Fix scanpy by using profile

[mvdbeek]

numba write to the code directory or the home directory, neither of which is or should be writable. The profile version ensures this is written to an isolated home_dir for the job.

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[mvdbeek]

Huh, containerized test passed while the Conda test fails with

| Dataset Job Standard Error:
|  Traceback (most recent call last):
|  File "/tmp/tmppX0FjK/job_working_directory/000/2/tmpcO_7Mi", line 21, in <module>
|  copy=False)
|  File "/home/travis/miniconda3/envs/mulled-v1-141253bb58fad23ac50749589168696eca3ed3ab1e99608dbf718dbfa9556234/lib/python3.6/site-packages/scanpy/tools/_louvain.py", line 120, in louvain
|  import louvain
|  ModuleNotFoundError: No module named 'louvain'

[mvdbeek]

OK, louvain has actually been removed at bioconda/bioconda-recipes@8cbb444#diff-42a29748c004d0dde077e3b41b022f3c, but the container wasn't rebuilt. So I guess we should add louvain as a separate requirement.

[bgruening]

Mh, the container is here: 1.4.4.post1--py_1 ... https://quay.io/repository/biocontainers/scanpy?tab=tags isn't it?

[mvdbeek]

Hmm, the container seems to contain louvain, which it shouldn't according to the recipe ...:

Unable to find image 'quay.io/biocontainers/scanpy:1.4.4.post1--py_1' locally
1.4.4.post1--py_1: Pulling from biocontainers/scanpy
a3ed95caeb02: Already exists
b0dc45cd432d: Already exists
9466b3513669: Already exists
ddd482ea7b54: Already exists
4d69f833b9d8: Already exists
e7c454e5167d: Already exists
e38092b005c0: Already exists
f879b42dfe2b: Already exists
bc6d8d5a56f8: Pull complete
Digest: sha256:4cd4cd9a9c555c8178464ba0b69748938459009958d743dbdd1e100436b4fb0d
Status: Downloaded newer image for quay.io/biocontainers/scanpy:1.4.4.post1--py_1
bash-4.2# python
Python 3.7.3 | packaged by conda-forge | (default, Jul  1 2019, 21:52:21)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import louvain
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'louvain'
>>> import scanpy as sc
>>> sc.tl.louvain
<function louvain at 0x7fe4b2579730>
>>> sc.tl.louvain()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: louvain() missing 1 required positional argument: 'adata'
>>> sc.tl.louvain('')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.7/site-packages/scanpy/tools/_louvain.py", line 95, in louvain
    if adjacency is None and 'neighbors' not in adata.uns:
AttributeError: 'str' object has no attribute 'uns'

Hah, it doesn't contain louvain, and yet it's not failing ... that isn't good :/
fwiw the louvain import is buried here: https://github.com/theislab/scanpy/blob/master/scanpy/tools/_louvain.py#L131
In any case we need to add louvain as a dependency to scanpy_cluster_reduce_dimension

[bebatut]

Yep we will need louvain for sure.
I have also some local changes to the wrappers and was planning also to update to the latest version. I will wait for your changes to add mine

[mvdbeek]

This is ready for review

[bgruening]

@bebatut do you want to add your changes to this branch?

[mvdbeek]

Let's try to keep the changes frequent and small, this will help with debugging and reviewing.

[bebatut]

I will add the changes in another PR as they are not ready