Antoine

[AntoinePassemiers]

• Combined pycistopic and scenicplus into a single script.
• Added TF list to the single-omics methods that allow it.
• Added TF list to reg2 evaluation method.

NOTE: I think using anndata to save the results of reg1 and reg2 is not appropriate, as anndata was not designed to store such data. Moreover, reg2 now gives me the following error:
Traceback (most recent call last):
File "/viash_automount/tmp/viash-run-regression_2-jvcvex.py", line 66, in
output = ad.AnnData(
^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/anndata/_core/anndata.py", line 291, in init
self._init_as_actual(
File "/usr/local/lib/python3.11/site-packages/anndata/_core/anndata.py", line 475, in _init_as_actual
{'dataset_id': 'scgen_pearson', 'method_id': 'reg2-None', 'metric_ids': array(['static-theta-0.0', 'static-theta-0.5', 'static-theta-1.0', 'Mean'],
dtype=object), 'metric_values': array([0.03201749, 0.24454853, 0.51412799, 0.26356467])}
X = np.array(X, dtype, copy=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Unable to avoid copy while creating an array as requested.
If using np.array(obj, copy=False) replace it with np.asarray(obj) to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.

A simpler file format such as json or csv (as it used to be) would be more appropriate.

[janursa]

PR reviewed