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@gorostiolam Great talktorial, thanks for your contribution! I reviewed the theory part for now, and only added small comments (see above). Let me know if you have any questions.
@dominiquesydow fell free to continue with the code parts.

Great, thanks a lot - I'll take over tomorrow evening!

@AndreaVolkamer thanks for the comments! I have implemented them and will do the same when the code revision by @dominiquesydow is done.

Hi everyone,

This is shaping up beautifully!!

I am pushing the following updates:

• By default no email address (instructions for user to set email if interested in using ClustalO with their own data; otherwise using pre-calculated aligned_sequences.aln-fasta.fasta; updated gitignore accordingly --- definitely up for discussion
• Enabled website rendering, if you'd like to see the rendering for yourself, follow instructions here
• Minor sorting update on imports, e.g. no paragraphs between third party imports
• Uniprot > UniProt (was a mix)
• Fix website rendering issues, e.g. always new paragraph before lists

Open TODOs still:

• Proofread the rendered website (apparently, we cannot have HTML tags such as <b> but need Markdown **, at least I do not see any formatting)
• At the end: Env file and CI set for all notebooks (currently only T032 for a faster CI check)
• At the end: black-nb and README generator
• @AndreaVolkamer, thanks a lot for looking into ClustalO alternatives! I do not have the bandwidth at the moment to adapt this; ClustalO seems like a commonly used service for this task, hence IMO good to showcase it here but definitely worth looking into the alternative more (maybe as a start raising this in the discussion and adapt in the future?)

Hi everyone,

This is shaping up beautifully!!

I am pushing the following updates:

• By default no email address (instructions for user to set email if interested in using ClustalO with their own data; otherwise using pre-calculated aligned_sequences.aln-fasta.fasta; updated gitignore accordingly --- definitely up for discussion
• Enabled website rendering, if you'd like to see the rendering for yourself, follow instructions here
• Minor sorting update on imports, e.g. no paragraphs between third party imports
• Uniprot > UniProt (was a mix)
• Fix website rendering issues, e.g. always new paragraph before lists

Open TODOs still:

• Proofread the rendered website (apparently, we cannot have HTML tags such as <b> but need Markdown **, at least I do not see any formatting)
• At the end: Env file and CI set for all notebooks (currently only T032 for a faster CI check)
• At the end: black-nb and README generator
• @AndreaVolkamer, thanks a lot for looking into ClustalO alternatives! I do not have the bandwidth at the moment to adapt this; ClustalO seems like a commonly used service for this task, hence IMO good to showcase it here but definitely worth looking into the alternative more (maybe as a start raising this in the discussion and adapt in the future?)

Hi!

These commits seem very appropriate! I agree that adding the option to read pre-computed ClustalO alignment or otherwise use your own email is probably the easiest fix here!

Regarding website rendering, I also cannot see formatting so indeed HTML tags will need to be substituted by Markdown. I have committed an update from HTML to Markdown formatting and now it renders correctly for me.

Hi @gorostiolam, my apologies for the hold-up from my side, I will get back onto this PR tonight - thank you very much for the updates on the Markdown rendering!

@AndreaVolkamer, I am trying out if installing the pip dependencies within the notebook itself works as an intermediate solution (would avoid installing many new packages for the full TOC stack).

Would look like this in the notebook:

Before we start, let's install a few packages that are not part of TeachOpenCADD's global enviroment file because they are only relevant to this notebook (this setup will change in the future, see discussion here).
!pip install prodec rich-msa xmltramp2
!pip install git+https://github.com/OlivierBeq/Papyrus-scripts.git

With a comment in our env file:

Remaining TODOs:

• Set env file and CI for all notebooks (currently only T032 for a faster CI check)
• Check upcoming CI fails
• Check Windows fail for T032 > for now no support under Windows: Note: T032 not available under Windows #318

In 8769fd5, T018 fails in this new environment for all but Ubuntu Python 3.9. Difference in environment:

# packages in passing Ubuntu Py3.9 version - 426
# packages in failing Ubuntu Py3.8 version - 425

name            python
pass_version    3.9.15
fail_version    3.8.15
Name: 306, dtype: object
name            python_abi
pass_version           3.9
fail_version           3.8
Name: 312, dtype: object
name            tzdata
pass_version     2022g
fail_version       NaN
Name: 388, dtype: object

Wait for next CI run to end - same issue?

Locally (MacOS, M1 chip) all tests pass for Python 3.9:

986 passed, 2 skipped, 56 warnings

we observed this issue #358 when running the code locally, needs to be addressed, before potential merge.

@mbackenkoehler just wondering if we could include this now, given that we are updating the environments anyways?