Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Set pdiff as nf-test differ in Docker image for Gitpod #2642

Merged
merged 3 commits into from
Jan 8, 2024
Merged

Set pdiff as nf-test differ in Docker image for Gitpod #2642

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
2f3e38f
set pdiff is nf-test differ in docker image for gitpod
mashehu Jan 8, 2024
f54f1f0
[automated] Update CHANGELOG.md [no ci]
nf-core-bot Jan 8, 2024
22613c5
update changelog [no ci]
mashehu Jan 8, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 0 additions & 5 deletions .gitpod.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,6 @@ tasks:
command: |
unset JAVA_TOOL_OPTIONS

- name: Use pdiff for nf-test diff viewing
command: |
export NFT_DIFF="pdiff"
export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"

vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
Expand Down
2 changes: 1 addition & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@
### Template

- Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
- Use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640))

### Download

Expand All @@ -22,6 +21,7 @@
- Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([#2630](https://github.com/nf-core/tools/pull/2630))
- Update mshick/add-pr-comment action to v2 ([#2632](https://github.com/nf-core/tools/pull/2632))
- update python image version in docker file ([#2636](https://github.com/nf-core/tools/pull/2636))
- Set pdiff as nf-test differ in Docker image for Gitpod ([#2642](https://github.com/nf-core/tools/pull/2642))

# [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]

Expand Down
6 changes: 5 additions & 1 deletion nf_core/gitpod/gitpod.Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62,4 +62,8 @@ RUN conda config --add channels defaults && \
RUN nextflow self-update

# Install nf-core
RUN python -m pip install .
RUN python -m pip install . --no-cache-dir

# Setup pdiff for nf-test diffs
RUN export NFT_DIFF="pdiff" && \
export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
5 changes: 1 addition & 4 deletions nf_core/pipeline-template/.gitpod.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,7 @@ tasks:
- name: unset JAVA_TOOL_OPTIONS
command: |
unset JAVA_TOOL_OPTIONS
- name: Use pdiff for nf-test diff viewing
command: |
export NFT_DIFF="pdiff"
export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"

vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
Expand Down