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Update README with workflow and CSV editing notes#3

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Yuri05 merged 5 commits into
Open-Systems-Pharmacology:mainfrom
rwmcintosh:main
Feb 19, 2026
Merged

Update README with workflow and CSV editing notes#3
Yuri05 merged 5 commits into
Open-Systems-Pharmacology:mainfrom
rwmcintosh:main

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@rwmcintosh

@rwmcintosh rwmcintosh commented Feb 18, 2026

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Added notes on enabling workflows and editing CSV files.

Summary by CodeRabbit

  • Documentation
    • Restructured report-creation workflows into numbered, action-focused steps for clarity.
    • Added guidance for enabling workflows on forked repositories and a note warning against editing CSVs with Excel.
    • Expanded post-report-creation guidance with explicit next steps and PR considerations.
    • Updated images with descriptive alt text and adjusted captions for improved accessibility and usability.

Added notes on enabling workflows and editing CSV files.
@coderabbitai

coderabbitai Bot commented Feb 18, 2026

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📝 Walkthrough

Walkthrough

Restructures README guidance into explicit, ordered steps for creating model evaluation and qualification reports; adds an "Enable Workflows on your forked repository" instruction, a CSV-editing warning, and alt-texted images. Replaces commented rebasing sequences in two GitHub Actions with an active "Configure git" step that sets core.longpaths to true.

Changes

Cohort / File(s) Summary
Documentation Rework
README.md
Replaced narrative/bullet guidance with numbered, action-focused workflows for model evaluation and qualification reports; added "Enable Workflows on your forked repository" bullet, decorative image block, a Notes warning about editing CSVs with Excel, alt text for images, and updated post-report instructions.
Evaluation workflow
.github/workflows/create-evaluation_reports.yml
Removed/commented rebasing block and added an explicit Configure git step that runs git config --global core.longpaths true; other steps left intact.
Qualification workflow
.github/workflows/create-qualification_reports.yml
Removed/commented rebasing block and added an explicit Configure git step that runs git config --global core.longpaths true in the qualification job; rest of workflow preserved.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

  • Initial commit #1 — Modifies the same workflow files and replaces commented rebasing steps with an active Configure git step.

Poem

🐇 I hopped through docs and lines of code,
Steps in order, down the road.
Git tweaked gently, CSVs kept neat,
Reports now run with lighter feet.
A tiny rabbit cheers — success tastes sweet! 🎉

🚥 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 accurately describes the main changes: updates to README with workflow instructions and CSV editing guidance, plus workflow file refinements.

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

✨ Finishing Touches
🧪 Generate unit tests (beta)
  • Create PR with unit tests
  • Post copyable unit tests in a comment

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Actionable comments posted: 3

🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@README.md`:
- Around line 32-33: The Qualifications section currently tells users to update
qualifications.csv and verify the "Validate qualifications.csv" GitHub Actions
check but omits the necessary step to push the branch to trigger that check;
update the wording around the qualifications.csv step to explicitly tell users
to push the new branch to their fork (e.g., "push the new branch to your fork
and verify that the check [Validate qualifications.csv] was successful") so it
matches the Model evaluation step and ensures the action runs after updating
qualifications.csv and before verifying the check.
- Line 27: The <img> tag in README.md is missing an alt attribute which breaks
accessibility; update the <img> element (the one with src
"https://github.com/user-attachments/assets/d787ddc6-db2a-47c0-ab98-82bcb0051bb4")
to include a meaningful alt="..." value (not just empty) and consider improving
the existing alt for the other image too so both provide descriptive text for
screen readers.
- Line 24: Update the broken in-page anchor references that currently use
"(`#next-step`)" to the actual generated heading ID
"(`#what-to-do-when-reports-are-created`)"; specifically change the two
occurrences of "#next-step" found near the lines referencing "Adjust the commit
message..." and the other similar line so they point to the existing heading "##
What to do when reports are created" (i.e., replace "#next-step" with
"#what-to-do-when-reports-are-created").

Comment thread README.md
Comment thread README.md Outdated
Comment thread README.md Outdated
rwmcintosh and others added 4 commits February 18, 2026 12:05
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Updated instructions to include pushing the new branch before verification.

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🧹 Nitpick comments (2)
.github/workflows/create-evaluation_reports.yml (1)

94-97: LGTM — minor placement note.

The --global scope is the right choice for an ephemeral Windows runner, and the step correctly precedes the heavy git operations (report-evaluation action and create-pull-request). The initial actions/checkout@v6 above it operates on the workflow repo itself, which is unlikely to contain >260-character paths, so the ordering is acceptable in practice.

Optionally, moving this step before the Checkout repository step would make long-path support apply to every git operation in the job without relying on that assumption:

♻️ Optional: move Configure git before Checkout
+    - name: Configure git
+      run: |
+        git config --global core.longpaths true
+      shell: bash
+
     - name: Checkout repository
       uses: actions/checkout@v6
 
-    - name: Configure git
-      run: |
-        git config --global core.longpaths true
-      shell: bash
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In @.github/workflows/create-evaluation_reports.yml around lines 94 - 97, Move
the "Configure git" step so it runs before the "Checkout repository" step:
currently the step named "Configure git" (which runs git config --global
core.longpaths true) comes after actions/checkout@v6; reposition it to precede
the initial checkout so the longpaths setting applies to every git operation in
the job (including actions/checkout@v6) and thus covers subsequent steps like
the report-evaluation and create-pull-request actions as well.
.github/workflows/create-qualification_reports.yml (1)

94-97: LGTM — same reasoning as create-evaluation_reports.yml.

Identical, correct addition. The same optional refactor applies: placing this step before Checkout repository would make long-path support unconditional for every git operation in the job, including the initial checkout.

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

In @.github/workflows/create-qualification_reports.yml around lines 94 - 97, The
`Configure git` step that sets `git config --global core.longpaths true` is
currently after the `Checkout repository` step, so long-path support doesn’t
apply to the initial checkout; move the `Configure git` step to before the
`Checkout repository` step in the workflow so the `git config` is applied
unconditionally to all git operations (identify the step by its name "Configure
git" and reposition it to precede the "Checkout repository" step).
🤖 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/create-evaluation_reports.yml:
- Around line 94-97: Move the "Configure git" step so it runs before the
"Checkout repository" step: currently the step named "Configure git" (which runs
git config --global core.longpaths true) comes after actions/checkout@v6;
reposition it to precede the initial checkout so the longpaths setting applies
to every git operation in the job (including actions/checkout@v6) and thus
covers subsequent steps like the report-evaluation and create-pull-request
actions as well.

In @.github/workflows/create-qualification_reports.yml:
- Around line 94-97: The `Configure git` step that sets `git config --global
core.longpaths true` is currently after the `Checkout repository` step, so
long-path support doesn’t apply to the initial checkout; move the `Configure
git` step to before the `Checkout repository` step in the workflow so the `git
config` is applied unconditionally to all git operations (identify the step by
its name "Configure git" and reposition it to precede the "Checkout repository"
step).

@Yuri05

Yuri05 commented Feb 18, 2026

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@rwmcintosh PR ready for review?

@rwmcintosh

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@rwmcintosh PR ready for review?

Yes, I can't select reviewers for some reason.

image

@Yuri05 Yuri05 merged commit db6c95b into Open-Systems-Pharmacology:main Feb 19, 2026
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2 participants