Skip to content
New issue

Have a question about this project? # for a free GitHub account to open an issue and contact its maintainers and the community.

#

By clicking “#”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? # to your account

Jump to bottom

module 'numpy' has no attribute 'float'. Did you mean: 'cfloat'? #1181

Closed
Maarten-vd-Sande opened this issue Jan 2, 2023 · 3 comments
Closed

module 'numpy' has no attribute 'float'. Did you mean: 'cfloat'? #1181

Maarten-vd-Sande opened this issue Jan 2, 2023 · 3 comments

Comments

@Maarten-vd-Sande
Copy link

When running computematrix:

Traceback (most recent call last):
  File "/var/lib/jenkins/workspace/seq2science_PR-944/miniconda/envs/s2s/lib/python3.8/site-packages/seq2science/.snakemake/37f425be7a38235ae34f7926399c06aa_/bin/computeMatrix", line 14, in <module>
    main(args)
  File "/var/lib/jenkins/workspace/seq2science_PR-944/miniconda/envs/s2s/lib/python3.8/site-packages/seq2science/.snakemake/37f425be7a38235ae34f7926399c06aa_/lib/python3.10/site-packages/deeptools/computeMatrix.py", line 438, in main
    hm.save_matrix(args.outFileName)
  File "/var/lib/jenkins/workspace/seq2science_PR-944/miniconda/envs/s2s/lib/python3.8/site-packages/seq2science/.snakemake/37f425be7a38235ae34f7926399c06aa_/lib/python3.10/site-packages/deeptools/heatmapper.py", line 855, in save_matrix
    np.float(score_list[idx])
  File "/var/lib/jenkins/workspace/seq2science_PR-944/miniconda/envs/s2s/lib/python3.8/site-packages/seq2science/.snakemake/37f425be7a38235ae34f7926399c06aa_/lib/python3.10/site-packages/numpy/__init__.py", line 284, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float'. Did you mean: 'cfloat'?
@Maarten-vd-Sande
Copy link
Author

Related to the latest numpy release where these have been deprecated: https://numpy.org/doc/stable/release/1.24.0-notes.html#expired-deprecations

@Maarten-vd-Sande
Copy link
Author

Maarten-vd-Sande commented Jan 3, 2023 •
edited
Loading

I updated the bioconda recipe to reflect this change:

https://github.com/bioconda/bioconda-recipes/blob/0f0f2c781fe176a6de1107050eda3de4fdb45750/recipes/deeptools/meta.yaml#L21

adRn-s pushed a commit that referenced this issue Jan 5, 2023
Addressing #1181
4c0c4fa
@y9c
Copy link

y9c commented Jan 19, 2023

#1184

@adRn-s adRn-s closed this as completed Jan 19, 2023
adRn-s added a commit that referenced this issue Feb 3, 2023
@adRn-s @gallardoalba
@bgruening @LeilyR @lldelisle
Develop (#1185)
3005380 
* Fix label options

* add pool

* trigger test

* new azure syntax?

* run also on PR

* fix #1159

* fixes #1172

* Addressing #1181

* Bigwig average (#1169)

* Fixes #1159

* Revert "dendogram of plotCorrelation now matches each cell correctly"

* add bigwigAverage

* linting

* remove forgotten prints

* make bigwigAverage executable

* fix galaxy tests

Co-authored-by: A.s <62971995+adRn-s@users.noreply.github.com>
Co-authored-by: LeilyR <25766687+LeilyR@users.noreply.github.com>

* Addresses #1183

* Fix galaxy tests (#1186)

* upload artifact

* allow 1 or 2 lines diff for bowtie2 program

* change github action to get artifacts

* fix plotPCA

* try to fix old samtools installed

* add forgotten channels

---------

Co-authored-by: Cristóbal Gallardo <gallardo@informatik.uni-freiburg.de>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: LeilyR <25766687+LeilyR@users.noreply.github.com>
Co-authored-by: Lucille Delisle <lucille.delisle@epfl.ch>
Co-authored-by: adRn-s <salatino@omics.dev>
# for free to join this conversation on GitHub. Already have an account? # to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@y9c @Maarten-vd-Sande @adRn-s