Better doc #82
Better doc #82
Conversation
calour/analysis.py
Outdated
|
|
||
| Returns | ||
| ------- | ||
| newexp : :class:`.Experiment` | ||
| The experiment with only significant (FDR<=maxfval) difference, sorted according to difference | ||
| ''' | ||
| if random_seed is not None: |
There was a problem hiding this comment.
what is the behavior if it is None?
There was a problem hiding this comment.
it says in the docstring... added also a comment before this line.
The idea is if None, don't touch it (so each time you get random results)
| try: | ||
| lines.append('feature IDs: %r' % self.feature_metadata.index) | ||
| except AttributeError: | ||
| lines.append('No feature metadata') |
There was a problem hiding this comment.
you think it prints too much? :)
There was a problem hiding this comment.
then could you rewrite the printout? like we don't need ------- any more.
There was a problem hiding this comment.
changed to:
class (description) with X samples, Y features
calour/filtering.py
Outdated
| @@ -422,6 +422,10 @@ def filter_abundance(exp: Experiment, min_abundance, **kwargs): | |||
| min_abundance : numeric | |||
| The minimal total abundance for each feature over all samples | |||
|
|
|||
| Other parameters | |||
There was a problem hiding this comment.
let's call this kwargs parameters?
There was a problem hiding this comment.
"Other parameters" is hard coded into docrep (part of the numpy doc standard)
Since docrep is just one file (the init.py), we can copy it into calour and then change it so it will also include kwargs parameters etc.
I think it will also be better to include it in calour since then we remove the dependency on a (very small) package that may change in the future without us knowing.
Alternatively, we can fork docrep and use the fork for installation (but then install will be via github... but that's also fine...).
or we can use the current docrep from its repository and keep it as Other Parameters...
what do you think?
There was a problem hiding this comment.
ok - let's copy it? if license allows
There was a problem hiding this comment.
license is currently GPL-2. I posted a question to the author if it's ok to copy/modify and use in our BSD-3 project. Let's hope he says it ok :).
calour/filtering.py
Outdated
|
|
||
| Parameters | ||
| ---------- | ||
| cutoff : float (optional) | ||
| The minimal mean abundance fraction (out of the mean of total abundance per sample) for a feature in order | ||
| to keep it. Default is 0.01 - keep features with mean abundance >=1% of mean total abundance per sample | ||
|
|
||
| Other parameters |
calour/heatmap/heatmap.py
Outdated
|
|
||
|
|
||
| logger = getLogger(__name__) | ||
|
|
||
|
|
||
| def _create_plot_gui(exp, gui='cli', databases=('dbbact',), tree_size=0): | ||
| def _create_plot_gui(exp: Experiment, gui='cli', databases=('dbbact',), tree_size=0): |
There was a problem hiding this comment.
this should not need type hint of ": Experiment", but it does not hurt.
There was a problem hiding this comment.
removed for consistency
| This GUI only enables the zooming/panning and displays information following a mouse click | ||
| in the terminal window | ||
|
|
||
| Other Parameters |
| def __init__(self, *kargs, **kwargs): | ||
| '''Init the GUI using the Qt5 framework. | ||
|
|
||
| Other Parameters |
| @@ -63,6 +67,10 @@ def sort_centroid(exp: Experiment, transform=log_n, inplace=False, **kwargs): | |||
| kwargs : dict | |||
| additional keyword parameters passed to ``transform``. | |||
|
|
|||
| Other Parameters | |||
| ---------------- | |||
| @@ -14,3 +14,4 @@ ipywidgets | |||
| numpydoc | |||
| sphinx | |||
| sphinx_bootstrap_theme | |||
| pandoc | |||
There was a problem hiding this comment.
pandoc is required for the nbsphinx. since nbsphinx is not in conda, we pip install it, but better to have pandoc from conda?
or do you think there's a better way to do it?
calour/training.py
Outdated
|
|
||
| # See Also | ||
| # -------- | ||
| # :class:`sklearn.preprocessing.OneHotEncoder` |
There was a problem hiding this comment.
understand you changed repr, but why other lines of docstring are commented out?
There was a problem hiding this comment.
uncommented and fixed to new repr results
|
and |
|
should we remove or merge the |
|
ok, fixed everything except the "Other Parameters" (since hardcoded in docrep) and the location for the docs notebooks |
calour/io.py
Outdated
| @@ -466,6 +382,90 @@ def read_amplicon(data_file, sample_metadata_file=None, | |||
| return exp | |||
|
|
|||
|
|
|||
| @ds.with_indent(4) | |||
| def read_open_ms(data_file, sample_metadata_file=None, gnps_file=None, feature_metadata_file=None, | |||
There was a problem hiding this comment.
this whole function is relocated? it's hard to see if there is any changes...
There was a problem hiding this comment.
just relocated since i think otherwise docrep has problems since the function for which we need the kwargs parameters list is after the function that needs to print them.
not changes otherwise
|
ok. |
|
ok, fixed the kwargs and moved notebooks to /docs/source/notebooks/ |
improve sphinx documentation:
Remove travis sphinx error which is due to sphinx-autodoc-typehints and the way we add functions to the Experiment class. Currently just removed sphinx-autodoc-typehints. Maybe can fix deeper
Change the Experiment.repr to remove the sample and feature list since in most cases it is huge, ugly and not useful
Add random_seed to diff_abundance to enable totally reproducible results.
and small goodies