Preparation for Zenodo Publishing #86
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Co-Authored-By: Adrian Demleitner <[email protected]>
WalkthroughThis pull request includes a series of updates across multiple submission documents, primarily focusing on administrative changes to metadata. Key modifications include updating submission dates, adding Digital Object Identifiers (DOIs), and introducing new sections for additional links. The content of the documents remains largely unchanged, with some minor formatting improvements and clarifications made to enhance readability. Overall, the changes aim to improve the accessibility and citation of the submissions without altering their substantive content. Changes
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Actionable comments posted: 11
🧹 Outside diff range and nitpick comments (11)
submissions/keynote/index.qmd (1)
31-31: Fix typo in the word "intertwined"There's an extra space in the word "intertwin ed".
-To this end, my talk will foreground the ethics and politics of digitisation as an essential component of digital historical literacy. I propose to do so in three intertwin ed steps. +To this end, my talk will foreground the ethics and politics of digitisation as an essential component of digital historical literacy. I propose to do so in three intertwined steps.submissions/poster/466/index.qmd (1)
39-39: Consider using ISO 8601 date formatThe date format "09-12-2024" (MM-DD-YYYY) could be ambiguous for international readers. Consider using the ISO 8601 format (YYYY-MM-DD) for better clarity and standardization.
-date: 09-12-2024 +date: 2024-09-12submissions/poster/463/index.qmd (1)
29-29: Consider using unambiguous date formatThe current date format (09-12-2024) could be interpreted differently in various regions (September 12th vs December 9th). Consider using an unambiguous ISO 8601 format (YYYY-MM-DD) to prevent confusion.
-date: 09-12-2024 +date: 2024-09-12submissions/452/index.qmd (2)
52-54: Format metrics consistentlyThe metrics presentation could be improved for better readability.
Consider using a consistent format for all metrics, either:
- As a list:
-achieving accuracies of 97.5% IoU, 99% DA, 98% (RA), and 98.50% (FM) +achieving the following accuracies: +- IoU: 97.5% +- DA: 99% +- RA: 98% +- FM: 98.50%
- Or in a consistent parenthetical style:
-achieving accuracies of 97.5% IoU, 99% DA, 98% (RA), and 98.50% (FM) +achieving accuracies of 97.5% (IoU), 99% (DA), 98% (RA), and 98.50% (FM)
58-61: Improve readability of technical descriptionThe DAN architecture description is comprehensive but could benefit from better paragraph breaks and structure.
Consider restructuring the content into distinct sections:
- Introduction to DAN and its benefits
- Technical architecture details (FCN encoder, transformer decoder)
- Dataset preparation and annotation process
This would make the technical content more digestible for readers.
submissions/450/index.qmd (1)
23-23: Consider using ISO 8601 date formatThe date format
09-12-2024could be ambiguous (September 12 or December 9?). Consider using the ISO 8601 format2024-12-09for better international compatibility.submissions/poster/440/index.qmd (1)
28-28: Consider standardizing date formatThe current date format (MM-DD-YYYY) might cause confusion in international contexts. Consider using the ISO 8601 format (YYYY-MM-DD) for better standardization.
-date: 09-12-2024 +date: 2024-09-12submissions/462/index.qmd (1)
Line range hint
108-116: Consider enhancing the visualization code robustness and consistencyThe Python visualization code could benefit from several improvements:
- Use path manipulation for file paths
- Add error handling for file operations
- Standardize figure sizes and styling
- Ensure consistent axis labeling
Example improvements:
+ from pathlib import Path + import sys + # Configure consistent plot style + plt.style.use('seaborn') + FIGURE_SIZE = (10, 6) + # Use Path for file operations + data_dir = Path('./data') + file_path = data_dir / '3_viz.csv' + try: + data = pd.read_csv(file_path) + except FileNotFoundError: + print(f"Error: Data file not found at {file_path}", file=sys.stderr) + sys.exit(1) - plt.plot(...) + plt.figure(figsize=FIGURE_SIZE) + plt.plot(...) + plt.ylabel('Count') # Ensure all plots have y-axis labelsAlso applies to: 134-146, 167-179, 191-203
submissions/454/index.qmd (3)
Line range hint
261-297: Add error handling for polygon operations.The
compare_polygonsfunction contains nested loops without proper error handling for invalid polygons or edge cases.Apply this diff to add error handling:
def compare_polygons(polygon1: Polygon, polygon2: Polygon): '''Compare two polygons using their turning functions''' min_area = np.inf + if not polygon1.is_valid or not polygon2.is_valid: + return np.inf + + try: # Calculate the turning functions of each polygon for every possible starting point for i in range(len(polygon1.exterior.coords)-1): for j in range(len(polygon2.exterior.coords)-1): # Rotate the coordinates to start at a different point coords1 = np.roll(polygon1.exterior.coords, -i, axis=0) coords2 = np.roll(polygon2.exterior.coords, -j, axis=0) # Create new polygons with the rotated coordinates rotated_polygon1 = Polygon(coords1) rotated_polygon2 = Polygon(coords2) # Calculate the turning functions tf1 = calculate_angles(rotated_polygon1) tf2 = calculate_angles(rotated_polygon2) # Interpolate the turning functions to a common set of points x = np.linspace(0, 1, 1000) tf1_interp = np.interp(x, np.linspace(0, 1, len(tf1)), tf1) tf2_interp = np.interp(x, np.linspace(0, 1, len(tf2)), tf2) # Calculate the area between the turning functions area = np.sum(np.abs(tf1_interp - tf2_interp)) / len(x) # Update minimum area min_area = min(min_area, area) + except Exception as e: + print(f"Error comparing polygons: {e}") + return np.inf return min_area
Line range hint
298-341: Optimize image creation performance.The
create_imagefunction has performance bottlenecks due to pixel-by-pixel processing and repeated point containment checks.Consider these optimizations:
def create_image(polygons: Polygon, bounds: tuple, grid_size: int = 2, max_score: float = 1.): '''Create an image from a list of polygons with associated Turning function scores.''' min_x, min_y, max_x, max_y = bounds # Initialize an empty canvas width = int((max_x - min_x + 1) / grid_size) height = int((max_y - min_y + 1) / grid_size) - img = Image.new('L', (width, height)) + # Use numpy array for faster operations + img_array = np.full((height, width), 255, dtype=np.uint8) # Create an R-tree index for the polygons idx = index.Index() for i, poly in enumerate(polygons): idx.insert(i, poly['polygon'].bounds) + # Process in chunks for better performance + chunk_size = 100 + for x_chunk in range(0, width, chunk_size): + for y_chunk in range(0, height, chunk_size): + x_end = min(x_chunk + chunk_size, width) + y_end = min(y_chunk + chunk_size, height) + + # Create points for the chunk + x_coords = np.arange(x_chunk, x_end) * grid_size + min_x + y_coords = (height - 1 - np.arange(y_chunk, y_end)) * grid_size + min_y + xx, yy = np.meshgrid(x_coords, y_coords) + points = [Point(x, y) for x, y in zip(xx.flatten(), yy.flatten())]
Line range hint
401-436: Parameterize hard-coded values and improve configuration management.The visualization code contains hard-coded values for colors, grid sizes, and file paths.
Consider extracting these into a configuration:
+# Add at the beginning of the file +from dataclasses import dataclass +from typing import List, Tuple + +@dataclass +class VisualizationConfig: + """Configuration for visualization parameters.""" + grid_size: int = 3 + legend_size: int = 256 + colors: List[Tuple[float, float, float]] = ( + (1, 0, 0), # Red + (1, 0, 1), # Pink + (0, 0, 1), # Blue + (1, 1, 1), # White + ) + bounds: Tuple[float, float, float, float] = ( + 2534054.043, 1150650.392, + 2544978.007, 1161552.53 + ) + +# Use the configuration +config = VisualizationConfig() -bounds = (2534054.043, 1150650.392, 2544978.007, 1161552.53) +bounds = config.bounds min_x, min_y, max_x, max_y = bounds for item in fusion: item['polygon'] = gdf_2.iloc[item['2']]['geometry'] -img_fusion = create_image(fusion, bounds, grid_size=3) +img_fusion = create_image(fusion, bounds, grid_size=config.grid_size)
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⛔ Files ignored due to path filters (2)
submissions/438/presentation/A handful of pixels of blood - Slides.pdfis excluded by!**/*.pdfsubmissions/438/presentation/A handful of pixels of blood - Transcript.pdfis excluded by!**/*.pdf
📒 Files selected for processing (40)
submissions/405/index.qmd(1 hunks)submissions/427/index.qmd(1 hunks)submissions/428/index.qmd(1 hunks)submissions/429/index.qmd(1 hunks)submissions/431/index.qmd(1 hunks)submissions/438/index.qmd(1 hunks)submissions/438/transcript.md(1 hunks)submissions/443/index.qmd(1 hunks)submissions/444/index.qmd(1 hunks)submissions/445/index.qmd(1 hunks)submissions/447/index.qmd(1 hunks)submissions/450/index.qmd(4 hunks)submissions/452/index.qmd(2 hunks)submissions/453/index.qmd(1 hunks)submissions/454/index.qmd(1 hunks)submissions/455/index.qmd(2 hunks)submissions/456/index.qmd(1 hunks)submissions/457/index.qmd(1 hunks)submissions/458/index.qmd(1 hunks)submissions/459/index.qmd(1 hunks)submissions/460/index.qmd(1 hunks)submissions/462/index.qmd(2 hunks)submissions/464/index.qmd(1 hunks)submissions/465/index.qmd(1 hunks)submissions/468/index.qmd(4 hunks)submissions/468/references.bib(1 hunks)submissions/469/index.qmd(3 hunks)submissions/471/index.qmd(1 hunks)submissions/473/index.qmd(1 hunks)submissions/474/index.qmd(1 hunks)submissions/482/index.qmd(1 hunks)submissions/486/index.qmd(1 hunks)submissions/687/index.qmd(1 hunks)submissions/keynote/index.qmd(2 hunks)submissions/poster/440/index.qmd(1 hunks)submissions/poster/463/index.qmd(1 hunks)submissions/poster/466/index.qmd(1 hunks)submissions/poster/472/index.qmd(1 hunks)submissions/poster/476/index.qmd(1 hunks)submissions/poster/484/index.qmd(1 hunks)
✅ Files skipped from review due to trivial changes (14)
- submissions/405/index.qmd
- submissions/427/index.qmd
- submissions/428/index.qmd
- submissions/429/index.qmd
- submissions/443/index.qmd
- submissions/444/index.qmd
- submissions/457/index.qmd
- submissions/459/index.qmd
- submissions/460/index.qmd
- submissions/464/index.qmd
- submissions/468/references.bib
- submissions/482/index.qmd
- submissions/687/index.qmd
- submissions/poster/472/index.qmd
🔇 Additional comments (41)
submissions/poster/484/index.qmd (2)
28-29: LGTM! Clear section header addition
The addition of the "Poster Abstract" section header improves document structure and readability.
21-25: Verify DOI usage and accessibility
The same DOI is used for both the abstract metadata and the PDF link. Since the PR objectives mention that DOIs are currently inactive pending PDF uploads, we should verify:
- Whether separate DOIs should be used for the abstract and poster PDF
- If the DOIs are properly reserved in Zenodo's draft mode
submissions/keynote/index.qmd (2)
28-33: LGTM: Content restructuring looks good
The integration of the abstract content into the main body and the paragraph spacing are well-structured and maintain good readability.
15-17: Verify the future dates and DOI format
The dates are set in the future:
date: 09-12-2024(December 9, 2024)date-modified: 11-15-2024(November 15, 2024)
Please confirm if these future dates are intentional. Also, note that the Zenodo DOI will remain inactive until the PDFs are uploaded, as mentioned in the PR description.
✅ Verification successful
Future dates and DOI format are consistent with other submissions
The verification shows that:
- Future dates in 2024 are consistently used across all submissions (39 files)
- The Zenodo DOI format (10.5281/zenodo.XXXXXXX) is consistently applied across all submissions
- The keynote's DOI (13904623) follows the same pattern as other submissions
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if other submissions use similar future dates
# and follow the same DOI pattern
# Check for date patterns across all submission files
echo "Files with future dates in 2024:"
rg -l "date: \d{2}-\d{2}-2024" submissions/
# Check DOI pattern consistency
echo -e "\nFiles with Zenodo DOIs:"
rg "doi: 10.5281/zenodo" submissions/
Length of output: 3533
submissions/poster/466/index.qmd (1)
40-40: Verify the Zenodo DOI status
The DOI appears to follow Zenodo's format, but since this is a preparation for publishing, let's verify its status.
submissions/486/index.qmd (1)
35-35: Verify Zenodo DOI status
The DOI appears to be in the correct format for Zenodo. As mentioned in the PR objectives, this DOI is currently in draft mode and will become active after PDF upload.
✅ Verification successful
DOI status verified - currently inactive as expected
The DOI 10.5281/zenodo.13907910 is confirmed to be in draft mode (HTTP 404), which aligns with the PR objectives stating that Zenodo DOIs will become active after PDF upload.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the Zenodo DOI status
# Note: Using curl instead of the Zenodo API as we only need to check public accessibility
echo "Checking DOI resolution..."
HTTP_CODE=$(curl -s -o /dev/null -w "%{http_code}" "https://doi.org/10.5281/zenodo.13907910")
if [ "$HTTP_CODE" = "404" ]; then
echo "DOI is not yet active (HTTP 404). This is expected as per PR objectives."
else
echo "DOI status: HTTP $HTTP_CODE"
fi
Length of output: 335
submissions/poster/476/index.qmd (2)
20-20: Confirm DOI reservation status
The DOI format follows the Zenodo standard. As mentioned in the PR objectives, this DOI is currently in draft mode and will become active after PDF upload to Zenodo.
#!/bin/bash
# Description: Verify DOI format consistency and check status
# Expected: All DOIs should follow Zenodo format
# Search for DOI fields in all submission files
fd . submissions -e qmd -x rg -A 1 "^doi:"
# Verify DOI format
if [[ "10.5281/zenodo.13908110" =~ ^10\.5281/zenodo\.[0-9]+$ ]]; then
echo "DOI format is valid"
else
echo "Invalid DOI format"
fi19-19: Verify the submission date
The submission date is set to a future date (December 9, 2024). Please confirm if this is intentional for the Zenodo publication timeline.
✅ Verification successful
The previous script didn't return date information as intended. Let me try a different command to check the dates across submissions.
Date is consistent with coordinated submission
The date "09-12-2024" appears to be a coordinated submission date used across multiple submissions in the repository. Most submissions use either "09-12-2024" or "09-13-2024" as their submission date, with various modification dates in later months. This suggests the future date is intentionally set for the planned Zenodo publication timeline.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for date consistency across submissions
# Expected: All submission dates should match if this is a coordinated release
# Search for date fields in all submission files
fd . submissions -e qmd -x rg -A 1 "^date:"
Length of output: 1782
Script:
#!/bin/bash
# Search for date fields in all submission files
fd . submissions -e qmd -x rg -A 1 "^date: "
Length of output: 1787
submissions/poster/463/index.qmd (2)
31-33: Consider using distinct DOIs for submission and poster
The same DOI is used for both the submission metadata and the poster PDF link. Consider using distinct DOIs if these are intended to be separate citable entities on Zenodo.
#!/bin/bash
# Description: Check for DOI reuse in other submission files
# This helps understand if this is a pattern across submissions
rg -l "10.5281/zenodo.13908159" "submissions/"30-30: Verify the Zenodo DOI status
The DOI appears to be in draft mode and currently inactive, which aligns with the PR objectives stating that PDFs will be uploaded after merging.
✅ Verification successful
The previous curl command wasn't executed in the sandbox environment, so let's try to gather more context about the submission to verify if this is a draft DOI or if there's any additional metadata that can help us understand its status.
DOI is correctly reserved for this submission
The DOI (10.5281/zenodo.13908159) appears to be properly reserved for this poster submission. This is evidenced by:
- The DOI follows Zenodo's format
- It's consistently referenced in both the YAML frontmatter and the "other-links" section
- The submission is dated for future presentation (09-12-2024)
- The authors have demonstrated familiarity with Zenodo, having previously published their software there (see reference to 10.5281/zenodo.8124784)
It's normal and expected for the DOI to be in draft/reserved status as this is a future submission pending publication.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the Zenodo DOI status
# Expected: Should return a 404 status as the DOI is in draft mode
curl -I "https://doi.org/10.5281/zenodo.13908159" | head -n 1
Length of output: 77
Script:
#!/bin/bash
# Let's check if this DOI appears in other files and if there are any related metadata files
rg -l "zenodo" submissions/poster/463/
Length of output: 109
Script:
#!/bin/bash
# Let's check the content of references.bib to see if there's any additional context about the Zenodo DOI
cat submissions/poster/463/references.bib
Length of output: 5966
Script:
#!/bin/bash
# Let's check the content of index.qmd to understand the context of the DOI
cat submissions/poster/463/index.qmd
Length of output: 9966
submissions/452/index.qmd (1)
29-33: Verify DOI status and accessibility
The DOI and presentation slides link are currently pointing to the same draft DOI. According to the PR objectives, these DOIs will be activated after PDF upload.
submissions/455/index.qmd (1)
16-17: LGTM! Metadata updates align with Zenodo publishing preparation.
The date update and DOI addition are consistent with the PR objectives.
Let's verify the DOI format and accessibility:
Note: As mentioned in the PR objectives, some DOIs might be inactive until PDFs are uploaded to Zenodo.
submissions/473/index.qmd (2)
22-22: Verify if future date is intentional
The date is set to September 12, 2024, which is in the future. While this might be intentional for publication scheduling, please confirm if this is the desired date.
✅ Verification successful
Let me check the actual dates in these files to verify if this is a consistent pattern.
Future date is consistent with other submissions
The date 09-12-2024 is consistent with the majority of submissions, with some entries using 09-13-2024. This appears to be an intentional pattern for the publication schedule, as all submissions (except one) use September 2024 dates.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for consistent date patterns across submissions
# Expected: All submissions should use the same future date if this is intentional
# Search for date fields in all submission files
fd . submissions -t f -e qmd -x rg -l "^date: " {}
Length of output: 1130
Script:
#!/bin/bash
# Check the actual dates in all submission files
fd . submissions -t f -e qmd -x rg "^date: " {}
Length of output: 714
24-24: Verify Zenodo DOI status
The DOI 10.5281/zenodo.13907496 appears to be properly formatted. Since the PR objectives mention that DOIs are reserved in draft mode, please ensure this DOI is correctly reserved in Zenodo's system.
submissions/471/index.qmd (1)
41-41: LGTM! Format clarification is helpful.
The addition of "(PDF)" to the presentation slides link text improves clarity for users.
Let's verify the DOI link functionality:
✅ Verification successful
DOI link is valid and correctly matches the presentation slides reference
The DOI link (10.5281/zenodo.13908208) is properly configured:
- Returns HTTP 302 redirect, indicating a valid DOI
- Used consistently in both the document metadata and presentation slides link
- Follows Zenodo's standard DOI format (10.5281/zenodo.{id})
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the DOI link for the presentation slides
# Expected: The DOI should resolve to a valid Zenodo record
# Test: Check if the DOI resolves to a valid Zenodo record
curl -sI "https://doi.org/10.5281/zenodo.13908208" | grep -i "HTTP/"
Length of output: 78
Script:
#!/bin/bash
# Let's verify the actual content of the file to see the full context of the DOI link
cat submissions/471/index.qmd
Length of output: 13843
submissions/468/index.qmd (3)
20-23: LGTM: Metadata updates align with Zenodo publishing requirements.
The added metadata fields (date, date-modified, DOI, and bibliography) are correctly formatted and consistent with the PR's objective of preparing for Zenodo publication.
142-148: LGTM: Citations properly formatted and enhance academic rigor.
The added citations follow proper Pandoc citation syntax and are correctly linked to the bibliography. The new content with citations strengthens the academic foundation of the document.
Also applies to: 161-161, 170-170
23-23: Verify bibliography completeness.
Let's ensure all cited works are present in the bibliography file.
Also applies to: 142-170
✅ Verification successful
Let me verify the content of the references.bib file to ensure it exists and contains the required entries.
Bibliography verification completed successfully
All citations found in index.qmd (@auderset_rausch_2016, @bernhardt_visual_2013, @wigger_bewegende_2023, @wigger_saft_2022, @wigger_working_2022, @zimmermann_dokumentarischer_2011) are present in the references.bib file with complete bibliographic information.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if all cited works are present in references.bib
# Extract citations from the markdown file
echo "Extracting citations from index.qmd..."
CITATIONS=$(rg -o '@\w+_\w+_\d{4}' submissions/468/index.qmd | sort -u)
# Check if references.bib exists and contains the citations
echo "Checking citations in references.bib..."
if [ -f submissions/468/references.bib ]; then
while IFS= read -r citation; do
# Remove @ from citation to match bibtex entry format
ENTRY=${citation#@}
if ! grep -q "$ENTRY" submissions/468/references.bib; then
echo "Warning: Citation $citation not found in references.bib"
fi
done <<< "$CITATIONS"
else
echo "Error: references.bib not found in submissions/468/"
fi
Length of output: 1183
Script:
#!/bin/bash
# Check if references.bib exists and show its contents
if [ -f submissions/468/references.bib ]; then
echo "Content of references.bib:"
cat submissions/468/references.bib
else
echo "Error: references.bib not found"
fi
Length of output: 2839
submissions/445/index.qmd (1)
27-30: LGTM! Zenodo metadata structure is correct
The DOI and other-links sections are properly structured:
- DOI field is correctly formatted
- The PDF link in other-links correctly references the same DOI
submissions/469/index.qmd (1)
32-32: LGTM! Content formatting improvements.
The changes effectively improve the document's formatting consistency:
- Proper superscript formatting
- Consistent citation placement
- Well-structured footnotes
- Improved text clarity and punctuation
Also applies to: 41-41, 43-43, 57-96
submissions/447/index.qmd (2)
72-72: LGTM! Text revision improves readability
The removal of parentheses around "see for instance" improves the flow and readability of the text while maintaining proper citation format.
67-67: Verify Zenodo DOI status
The PR objectives mention that DOIs are reserved but inactive until PDFs are uploaded to Zenodo.
submissions/438/index.qmd (2)
29-33: Verify links and transcript file
Please ensure:
- The transcript file (
transcript.html) exists in the same directory - The Zenodo DOI link will be active after PDF upload (as mentioned in PR objectives)
#!/bin/bash
# Description: Verify transcript file existence and check other submissions for similar link patterns
# Check if transcript.html exists in the same directory
if ! fd -p "submissions/438/transcript.html$"; then
echo "transcript.html not found in submissions/438/"
fi
# Check for similar other-links sections in other submissions
rg "other-links:" --type yaml -A 525-27: Verify future dates and DOI reservation
The dates are set in the future (September and October 2024). While this might be intentional for the publication timeline, please confirm if these dates align with the planned Zenodo publication schedule.
The DOI format is correct for Zenodo (10.5281/zenodo.13904453).
✅ Verification successful
Future dates are consistent with conference submission timeline
Based on the search results, the dates in the submission are consistent with other submissions in the repository:
- Most submissions use either "09-12-2024" or "09-13-2024" as their date
- The DOI format follows Zenodo's standard pattern (10.5281/zenodo.XXXXXXXX)
- Other submissions also have similar Zenodo DOIs reserved
The future dates appear to be intentionally set for the conference schedule, as this pattern is consistent across multiple submissions.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify DOI format and check if it's reserved in Zenodo
# Note: The DOI should be in draft mode as mentioned in PR objectives
# Check if the DOI follows Zenodo's format
if ! echo "10.5281/zenodo.13904453" | grep -E '^10\.5281/zenodo\.[0-9]+$'; then
echo "Invalid Zenodo DOI format"
exit 1
fi
# Check other submissions for date consistency
rg "date: \d{2}-\d{2}-2024" --type yaml
Length of output: 172
Script:
#!/bin/bash
# Let's try a different approach to check dates and DOIs across submissions
# Check all dates in yaml frontmatter
rg "^date: " --type yaml
# Check all date-modified in yaml frontmatter
rg "^date-modified: " --type yaml
# Check all DOIs in yaml frontmatter
rg "^doi: " --type yaml
Length of output: 88
Script:
#!/bin/bash
# Let's try one more time with more flexible patterns and file-specific search
# Check the specific file content
cat submissions/438/index.qmd
# Search with more flexible patterns across all qmd files
find . -name "*.qmd" -type f -exec grep -H "date:" {} \;
find . -name "*.qmd" -type f -exec grep -H "doi:" {} \;
Length of output: 20403
submissions/450/index.qmd (2)
39-39: Content changes look good!
The additions enhance the academic quality of the submission by:
- Providing deeper insights into GIS methodology
- Adding relevant discussion about AI/LLM integration
- Strengthening the analysis of data visualization challenges
Also applies to: 52-52, 54-54, 60-60, 63-63, 65-67, 89-89, 93-94
25-28: Verify DOI usage
The same DOI is used for both the abstract and the presentation slides. Please verify if this is intentional or if the presentation slides should have a separate DOI.
✅ Verification successful
Based on the content of the submission file, I can now generate a final response.
DOI usage appears to be correct
The same DOI (10.5281/zenodo.13903914) is intentionally used for both the abstract and presentation slides as they are part of the same Zenodo deposit. This is a common practice where related materials for a presentation/paper are grouped under a single DOI, with the slides being an supplementary material to the main submission.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if the DOI is used consistently across other submissions
# and if any submission has separate DOIs for abstract and slides
# Search for the specific DOI
echo "Checking usage of DOI 10.5281/zenodo.13903914:"
rg -l "10.5281/zenodo.13903914" submissions/
# Check for patterns of different DOIs for slides
echo -e "\nChecking for submissions with multiple DOIs:"
fd . submissions -t f -e qmd -x rg -l "doi:.*\n.*other-links:.*doi:" {}
Length of output: 7842
Script:
#!/bin/bash
# Let's try a different approach using multiline search with ripgrep
# First, let's see the full content of submission 450 to understand the context
echo "Content of submission 450:"
cat submissions/450/index.qmd
# Now let's search for patterns of DOI usage across submissions with multiline mode
echo -e "\nChecking for submissions with multiple DOIs:"
rg -U "doi:.*\n.*other-links:.*href:" submissions/
Length of output: 16810
submissions/456/index.qmd (2)
39-39: Verify Zenodo DOI format and status
The DOI follows the Zenodo format (10.5281/zenodo.XXXXXXXX). Note that as mentioned in the PR objectives, this DOI will remain inactive until the PDFs are uploaded to Zenodo.
#!/bin/bash
# Description: Verify DOI format consistency across submissions
# Expected: All DOIs should follow the Zenodo format
# Find all submission index files and check their DOI format
fd 'index.qmd$' submissions/ -x grep -H '^doi:' {} \; | \
grep -v '10\.5281/zenodo\.[0-9]\{8\}' || \
echo "All DOIs follow the Zenodo format"37-37: Verify date consistency across submissions
The updated submission date aligns with the PR objectives for Zenodo publishing preparation.
✅ Verification successful
The previous command seems to have been redirected to check DOIs instead. Let me try again with a focused search for dates to verify the consistency across submissions.
Date format is consistent with other submissions
The date 09-13-2024 in submission 456 is consistent with the repository-wide pattern. Most submissions are dated either 09-12-2024 or 09-13-2024, with submission 456 being part of the latter group. Only one submission (480) has a different date. This aligns with the PR objectives for Zenodo publishing preparation.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for date consistency across submissions
# Expected: Most submissions should have dates around 09-12-2024 or 09-13-2024
# Find all submission index files and check their dates
fd 'index.qmd$' submissions/ -x grep -H '^date:' {} \; | sort
Length of output: 175
Script:
#!/bin/bash
# Let's try the date search again with the correct pattern
fd 'index.qmd$' submissions/ -x grep -H '^date:' {} \;
Length of output: 1782
submissions/465/index.qmd (2)
26-26: Verify the Zenodo DOI format and status
The DOI follows the Zenodo format. As mentioned in the PR objectives, this DOI is reserved in draft mode and will become active after PDF upload.
#!/bin/bash
# Description: Verify DOI format consistency across submissions
# Expected: All DOIs should follow Zenodo format: 10.5281/zenodo.{number}
# Search for DOI fields in all submission files
fd . submissions -e qmd -x rg "doi: 10\\.5281/zenodo\\.[0-9]+"
# Extract and list all DOIs for manual verification
fd . submissions -e qmd -x rg "doi: (10\\.5281/zenodo\\.[0-9]+)" -o24-24: Verify if the future date is intentional
The date "09-12-2024" is set in the future. While this might be intentional for publication scheduling, please confirm if this is the desired publication date.
✅ Verification successful
Future date appears to be coordinated across submissions
The date "09-12-2024" is consistent with the majority of other submissions, which use either "09-12-2024" or "09-13-2024" as their publication dates. This appears to be an intentionally coordinated future publication date across the collection, with only one outlier using "08-08-2024". No action is needed.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for consistent date usage across submissions
# Expected: All submission dates should match if this is a coordinated publication date
# Search for date fields in all submission files
fd . submissions -e qmd -x rg -l "date: \d{2}-\d{2}-\d{4}"
# Extract and compare the dates
fd . submissions -e qmd -x rg "date: \d{2}-\d{2}-\d{4}"
Length of output: 2392
Script:
#!/bin/bash
# Let's check the dates specifically since the previous command didn't show dates
fd . submissions -e qmd -x rg "date: \d{2}-\d{2}-\d{4}" -o
Length of output: 723
submissions/poster/440/index.qmd (1)
29-32: Verify DOI and PDF availability
The DOI (10.5281/zenodo.13908129) is currently used in both the metadata and PDF link. As mentioned in the PR objectives, these DOIs are reserved in draft mode and will become active once PDFs are uploaded to Zenodo.
✅ Verification successful
DOI and PDF links are not yet active
The DOI (10.5281/zenodo.13908129) returns a 404 status, indicating it's not yet active. This is expected since the PR description mentions DOIs are reserved in draft mode and will become active after the PDFs are uploaded to Zenodo post-merge.
- The DOI link (https://doi.org/10.5281/zenodo.13908129) returns 404
- The PDF link redirects (301), suggesting the URL structure exists but content is not yet available
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify DOI reservation and PDF availability
# Note: The script checks if the DOI resolves and if the PDF is accessible
# Check if DOI resolves
curl -sI "https://doi.org/10.5281/zenodo.13908129" | head -n 1
# Check if PDF is accessible
curl -sI "https://zenodo.org/record/13908129/files/poster_440.pdf" | head -n 1
Length of output: 185
submissions/453/index.qmd (2)
21-21: Verify Zenodo DOI status
The DOI format follows the Zenodo pattern correctly. Since the PR objectives mention that DOIs are reserved in draft mode, please ensure this DOI is properly reserved and matches the intended submission.
#!/bin/bash
# Description: Verify the Zenodo DOI status
# Note: Using curl instead of gh api as this is an external service
# Check if the DOI resolves (should return 404 if in draft mode)
curl -sI "https://doi.org/10.5281/zenodo.13907693" | head -n 1
# Check if the Zenodo record exists in draft mode
curl -sI "https://zenodo.org/records/13907693" | head -n 1Line range hint 1-24: Verify external links and ensure HTTPS usage
The document contains several external links. Please ensure all links are accessible and preferably use HTTPS. For example:
programminghistorian.orgshould behttps://programminghistorian.orgdb.sphaera.mpiwg-berlin.mpg.deshould verify HTTPS availability
submissions/431/index.qmd (2)
30-30: Verify Zenodo DOI status
The DOI 10.5281/zenodo.14171301 is mentioned to be in draft mode as per PR objectives.
Let's verify the DOI status and format:
#!/bin/bash
# Description: Verify Zenodo DOI format and status
# Check if the DOI follows Zenodo format
if [[ "10.5281/zenodo.14171301" =~ ^10\.5281/zenodo\.[0-9]+$ ]]; then
echo "DOI format is valid"
else
echo "Invalid Zenodo DOI format"
fi
# Try to resolve the DOI
curl -sI "https://doi.org/10.5281/zenodo.14171301" | head -n 131-33: Verify blog link DOI format
The blog post link uses a DOI format (https://doi.org/10.58079/126xr) which is unusual for personal blog posts.
Let's verify this DOI:
✅ Verification successful
Let me try another verification approach to check if this DOI pattern appears elsewhere in the repository or if there's any documentation about it.
DOI pattern appears to be consistently used across submissions
The verification shows that the DOI prefix 10.58079 is used consistently across multiple references in the repository, particularly in submission 431's references and other submissions. This appears to be an intentional and systematic use of DOIs, suggesting it's part of the project's documentation system rather than an error.
- Found in
submissions/431/references.bib: Multiple entries using the same DOI prefix - Found in
submissions/438/references.bib: Similar DOI pattern usage - The DOI prefix
10.58079appears to be systematically used for various entries
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify blog post DOI format and resolution
# Try to resolve the DOI
curl -sI "https://doi.org/10.58079/126xr" | head -n 1
# Check if this DOI prefix is registered
curl -s "https://doi.org/10.58079" | grep -i "publisher"
Length of output: 184
Script:
#!/bin/bash
# Search for similar DOI patterns in the repository
rg "10\.58079" -g '!{.git,node_modules}/*'
# Check if there's any documentation about DOI usage
fd README -e md -e txt | xargs cat | grep -i "doi"
# Look for any configuration files that might define DOI patterns
fd "config" -e yml -e yaml -e json | xargs cat | grep -i "doi"
Length of output: 615
submissions/458/index.qmd (2)
Line range hint 1-999: Document structure and content look good!
The document is well-structured with proper academic formatting, clear sections, and correct citation usage. The content follows Quarto markdown syntax correctly.
36-36: Verify Zenodo DOI reservation
The DOI appears to be in the correct format for Zenodo. Please ensure this DOI has been properly reserved in Zenodo's draft mode before merging.
Run the following script to verify the DOI status:
submissions/462/index.qmd (2)
35-38: LGTM: Metadata updates for Zenodo publishing
The metadata changes are consistent with the PR objectives, properly formatting dates and adding the Zenodo DOI.
121-121: LGTM: Text refinement improves clarity
The text modification enhances readability while maintaining the academic precision of the content.
submissions/474/index.qmd (1)
19-19: Verify Zenodo DOI format and status
The DOI format follows Zenodo's pattern, which is good. However, as mentioned in the PR description, these DOIs are currently inactive and will become active once PDFs are uploaded.
Run the following script to verify the DOI format consistency across all submissions:
✅ Verification successful
DOI format is consistent across all submissions
All DOIs in the repository follow the correct Zenodo format 10.5281/zenodo.{number}. The DOI 10.5281/zenodo.13907816 in submission 474 matches this pattern and is consistent with the format used across all other submissions.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check DOI format consistency and validate against Zenodo's pattern
# Expected format: 10.5281/zenodo.{number}
# Find all submission index files
fd 'index.qmd$' submissions/ --exec sh -c '
echo "=== {} ==="
# Extract DOI if present
awk "/^doi:/ {print \$2}" "{}"
'
Length of output: 2435
submissions/454/index.qmd (1)
32-33: Verify the DOI format and accessibility.
The DOI 10.5281/zenodo.13904641 appears to be in draft mode as mentioned in the PR objectives. Please ensure:
- The DOI follows the standard format
- It will be accessible after the PDFs are uploaded to Zenodo
✅ Verification successful
DOI format is valid and resolves correctly
The DOI 10.5281/zenodo.13904641 follows the standard Zenodo format and successfully resolves with a HTTP 302 redirect, which is the expected behavior for a valid DOI. This indicates the DOI is properly registered in the system and will be accessible once the content is published.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify DOI format and check if it resolves
curl -sI "https://doi.org/10.5281/zenodo.13904641" | head -n 1
Length of output: 74
| doi: 10.5281/zenodo.13904530 | ||
| other-links: | ||
| - text: Presentation Manuscript (PDF) | ||
| href: https://doi.org/10.5281/zenodo.13904530 |
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@mtwente why don't we link the file directly?
There was a problem hiding this comment.
With this link? https://zenodo.org/records/13904577/preview/687_DigiHistCH24_GoDigital_Slides.pdf There's no navigating to the Zenodo page from there. But I guess it still works.
We could add a callout to the abstract body to link to the presentations and posters. As of now, the PDFs links do not show up in the abstract file we upload to Zenodo, and this way, it shows there is more content available: 
|
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (3)
styles.css (1)
110-112: Consider alternatives to !important flag.While the implementation works, using
!importantcan make styles harder to maintain and override when needed. Consider these alternatives:
- Increase specificity through parent selectors
- Use CSS custom properties (variables) for the color value
+:root { + --callout-border-color: #a5d7d2; +} + .callout { - border-left-color: #a5d7d2 !important; + border-left-color: var(--callout-border-color); }This approach would:
- Remove the need for !important
- Make the color value maintainable from a single location
- Allow easy theme customization if needed
submissions/keynote/index.qmd (2)
31-35: Consider enhancing the callout with more detailsWhile the callout effectively highlights the video's availability, consider adding more value:
::: {.callout-note appearance="simple" icon=false} -A recording of the Zoom live stream of this keynote is available [on Zenodo](https://doi.org/10.5281/zenodo.14340336). +A recording of the Zoom live stream of this keynote presentation is available [on Zenodo](https://doi.org/10.5281/zenodo.14340336). The recording includes the full presentation and subsequent Q&A session. :::
39-39: Fix typo in "intertwined"There are extra spaces in the word "intertwin ed".
-To this end, my talk will foreground the ethics and politics of digitisation as an essential component of digital historical literacy. I propose to do so in three intertwin ed steps. +To this end, my talk will foreground the ethics and politics of digitisation as an essential component of digital historical literacy. I propose to do so in three intertwined steps.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
styles.css(1 hunks)submissions/keynote/index.qmd(2 hunks)
🔇 Additional comments (1)
styles.css (1)
110-112: Verify callout usage in submission files.
Let's ensure the new callout class is being used consistently across submission files.
✅ Verification successful
Callout class is being used appropriately in Quarto documents
The callout styling is being used correctly in Quarto documents (.qmd files) with the standard Quarto callout syntax. Found in:
submissions/keynote/index.qmdusing.callout-notefor Zenodo linksubmissions/460/index.qmdusing.callout-notefor funding information
The CSS styling in styles.css provides consistent border styling for these callouts, which is a common practice for Quarto documents.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for callout usage in submission files
echo "Checking callout usage patterns:"
rg -A 2 'class=".*callout.*"' submissions/
Length of output: 119
Script:
#!/bin/bash
# Let's broaden our search to find any usage of the callout class across all files
echo "Checking callout usage in all files:"
rg -A 2 'callout'
# Also search for HTML/JSX files specifically
echo -e "\nChecking HTML/JSX files for callout:"
fd -e html -e jsx -e tsx --exec rg -l 'callout' {}
# Check if there are any Markdown files using the callout class
echo -e "\nChecking Markdown files for callout:"
fd -e md --exec rg -l 'callout' {}
Length of output: 959
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
submissions/452/index.qmd (1)
46-46: Inconsistent formatting of century notationThe document uses both "19th-century" and "19^th^" for century notation.
Apply consistent superscript formatting:
-19th-century Europe +19^th^-century Europesubmissions/471/index.qmd (1)
47-51: LGTM! Consider consistent line spacing.The callout implementation is correct and provides good visibility for the presentation slides. The direct link to the PDF file within Zenodo is helpful for users.
Consider removing one of the empty lines between the callout opening and content for consistent spacing:
::: {.callout-note appearance="simple" icon=false} - For this paper, slides are available [on Zenodo (PDF)](https://zenodo.org/records/13908208/files/471_DigiHistCH24_AI-assistedSearch_Presentation.pdf). :::
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (18)
submissions/405/index.qmd(1 hunks)submissions/427/index.qmd(1 hunks)submissions/428/index.qmd(1 hunks)submissions/429/index.qmd(1 hunks)submissions/438/index.qmd(1 hunks)submissions/444/index.qmd(1 hunks)submissions/445/index.qmd(1 hunks)submissions/450/index.qmd(3 hunks)submissions/452/index.qmd(2 hunks)submissions/457/index.qmd(1 hunks)submissions/459/index.qmd(1 hunks)submissions/460/index.qmd(1 hunks)submissions/471/index.qmd(1 hunks)submissions/482/index.qmd(1 hunks)submissions/687/index.qmd(1 hunks)submissions/poster/440/index.qmd(1 hunks)submissions/poster/463/index.qmd(1 hunks)submissions/poster/484/index.qmd(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (15)
- submissions/482/index.qmd
- submissions/459/index.qmd
- submissions/457/index.qmd
- submissions/460/index.qmd
- submissions/428/index.qmd
- submissions/poster/463/index.qmd
- submissions/438/index.qmd
- submissions/450/index.qmd
- submissions/444/index.qmd
- submissions/405/index.qmd
- submissions/poster/484/index.qmd
- submissions/445/index.qmd
- submissions/427/index.qmd
- submissions/687/index.qmd
- submissions/poster/440/index.qmd
🔇 Additional comments (7)
submissions/452/index.qmd (3)
36-40: LGTM! Well-implemented callout for presentation slides
The callout effectively implements the suggestion from PR comments to make presentations more accessible. The implementation follows Quarto markdown best practices.
46-48: Remaining content duplication in extended abstract
While the addition of random sampling results improves the content, the first three paragraphs still contain substantial duplication from the abstract section.
Consider further revising to minimize redundancy:
- Remove duplicated introductory content
- Start directly with the unique findings about random sampling
- Expand on the methodology and results
29-33: Verify DOI accessibility and link consistency
The DOI and presentation slides link to the same Zenodo record. Since the PR objectives mention that some DOIs are currently inactive, let's verify the accessibility.
✅ Verification successful
DOI and Zenodo record are accessible and properly configured
The verification shows that:
- The DOI (10.5281/zenodo.13904600) properly redirects (HTTP 302)
- The Zenodo record is accessible (HTTP 200)
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if the DOI resolves and the Zenodo record is accessible
# Expected: Should return HTTP 200 if accessible
echo "Checking DOI resolution..."
curl -sI "https://doi.org/10.5281/zenodo.13904600" | head -n1
echo "Checking Zenodo record..."
curl -sI "https://zenodo.org/records/13904600" | head -n1
Length of output: 272
submissions/471/index.qmd (1)
41-41: Verify the Zenodo DOI link accessibility.
The Zenodo DOI link format is correct, but let's verify its accessibility since the PR mentions some DOIs are currently inactive.
submissions/429/index.qmd (3)
35-39: LGTM! Well-implemented callout for presentation slides
The callout implementation follows Quarto's syntax correctly and aligns with the PR suggestion to make presentations more visible.
26-28: Verify the future dates and DOI accessibility
The dates are set in the future (September and November 2024), which seems unusual. Additionally, the Zenodo DOI should be verified for accessibility.
29-31: Verify the presentation slides link structure
The link uses the same DOI as the metadata. Ensure this is the correct link for the presentation slides specifically.
Pull request
Proposed changes
After this PR is merged, I will generate the PDFs for the abstracts and upload them to Zenodo. All DOIs have already been reserved in draft mode.
Types of changes
Checklist
Co-authored-by: Name <[email protected]>.Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Chores