From d7937673fb6d72a3ce3e2a374d95468ac0bfd0ce Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 18 Feb 2025 22:33:22 +0100 Subject: [PATCH 1/4] Missed gitpod file paths --- docs/nextflow_run/01_orientation.md | 2 +- docs/nf4_science/genomics/00_orientation.md | 2 +- docs/side_quests/orientation.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/nextflow_run/01_orientation.md b/docs/nextflow_run/01_orientation.md index d731b92d4..1be4247f1 100644 --- a/docs/nextflow_run/01_orientation.md +++ b/docs/nextflow_run/01_orientation.md @@ -40,7 +40,7 @@ If you run this inside `run-nextflow`, you should see the following output: [TOD If for whatever reason you move out of this directory, you can always run this command to return to it: ```bash - cd /workspace/gitpod/run-nextflow + cd /workspaces/training/run-nextflow ``` Now, to begin the course, click on the arrow in the bottom right corner of this page. diff --git a/docs/nf4_science/genomics/00_orientation.md b/docs/nf4_science/genomics/00_orientation.md index 2d05f7379..deab50ad3 100644 --- a/docs/nf4_science/genomics/00_orientation.md +++ b/docs/nf4_science/genomics/00_orientation.md @@ -65,7 +65,7 @@ _Completed workflows (solutions) will be added in the near future._ If for whatever reason you move out of this directory, you can always run this command to return to it: ```bash - cd /workspace/gitpod/nf4-science/genomics + cd /workspaces/training/nf4-science/genomics ``` Now, to begin the course, click on the arrow in the bottom right corner of this page. diff --git a/docs/side_quests/orientation.md b/docs/side_quests/orientation.md index a867a338a..56762be3e 100644 --- a/docs/side_quests/orientation.md +++ b/docs/side_quests/orientation.md @@ -40,7 +40,7 @@ If you run this inside `tapas`, you should see the following output: [TODO] If for whatever reason you move out of this directory, you can always run this command to return to it: ```bash - cd /workspace/gitpod/tapas + cd /workspaces/training/tapas ``` Now, to begin the course, click on the arrow in the bottom right corner of this page. From 9222c575ba6de71a3e209b16c489f7a6bcf7bede Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 18 Feb 2025 22:33:46 +0100 Subject: [PATCH 2/4] Delete Gitpod config files --- .gitpod.yml | 52 ---------------------------------------- gitpod-ws.code-workspace | 46 ----------------------------------- 2 files changed, 98 deletions(-) delete mode 100644 .gitpod.yml delete mode 100644 gitpod-ws.code-workspace diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index da79e25ce..000000000 --- a/.gitpod.yml +++ /dev/null @@ -1,52 +0,0 @@ -workspaceLocation: gitpod/gitpod-ws.code-workspace -checkoutLocation: gitpod - -github: - prebuilds: - # enable for the master/default branch (defaults to true) - master: true - # enable for all branches in this repo (defaults to false) - branches: false - # enable for pull requests coming from this repo (defaults to true) - pullRequests: true - # enable for pull requests coming from forks (defaults to false) - pullRequestsFromForks: true - # add a "Review in Gitpod" button as a comment to pull requests (defaults to true) - addComment: true - # add a "Review in Gitpod" button to pull requests (defaults to false) - addBadge: false - -# See .github/Dockerfile -image: ghcr.io/nextflow-io/training:latest - -tasks: - - before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit - - - name: Start web server - command: gp ports await 23000 && gp preview https://training.nextflow.io/hello_nextflow - - - name: Load Nextflow Tutorial - command: docker pull -q nextflow/rnaseq-nf - - - name: Start Nextflow Tutorial - env: - NXF_HOME: "/workspace/gitpod/.nextflow" - command: | - cd hello-nextflow - source $HOME/.bashrc - export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] ' - unset JAVA_TOOL_OPTIONS - clear - -vscode: - extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - - cssho.vscode-svgviewer # SVG viewer - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - # - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - - nextflow.nextflow # Nextflow syntax highlighting - # - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - ms-vscode.live-server diff --git a/gitpod-ws.code-workspace b/gitpod-ws.code-workspace deleted file mode 100644 index f6865101f..000000000 --- a/gitpod-ws.code-workspace +++ /dev/null @@ -1,46 +0,0 @@ -{ - "folders": [ - { "path": "./hello-nextflow" }, - { "path": "./nf4-science" }, - { "path": "./nf-training" }, - { "path": "./nf-training-advanced" }, - ], - "settings": { - "typescript.tsdk": "gitpod/node_modules/typescript/lib", - "[javascript]": { - "editor.defaultFormatter": "esbenp.prettier-vscode", - "editor.formatOnSave": true, - }, - "[typescript]": { - "editor.defaultFormatter": "esbenp.prettier-vscode", - "editor.formatOnSave": true, - }, - "[json]": { - "editor.insertSpaces": true, - "editor.tabSize": 2, - }, - "[yaml]": { - "editor.insertSpaces": true, - "editor.tabSize": 2, - }, - "[go]": { - "editor.formatOnSave": true, - }, - "[tf]": { - "editor.insertSpaces": true, - "editor.tabSize": 2, - }, - "go.formatTool": "goimports", - "go.useLanguageServer": true, - "workspace.supportMultiRootWorkspace": true, - "launch": {}, - "files.exclude": { - "**/.git": true, - }, - "go.lintTool": "golangci-lint", - "gopls": { - "allowModfileModifications": true, - }, - "prettier.configPath": ".prettierrc.json", - }, -} From 81aaeea9b23befcc7a2c4b999ffb569dd0302b0f Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 18 Feb 2025 22:37:08 +0100 Subject: [PATCH 3/4] Add gitpod deprecation note to envsetup, instead of docs homepage --- docs/envsetup/index.md | 12 ++++++++++++ docs/index.md | 9 --------- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/docs/envsetup/index.md b/docs/envsetup/index.md index 95c067729..6905a1e94 100644 --- a/docs/envsetup/index.md +++ b/docs/envsetup/index.md @@ -9,3 +9,15 @@ If you already have a GitHub Codespaces account, click on the button below, othe Let's get started! [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) + +For more detailed instructions for GitHub Codespaces, see the [GitHub Codespaces env-setup docs](01_setup.md). +If you cannot use GitHub Codespaces and wish to use a local development environment, see the [documentation for local installation](02_local.md). + +!!! note + + Nextflow Training used to use [Gitpod](https://gitpod.io) until February 2025. + However, the makers of Gitpod have decided to retire the free functionality in favor of their new [Gitpod Flex](https://www.gitpod.io/blog/introducing-gitpod-flex) system. + For that reason, we have switched to using GitHub Codespaces, which also offer a one-click developer environment with no prior setup. + + Depending on when you signed up to GitPod and when exactly they retire the service, you may still be able to launch the training in their old cloud IDE, though we cannot guarantee reliable access going forward: + [Open in Gitpod](https://gitpod.io/#https://github.com/nextflow-io/training). diff --git a/docs/index.md b/docs/index.md index 0015c4ba0..dfbb906a1 100644 --- a/docs/index.md +++ b/docs/index.md @@ -22,15 +22,6 @@ When you're ready to get down to work, click on the 'Open in GitHub Codespaces' [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) -!!! note - - Nextflow Training used to use [Gitpod](https://gitpod.io) until February 2025. - However, the makers of Gitpod have decided to retire the free functionality in favor of their new [Gitpod Flex](https://www.gitpod.io/blog/introducing-gitpod-flex) system. - For that reason, we have switched to using GitHub Codespaces, which also offer a one-click developer environment with no prior setup. - - Depending on when you signed up to GitPod and when exactly they retire the service, you may still be able to launch the training in their old cloud IDE, though we cannot guarantee reliable access going forward: - [Open in Gitpod](https://gitpod.io/#https://github.com/nextflow-io/training). - ## Training Environment Setup !!! exercise "Environment Setup" From 6d837fc39a4f5b3fe6073c144b6e1938e5e002ec Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 18 Feb 2025 22:56:42 +0100 Subject: [PATCH 4/4] Finetune admonitions --- docs/envsetup/index.md | 2 +- docs/index.md | 22 +++++++++++++--------- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/docs/envsetup/index.md b/docs/envsetup/index.md index 6905a1e94..c04f6dda9 100644 --- a/docs/envsetup/index.md +++ b/docs/envsetup/index.md @@ -13,7 +13,7 @@ Let's get started! For more detailed instructions for GitHub Codespaces, see the [GitHub Codespaces env-setup docs](01_setup.md). If you cannot use GitHub Codespaces and wish to use a local development environment, see the [documentation for local installation](02_local.md). -!!! note +!!! info "Deprecation of GitPod" Nextflow Training used to use [Gitpod](https://gitpod.io) until February 2025. However, the makers of Gitpod have decided to retire the free functionality in favor of their new [Gitpod Flex](https://www.gitpod.io/blog/introducing-gitpod-flex) system. diff --git a/docs/index.md b/docs/index.md index dfbb906a1..605b0cbf7 100644 --- a/docs/index.md +++ b/docs/index.md @@ -26,7 +26,7 @@ When you're ready to get down to work, click on the 'Open in GitHub Codespaces' !!! exercise "Environment Setup" - !!! quote inline end "" + !!! tip inline end "" :material-lightbulb: Set up your environment for the first time. @@ -40,7 +40,7 @@ These are foundational, domain-agnostic courses intended for those who are compl !!! exercise "Hello Nextflow" - !!! quote inline end "" + !!! tip inline end "" :material-run-fast: Learn to develop pipelines in Nextflow. @@ -48,12 +48,14 @@ These are foundational, domain-agnostic courses intended for those who are compl [Launch the Hello Nextflow training :material-arrow-right:](hello_nextflow/index.md){ .md-button .md-button--primary } -**Coming soon:** "Nextflow Run" — Learn to run Nextflow pipelines (run only, no code development) +!!! info "" + + **Coming soon:** "Nextflow Run" — Learn to run Nextflow pipelines (run only, no code development)