[averissimo]

Pull request

Update dev branch with latest development in main

[Copilot]

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[Copilot]

🟡 Changes recommended

Cypress 16 is incompatible with the workflow’s Node 20 runtime, and the new setup and manual-update workflows contain blocking errors.

12 open findings

• Dependency setup assumes missing root DESCRIPTION and renv.lock · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Cypress 16 requires Node 22, but workflow selects Node 20 · New
• Use standard product name capitalization · New
• Manual update selects incompatible Bash-only commit step · New

What changed in this PR

Synchronizes dev with recent deployment, dependency, testing, and documentation changes from main.

Changes:

• Upgrades Cypress dependencies and standardizes browser/timeouts.
• Revises channel-aware renv dependency handling.
• Updates contributor documentation and Copilot agent setup.

File	Description
safety/​tests/​package.json	Upgrades test dependencies.
safety/​tests/​package-lock.json	Locks upgraded dependencies.
safety/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
safety/​tests/​cypress.config.js	Defaults to Chrome.
RNA-seq/​tests/​package.json	Upgrades test dependencies.
RNA-seq/​tests/​package-lock.json	Locks upgraded dependencies.
RNA-seq/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
RNA-seq/​tests/​cypress.config.js	Defaults to Chrome.
README.md	Updates deployment documentation.
patient-profile/​tests/​package.json	Upgrades test dependencies.
patient-profile/​tests/​package-lock.json	Locks upgraded dependencies.
patient-profile/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
patient-profile/​tests/​cypress.config.js	Defaults to Chrome.
longitudinal/​tests/​package.json	Upgrades test dependencies.
longitudinal/​tests/​package-lock.json	Locks upgraded dependencies.
longitudinal/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
longitudinal/​tests/​cypress/​e2e/​app.cy.js	Extends tab discovery timeout.
longitudinal/​tests/​cypress.config.js	Defaults to Chrome.
exploratory/​tests/​package.json	Upgrades test dependencies.
exploratory/​tests/​package-lock.json	Locks upgraded dependencies.
exploratory/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
exploratory/​tests/​cypress.config.js	Defaults to Chrome.
efficacy/​tests/​package.json	Upgrades test dependencies.
efficacy/​tests/​package-lock.json	Locks upgraded dependencies.
efficacy/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
efficacy/​tests/​cypress.config.js	Defaults to Chrome.
delayed-data/​tests/​package.json	Upgrades test dependencies.
delayed-data/​tests/​package-lock.json	Locks upgraded dependencies.
delayed-data/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
delayed-data/​tests/​cypress.config.js	Defaults to Chrome.
custom-transform/​tests/​package.json	Upgrades test dependencies.
custom-transform/​tests/​package-lock.json	Locks upgraded dependencies.
custom-transform/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
custom-transform/​tests/​cypress.config.js	Defaults to Chrome.
basic-teal/​tests/​package.json	Upgrades Cypress.
basic-teal/​tests/​package-lock.json	Locks upgraded Cypress dependencies.
basic-teal/​tests/​cypress/​support/​commands.js	Reduces stability timeout.
basic-teal/​tests/​cypress.config.js	Defaults to Chrome.
.github/​workflows/​deploy.yml	Revises channel-specific dependency recording.
.github/​workflows/​copilot-setup-steps.yml	Adds Copilot R environment setup.

Files not reviewed (9)

• RNA-seq/tests/package-lock.json: Generated file
• basic-teal/tests/package-lock.json: Generated file
• custom-transform/tests/package-lock.json: Generated file
• delayed-data/tests/package-lock.json: Generated file
• efficacy/tests/package-lock.json: Generated file
• exploratory/tests/package-lock.json: Generated file
• longitudinal/tests/package-lock.json: Generated file
• patient-profile/tests/package-lock.json: Generated file
• safety/tests/package-lock.json: Generated file

🧠 Review effort: Balanced

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[llrs-roche]

When I compare update_main with dev I see more changes. Probably because dev already was using teal.picks.

I noticed the **/tests/cypress/support/commands.js have now a shorter timeout, I would have expected the opposite, specially since app.cy.js increase of timeout.