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WalkthroughThe changes introduce a new "User Guide" page into the Streamlit application's navigation, referencing a new Python module that dynamically renders a Markdown-based user guide with embedded images and error handling for missing assets. The Markdown file for the user guide is added, providing comprehensive documentation for users. An old multi-page documentation viewer Python file is deleted, consolidating documentation into the new user guide system. No changes are made to exported or public entities, and no modifications to control flow outside of the documentation navigation are introduced. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant StreamlitApp
participant user_guide.py
participant user_guide.md
participant ImagesFolder
User->>StreamlitApp: Select "User Guide" from navigation
StreamlitApp->>user_guide.py: Load page
user_guide.py->>user_guide.md: Read Markdown content
loop For each line in Markdown
alt Markdown image syntax
user_guide.py->>ImagesFolder: Load referenced image
alt Image found
user_guide.py->>StreamlitApp: Display image with caption
else Image missing
user_guide.py->>StreamlitApp: Display warning
end
else Regular Markdown
user_guide.py->>StreamlitApp: Render Markdown line
end
end
StreamlitApp->>User: Display user guide with images and text
Poem
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Actionable comments posted: 1
🧹 Nitpick comments (12)
content/user_guide.md (9)
30-30: Use proper Markdown link formatting.Replace the bare URL with proper Markdown link formatting for better readability and accessibility.
-4. If you want to know more about each parameter go to this link: https://openms.de/FLASHDeconv +4. If you want to know more about each parameter, visit the [FLASHDeconv documentation](https://openms.de/FLASHDeconv).🧰 Tools
🪛 LanguageTool
[style] ~30-~30: Consider using an alternative to strengthen your wording.
Context: ...* for deconvolution accuracy. 4. If you want to know more about each parameter go to...(WANT_KEEN)
🪛 markdownlint-cli2 (0.17.2)
30-30: Bare URL used
null(MD034, no-bare-urls)
133-134: Vary sentence structure for better readability.Consecutive sentences starting with the same word make the text repetitive.
-3. Click the **"Database"** tab to upload the necessary **FASTA** database files. -4. Click **"Add Database"** to confirm the upload. +3. Click the **"Database"** tab to upload the necessary **FASTA** database files. +4. Select **"Add Database"** to confirm the upload.🧰 Tools
🪛 LanguageTool
[style] ~134-~134: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: ... necessary FASTA database files. 4. Click "Add Database" to confirm the uploa...(ENGLISH_WORD_REPEAT_BEGINNING_RULE)
131-137: Use consistent image captions.Multiple images use the same generic caption "Download Results" despite showing different features.
- + - +🧰 Tools
🪛 LanguageTool
[style] ~134-~134: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: ... necessary FASTA database files. 4. Click "Add Database" to confirm the uploa...(ENGLISH_WORD_REPEAT_BEGINNING_RULE)
🪛 markdownlint-cli2 (0.17.2)
137-137: Heading style
Expected: atx; Actual: setext(MD003, heading-style)
154-155: Use consistent image captions.Multiple images use the same generic caption.
- - + +
166-166: Use consistent image captions.Generic caption needs to be more specific.
- +
181-181: Use consistent image captions.Generic caption needs to be more specific.
- +
190-190: Use consistent image captions.Generic caption needs to be more specific.
- +
199-199: Use consistent image captions.Generic caption needs to be more specific.
- +
210-210: Use consistent image captions.Generic caption needs to be more specific.
- +content/user_guide.py (3)
18-18: Unnecessary f-string.The f-string doesn't contain any interpolated variables.
- st.error(f"🚨 Error: Could not find {md_file}") + st.error("🚨 Error: Could not find " + str(md_file))
35-36: Use alt text for captions.The image caption could use the alt text from the Markdown image syntax instead of just the filename.
- image_name = line[start:end].split("/")[-1] - image_path = image_folder / image_name + image_path_str = line[start:end] + image_name = image_path_str.split("/")[-1] + image_path = image_folder / image_name + + # Extract alt text for caption + alt_start = line.find("![") + 2 + alt_end = line.find("](") + caption = line[alt_start:alt_end] if alt_start < alt_end else image_nameAnd update the image display code:
- st.image(str(image_path), caption=image_name, width=800) + st.image(str(image_path), caption=caption, width=800)
31-42: Handle image widths dynamically.Currently, there's inconsistent image width handling (300px for the custom image vs 800px for all others). Consider making widths dynamic based on image content or user preferences.
# Markdown-style image (e.g., ) elif line.strip().startswith("!["): start = line.find("(") + 1 end = line.find(")") image_name = line[start:end].split("/")[-1] image_path = image_folder / image_name + + # Set appropriate width based on image type + if "configure" in image_name.lower(): + width = 700 # Configuration screenshots often need more detail + elif "viewer" in image_name.lower() or "layout" in image_name.lower(): + width = 800 # Full UI screenshots + else: + width = 600 # Default width for other images if image_path.exists(): - st.image(str(image_path), caption=image_name, width=800) + st.image(str(image_path), caption=image_name, width=width) else: st.warning(f"⚠️ Missing image: {image_name}")
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⛔ Files ignored due to path filters (20)
content/FLASHTnT/img.pngis excluded by!**/*.pngcontent/FLASHTnT/img_1.pngis excluded by!**/*.pngcontent/FLASHTnT/img_2.pngis excluded by!**/*.pngstatic/images/FlashTnT_Viewer.pngis excluded by!**/*.pngstatic/images/download_tnt.pngis excluded by!**/*.pngstatic/images/flashTnT_configure2.pngis excluded by!**/*.pngstatic/images/flashTnT_databaseupload.pngis excluded by!**/*.pngstatic/images/flashTnT_upload.pngis excluded by!**/*.pngstatic/images/flashdeconv_configure.pngis excluded by!**/*.pngstatic/images/flashdeconv_download.pngis excluded by!**/*.pngstatic/images/flashdeconv_example_data.pngis excluded by!**/*.pngstatic/images/flashdeconv_layout_manager.pngis excluded by!**/*.pngstatic/images/flashdeconv_manual_upload.pngis excluded by!**/*.pngstatic/images/flashdeconv_run.pngis excluded by!**/*.pngstatic/images/flashdeconv_upload.pngis excluded by!**/*.pngstatic/images/flashdeconv_viewer.pngis excluded by!**/*.pngstatic/images/flashtnt_configure.pngis excluded by!**/*.pngstatic/images/flashtnt_run.pngis excluded by!**/*.pngstatic/images/layoutmanager_tnt.pngis excluded by!**/*.pngstatic/images/manual_result_upload.pngis excluded by!**/*.png
📒 Files selected for processing (4)
app.py(1 hunks)content/TODO_Update/documentation.py(0 hunks)content/user_guide.md(1 hunks)content/user_guide.py(1 hunks)
💤 Files with no reviewable changes (1)
- content/TODO_Update/documentation.py
🧰 Additional context used
🧬 Code Graph Analysis (1)
content/user_guide.py (1)
src/common/common.py (1)
page_setup(91-228)
🪛 LanguageTool
content/user_guide.md
[style] ~30-~30: Consider using an alternative to strengthen your wording.
Context: ...* for deconvolution accuracy. 4. If you want to know more about each parameter go to...
(WANT_KEEN)
[style] ~134-~134: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: ... necessary FASTA database files. 4. Click "Add Database" to confirm the uploa...
(ENGLISH_WORD_REPEAT_BEGINNING_RULE)
🪛 markdownlint-cli2 (0.17.2)
content/user_guide.md
30-30: Bare URL used
null
(MD034, no-bare-urls)
137-137: Heading style
Expected: atx; Actual: setext
(MD003, heading-style)
⏰ Context from checks skipped due to timeout of 90000ms (2)
- GitHub Check: build-openms
- GitHub Check: build-full-app
🔇 Additional comments (2)
content/user_guide.md (1)
16-16:Details
❌ Incorrect review comment
Verify image paths are correct.
The image path uses lowercase "images" while the Python code looks for them in "static/Images" (with uppercase I).
Check that the image paths match the actual directory structure:
🏁 Script executed:
#!/bin/bash # Check image folder structure and case sensitivity ls -la static/ if [ -d "static/Images" ]; then echo "Directory 'static/Images' exists" ls -la static/Images | head -n 10 elif [ -d "static/images" ]; then echo "Directory 'static/images' exists" ls -la static/images | head -n 10 else echo "Neither 'static/Images' nor 'static/images' directory exists" fiLength of output: 989
🏁 Script executed:
#!/bin/bash # Search for any references to an uppercase “Images” folder in the codebase rg -n "/static/Images"Length of output: 22
Image path is correct – no uppercase “Images” directory detected
The markdown reference uses
/static/imagesand the filesystem only containsstatic/images. A search for any/static/Imagesreferences in the codebase returned no matches, so there’s no case mismatch to address. No changes needed.Likely an incorrect or invalid review comment.
app.py (1)
9-11: LGTM: Clean navigation integration.The User Guide page is properly integrated into the navigation structure with appropriate icon and title.
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 0
🧹 Nitpick comments (3)
content/user_guide.py (3)
21-39: Consider a more robust approach to Markdown renderingThe current line-by-line approach may not correctly render multi-line Markdown elements like lists, code blocks, or blockquotes that require context from surrounding lines.
Instead of processing line-by-line, consider:
-# Process Markdown content and replace image references -for line in content: - - # Markdown-style image (e.g., ) - if line.strip().startswith("!["): - start = line.find("(") + 1 - end = line.find(")") - image_name = line[start:end].split("/")[-1] - image_path = image_folder / image_name - - if image_path.exists(): - st.image(str(image_path), caption=image_name, width=800) - else: - st.warning(f"⚠️ Missing image: {image_name}") - - # Normal markdown text - else: - st.markdown(line) +# Read the entire content +markdown_content = "" + +# Process Markdown content and replace image references +for line in content: + # Markdown-style image (e.g., ) + if line.strip().startswith("!["): + # First, render any accumulated markdown + if markdown_content: + st.markdown(markdown_content) + markdown_content = "" + + # Then handle the image + start = line.find("(") + 1 + end = line.find(")") + image_name = line[start:end].split("/")[-1] + image_path = image_folder / image_name + + if image_path.exists(): + st.image(str(image_path), caption=image_name, width=800) + else: + st.warning(f"⚠️ Missing image: {image_name}") + # Normal markdown text + else: + markdown_content += line + +# Render any remaining markdown content +if markdown_content: + st.markdown(markdown_content)This approach accumulates regular Markdown content and only interrupts to render images, which should preserve proper Markdown formatting.
25-30: Improve image path extractionThe current image extraction logic is simple but might break with complex Markdown syntax. It doesn't handle cases with escaped parentheses or when multiple images are on the same line.
Consider using a more robust approach with regular expressions:
- # Markdown-style image (e.g., ) - if line.strip().startswith("!["): - start = line.find("(") + 1 - end = line.find(")") - image_name = line[start:end].split("/")[-1] - image_path = image_folder / image_name + # Markdown-style image (e.g., ) + import re + image_pattern = r'!\[.*?\]\((.*?)\)' + if line.strip().startswith("!["): + match = re.search(image_pattern, line) + if match: + image_path_str = match.group(1) + image_name = image_path_str.split("/")[-1] + image_path = image_folder / image_name
31-34: Consider responsive image sizingSetting a fixed width of 800 pixels for all images might not be optimal for all screen sizes and images.
Consider using Streamlit's responsive options or conditionally setting width based on image size:
- if image_path.exists(): - st.image(str(image_path), caption=image_name, width=800) - else: - st.warning(f"⚠️ Missing image: {image_name}") + if image_path.exists(): + # Either use responsive sizing or set a percentage of container width + st.image(str(image_path), caption=image_name, use_column_width="auto") + else: + st.warning(f"⚠️ Missing image: {image_name}")The
use_column_width="auto"option will make the image responsive while maintaining its aspect ratio.
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content/user_guide.py (1)
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🔇 Additional comments (2)
content/user_guide.py (2)
1-7: Nicely structured page setup! 👍Good job using the common
page_setup()function for consistent UI configuration across the app, and setting a clear title for the user guide.
13-19: Good error handling for missing filesThe implementation properly handles the case where the Markdown file doesn't exist and provides a clear error message to the user.
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