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[BUG]: relative path in with block in YAML is interpreted relative from YAML, but copy operation to junifer jobs directory interprets relative to working directory. #224

Merged
synchon merged 3 commits from fix/with-section-file-copying into main 2023-11-17 11:44:50 +00:00
Conversation 9 Commits 3 Files changed 3 +13 -1
synchon commented 2023-11-07 15:37:03 +00:00 (Migrated from github.com)
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Is there an existing issue for this?

  • I have searched the existing issues

Current Behavior

I have the following directory structure:

❱ tree                                                                                                                                                   1 !
.
├── 01_queue.sh
├── junifer_extensions
│   ├── juni-farm
│   │   ├── juni_farm
│   │   │   └── datagrabber
│   │   │       ├── hcp_aging.py
│   │   │       ├── hcp_early_psychosis.py
│   │   │       ├── hcp_ya_confounds_cat.py
│   │   │       └── __pycache__
│   │   │           └── hcp_ya_confounds_cat.cpython-310.pyc
│   │   ├── LICENSE
│   │   └── README.md
│   ├── markers
│   └── parcellations
│       ├── data
│       │   ├── README.md
│       │   └── shen_1mm_268_parcellation.nii.gz
│       ├── __pycache__
│       │   └── register_parcellations.cpython-310.pyc
│       └── register_parcellations.py
├── junifer_jobs
│   └── PREPROCESS_HCP1200
└── yamls
    └── hcp_ya.yaml

The top level directory here is my working directory. The code in 01_queue.sh is:

#!/usr/bin/zsh
# 
# Run this code to create the junifer_jobs directory
junifer queue yamls/${1}.yaml

I run 01_queue.sh hcp_ya which performs junifer queue with the hcp_ya.yaml

The content of that yaml file is:

❱ cat yamls/hcp_ya.yaml                                                                                                                                  1 !
workdir: /tmp

with:
  - ../junifer_extensions/parcellations/register_parcellations.py
  - ../junifer_extensions/juni-farm/juni_farm/datagrabber/hcp_ya_confounds_cat.py


datagrabber:
    kind: MultipleHCP
    tasks:
      - REST1
      - REST2

preprocess:
    kind: fMRIPrepConfoundRemover
    detrend: true
    standardize: true
    strategy:
        wm_csf: full
        global_signal: full
    low_pass: 0.08
    high_pass: 0.01
    masks:
      - compute_epi_mask
      - compute_brain_mask
      - threshold: 0

storage:
  kind: HDF5FeatureStorage
  uri: ../../../data/junifer_storage/hcp_ya/hcp_ya.hdf5


markers:
   
  - name: parc-Finn2015Shen268_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: Finn2015Shen268
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
  
  - name: parccortical-Schaefer100x17FSLMNI_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer100x17
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
        
  - name: parccortical-Schaefer200x17FSLMNI_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer200x17
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
  
  - name: parccortical-Schaefer400x17FSLMNI_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer400x17
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit

  - name: parccortical-Schaefer100x7FSLMNI_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer100x7
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
        
  - name: parccortical-Schaefer200x7FSLMNI_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer200x7
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
  
  - name: parccortical-Schaefer400x7FSLMNI_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer400x7
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
  

queue:
  jobname: PREPROCESS_HCP1200
  kind: HTCondor
  env:
    kind: conda
    name: network-stacking-env
  mem: 8G
  verbose: 8

Of course, looking at the with block in the yaml, the file paths are relative from the YAML file:


with:
  - ../junifer_extensions/parcellations/register_parcellations.py
  - ../junifer_extensions/juni-farm/juni_farm/datagrabber/hcp_ya_confounds_cat.py

However when I run this I get:

❱ ./01_queue.sh hcp_ya                  
2023-05-10 08:45:29,730 - JUNIFER - INFO - ===== Lib Versions =====
2023-05-10 08:45:29,730 - JUNIFER - INFO - numpy: 1.23.5
2023-05-10 08:45:29,731 - JUNIFER - INFO - scipy: 1.10.1
2023-05-10 08:45:29,731 - JUNIFER - INFO - pandas: 1.5.3
2023-05-10 08:45:29,731 - JUNIFER - INFO - nilearn: 0.10.0
2023-05-10 08:45:29,731 - JUNIFER - INFO - nibabel: 4.0.2
2023-05-10 08:45:29,731 - JUNIFER - INFO - junifer: 0.0.3.dev71
2023-05-10 08:45:29,731 - JUNIFER - INFO - ========================
2023-05-10 08:45:29,731 - JUNIFER - INFO - Parsing yaml file: /data/project/identification_prediction/projects/network-stacking/code/preprocessing/yamls/hcp_ya.yaml
================================================================================
Registering: Finn2015Shen268
================================================================================
2023-05-10 08:45:29,761 - JUNIFER - INFO - Registering HCPCATConfounds in datagrabber
2023-05-10 08:45:29,761 - JUNIFER - INFO - Registering MultipleHCP in datagrabber
2023-05-10 08:45:29,761 - JUNIFER - INFO - Creating job in /data/project/identification_prediction/projects/network-stacking/code/preprocessing/junifer_jobs/PREPROCESS_HCP1200
Traceback (most recent call last):
  File "/home/lsasse/miniconda3/envs/network-stacking-env/bin/junifer", line 8, in <module>
    sys.exit(cli())
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/cli.py", line 250, in queue
    api_queue(
  File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/functions.py", line 264, in queue
    shutil.copy(item, jobdir)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/shutil.py", line 417, in copy
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/shutil.py", line 254, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '../junifer_extensions/parcellations/register_parcellations.py'

Thinking, that maybe files have to be relative from working directory, I then tried to change this to:

with:
  - junifer_extensions/parcellations/register_parcellations.py
  - junifer_extensions/juni-farm/juni_farm/datagrabber/hcp_ya_confounds_cat.py

But using that I get:

❱ ./01_queue.sh hcp_ya                                                                                                                                   1 !
2023-05-10 08:47:09,779 - JUNIFER - INFO - ===== Lib Versions =====
2023-05-10 08:47:09,779 - JUNIFER - INFO - numpy: 1.23.5
2023-05-10 08:47:09,779 - JUNIFER - INFO - scipy: 1.10.1
2023-05-10 08:47:09,779 - JUNIFER - INFO - pandas: 1.5.3
2023-05-10 08:47:09,779 - JUNIFER - INFO - nilearn: 0.10.0
2023-05-10 08:47:09,779 - JUNIFER - INFO - nibabel: 4.0.2
2023-05-10 08:47:09,779 - JUNIFER - INFO - junifer: 0.0.3.dev71
2023-05-10 08:47:09,779 - JUNIFER - INFO - ========================
2023-05-10 08:47:09,779 - JUNIFER - INFO - Parsing yaml file: /data/project/identification_prediction/projects/network-stacking/code/preprocessing/yamls/hcp_ya.yaml
2023-05-10 08:47:09,808 - JUNIFER - ERROR - File in 'with' section does not exist: yamls/junifer_extensions/parcellations/register_parcellations.py
Traceback (most recent call last):
  File "/home/lsasse/miniconda3/envs/network-stacking-env/bin/junifer", line 8, in <module>
    sys.exit(cli())
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/cli.py", line 244, in queue
    config = parse_yaml(filepath)  # type: ignore
  File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/parser.py", line 59, in parse_yaml
    raise_error(
  File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/utils/logging.py", line 289, in raise_error
    raise klass(msg)
ValueError: File in 'with' section does not exist: yamls/junifer_extensions/parcellations/register_parcellations.py

Expected Behavior

I think it should just work with relative paths, relative from the YAML directory, even if the working directory is another.

Just to be clear I fixed the issue by adjusting the code in 01_queue.sh to this:

#!/usr/bin/zsh
# 
# Run this code to create the junifer_jobs directory
cd yamls
junifer queue ${1}.yaml
cd ..

With that it works, but I think that is somewhat beside the point. In my understanding the previous version should also work.
Also, of course, this puts the junifer jobs directory under the yamls directory which is not what i want. I could also put absolute paths (and will for now), but I would prefer relative paths.

Steps To Reproduce

I think I gave everything needed above. Junifer wtf is below.

Environment

❱ junifer wtf
junifer:
  version: 0.0.3.dev71
python:
  version: 3.10.8
  implementation: CPython
dependencies:
  click: 8.1.3
  numpy: 1.23.5
  datalad: 0.18.3
  pandas: 1.5.3
  nibabel: 4.0.2
  nilearn: 0.10.0
  sqlalchemy: 1.4.47
  ruamel.yaml: 0.17.26
system:
  platform: Linux-4.19.0-21-amd64-x86_64-with-glibc2.28
environment:
  LC_CTYPE: en_US.UTF-8
  PATH: 
    /home/lsasse/miniconda3/envs/network-stacking-env/bin:/home/lsasse/miniconda3/condabin:/home/lsasse/bin:/home/lsasse/.dotfiles/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games





### Relevant log output

_No response_

### Anything else?

_No response_
### Is there an existing issue for this? - [X] I have searched the existing issues ### Current Behavior I have the following directory structure: ``` ❱ tree 1 ! . ├── 01_queue.sh ├── junifer_extensions │   ├── juni-farm │   │   ├── juni_farm │   │   │   └── datagrabber │   │   │   ├── hcp_aging.py │   │   │   ├── hcp_early_psychosis.py │   │   │   ├── hcp_ya_confounds_cat.py │   │   │   └── __pycache__ │   │   │   └── hcp_ya_confounds_cat.cpython-310.pyc │   │   ├── LICENSE │   │   └── README.md │   ├── markers │   └── parcellations │   ├── data │   │   ├── README.md │   │   └── shen_1mm_268_parcellation.nii.gz │   ├── __pycache__ │   │   └── register_parcellations.cpython-310.pyc │   └── register_parcellations.py ├── junifer_jobs │   └── PREPROCESS_HCP1200 └── yamls └── hcp_ya.yaml ``` The top level directory here is my working directory. The code in 01_queue.sh is: ``` #!/usr/bin/zsh # # Run this code to create the junifer_jobs directory junifer queue yamls/${1}.yaml ``` I run `01_queue.sh hcp_ya` which performs `junifer queue` with the `hcp_ya.yaml` The content of that yaml file is: ``` ❱ cat yamls/hcp_ya.yaml 1 ! workdir: /tmp with: - ../junifer_extensions/parcellations/register_parcellations.py - ../junifer_extensions/juni-farm/juni_farm/datagrabber/hcp_ya_confounds_cat.py datagrabber: kind: MultipleHCP tasks: - REST1 - REST2 preprocess: kind: fMRIPrepConfoundRemover detrend: true standardize: true strategy: wm_csf: full global_signal: full low_pass: 0.08 high_pass: 0.01 masks: - compute_epi_mask - compute_brain_mask - threshold: 0 storage: kind: HDF5FeatureStorage uri: ../../../data/junifer_storage/hcp_ya/hcp_ya.hdf5 markers: - name: parc-Finn2015Shen268_marker-empiricalFC kind: FunctionalConnectivityParcels parcellation: Finn2015Shen268 cor_method: correlation cor_method_params: empirical: true masks: - inherit - name: parccortical-Schaefer100x17FSLMNI_marker-empiricalFC kind: FunctionalConnectivityParcels parcellation: Schaefer100x17 cor_method: correlation cor_method_params: empirical: true masks: - inherit - name: parccortical-Schaefer200x17FSLMNI_marker-empiricalFC kind: FunctionalConnectivityParcels parcellation: Schaefer200x17 cor_method: correlation cor_method_params: empirical: true masks: - inherit - name: parccortical-Schaefer400x17FSLMNI_marker-empiricalFC kind: FunctionalConnectivityParcels parcellation: Schaefer400x17 cor_method: correlation cor_method_params: empirical: true masks: - inherit - name: parccortical-Schaefer100x7FSLMNI_marker-empiricalFC kind: FunctionalConnectivityParcels parcellation: Schaefer100x7 cor_method: correlation cor_method_params: empirical: true masks: - inherit - name: parccortical-Schaefer200x7FSLMNI_marker-empiricalFC kind: FunctionalConnectivityParcels parcellation: Schaefer200x7 cor_method: correlation cor_method_params: empirical: true masks: - inherit - name: parccortical-Schaefer400x7FSLMNI_marker-empiricalFC kind: FunctionalConnectivityParcels parcellation: Schaefer400x7 cor_method: correlation cor_method_params: empirical: true masks: - inherit queue: jobname: PREPROCESS_HCP1200 kind: HTCondor env: kind: conda name: network-stacking-env mem: 8G verbose: 8 ``` Of course, looking at the with block in the yaml, the file paths are relative from the YAML file: ``` with: - ../junifer_extensions/parcellations/register_parcellations.py - ../junifer_extensions/juni-farm/juni_farm/datagrabber/hcp_ya_confounds_cat.py ``` However when I run this I get: ``` ❱ ./01_queue.sh hcp_ya 2023-05-10 08:45:29,730 - JUNIFER - INFO - ===== Lib Versions ===== 2023-05-10 08:45:29,730 - JUNIFER - INFO - numpy: 1.23.5 2023-05-10 08:45:29,731 - JUNIFER - INFO - scipy: 1.10.1 2023-05-10 08:45:29,731 - JUNIFER - INFO - pandas: 1.5.3 2023-05-10 08:45:29,731 - JUNIFER - INFO - nilearn: 0.10.0 2023-05-10 08:45:29,731 - JUNIFER - INFO - nibabel: 4.0.2 2023-05-10 08:45:29,731 - JUNIFER - INFO - junifer: 0.0.3.dev71 2023-05-10 08:45:29,731 - JUNIFER - INFO - ======================== 2023-05-10 08:45:29,731 - JUNIFER - INFO - Parsing yaml file: /data/project/identification_prediction/projects/network-stacking/code/preprocessing/yamls/hcp_ya.yaml ================================================================================ Registering: Finn2015Shen268 ================================================================================ 2023-05-10 08:45:29,761 - JUNIFER - INFO - Registering HCPCATConfounds in datagrabber 2023-05-10 08:45:29,761 - JUNIFER - INFO - Registering MultipleHCP in datagrabber 2023-05-10 08:45:29,761 - JUNIFER - INFO - Creating job in /data/project/identification_prediction/projects/network-stacking/code/preprocessing/junifer_jobs/PREPROCESS_HCP1200 Traceback (most recent call last): File "/home/lsasse/miniconda3/envs/network-stacking-env/bin/junifer", line 8, in <module> sys.exit(cli()) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/cli.py", line 250, in queue api_queue( File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/functions.py", line 264, in queue shutil.copy(item, jobdir) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/shutil.py", line 417, in copy copyfile(src, dst, follow_symlinks=follow_symlinks) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/shutil.py", line 254, in copyfile with open(src, 'rb') as fsrc: FileNotFoundError: [Errno 2] No such file or directory: '../junifer_extensions/parcellations/register_parcellations.py' ``` Thinking, that maybe files have to be relative from working directory, I then tried to change this to: ``` with: - junifer_extensions/parcellations/register_parcellations.py - junifer_extensions/juni-farm/juni_farm/datagrabber/hcp_ya_confounds_cat.py ``` But using that I get: ``` ❱ ./01_queue.sh hcp_ya 1 ! 2023-05-10 08:47:09,779 - JUNIFER - INFO - ===== Lib Versions ===== 2023-05-10 08:47:09,779 - JUNIFER - INFO - numpy: 1.23.5 2023-05-10 08:47:09,779 - JUNIFER - INFO - scipy: 1.10.1 2023-05-10 08:47:09,779 - JUNIFER - INFO - pandas: 1.5.3 2023-05-10 08:47:09,779 - JUNIFER - INFO - nilearn: 0.10.0 2023-05-10 08:47:09,779 - JUNIFER - INFO - nibabel: 4.0.2 2023-05-10 08:47:09,779 - JUNIFER - INFO - junifer: 0.0.3.dev71 2023-05-10 08:47:09,779 - JUNIFER - INFO - ======================== 2023-05-10 08:47:09,779 - JUNIFER - INFO - Parsing yaml file: /data/project/identification_prediction/projects/network-stacking/code/preprocessing/yamls/hcp_ya.yaml 2023-05-10 08:47:09,808 - JUNIFER - ERROR - File in 'with' section does not exist: yamls/junifer_extensions/parcellations/register_parcellations.py Traceback (most recent call last): File "/home/lsasse/miniconda3/envs/network-stacking-env/bin/junifer", line 8, in <module> sys.exit(cli()) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/lsasse/miniconda3/envs/network-stacking-env/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/cli.py", line 244, in queue config = parse_yaml(filepath) # type: ignore File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/api/parser.py", line 59, in parse_yaml raise_error( File "/data/project/identification_prediction/projects/network-stacking/envs/junifer/junifer/utils/logging.py", line 289, in raise_error raise klass(msg) ValueError: File in 'with' section does not exist: yamls/junifer_extensions/parcellations/register_parcellations.py ``` ### Expected Behavior I think it should just work with relative paths, relative from the YAML directory, even if the working directory is another. Just to be clear I fixed the issue by adjusting the code in `01_queue.sh` to this: ``` #!/usr/bin/zsh # # Run this code to create the junifer_jobs directory cd yamls junifer queue ${1}.yaml cd .. ``` With that it works, but I think that is somewhat beside the point. In my understanding the previous version should also work. Also, of course, this puts the junifer jobs directory under the yamls directory which is not what i want. I could also put absolute paths (and will for now), but I would prefer relative paths. ### Steps To Reproduce I think I gave everything needed above. Junifer wtf is below. ### Environment ```markdown ❱ junifer wtf junifer: version: 0.0.3.dev71 python: version: 3.10.8 implementation: CPython dependencies: click: 8.1.3 numpy: 1.23.5 datalad: 0.18.3 pandas: 1.5.3 nibabel: 4.0.2 nilearn: 0.10.0 sqlalchemy: 1.4.47 ruamel.yaml: 0.17.26 system: platform: Linux-4.19.0-21-amd64-x86_64-with-glibc2.28 environment: LC_CTYPE: en_US.UTF-8 PATH: /home/lsasse/miniconda3/envs/network-stacking-env/bin:/home/lsasse/miniconda3/condabin:/home/lsasse/bin:/home/lsasse/.dotfiles/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games ``` ``` ### Relevant log output _No response_ ### Anything else? _No response_
fraimondo commented 2023-11-07 11:04:58 +00:00 (Migrated from github.com)
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TODO: Fix the with value of the config dict with the absolute path here: github.com/juaml/junifer@f203cd853e/junifer/api/parser.py (L67)

TODO: Fix the `with` value of the `config` dict with the absolute path here: https://github.com/juaml/junifer/blob/f203cd853efab91419a9c380b25d3925db69e2bc/junifer/api/parser.py#L67
synchon commented 2023-11-07 15:37:59 +00:00 (Migrated from github.com)
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@LeSasse Could you check if this branch works with your project setup as you described?

@LeSasse Could you check if this branch works with your project setup as you described?
codecov[bot] commented 2023-11-07 15:38:15 +00:00 (Migrated from github.com)
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Codecov Report

Merging #224 (62567ad) into main (50d0f97) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Additional details and impacted files

Impacted file tree graph

@@           Coverage Diff           @@
##             main     #224   +/-   ##
=======================================
  Coverage   89.80%   89.81%           
=======================================
  Files          99       99           
  Lines        4367     4371    +4     
  Branches      842      842           
=======================================
+ Hits         3922     3926    +4     
  Misses        305      305           
  Partials      140      140
Flag Coverage Δ
docs 100.00% <ø> (ø)
junifer 89.81% <100.00%> (+<0.01%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
junifer/api/parser.py 95.34% <100.00%> (+0.47%) ⬆️
## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/224?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report > Merging [#224](https://app.codecov.io/gh/juaml/junifer/pull/224?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (62567ad) into [main](https://app.codecov.io/gh/juaml/junifer/commit/50d0f970c75baa697fe2949ee14dde29eb82f28a?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (50d0f97) will **increase** coverage by `0.00%`. > The diff coverage is `100.00%`. <details><summary>Additional details and impacted files</summary> [![Impacted file tree graph](https://app.codecov.io/gh/juaml/junifer/pull/224/graphs/tree.svg?width=650&height=150&src=pr&token=5H21JuZXMw&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)](https://app.codecov.io/gh/juaml/junifer/pull/224?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #224 +/- ## ======================================= Coverage 89.80% 89.81% ======================================= Files 99 99 Lines 4367 4371 +4 Branches 842 842 ======================================= + Hits 3922 3926 +4 Misses 305 305 Partials 140 140 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/224/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [docs](https://app.codecov.io/gh/juaml/junifer/pull/224/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `100.00% <ø> (ø)` | | | [junifer](https://app.codecov.io/gh/juaml/junifer/pull/224/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `89.81% <100.00%> (+<0.01%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/juaml/junifer/pull/224?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [junifer/api/parser.py](https://app.codecov.io/gh/juaml/junifer/pull/224?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9hcGkvcGFyc2VyLnB5) | `95.34% <100.00%> (+0.47%)` | :arrow_up: | </details>
github-actions[bot] commented 2023-11-07 15:43:01 +00:00 (Migrated from github.com)
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PR Preview Action v1.4.4
Preview removed because the pull request was closed.
2023-11-17 11:48 UTC
[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.4 :---: Preview removed because the pull request was closed. 2023-11-17 11:48 UTC <!-- Sticky Pull Request Commentpr-preview -->
LeSasse commented 2023-11-07 17:45:20 +00:00 (Migrated from github.com)
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@LeSasse Could you check if this branch works with your project setup as you described?

I can likely do it on friday or early next week.

> @LeSasse Could you check if this branch works with your project setup as you described? I can likely do it on friday or early next week.
synchon commented 2023-11-08 10:33:45 +00:00 (Migrated from github.com)
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@LeSasse Could you check if this branch works with your project setup as you described?

I can likely do it on friday or early next week.

Sure, take your time.

> > @LeSasse Could you check if this branch works with your project setup as you described? > > I can likely do it on friday or early next week. Sure, take your time.
LeSasse commented 2023-11-17 08:05:46 +00:00 (Migrated from github.com)
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@synchon this works in my project folder now.

@synchon this works in my project folder now.
synchon commented 2023-11-17 09:32:02 +00:00 (Migrated from github.com)
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@synchon this works in my project folder now.

Thanks for verifying :)

> @synchon this works in my project folder now. Thanks for verifying :)
fraimondo (Migrated from github.com) approved these changes 2023-11-17 10:09:10 +00:00
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