pyopenms-docs

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formula notation not correct

10

**Describe the problem you encountered**  should be something like [2M+H]^{2+} **Documentation version**

timosachsenberg

Find a way to automatically update versions at release

2

in conf.py and switcher.json

jpfeuffer

Create Vector wrapper for PeptideIdentifications and ProteinIdentifications

1

And provide overloads for certain functions that return a list of PeptideIdentifications to return this Wrapper instead. Avoids copying everything, allows us to provide convenience functions (toNDArray, toArrow) and iteration...

jpfeuffer

They are apparently declared as "output" not "python" because they are not working. ``` --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) Cell In[8], line 34 31 consumer = oms.PlainMSDataWritingConsumer(outputfile) 32...

jpfeuffer

Translate dataframes functions to cython

1

Faster and avoids monkeypatching the original class.

jpfeuffer

To get rid of the awkward master+ipynb branch. Just copy the action to postBuild.

jpfeuffer

:py:class: references look weird in ipynb notebooks

1

We either need another pandoc filter to convert them to something meaningful, or try a different converter e.g. jupytext.

jpfeuffer

Update wrap_classes.rst with newest changes in autowrap

1

I think parts of it are not up-to-date anymore. E.g. I think you should use `const` specifiers now. Especially on libcpp objects like lists, where you can skip the copy-back...

jpfeuffer

500+ warnings and a few errors on RTD and local

1

Ref: ### RTD - https://readthedocs.org/api/v2/build/17828710.txt - example: https://github.com/search?q=org%3AOpenMS+pseudocode&type=code ### Local

tapaswenipathak

timosachsenberg