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incorrectly formatted yaml file for long file name #3119
Description
Is there an existing issue for this?
- I have searched the existing issues
Operating System
windows
DeepLabCut version
'3.0.0rc13'
What engine are you using?
pytorch
DeepLabCut mode
single animal
Device type
5090
Bug description 🐛
Hi,
The config YAML cannot handle a long file name with a space; whenever I call deeplabcut.convertcsv2h5, it attempts to format my config file and eventually make the YAML invalid. I think the root cause is that ruamel.yaml cannot reliably store the YAML setting. Here is a simple repex
from ruamel.yaml import YAML
ruamelFile = YAML()
# a dummpy config file
cfg = {
'video_sets': {
'G:/My Drive/lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllong_name.mp4': {
'crop': [0, 1280, 0, 720]
}
}
}
# save to yaml
with open("test.yaml", "w") as cf:
ruamelFile.dump(cfg, cf)
# Error: mapping values are not allowed here
with open("test.yaml", "r") as f:
cfg = ruamelFile.load(f)
Here is the resulting YAML:
video_sets:
G:/My
Drive/lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllong_name.mp4:
crop:
- 0
- 1280
- 0
- 720
It seems like ruamelFile.dump is not happy with the space in the video path. However, there is no way for me to avoid it since it is a Google Drive. using ruamelFile = YAML(typ="full") can solve the issue, but it will result in an unreadable YAML (I assume the motivation for using ruamel is readability? Otherwise yaml package can dump the data perfectly fine)
I found a similar issue in this repository: #3063
Steps To Reproduce
No response
Relevant log output
Anything else?
This is the actual config file deeplabcut.convertcsv2h5 will create
# Project definitions (do not edit)
Task: Sleap_Rat_test
scorer: T
date: Oct2
multianimalproject: false
identity:
# Project path (change when moving around)
project_path: G:\My
Drive\projects\Green_Tom\rat_pose\post_model\projects\rat_pose
# Default DeepLabCut engine to use for shuffle creation (either pytorch or tensorflow)
engine: pytorch
# Annotation data set configuration (and individual video cropping parameters)
video_sets:
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai1.mp4:
crop: 0, 1280, 0, 720
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai2.mp4:
crop: 0, 1280, 0, 720
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai3.mp4:
crop: 0, 1280, 0, 720
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai4.mp4:
crop: 0, 1280, 0, 720
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai5.mp4:
crop: 0, 1280, 0, 720
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai6.mp4:
crop: 0, 1280, 0, 720
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai7.mp4:
crop: 0, 1280, 0, 720
G:/My
Drive/projects/Green_Tom/rat_pose/post_model/projects/rat_pose/videos/ai8.mp4:
crop: 0, 1280, 0, 720
G:\My Drive\projects\Green Tom\rat_pose\post_model\videos\Camera4_stitched.mp4:
crop: 0, 1280, 0, 720
G:\My Drive\projects\Green Tom\rat_pose\post_model\videos\RAT 11 FR1.mp4:
crop: 0, 1280, 0, 720
bodyparts:
- head
- nose
- spine1
- spine2
- spine3
- tailbase
- tail1
- tail2
- tail_tip
- L_hip
- L_backpaw
- R_backpaw
- L_shoulder
- R_frontpaw
- R_shoulder
- R_hip
- R_knee
- L_knee
- L_frontpaw
# Fraction of video to start/stop when extracting frames for labeling/refinement
start: 0
stop: 1
numframes2pick: 20
# Plotting configuration
skeleton:
- - head
- nose
- - head
- spine1
- - spine1
- spine2
- - spine2
- spine3
- - spine1
- L_shoulder
- - L_shoulder
- L_frontpaw
- - spine3
- L_hip
- - L_hip
- L_knee
- - L_knee
- L_backpaw
- - spine3
- tailbase
- - tailbase
- tail1
- - tail1
- tail2
- - tail2
- tail_tip
- - spine1
- R_shoulder
- - R_shoulder
- R_frontpaw
- - spine3
- R_hip
- - R_hip
- R_knee
- - R_knee
- R_backpaw
skeleton_color: black
pcutoff: 0.6
dotsize: 12
alphavalue: 0.7
colormap: rainbow
# Training,Evaluation and Analysis configuration
TrainingFraction:
- 0.95
iteration: 0
default_net_type: resnet_50
default_augmenter: default
snapshotindex: -1
detector_snapshotindex: -1
batch_size: 8
detector_batch_size: 1
# Cropping Parameters (for analysis and outlier frame detection)
cropping: false
#if cropping is true for analysis, then set the values here:
x1: 0
x2: 640
y1: 277
y2: 624
# Refinement configuration (parameters from annotation dataset configuration also relevant in this stage)
corner2move2:
- 50
- 50
move2corner: true
# Conversion tables to fine-tune SuperAnimal weights
SuperAnimalConversionTables:
It might be somehow related to the recent change in ruamel-yaml. Downgrading ruamel in the package requirement might help.
https://sourceforge.net/p/ruamel-yaml/tickets/546/
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Activity
toniklenk commentedon Nov 4, 2025
i have a similar issue, triggered if a long filename gets a line break inserted upon using deeplabcut.add_new_video
AlexEMG commentedon Nov 5, 2025
Ok, here is a quick fix for the broken config file, can you just manually write:
Fix ruamel.yaml dumping issue causing YAML corruption for long video …
Jiefei-Wang commentedon Nov 13, 2025
Thanks for the reply. I see DEEPLABCUT always format my relative path to the full path. Is there any motivation to use the full video path in the config file? Since the videos are always in the project folder, I'm having a feeling that a relative path (relative to the project path) is a better way to store the path.
deruyter92 commentedon Dec 18, 2025
@Jiefei-Wang, glad the quick fix worked for you. It was an issue with one of the packages that we are using, and we are currently implementing a more permanent fix to prevent this happening in the future. To address your last question: for some functions (e.g. video inference) the videos don't need to be inside the project folder. Also some of our scripts change the current working directory. Specifying the full path is a design choice that currently works best. Thanks nevertheless for sharing your feedback.
Fix ruamel.yaml dumping issue causing YAML corruption for long video …
fix ruamel.yaml dumping newline for long filenames (DeepLabCut#3140)