed Feb 16, 2024

View reviewed changes

make testing for armv7/ppc64le/s390x on-demmand in master branch only…

c4e687e

… because it took too long to finish. we only keep aarch64 or arm v8 in the standard non-x86 test

taoliu merged commit ab5e3e3 into master Feb 16, 2024
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v3.0.1: Add JI method to test similarity of outputs; Sphinx documentations; Dependencies adjustment #619

v3.0.1: Add JI method to test similarity of outputs; Sphinx documentations; Dependencies adjustment #619

taoliu commented Feb 16, 2024

philippadoherty left a comment

v3.0.1: Add JI method to test similarity of outputs; Sphinx documentations; Dependencies adjustment #619

v3.0.1: Add JI method to test similarity of outputs; Sphinx documentations; Dependencies adjustment #619

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taoliu commented Feb 16, 2024

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