Fixes #5 Add a troubleshooting guide#6
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…instructions (#116) * Initial plan * docs: improve troubleshooting guide and link from README Co-authored-by: Yuri05 <25061876+Yuri05@users.noreply.github.com> * docs: add troubleshooting intro sentence Co-authored-by: Yuri05 <25061876+Yuri05@users.noreply.github.com> * Update README.md * Update Troubleshooting.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: Yuri05 <25061876+Yuri05@users.noreply.github.com> Co-authored-by: Juri Solodenko <Yuri05@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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📝 WalkthroughWalkthroughAdds documentation tips and a new Troubleshooting guide; updates two GitHub Actions workflows to sanitize matrix-provided repository names before creating PR branches. Changes
Sequence Diagram(s)sequenceDiagram
autonumber
participant Matrix as Matrix Job
participant Runner as GH Actions Runner
participant Sanitize as Sanitize Step
participant GitHubAPI as GitHub API (Create PR)
Rect rgba(100,150,250,0.5)
Matrix->>Runner: provide matrix['Repository name'] and run_number
end
Runner->>Sanitize: run bash to strip invalid chars -> outputs repo_name
Sanitize-->>Runner: outputs.repo_name
Runner->>GitHubAPI: create branch using outputs.repo_name + -run_number and open PR
GitHubAPI-->>Runner: PR created / errors
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~20 minutes Possibly related PRs
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🚥 Pre-merge checks | ✅ 2✅ Passed checks (2 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches🧪 Generate unit tests (beta)
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Actionable comments posted: 1
🧹 Nitpick comments (1)
Troubleshooting.md (1)
59-76: Normalize strong emphasis style to satisfy MD050.markdownlint expects underscores for strong emphasis; switch
**...**to__...__in the flagged lines to match the configured style.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@Troubleshooting.md` around lines 59 - 76, Several strong-emphasis instances use asterisks instead of the configured underscore style (MD050); find occurrences like "**Explain Error**", "**Run workflow**", "**Create qualification reports** and "**Create evaluation reports and projects**" and replace the asterisk-based bold with underscore-based bold (e.g., **text** -> __text__) so the document uses __Explain Error__, __Run workflow__, __Create qualification reports__, etc.; ensure all remaining double-asterisk strong emphasis in the provided snippet are converted to double-underscore equivalents to satisfy markdownlint MD050.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@Troubleshooting.md`:
- Around line 7-62: The Markdown file Troubleshooting.md contains multiple <img>
tags missing alt attributes; update every <img ... src="..."> element (e.g., the
images with src values like f8a55fe8-97ad-4caa-99da-c00e57e8ca83,
1c7281b7-410a-40e5-8f28-2bcd5a898df8, f7583d97-2075-4395-b892-6d24a3afa76f,
8c619837-a1c0-4ebe-bae5-3c01771db2b7, 21128c32-d27f-4713-bceb-cfca9b51c288,
9d3eee4c-d267-4c7f-bd45-3507bcfd35c6, ccd37155-403e-4db3-aa02-f07611fb1597,
a1d2dcf9-bced-424c-bfdf-6144c1ac0f94) by adding concise descriptive alt text
(one short phrase per image describing the screenshot content, e.g., "GitHub
Actions workflow run button", "Validation workflow error list", "Artifact log
file path example"); ensure each <img> tag has an alt attribute and keep
descriptions brief and meaningful for screen readers.
---
Nitpick comments:
In `@Troubleshooting.md`:
- Around line 59-76: Several strong-emphasis instances use asterisks instead of
the configured underscore style (MD050); find occurrences like "**Explain
Error**", "**Run workflow**", "**Create qualification reports** and "**Create
evaluation reports and projects**" and replace the asterisk-based bold with
underscore-based bold (e.g., **text** -> __text__) so the document uses
__Explain Error__, __Run workflow__, __Create qualification reports__, etc.;
ensure all remaining double-asterisk strong emphasis in the provided snippet are
converted to double-underscore equivalents to satisfy markdownlint MD050.
Yuri05
commented
Feb 23, 2026
Comment on lines
+59
to
+60
| > [!TIP] | ||
| > If the model repository does not come from _Open-Systems-Pharmacology_, enter it like this:<br> `../<GITHUB_ACCOUNT_NAME>/<REPOSITORY_NAME>` (e.g. `../Yuri05/7E3-Model`) |
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It really works like this (the GHA currently always uses the prefix https://github.com/Open-Systems-Pharmacology/ and with .. I can switch to another GitHub account (the same applies for the validate actions).
Would be better of course to check if the repo name contains / and don't insert Open-Systems-Pharmacology - but I really don't want to modify everything again.
Member
Author
|
Failing link checks can be ignored. The checks are made for the reports created by end users (which always live in separate folders) and fail for md files in the root folder of the repo. |
* Update create-evaluation_reports.yml * Update create-qualification_reports.yml * Update tools.csv
Yuri05
commented
Feb 24, 2026
Comment on lines
+123
to
+134
| - name: Sanitize repository name for branch | ||
| id: sanitize | ||
| shell: bash | ||
| run: | | ||
| # Remove characters that can make a branch name invalid | ||
| sanitized="$(printf '%s' "${{ matrix['Repository name'] }}" | tr -d './\\')" | ||
| echo "repo_name=$sanitized" >> "$GITHUB_OUTPUT" | ||
|
|
||
| - name: Create Pull Request | ||
| uses: peter-evans/create-pull-request@v8 | ||
| with: | ||
| branch: ${{ matrix['Repository name'] }}-${{ github.run_number }} | ||
| branch: ${{ steps.sanitize.outputs.repo_name }}-${{ github.run_number }} |
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The branch name is built from the repo name.
If the repo comes from a local account (e.g. ../Yuri05/MyRepo) - we need to remove characters which are not allowed in a branch name (e.g. /)
Yuri05
commented
Feb 24, 2026
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Also updated the tools to the versions used in the last OSP release (12.2)
PavelBal
previously approved these changes
Feb 24, 2026
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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 @.github/workflows/create-evaluation_reports.yml:
- Line 150: Remove the extra trailing blank line flagged by YAMLlint in the
create-evaluation_reports.yml workflow file so there are no consecutive blank
lines at the end of the file; open the create-evaluation_reports.yml content and
delete the redundant empty line (leaving a single trailing newline if needed) to
resolve the "too many blank lines" lint error.
- Around line 123-129: The sanitize step currently injects `${{
matrix['Repository name'] }}` directly into the shell, risking command
injection; change the job step with id "sanitize" to pass the repository name
via the step's env (e.g., set an env key like REPO_NAME: ${{ matrix['Repository
name'] }}) and then reference that env var inside the run script (use
"$REPO_NAME" when building the sanitized variable and when writing to
"$GITHUB_OUTPUT"); keep the same sanitization transform (printf ... | tr -d
'./\\') but operate on the env variable rather than the evaluated `${{ ... }}`
expression.
In @.github/workflows/create-qualification_reports.yml:
- Around line 122-128: The "Sanitize repository name for branch" step (id:
sanitize) is vulnerable because it interpolates ${{ matrix['Repository name'] }}
directly into the shell run; change the step to pass the matrix value via env
(e.g., REPO_NAME) and reference that env var inside the run to avoid shell
injection, then perform the same sanitization on the env var
(sanitized="$(printf '%s' "$REPO_NAME" | tr -d './\\')" ) and echo
"repo_name=$sanitized" >> "$GITHUB_OUTPUT"; update references to the sanitized
variable and keep the step id sanitize unchanged.
ℹ️ Review info
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
⛔ Files ignored due to path filters (1)
tools.csvis excluded by!**/*.csv
📒 Files selected for processing (2)
.github/workflows/create-evaluation_reports.yml.github/workflows/create-qualification_reports.yml
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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♻️ Duplicate comments (1)
.github/workflows/create-evaluation_reports.yml (1)
152-152:⚠️ Potential issue | 🟡 MinorRemove the extra trailing blank line to satisfy YAMLlint.
Two consecutive blank lines at the end of the file trigger a YAMLlint
too many blank lines (2 > 0)warning. Delete one of the trailing blank lines.🧹 Proposed fix
# reviewers: ${{ github.actor }} -🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In @.github/workflows/create-evaluation_reports.yml at line 152, The workflow file create-evaluation_reports.yml ends with two consecutive blank lines causing a YAMLlint "too many blank lines" error; open create-evaluation_reports.yml and remove one of the trailing blank lines at the end so the file ends with only a single newline (no extra empty line).
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Duplicate comments:
In @.github/workflows/create-evaluation_reports.yml:
- Line 152: The workflow file create-evaluation_reports.yml ends with two
consecutive blank lines causing a YAMLlint "too many blank lines" error; open
create-evaluation_reports.yml and remove one of the trailing blank lines at the
end so the file ends with only a single newline (no extra empty line).
ℹ️ Review info
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (2)
.github/workflows/create-evaluation_reports.yml.github/workflows/create-qualification_reports.yml
rwmcintosh
approved these changes
Feb 24, 2026
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