Hi,
On Wed, 11 Nov 2020 11:56:10 +0800 Drew Parsons <dpars...@debian.org> wrote:
> Package: python3-biom-format
> Version: 2.1.9-2
> Severity: normal
>
> debci tests for python3-biom-format are show test error triggered by
> python3-h5py 3.1.0-1exp1 from experimental.
>
> The odd thing is that the error trace does not directly refer to h5py,
> it's a json problem:
>
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/biom/assets/exercise_api.py",
line 95, in <module>
> out.write(table.to_json('rc-testing'))
> File "/usr/lib/python3/dist-packages/biom/table.py", line 4720, in to_json
> dumps(samp[1]), dumps(samp[2])))
> File "/usr/lib/python3.8/json/__init__.py", line 231, in dumps
> return _default_encoder.encode(obj)
> File "/usr/lib/python3.8/json/encoder.py", line 199, in encode
> chunks = self.iterencode(o, _one_shot=True)
> File "/usr/lib/python3.8/json/encoder.py", line 257, in iterencode
> return _iterencode(o, 0)
> File "/usr/lib/python3.8/json/encoder.py", line 179, in default
> raise TypeError(f'Object of type {o.__class__.__name__} '
> TypeError: Object of type bytes is not JSON serializable
>
Thanks for this bug report!
Just uploaded a new upstream revision for python-biom-format, the
autopkgtests seem fine locally now:
autopkgtest [13:08:06]: test run-unit-test: [-----------------------
System information
==================
Platform: linux
Python version: 3.9.0+ (default, Oct 19 2020, 09:51:18) [GCC 10.2.0]
Python executable: /usr/bin/python3
Dependency versions
===================
click version: 7.1.2
NumPy version: 1.19.4
SciPy version: 1.5.3
h5py version: 3.1.0
biom-format package information
===============================
biom-format version: 2.1.10
The input file is a valid BIOM-formatted file.
The input file is a valid BIOM-formatted file.
The input file is a valid BIOM-formatted file.
The input file is a valid BIOM-formatted file.
+ table=examples/min_sparse_otu_table_hdf5.biom
+ obsmd=examples/obs_md.txt
+ [ ! -f examples/min_sparse_otu_table_hdf5.biom ]
+ biom show-install-info
System information
==================
Platform: linux
Python version: 3.9.0+ (default, Oct 19 2020, 09:51:18) [GCC 10.2.0]
Python executable: /usr/bin/python3
Dependency versions
===================
click version: 7.1.2
NumPy version: 1.19.4
SciPy version: 1.5.3
h5py version: 3.1.0
biom-format package information
===============================
biom-format version: 2.1.10
+ biom validate-table -i examples/min_sparse_otu_table_hdf5.biom
The input file is a valid BIOM-formatted file.
+ biom add-metadata -i examples/min_sparse_otu_table_hdf5.biom -o
test_add_metadata.biom --observation-metadata-fp examples/obs_md.txt
--sc-separated taxonomy
+ biom convert -i examples/min_sparse_otu_table_hdf5.biom -o
test_json.biom --to-json
+ biom convert -i examples/min_sparse_otu_table_hdf5.biom -o
test_tsv.txt --to-tsv
+ biom validate-table -i test_json.biom
The input file is a valid BIOM-formatted file.
+ biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5
+ biom validate-table -i test_hdf5.biom
The input file is a valid BIOM-formatted file.
+ biom convert -i test_json.biom -o test_tsv.txt --to-tsv
+ biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type
OTU table
+ biom validate-table -i test_hdf5.biom
The input file is a valid BIOM-formatted file.
+ biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type
OTU table
+ biom validate-table -i test_json.biom
The input file is a valid BIOM-formatted file.
+ biom head -i examples/min_sparse_otu_table_hdf5.biom
# Constructed from biom file
#OTU ID Sample1 Sample2 Sample3 Sample4 Sample5
GG_OTU_1 0.0 0.0 1.0 0.0 0.0
GG_OTU_2 5.0 1.0 0.0 2.0 3.0
GG_OTU_3 0.0 0.0 1.0 4.0 0.0
GG_OTU_4 2.0 1.0 1.0 0.0 0.0
GG_OTU_5 0.0 1.0 1.0 0.0 0.0
+ biom table-ids -i examples/min_sparse_otu_table_hdf5.biom
Sample1
Sample2
Sample3
Sample4
Sample5
Sample6
+ biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o
test_norm.biom -p
+ cat
+ biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o
test_subset.biom -a observation -s ids.txt
/usr/lib/python3/dist-packages/biom/table.py:4077: FutureWarning: arrays
to stack must be passed as a "sequence" type such as list or tuple.
Support for non-sequence iterables such as generators is deprecated as
of NumPy 1.16 and will raise an error in the future.
data = np.hstack(h5_data[start:end]
/usr/lib/python3/dist-packages/biom/table.py:4079: FutureWarning: arrays
to stack must be passed as a "sequence" type such as list or tuple.
Support for non-sequence iterables such as generators is deprecated as
of NumPy 1.16 and will raise an error in the future.
indices = np.hstack(h5_indices[start:end]
+ biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom
Num samples: 6
Num observations: 5
Total count: 27
Table density (fraction of non-zero values): 0.500
Counts/sample summary:
Min: 3.000
Max: 7.000
Median: 4.000
Mean: 4.500
Std. dev.: 1.500
Sample Metadata Categories: None provided
Observation Metadata Categories: None provided
Counts/sample detail:
Sample2: 3.000
Sample5: 3.000
Sample3: 4.000
Sample6: 4.000
Sample4: 6.000
Sample1: 7.000
+ cat
+ biom from-uc -i uctest -o test_uc.biom
+ echo If this message was shown, then all commands executed without failure
If this message was shown, then all commands executed without failure
autopkgtest [13:08:27]: test run-unit-test: -----------------------]
autopkgtest [13:08:27]: test run-unit-test: - - - - - - - - - - results
- - - - - - - - - -
run-unit-test PASS
autopkgtest [13:08:27]: test autodep8-python3: preparing testbed
But lets wait for debci results
Regards,
Nilesh
