Dev -> Master for v2.10 #2440

mirpedrol · 2023-09-25T11:11:29Z

PR checklist

This comment contains a description of changes (with reason)
CHANGELOG.md is updated
If you've fixed a bug or added code that should be tested, add tests!
Documentation in docs is updated

bump to 2.10dev

…flaky.

…s solution was prone to false positives and negatives.

…ne string which I abused as comment.

…w class are stateful, i.e. if the function is called without a parameter that was provided in a previous call, then it is still present.

…s happy.

params.fasta - add TODO

Remove bare URL in MD file. Plus we already have this exact link in the tool name.

Update modules in TEMPLATE

Fix link template PR message

Remove bare URL in CITATIONS.md

Update Gitpod profile to reflect environment allowance

…ainer downloads in test.

…_download Download: Fix unintentional downloading of containers in test

Bump Python 3.8 -> 3.11 for most CI tasks, plus docker base image.

Updated devcontainer.json permissions for using devcontainers in Codespaces/VS Code

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Only test min + max supported Python versions

fix subworkflow template jinja variable for subworkflow name

add bluesky automatic release anonuncement

bump to 2.10 for release

remove unwanted changes in changelog

codecov · 2023-09-25T11:54:25Z

Codecov Report

Merging #2440 (314aa0b) into master (e5ce6ce) will decrease coverage by 2.11%.
The diff coverage is 81.29%.

@@            Coverage Diff             @@
##           master    #2440      +/-   ##
==========================================
- Coverage   72.75%   70.64%   -2.11%     
==========================================
  Files          78       87       +9     
  Lines        8889     9431     +542     
==========================================
+ Hits         6467     6663     +196     
- Misses       2422     2768     +346

Files Changed	Coverage Δ
nf_core/components/components_utils.py	`48.19% <ø> (ø)`
nf_core/launch.py	`63.26% <0.00%> (ø)`
nf_core/lint/files_exist.py	`78.00% <ø> (ø)`
nf_core/modules/lint/meta_yml.py	`60.00% <ø> (ø)`
nf_core/modules/test_yml_builder.py	`50.90% <ø> (-0.46%)`	⬇️
nf_core/subworkflows/__init__.py	`100.00% <ø> (ø)`
nf_core/subworkflows/lint/__init__.py	`28.37% <ø> (ø)`
nf_core/subworkflows/lint/main_nf.py	`9.70% <ø> (ø)`
nf_core/subworkflows/lint/meta_yml.py	`10.90% <ø> (ø)`
nf_core/subworkflows/lint/subworkflow_changes.py	`30.00% <ø> (ø)`
... and 29 more

... and 1 file with indirect coverage changes

install default-jre instead of openjdk-11-jre

mirpedrol and others added 30 commits July 4, 2023 17:18

bump to 2.10dev

7e09b8f

Merge pull request #2363 from mirpedrol/bump-2.10dev

d21770d

bump to 2.10dev

Remove loop for resolution of container source priority. This is too …

56086b1

…flaky.

New helper function to prioritize direct download URLs, since previou…

60358e9

…s solution was prone to false positives and negatives.

New test allows to test specific container notations in mock modules.

d7784e3

Old DSL2 modules resolve correctly for the first time

d8fadae

Got rid of a DeprecationWarning, that was triggered due to a multi-li…

c3523c9

…ne string which I abused as comment.

Changelog changes.

60c9cef

params.fasta - add TODO

d0e11f4

I had never really realized that the functions in the DownloadWorkflo…

1ab228b

…w class are stateful, i.e. if the function is called without a parameter that was provided in a previous call, then it is still present.

Remove trailing whitespace from mock module so editorconfig-checker i…

5a6de12

…s happy.

Run prettier on CHANGELOG.

47388c3

Merge pull request #2365 from nf-core/fasta-todo

2d17961

params.fasta - add TODO

Update CITATIONS.md

c004744

Remove bare URL in MD file. Plus we already have this exact link in the tool name.

Update modules in TEMPLATE

3671081

Update main.nf

3d2aa97

Update main.nf

7f6d259

Update main.nf

2f38903

Update main.nf

8dfc0d3

add update step to release checklist

99300ba

Merge pull request #2368 from nf-core/update-modules

db33330

Update modules in TEMPLATE

Fix link to point to new website page

91a3b65

Merge pull request #2371 from nf-core/fix-link-template-pr

89167f0

Fix link template PR message

Merge pull request #2367 from nf-core/maxulysse-patch-1

f685aee

Remove bare URL in CITATIONS.md

fix multiqc_config.yml links

c50abf4

remove version from multiqc_config.yml and adapt linting accordingly

71191da

update changelog

02455fc

add the version back

c62367b

update changelog

ed4babf

Commit review suggestions by @mirpedrol.

e459c66

mahesh-panchal and others added 23 commits September 19, 2023 15:36

Merge pull request #2423 from mahesh-panchal/update_gitpod_profile

f61e523

Update Gitpod profile to reflect environment allowance

Dump pipeline parameters into a json file

3a9f229

Apply review sugestions

0a751ff

Update docs

d1d9f60

Mock DownloadWorkflow.get_singularity_images() to prevent actual cont…

535e7f9

…ainer downloads in test.

fix subworkflow template jinja variable for subworkflow name

b6488d3

Update Changelog

7592320

update changelog

b156469

Merge pull request #2425 from JoseEspinosa/dump_params

6483100

Merge pull request #2434 from MatthiasZepper/prevent_pytest_container…

4570ea4

…_download Download: Fix unintentional downloading of containers in test

bump to 2.10 for release

5ddf7e9

Merge branch 'dev' into codespaces

0338dfe

Only test min + max supported Python versions

f1fdd02

Bump Python 3.8 -> 3.11 for most CI tasks, plus docker base image.

Merge pull request #2422 from CarsonJM/codespaces

b2fdc4e

Updated devcontainer.json permissions for using devcontainers in Codespaces/VS Code

Update .github/workflows/tools-api-docs-release.yml

b05817c

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Merge pull request #2438 from ewels/update-python

aa7e69b

Only test min + max supported Python versions

Merge pull request #2435 from mirpedrol/fix-subworkflows-create-name

54d06e8

fix subworkflow template jinja variable for subworkflow name

add bluesky automatic release anonuncement

209c1ff

Merge pull request #2439 from mirpedrol/bluesky-automation

9abaacc

add bluesky automatic release anonuncement

Merge branch 'dev' into bump-2.10

dfade38

Merge pull request #2437 from mirpedrol/bump-2.10

cacef8a

bump to 2.10 for release

remove unwanted changes in changelog

9db67a3

Merge pull request #2441 from mirpedrol/changelog

5f32dd7

remove unwanted changes in changelog

mashehu approved these changes Sep 25, 2023

View reviewed changes

install default-jre instead of openjdk-11-jre

985ae1c

mirpedrol changed the title ~~DevDev -> Master for v2.10~~ Dev -> Master for v2.10 Sep 25, 2023

github-actions bot and others added 2 commits September 25, 2023 13:15

Generate new screengrabs with rich-codex

63c0006

Merge pull request #2442 from nf-core/fix-dockerfile

314aa0b

install default-jre instead of openjdk-11-jre

mirpedrol merged commit 9ab896c into master Sep 25, 2023
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Dev -> Master for v2.10 #2440

Dev -> Master for v2.10 #2440

mirpedrol commented Sep 25, 2023

codecov bot commented Sep 25, 2023 •

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Dev -> Master for v2.10 #2440

Dev -> Master for v2.10 #2440

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mirpedrol commented Sep 25, 2023

PR checklist

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Codecov Report

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