rnaglib issues
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues
2023-02-27T14:31:53Z
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/14
`graph_from_pdbid` add automatic download if pdb missing
2023-02-27T14:31:53Z
Carlos GO
`graph_from_pdbid` add automatic download if pdb missing
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/1
error when running main.py in prepare_data
2022-01-12T16:47:53Z
Seraphin Bassas
error when running main.py in prepare_data
Hi,
I've been following the instructions to prepare PDB data as indicated in the README.md in rnaglib/rnaglib/prepare_data and I've been running into a few errors:
1. for main.py and the first example I was trying to run from rnaglib, I...
Hi,
I've been following the instructions to prepare PDB data as indicated in the README.md in rnaglib/rnaglib/prepare_data and I've been running into a few errors:
1. for main.py and the first example I was trying to run from rnaglib, I was denied access when trying to run the scripts and have to run the `chmod` command to get permission to access the files
2. once this is done, the files are not executable as python files on my machine and I have to shebang them to get them to recognize the import statements being used. But once I do this it seems like things work.
3. when running main.py in prepare_data, I keep running into two problems: either the options mentioned in the README.md and in the argparser in the main.py file are not recognized:
![Screen_Shot_2021-10-07_at_8.05.45_PM](/uploads/20618b83769f1a1a300d6ba3abf3e4a5/Screen_Shot_2021-10-07_at_8.05.45_PM.png)
or I get the following error message:
![Screen_Shot_2021-10-07_at_8.09.28_PM](/uploads/d619c5f403f3759f744c682fc2ea98f7/Screen_Shot_2021-10-07_at_8.09.28_PM.png)
I'm running on IOS with Python 3.8.8
Thank you,
Séraphin
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/13
Include necessary download calls for examples to work
2023-01-12T15:23:34Z
Carlos GO
Include necessary download calls for examples to work
Example 2 doesn't work if you don't pass the right flags to `rnaglib_download`
Example 2 doesn't work if you don't pass the right flags to `rnaglib_download`
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/6
Linkify missing with docs build
2021-11-24T10:31:55Z
Carlos GO
Linkify missing with docs build
It seems 'linkify' was enabled in the conf.py. After I `pip install linkify` I still get the error:
```
/anaconda3/envs/rnaglib/lib/python3.9/site-packages/markdown_it/rules_core/linkify.py", line 31, in linkify
raise ModuleNotFoun...
It seems 'linkify' was enabled in the conf.py. After I `pip install linkify` I still get the error:
```
/anaconda3/envs/rnaglib/lib/python3.9/site-packages/markdown_it/rules_core/linkify.py", line 31, in linkify
raise ModuleNotFoundError("Linkify enabled but not installed.")
ModuleNotFoundError: Linkify enabled but not installed.
```
Is this module necessary or am i doing something wrong to build the docs?
```
make html
```
Jonathan Broadbent
Jonathan Broadbent
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/12
rna_draw save option sends file to path in site-packages
2022-07-25T14:13:48Z
Carlos GO
rna_draw save option sends file to path in site-packages
See line https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/blob/main/rnaglib/drawing/rna_draw.py#L157
Should just accept the value of `save` e.g.
```python
rna_draw(g, save='/my/path.pdf')
```
See line https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/blob/main/rnaglib/drawing/rna_draw.py#L157
Should just accept the value of `save` e.g.
```python
rna_draw(g, save='/my/path.pdf')
```
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/9
Testing issue creation with fresh profile
2021-11-30T15:18:12Z
Vincent MALLET
Testing issue creation with fresh profile
Hello, this is Vincent trying to submit an issue with a fresh profile
Hello, this is Vincent trying to submit an issue with a fresh profile