Develop #1243

WardDeb · 2023-08-28T13:04:41Z

dependencies and metadata are defined in the toml file (setup.py & requirements deprecated)
scripts / entrypoints are defined here as well (bin folder deprecated)
wheels are built with setuptools / toml file now (python >= 3.7)
deeptools' version is defined in the toml file as well (no more _version.py, keep importlib as a requirement until we drop python 3.7 support). --version flags have been changed to use importlib in all executables.
usage standardized per executable
matplotlib version pin has been removed, some changes in the cm.py for newer version.
nosetests are deprecated and ported to pytests
pytests now run on proposed wheel with version 3.7 - 3.11
dependency on the custom typescript action (https://github.com/deeptools/github-actions) has been deprecated in favor of micromamba/python/miniconda-setup actions
planemo tests and pytests use conda environment(.github/test_and_build.yml), historical 'foo' name is dropped.
planemo tests expected pngs are slightly changed (due to mpl updates) expected qual metrics in plotfingerprint changed, not 100% where exactly the rounding difference comes from
planemo tests run on galaxy 23.1
stricter label checks and validator in galaxy wrapper
deprecation of np types for builtin types

Bumps [requests](https://github.com/psf/requests) from 2.27.1 to 2.31.0. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.27.1...v2.31.0) --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>

Keeping branches in sync

Bumps [scipy](https://github.com/scipy/scipy) from 1.8.0 to 1.10.0. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.8.0...v1.10.0) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>

Bumps [pygments](https://github.com/pygments/pygments) from 2.12.0 to 2.15.0. - [Release notes](https://github.com/pygments/pygments/releases) - [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES) - [Commits](pygments/pygments@2.12.0...2.15.0) --- updated-dependencies: - dependency-name: pygments dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>

Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.12.7 to 2023.7.22. - [Commits](certifi/python-certifi@2022.12.07...2023.07.22) --- updated-dependencies: - dependency-name: certifi dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>

Bump certifi from 2022.12.7 to 2023.7.22

Bump pygments from 2.12.0 to 2.15.0

Bump scipy from 1.8.0 to 1.10.0

stricter label checks

Bump requests from 2.27.1 to 2.31.0

np.{type} to {type}

Co-authored-by: Björn Grüning <[email protected]>

…re restriction

toml install / requirements version boost

update galaxy version & tool version in galaxy xml

round getJSDcommon to 16 decimals

JSD round to 15 decimals

The profile version does not need to be the latest Galaxy version. It specifies the latest version in which those tools will work. So it would be better to keep it a bit lower. Otherwise, older Galaxy instances can not install this tool.

bgruening

Ship it! Thanks a lot.

dependabot bot and others added 30 commits May 23, 2023 03:56

stricter label checks

6fcb275

add validator

9d75226

add validator

252920b

Merge pull request #1230 from deeptools/master

8e7be7e

Keeping branches in sync

np.{type} to {type}

b7f0ac6

Merge pull request #1237 from deeptools/dependabot/pip/certifi-2023.7.22

ddfc6ff

Bump certifi from 2022.12.7 to 2023.7.22

Merge pull request #1234 from deeptools/dependabot/pip/pygments-2.15.0

509c0bc

Bump pygments from 2.12.0 to 2.15.0

Merge pull request #1232 from deeptools/dependabot/pip/scipy-1.10.0

e9fedc7

Bump scipy from 1.8.0 to 1.10.0

Merge pull request #1227 from deeptools/label_check

47c0c57

stricter label checks

Merge pull request #1216 from deeptools/dependabot/pip/requests-2.31.0

8009bb4

Bump requests from 2.27.1 to 2.31.0

float64 to float

5e9603e

Merge pull request #1235 from ggraham/np_types

2034250

np.{type} to {type}

bin execs replaced by toml scripts

4826ebd

replace version check for tests with toml version definition

0c609de

remove _version file

288ba70

version checks with importlib

fb0a242

version check docs update to importlib

45dea00

purge reqs & setup.py

6ca54b0

init toml

c986db9

update cm for mpl > 3.7

ce327bc

port nosetests to pytest

6352657

escape sysargv check in case of pytests

2e7e4ac

deprecate nosetest in favor of pytest

4b8d38c

rollback heatmapperr imgs test until later

2cc7977

flake8

df18b1d

add conda env for workflows

4294a3b

WardDeb and others added 28 commits August 21, 2023 15:23

rollback galaxy again

6b4ad36

update installation instructions doc

f0ad1f0

qual metrics 14

e5a051d

usage and -h for all executables

d7543b1

flakes

3a5279c

switch pytest to -v

fff9904

switch pytest to -v in init build as well

ac43356

Update .github/workflows/planemo.yml

70c8274

Co-authored-by: Björn Grüning <[email protected]>

python >=3.7, combine env/planemo envs, planemo test galaxy 23.1

8d3c964

force conda prefix to micromamba env dir on runner

b0496a7

include pytests for 3.11

558442d

bring back no dependency resolution planemo

ad57435

parse toml for tool tests + verify version

8df4889

fstring tests

bfda737

1 env for test/builds, pip planemo, python min version 3.7, drop allu…

21d1326

…re restriction

setup-miniconda runner instead of micromamba for planemo test

c238997

print planemo version in shell runner

b80278a

flake fixes tests

5d00cb5

drop channelprio / planemo fingerprint back to 13 (again)

04b7a67

update changelog

ba71cbe

Merge pull request #1242 from WardDeb/pyproject

3f8010c

toml install / requirements version boost

update galaxy version & tool version in galaxy xml

f536776

Merge pull request #1245 from WardDeb/galaxy_wrapper_version

b43621a

update galaxy version & tool version in galaxy xml

round getJSDcommon to 16 decimals, attempt to fix planemo test

816033d

Merge pull request #1246 from WardDeb/plotFP_nd

ce053ac

round getJSDcommon to 16 decimals

JSD round to 15 decimals

2402f0e

Merge pull request #1247 from WardDeb/plotFP_nd

96b2da1

JSD round to 15 decimals

decrease galaxy profile version

292b492

The profile version does not need to be the latest Galaxy version. It specifies the latest version in which those tools will work. So it would be better to keep it a bit lower. Otherwise, older Galaxy instances can not install this tool.

bgruening approved these changes Aug 28, 2023

View reviewed changes

WardDeb merged commit 83f1929 into master Aug 29, 2023
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Develop #1243

Develop #1243

WardDeb commented Aug 28, 2023

bgruening left a comment

Develop #1243

Develop #1243

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