this is new...haven't got this in my earlier PRs ?...
# lintings
Sateesh_Peri
10/18/2024, 9:48 AMthis is new...haven't got this in my earlier PRs ?
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╭─ [✗] 1 Pipeline Test Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_unchanged: LICENSE does not match the template │
│ Copy code
nf-core pipelines lint --dir . --fix files_unchanged Copy code
INFO Testing pipeline: .
INFO Attempting to automatically fix failing tests
CRITICAL Critical error: Uncommitted changes found in pipeline directory!
Please commit these before running with '--fix'
INFO Stopping tests...
gitpod /workspace/methylseq (dev) $ git status
On branch dev
Your branch is ahead of 'origin/dev' by 1 commit.
(use "git push" to publish your local commits)m
mashehu
10/18/2024, 9:51 AMcan you run
nf-core -v pipelines lint --dir . --fix files_unchangeds
Sateesh_Peri
10/18/2024, 9:51 AM Copy code
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/workspace/methylseq, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Using config file: .nf-core.yml utils.py:1188
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Popen(['git', 'version'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Got '/home/gitpod/.config/nfcore/nf-core/modules' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json utils.py:290
DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1188
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Using config file: .nf-core.yml utils.py:1188
DEBUG The following files were modified by prettier: lint_utils.py:99
modules.json
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Registry set to <http://quay.io|quay.io> __init__.py:163
DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Got '/home/gitpod/.config/nfcore/nf-core/modules' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json utils.py:290
DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1188
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Using config file: .nf-core.yml utils.py:1188
DEBUG The following files were modified by prettier: lint_utils.py:99
modules.json
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Registry set to <http://quay.io|quay.io> __init__.py:163
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Using config file: .nf-core.yml utils.py:1188
DEBUG Got '.' as path utils.py:256
DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-4c7417c306d72b064574535d1.json utils.py:290
DEBUG Using config file: .nf-core.yml utils.py:1188
INFO Testing pipeline: . __init__.py:196
INFO Attempting to automatically fix failing tests __init__.py:228
DEBUG Popen(['git', 'diff', '--cached', '--abbrev=40', '--full-index', '--raw'], cwd=/workspace/methylseq, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'diff', '--abbrev=40', '--full-index', '--raw'], cwd=/workspace/methylseq, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'status', '--porcelain', '--untracked-files'], cwd=/workspace/methylseq, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
CRITICAL Critical error: Uncommitted changes found in pipeline directory! __init__.py:641
Please commit these before running with '--fix'
INFO Stopping tests...m
mashehu
10/18/2024, 9:52 AMcan you try
git checkout TEMPLATE -- LICENSEmashehu
10/18/2024, 9:52 AMthat should do the fix manually
s
Sateesh_Peri
10/18/2024, 9:55 AMno change i think
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gitpod /workspace/methylseq (dev) $ git checkout TEMPLATE -- LICENSE
gitpod /workspace/methylseq (dev) $ git status
On branch dev
Your branch is ahead of 'origin/dev' by 1 commit.m
mashehu
10/18/2024, 9:56 AMand you still get the linting error?
s
Sateesh_Peri
10/18/2024, 9:58 AMyes
Sateesh_Peri
10/18/2024, 9:58 AMim on tools
3.0.2m
mashehu
10/18/2024, 10:00 AMhow about
git checkout origin/TEMPLATE -- LICENSEs
Sateesh_Peri
10/18/2024, 10:02 AMsame
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gitpod /workspace/methylseq (dev) $ git checkout origin/TEMPLATE -- LICENSE
gitpod /workspace/methylseq (dev) $ git status
On branch dev
Your branch is ahead of 'origin/dev' by 1 commit.
(use "git push" to publish your local commits)
Untracked files:
(use "git add <file>..." to include in what will be committed)
samplesheet.csv
nothing added to commit but untracked files present (use "git add" to track)
gitpod /workspace/methylseq (dev) $ nf-core pipelines lint --release
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 3.0.2 - <https://nf-co.re>
INFO Testing pipeline: .
INFO Including --release mode tests
╭─ [?] 4 Pipeline Tests Ignored ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_exist: File is ignored: lib/nfcore_external_java_deps.jar │
│ files_exist: File is ignored: conf/modules.config │
│ actions_ci: actions_ci │
│ modules_config: modules_config │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 1 Pipeline Test Failed ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_unchanged: LICENSE does not match the template │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 316 Tests Passed │
│ [?] 4 Tests Ignored │
│ [!] 0 Test Warnings │
│ [✗] 1 Test Failed │
╰───────────────────────╯
Tip: Some of these linting errors can automatically be resolved with the following command:
nf-core pipelines lint --dir . --fix files_unchangedm
mashehu
10/18/2024, 10:04 AMlast resort (if @Júlia Mir doesn't find the issue) ignore them for now in the nf-core.yml
https://nf-co.re/docs/nf-core-tools/api_reference/3.0.2/pipeline_lint_tests/files_unchanged
s
Sateesh_Peri
10/18/2024, 10:05 AMhere is my fork where im seeing this - https://github.com/sateeshperi/methylseq/tree/dev
m
Maxime Garcia
10/18/2024, 10:10 AMyou need to add yourself here as well: https://github.com/sateeshperi/methylseq/blob/dev/LICENSE#L3
s
Sateesh_Peri
10/18/2024, 10:13 AMyup...relaunched gitpod and now it was able to fix
m
mashehu
10/18/2024, 10:14 AMweird...
🤷 1