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Added build-nightly_13.yml#3444

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Yuri05 merged 2 commits intoOpen-Systems-Pharmacology:developfrom
Yuri05:build_v13
Mar 16, 2026
Merged

Added build-nightly_13.yml#3444
Yuri05 merged 2 commits intoOpen-Systems-Pharmacology:developfrom
Yuri05:build_v13

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@Yuri05 Yuri05 commented Mar 12, 2026

Description

  • Added build-nightly_13.yml (currently can be run only on_dispatch; will be run on schedule once V13 branch becomes develop)
  • Upgraded used "standard" GHA (checkout, upload-artifact) to the latest versions

Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.

Type of change

Please mark relevant options with an x in the brackets.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • This change requires documentation changes (link at least one user or developer documentation issue):
  • Algorithm update - updates algorithm documentation/questions/answers etc.
  • Other (please describe):

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

  • Integration tests
  • Unit tests
  • Manual tests
  • No tests required

Reviewer checklist

Mark everything that needs to be checked before merging the PR.

  • Check if the code is well documented
  • Check if the behavior is what is expected
  • Check if the code is well tested
  • Check if the code is readable and well formatted
  • Additional checks (document below if any)
  • Check if documentation update issue(s) are created if the option This change requires a documentation update above is selected

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Questions (if appropriate):

Summary by CodeRabbit

  • Chores
    • Updated GitHub Actions to use latest versions for improved compatibility and reliability in build workflows.
    • Added new build pipeline for version 13.0 with branch validation to ensure builds run from the correct source.

Upgraded used GHA to the latest versions
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coderabbitai bot commented Mar 12, 2026

📝 Walkthrough

Walkthrough

GitHub Actions workflow files updated across three configurations: version upgrades applied to checkout (v4→v6) and upload-artifact (v4→v7) actions in existing nightly and coverage workflows, plus a new nightly workflow added for version 13.0 with branch validation.

Changes

Cohort / File(s) Summary
GitHub Actions Version Upgrades
.github/workflows/build-nightly_12.3.yml, .github/workflows/coverage.yml
Updated GitHub Actions versions: actions/checkout@v4 upgraded to @v6, and actions/upload-artifact@v4 upgraded to @v7 in the nightly workflow.
New Version 13.0 Workflow
.github/workflows/build-nightly_v13.yml
New nightly workflow added for version 13.0 with manual trigger (workflow_dispatch). Includes branch validation step that enforces execution from the V13 branch, failing with an error message if run from other branches.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 Workflows dance in GitHub's light,
Actions upgraded to v6, so right!
V13 joins the nightly spree,
Branch guards keep the pipeline free!
CI/CD hops along with glee!

🚥 Pre-merge checks | ✅ 2
✅ Passed checks (2 passed)
Check name Status Explanation
Description Check ✅ Passed Check skipped - CodeRabbit’s high-level summary is enabled.
Title check ✅ Passed The title mentions adding build-nightly_13.yml, which is the primary change, but overlooks the equally significant upgrades to GitHub Actions versions in two existing workflows.

✏️ Tip: You can configure your own custom pre-merge checks in the settings.

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🧹 Nitpick comments (1)
.github/workflows/build-nightly_13.yml (1)

36-36: Deprecated bash arithmetic syntax in commented code.

The $[...] syntax is deprecated in modern bash. When this code is uncommented, consider using $((...)) instead for arithmetic expansion.

-#          timespan=$[now - commit]
+#          timespan=$((now - commit))

Note: The same deprecated syntax exists in build-nightly_12.3.yml at line 35 and could be fixed there as well.

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In @.github/workflows/build-nightly_13.yml at line 36, The commented arithmetic
assignment timespan=$[now - commit] uses deprecated $[...] syntax; update the
comment to use POSIX-friendly arithmetic expansion by replacing the deprecated
form with $((now - commit)) wherever it appears (including the similar
occurrence in build-nightly_12.3.yml) so that when uncommented it will work in
modern bash.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In @.github/workflows/build-nightly_13.yml:
- Line 36: The commented arithmetic assignment timespan=$[now - commit] uses
deprecated $[...] syntax; update the comment to use POSIX-friendly arithmetic
expansion by replacing the deprecated form with $((now - commit)) wherever it
appears (including the similar occurrence in build-nightly_12.3.yml) so that
when uncommented it will work in modern bash.

ℹ️ Review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: f0eb4b11-7d9d-46fb-aa61-626ac9e377ae

📥 Commits

Reviewing files that changed from the base of the PR and between 0a83906 and f363fb2.

📒 Files selected for processing (3)
  • .github/workflows/build-nightly_12.3.yml
  • .github/workflows/build-nightly_13.yml
  • .github/workflows/coverage.yml

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assuming the code in 13 is the same as in 12.3 except version

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🧹 Nitpick comments (1)
.github/workflows/build-nightly_v13.yml (1)

11-20: Consider using an environment variable for safer shell interpolation.

While the current implementation works correctly, directly interpolating ${{ github.ref_name }} into the shell script could be fragile if branch names ever contain special characters. Using an environment variable is a more robust pattern.

♻️ Suggested improvement
 jobs:
   check-branch:
     runs-on: ubuntu-latest
     steps:
     - name: Validate source branch
+      env:
+        BRANCH_NAME: ${{ github.ref_name }}
       run: |
-        if [ "${{ github.ref_name }}" != "V13" ]; then
+        if [ "$BRANCH_NAME" != "V13" ]; then
           echo "::error::Please call the workflow from the V13 branch"
           exit 1
         fi
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In @.github/workflows/build-nightly_v13.yml around lines 11 - 20, The step
"Validate source branch" in job check-branch currently interpolates ${{
github.ref_name }} directly into the shell; instead set an environment variable
(e.g., REF_NAME) from ${{ github.ref_name }} at the job or step level and
reference that in the run script using a quoted shell variable ("$REF_NAME") to
avoid word-splitting or special-character issues; update the run block in the
"Validate source branch" step to use the env var and ensure comparisons use the
quoted variable.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In @.github/workflows/build-nightly_v13.yml:
- Around line 11-20: The step "Validate source branch" in job check-branch
currently interpolates ${{ github.ref_name }} directly into the shell; instead
set an environment variable (e.g., REF_NAME) from ${{ github.ref_name }} at the
job or step level and reference that in the run script using a quoted shell
variable ("$REF_NAME") to avoid word-splitting or special-character issues;
update the run block in the "Validate source branch" step to use the env var and
ensure comparisons use the quoted variable.

ℹ️ Review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 28cfc06d-a931-4243-a51f-ac7b78ecc713

📥 Commits

Reviewing files that changed from the base of the PR and between f363fb2 and 489feba.

📒 Files selected for processing (1)
  • .github/workflows/build-nightly_v13.yml

@Yuri05
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Yuri05 commented Mar 12, 2026

assuming the code in 13 is the same as in 12.3 except version

Actually we don't need to do anything in build-nightly_v13.yml on the develop branch (except for the branch check).
The workflow should be only started from V13 branch (where it already exists)

@Yuri05 Yuri05 requested a review from msevestre March 12, 2026 14:45
@Yuri05 Yuri05 merged commit d3e4114 into Open-Systems-Pharmacology:develop Mar 16, 2026
6 checks passed
@Yuri05 Yuri05 deleted the build_v13 branch March 16, 2026 13:21
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3 participants