dgslos
commented
1 year ago Any progress on this?
Closed meren closed 1 year ago
dgslos
commented
1 year ago Any progress on this?
meren
commented
1 year ago anvio-dev is at Python 3.7 and it seems we will stay there for a while.
dgslos
commented
1 year ago Python 3.7 is also end-of-life :(
meren
commented
1 year ago OK. Let me open this issue so maybe someone would like to take a look into it.
In essence, we are at the mercy of the developers of other tools that anvi'o and its users depend on. In our previous attempt to go bump ourselves all the way to Python 3.10, we realized that snakemake was not compatible with it and the best we could do was 3.7. Perhaps that issue is resolved and someone needs to test it.
Just for posterity, testing is straightforward. One can use,
anvi-self-test --suite mini
anvi-self-test --suite metagenomics-full
anvi-self-test --suite pangenomics
anvi-self-test --suite workflow-metagenomics
anvi-self-test --suite database-migrationsBest wishes,
dgslos
commented
1 year ago anvi-self-test --suite mini
:: Output directory ...
/tmp/tmpzmf73az4
:: Can has interactive displays? ...
Yes, anvi'o will try to show you interactive displays that will require you to come back to the terminal and press CTRL+C to continue
:: Anvi'o version ...
Anvi'o .......................................: hope (v7.1-dev)
Profile database .............................: 38
Contigs database .............................: 20
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2
:: Initializing raw BAM files ...
Traceback (most recent call last):
File "/home/genomics/dslos/07_tools/anvio/bin/anvi-init-bam", line 80, in <module>
init_bam_file(args.input_file, args.output_file, args.num_threads)
File "/home/genomics/dslos/07_tools/anvio/bin/anvi-init-bam", line 49, in init_bam_file
progress.update('Sorting BAM File... May take a while depending on the size.')
File "/home/genomics/dslos/07_tools/anvio/anvio/terminal.py", line 308, in update
self.write('\r[%s] %s' % (self.pid, msg))
File "/home/genomics/dslos/07_tools/anvio/anvio/terminal.py", line 239, in write
sys.stderr.write(back.CYAN + fore.BLACK + c + style.RESET)
AttributeError: 'function' object has no attribute 'CYAN'
Config Error: According to the exit code ('1'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less.anvi-self-test --suite metagenomics-full
:: Output directory ...
/tmp/tmpnpi_7351
:: Can has interactive displays? ...
Yes, anvi'o will try to show you interactive displays that will require you to come back to the terminal and press CTRL+C to continue
:: Anvi'o version ...
Anvi'o .......................................: hope (v7.1-dev)
Profile database .............................: 38
Contigs database .............................: 20
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2
:: Reformat the contigs FASTA ...
./run_component_tests_for_metagenomics.sh: line 9: anvi-script-reformat-fasta: command not found
Config Error: According to the exit code ('127'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less.anvi-self-test --suite pangenomics
/tmp/tmpf7sehz76
:: Can has interactive displays? ...
Yes, anvi'o will try to show you interactive displays that will require you to come back to the terminal and press CTRL+C to continue
:: Anvi'o version ...
Anvi'o .......................................: hope (v7.1-dev)
Profile database .............................: 38
Contigs database .............................: 20
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2
:: Setting up the pan analysis directory ...
:: Generating an anvi'o genomes storage ...
WARNING
===============================================
Good news! Anvi'o found all these functions that are common to all of your
genomes and will use them for downstream analyses and is very proud of you:
'COG20_FUNCTION, COG20_PATHWAY, COG20_CATEGORY'.
Internal genomes .............................: 0 have been initialized.
Traceback (most recent call last):
File "/home/genomics/dslos/07_tools/anvio/bin/anvi-gen-genomes-storage", line 56, in <module>
genome_descriptions.load_genomes_descriptions()
File "/home/genomics/dslos/07_tools/anvio/anvio/genomedescriptions.py", line 306, in load_genomes_descriptions
self.init_external_genomes()
File "/home/genomics/dslos/07_tools/anvio/anvio/genomedescriptions.py", line 519, in init_external_genomes
contigs_db_summary = ContigSummarizer(c['contigs_db_path']).get_contigs_db_info_dict(gene_caller_to_use=self.gene_caller)
File "/home/genomics/dslos/07_tools/anvio/anvio/summarizer.py", line 1071, in get_contigs_db_info_dict
p_completion, p_redundancy, domain, domain_probabilities, info_text, results_dict = completeness.Completeness(self.contigs_db_path).get_info_for_splits(split_names if split_names else set(c.splits_basic_info.keys()))
File "/home/genomics/dslos/07_tools/anvio/anvio/completeness.py", line 45, in __init__
self.SCG_domain_predictor = scgdomainclassifier.Predict(argparse.Namespace(), run=terminal.Run(verbose=False), progress=self.progress)
File "/home/genomics/dslos/07_tools/anvio/anvio/scgdomainclassifier.py", line 234, in __init__
SCGDomainClassifier.__init__(self, args, run, progress)
File "/home/genomics/dslos/07_tools/anvio/anvio/scgdomainclassifier.py", line 73, in __init__
self.rf.initialize_classifier()
File "/home/genomics/dslos/07_tools/anvio/anvio/learning.py", line 103, in initialize_classifier
classifier_obj = pickle.load(open(self.classifier_object_path, 'rb'))
File "sklearn/tree/_tree.pyx", line 714, in sklearn.tree._tree.Tree.__setstate__
File "sklearn/tree/_tree.pyx", line 1418, in sklearn.tree._tree._check_node_ndarray
ValueError: node array from the pickle has an incompatible dtype:
- expected: {'names': ['left_child', 'right_child', 'feature', 'threshold', 'impurity', 'n_node_samples', 'weighted_n_node_samples', 'missing_go_to_left'], 'formats': ['<i8', '<i8', '<i8', '<f8', '<f8', '<i8', '<f8', 'u1'], 'offsets': [0, 8, 16, 24, 32, 40, 48, 56], 'itemsize': 64}
- got : [('left_child', '<i8'), ('right_child', '<i8'), ('feature', '<i8'), ('threshold', '<f8'), ('impurity', '<f8'), ('n_node_samples', '<i8'), ('weighted_n_node_samples', '<f8')]
Config Error: According to the exit code ('1'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less.
anvi-self-test --suite workflow-metagenomics
:: Output directory ...
/tmp/tmp49puzbva
:: Can has interactive displays? ...
Yes, anvi'o will try to show you interactive displays that will require you to come back to the terminal and press CTRL+C to continue
:: Anvi'o version ...
Anvi'o .......................................: hope (v7.1-dev)
Profile database .............................: 38
Contigs database .............................: 20
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2
:: Setting up the metagenomics analysis directory ...
:: Creating a default config for metagenomics workflow ...
WARNING
===============================================
If you publish results from this workflow, please do not forget to cite
snakemake (doi:10.1093/bioinformatics/bts480)
HMM profiles .................................: 9 sources have been loaded: Archaea_76 (76 genes, domain: archaea), Bacteria_71 (71 genes, domain: bacteria), Protista_83 (83 genes, domain: eukarya),
Ribosomal_RNA_12S (1 genes, domain: None), Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Ribosomal_RNA_23S (2 genes,
domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_5S (5 genes, domain: None)
WARNING
===============================================
We are initiating parameters for the metagenomics workflow
Default config file ..........................: Stored for workflow 'metagenomics' as 'default-config.json'.
:: List dependencies for metagenomics workflow with megahit ...
WARNING
===============================================
If you publish results from this workflow, please do not forget to cite
snakemake (doi:10.1093/bioinformatics/bts480)
HMM profiles .................................: 9 sources have been loaded: Archaea_76 (76 genes, domain: archaea), Bacteria_71 (71 genes, domain: bacteria), Protista_83 (83 genes, domain: eukarya),
Ribosomal_RNA_12S (1 genes, domain: None), Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Ribosomal_RNA_23S (2 genes,
domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_5S (5 genes, domain: None)
WARNING
===============================================
We are initiating parameters for the metagenomics workflow
MAX NUMBER OF CPU CORES HEURISTIC
===============================================
You haven't set a global `max_threads` value in your config file, and you
haven't declared the maximum number of CPUs you wish to assign to this job via
`--cores`. But anvi'o found out that for the rule `anvi_run_hmms` you asked for
20 threads , which is the largest number of threads among all rules. So, anvi'o
will set up your job by passing 20 as the maximum number of CPU cores to be used
by your workflow. If you'd like to assign more resources for your workflow,
please either use the global `max_threads` parameter in your config file, or
include a `--cores XX` parameter via the `--additional-params` mechanism, where
XX is the maximum number of CPUs you wish to assign to this job.
Traceback (most recent call last):
File "/home/genomics/dslos/07_tools/anvio/bin/anvi-run-workflow", line 77, in <module>
main(args)
File "/home/genomics/dslos/07_tools/anvio/bin/anvi-run-workflow", line 51, in main
M.go(skip_dry_run=args.skip_dry_run)
File "/home/genomics/dslos/07_tools/anvio/anvio/workflows/__init__.py", line 270, in go
self.dry_run()
File "/home/genomics/dslos/07_tools/anvio/anvio/workflows/__init__.py", line 321, in dry_run
self.progress.update('Quick dry run for an initial sanity check ...')
File "/home/genomics/dslos/07_tools/anvio/anvio/terminal.py", line 308, in update
self.write('\r[%s] %s' % (self.pid, msg))
File "/home/genomics/dslos/07_tools/anvio/anvio/terminal.py", line 239, in write
sys.stderr.write(back.CYAN + fore.BLACK + c + style.RESET)
AttributeError: 'function' object has no attribute 'CYAN'
Config Error: According to the exit code ('1'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less.anvi-self-test --suite database-migrations
anvi-self-test --suite database-migrations
Collecting h5py==2.8.0
Downloading h5py-2.8.0.tar.gz (274 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 274.6/274.6 kB 5.5 MB/s eta 0:00:00
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy>=1.7 in /opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages (from h5py==2.8.0) (1.24.4)
Requirement already satisfied: six in /opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages (from h5py==2.8.0) (1.16.0)
Building wheels for collected packages: h5py
Building wheel for h5py (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [4056 lines of output]
/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-310
creating build/lib.linux-x86_64-cpython-310/h5py
copying h5py/ipy_completer.py -> build/lib.linux-x86_64-cpython-310/h5py
copying h5py/highlevel.py -> build/lib.linux-x86_64-cpython-310/h5py
copying h5py/h5py_warnings.py -> build/lib.linux-x86_64-cpython-310/h5py
copying h5py/version.py -> build/lib.linux-x86_64-cpython-310/h5py
copying h5py/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py
creating build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/selections.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/files.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/base.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/group.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/filters.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/compat.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
copying h5py/_hl/dims.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
creating build/lib.linux-x86_64-cpython-310/h5py/tests
copying h5py/tests/common.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
copying h5py/tests/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
creating build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_h5t.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_file.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_dataset.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_selections.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_slicing.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_attrs_data.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_base.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_file_image.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_objects.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_h5d_direct_chunk_write.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_dimension_scales.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_datatype.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_h5f.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_h5p.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_group.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_h5.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
copying h5py/tests/old/test_attrs.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/old
creating build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_file.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_dataset_swmr.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_attribute_create.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_dataset_getitem.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_datatype.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_threads.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/test_filters.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
copying h5py/tests/hl/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/hl
running build_ext
Autodetected HDF5 1.10.7
********************************************************************************
Summary of the h5py configuration
Path to HDF5: None
HDF5 Version: '1.10.7'
MPI Enabled: False
Rebuild Required: True
********************************************************************************
Executing api_gen rebuild of defs
Executing cythonize()
[ 1/22] Cythonizing /tmp/pip-install-990qh8xu/h5py_447ed218a500438085f3341266b7d4cd/h5py/_conv.pyx
/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-990qh8xu/h5py_447ed218a500438085f3341266b7d4cd/h5py/_conv.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
from defs cimport *
^
------------------------------------------------------------
h5py/_conv.pxd:10:0: 'defs.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
^
------------------------------------------------------------
h5py/_conv.pyx:16:0: 'h5r.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
^
------------------------------------------------------------
h5py/_conv.pyx:16:0: 'h5r/Reference.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
^
------------------------------------------------------------
h5py/_conv.pyx:16:0: 'h5r/RegionReference.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
^
------------------------------------------------------------
h5py/_conv.pyx:16:0: 'h5r/hobj_ref_t.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
^
------------------------------------------------------------
h5py/_conv.pyx:16:0: 'h5r/hdset_reg_ref_t.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
^
------------------------------------------------------------
h5py/_conv.pyx:17:0: 'h5t.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
^
------------------------------------------------------------
h5py/_conv.pyx:17:0: 'h5t/H5PY_OBJ.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
^
------------------------------------------------------------
h5py/_conv.pyx:17:0: 'h5t/typewrap.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
^
------------------------------------------------------------
h5py/_conv.pyx:17:0: 'h5t/py_create.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
"""
Low-level type-conversion routines.
"""
from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
^
------------------------------------------------------------
h5py/_conv.pyx:17:0: 'h5t/TypeID.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
PyTypeObject PyArray_Type
object PyArray_NewFromDescr(PyTypeObject* subtype, np.dtype descr, int nd, np.npy_intp* dims, np.npy_intp* strides, void* data, int flags, object obj)
ctypedef int (*conv_operator_t)(void* ipt, void* opt, void* bkg, void* priv) except -1
ctypedef herr_t (*init_operator_t)(hid_t src, hid_t dst, void** priv) except -1
^
------------------------------------------------------------
h5py/_conv.pyx:61:9: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
PyTypeObject PyArray_Type
object PyArray_NewFromDescr(PyTypeObject* subtype, np.dtype descr, int nd, np.npy_intp* dims, np.npy_intp* strides, void* data, int flags, object obj)
ctypedef int (*conv_operator_t)(void* ipt, void* opt, void* bkg, void* priv) except -1
ctypedef herr_t (*init_operator_t)(hid_t src, hid_t dst, void** priv) except -1
^
------------------------------------------------------------
h5py/_conv.pyx:61:35: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
PyTypeObject PyArray_Type
object PyArray_NewFromDescr(PyTypeObject* subtype, np.dtype descr, int nd, np.npy_intp* dims, np.npy_intp* strides, void* data, int flags, object obj)
ctypedef int (*conv_operator_t)(void* ipt, void* opt, void* bkg, void* priv) except -1
ctypedef herr_t (*init_operator_t)(hid_t src, hid_t dst, void** priv) except -1
^
------------------------------------------------------------
h5py/_conv.pyx:61:46: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# repeat all the conversion boilerplate for every single callback.
#
# While this is somewhat slower than a custom function, the added overhead is
# likely small compared to the cost of the Python-side API calls required to
# implement the conversions.
cdef herr_t generic_converter(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:72:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# repeat all the conversion boilerplate for every single callback.
#
# While this is somewhat slower than a custom function, the added overhead is
# likely small compared to the cost of the Python-side API calls required to
# implement the conversions.
cdef herr_t generic_converter(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:72:30: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# repeat all the conversion boilerplate for every single callback.
#
# While this is somewhat slower than a custom function, the added overhead is
# likely small compared to the cost of the Python-side API calls required to
# implement the conversions.
cdef herr_t generic_converter(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:72:44: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# repeat all the conversion boilerplate for every single callback.
#
# While this is somewhat slower than a custom function, the added overhead is
# likely small compared to the cost of the Python-side API calls required to
# implement the conversions.
cdef herr_t generic_converter(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:72:58: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# While this is somewhat slower than a custom function, the added overhead is
# likely small compared to the cost of the Python-side API calls required to
# implement the conversions.
cdef herr_t generic_converter(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl, conv_operator_t op,
^
------------------------------------------------------------
h5py/_conv.pyx:74:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# likely small compared to the cost of the Python-side API calls required to
# implement the conversions.
cdef herr_t generic_converter(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl, conv_operator_t op,
init_operator_t initop, H5T_bkg_t need_bkg) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:75:44: 'H5T_bkg_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
ctypedef struct conv_size_t:
size_t src_size
size_t dst_size
int cset
cdef herr_t init_generic(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:145:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
ctypedef struct conv_size_t:
size_t src_size
size_t dst_size
int cset
cdef herr_t init_generic(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:145:25: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
ctypedef struct conv_size_t:
size_t src_size
size_t dst_size
int cset
cdef herr_t init_generic(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:145:36: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
Py_XDECREF(temp_encoded)
# =============================================================================
# VLEN to fixed-width strings
cdef herr_t init_vlen2fixed(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:273:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
Py_XDECREF(temp_encoded)
# =============================================================================
# VLEN to fixed-width strings
cdef herr_t init_vlen2fixed(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:273:28: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
Py_XDECREF(temp_encoded)
# =============================================================================
# VLEN to fixed-width strings
cdef herr_t init_vlen2fixed(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:273:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
sizes[0].src_size = H5Tget_size(src)
sizes[0].dst_size = H5Tget_size(dst)
return 0
cdef herr_t init_fixed2vlen(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:287:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
sizes[0].src_size = H5Tget_size(src)
sizes[0].dst_size = H5Tget_size(dst)
return 0
cdef herr_t init_fixed2vlen(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:287:28: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
sizes[0].src_size = H5Tget_size(src)
sizes[0].dst_size = H5Tget_size(dst)
return 0
cdef herr_t init_fixed2vlen(hid_t src, hid_t dst, void** priv) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:287:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# =============================================================================
# Conversion functions
cdef herr_t vlen2str(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:440:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# =============================================================================
# Conversion functions
cdef herr_t vlen2str(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:440:21: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# =============================================================================
# Conversion functions
cdef herr_t vlen2str(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:440:35: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# =============================================================================
# Conversion functions
cdef herr_t vlen2str(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:440:49: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# Conversion functions
cdef herr_t vlen2str(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:442:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2str, init_generic, H5T_BKG_YES)
cdef herr_t str2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:446:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2str, init_generic, H5T_BKG_YES)
cdef herr_t str2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:446:21: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2str, init_generic, H5T_BKG_YES)
cdef herr_t str2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:446:35: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2str, init_generic, H5T_BKG_YES)
cdef herr_t str2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:446:49: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2str, init_generic, H5T_BKG_YES)
cdef herr_t str2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:448:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_str2vlen, init_generic, H5T_BKG_NO)
cdef herr_t vlen2fixed(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:452:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_str2vlen, init_generic, H5T_BKG_NO)
cdef herr_t vlen2fixed(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:452:23: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_str2vlen, init_generic, H5T_BKG_NO)
cdef herr_t vlen2fixed(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:452:37: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_str2vlen, init_generic, H5T_BKG_NO)
cdef herr_t vlen2fixed(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:452:51: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_str2vlen, init_generic, H5T_BKG_NO)
cdef herr_t vlen2fixed(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:454:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2fixed, init_vlen2fixed, H5T_BKG_NO)
cdef herr_t fixed2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:458:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2fixed, init_vlen2fixed, H5T_BKG_NO)
cdef herr_t fixed2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:458:23: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2fixed, init_vlen2fixed, H5T_BKG_NO)
cdef herr_t fixed2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:458:37: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2fixed, init_vlen2fixed, H5T_BKG_NO)
cdef herr_t fixed2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:458:51: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2fixed, init_vlen2fixed, H5T_BKG_NO)
cdef herr_t fixed2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:460:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_fixed2vlen, init_fixed2vlen, H5T_BKG_NO)
cdef herr_t objref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:464:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_fixed2vlen, init_fixed2vlen, H5T_BKG_NO)
cdef herr_t objref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:464:25: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_fixed2vlen, init_fixed2vlen, H5T_BKG_NO)
cdef herr_t objref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:464:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_fixed2vlen, init_fixed2vlen, H5T_BKG_NO)
cdef herr_t objref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:464:53: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_fixed2vlen, init_fixed2vlen, H5T_BKG_NO)
cdef herr_t objref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:466:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_objref2pyref, init_generic, H5T_BKG_NO)
cdef herr_t pyref2objref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:470:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_objref2pyref, init_generic, H5T_BKG_NO)
cdef herr_t pyref2objref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:470:25: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_objref2pyref, init_generic, H5T_BKG_NO)
cdef herr_t pyref2objref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:470:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_objref2pyref, init_generic, H5T_BKG_NO)
cdef herr_t pyref2objref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:470:53: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_objref2pyref, init_generic, H5T_BKG_NO)
cdef herr_t pyref2objref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:472:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_pyref2objref, init_generic, H5T_BKG_NO)
cdef herr_t regref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:476:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_pyref2objref, init_generic, H5T_BKG_NO)
cdef herr_t regref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:476:25: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_pyref2objref, init_generic, H5T_BKG_NO)
cdef herr_t regref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:476:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_pyref2objref, init_generic, H5T_BKG_NO)
cdef herr_t regref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:476:53: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_pyref2objref, init_generic, H5T_BKG_NO)
cdef herr_t regref2pyref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:478:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_regref2pyref, init_generic, H5T_BKG_YES)
cdef herr_t pyref2regref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:482:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_regref2pyref, init_generic, H5T_BKG_YES)
cdef herr_t pyref2regref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:482:25: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_regref2pyref, init_generic, H5T_BKG_YES)
cdef herr_t pyref2regref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:482:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_regref2pyref, init_generic, H5T_BKG_YES)
cdef herr_t pyref2regref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:482:53: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_regref2pyref, init_generic, H5T_BKG_YES)
cdef herr_t pyref2regref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:484:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef struct conv_enum_t:
size_t src_size
size_t dst_size
cdef int enum_int_converter_init(hid_t src, hid_t dst,
^
------------------------------------------------------------
h5py/_conv.pyx:495:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef struct conv_enum_t:
size_t src_size
size_t dst_size
cdef int enum_int_converter_init(hid_t src, hid_t dst,
^
------------------------------------------------------------
h5py/_conv.pyx:495:44: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef struct conv_enum_t:
size_t src_size
size_t dst_size
cdef int enum_int_converter_init(hid_t src, hid_t dst,
H5T_cdata_t *cdata, int forward) except -1 with gil:
^
------------------------------------------------------------
h5py/_conv.pyx:496:33: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdata[0].need_bkg = H5T_BKG_NO
cdata[0].priv = info = <conv_enum_t*>malloc(sizeof(conv_enum_t))
info[0].src_size = H5Tget_size(src)
info[0].dst_size = H5Tget_size(dst)
cdef void enum_int_converter_free(H5T_cdata_t *cdata):
^
------------------------------------------------------------
h5py/_conv.pyx:504:34: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
info = <conv_enum_t*>cdata[0].priv
free(info)
cdata[0].priv = NULL
cdef int enum_int_converter_conv(hid_t src, hid_t dst, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:512:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
info = <conv_enum_t*>cdata[0].priv
free(info)
cdata[0].priv = NULL
cdef int enum_int_converter_conv(hid_t src, hid_t dst, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:512:44: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
info = <conv_enum_t*>cdata[0].priv
free(info)
cdata[0].priv = NULL
cdef int enum_int_converter_conv(hid_t src, hid_t dst, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:512:55: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdata[0].priv = NULL
cdef int enum_int_converter_conv(hid_t src, hid_t dst, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl, int forward) except -1 with gil:
^
------------------------------------------------------------
h5py/_conv.pyx:514:46: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
# Direction ("forward"): 1 = enum to int, 0 = int to enum
cdef herr_t enum_int_converter(hid_t src, hid_t dst, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:577:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
# Direction ("forward"): 1 = enum to int, 0 = int to enum
cdef herr_t enum_int_converter(hid_t src, hid_t dst, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:577:31: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
# Direction ("forward"): 1 = enum to int, 0 = int to enum
cdef herr_t enum_int_converter(hid_t src, hid_t dst, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:577:42: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
# Direction ("forward"): 1 = enum to int, 0 = int to enum
cdef herr_t enum_int_converter(hid_t src, hid_t dst, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:577:53: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# Direction ("forward"): 1 = enum to int, 0 = int to enum
cdef herr_t enum_int_converter(hid_t src, hid_t dst, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl, int forward) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:579:44: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return -2
return 0
cdef herr_t enum2int(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:596:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return -2
return 0
cdef herr_t enum2int(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:596:21: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return -2
return 0
cdef herr_t enum2int(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:596:35: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return -2
return 0
cdef herr_t enum2int(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:596:49: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef herr_t enum2int(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:598:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return enum_int_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, 1)
cdef herr_t int2enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:602:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return enum_int_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, 1)
cdef herr_t int2enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:602:21: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return enum_int_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, 1)
cdef herr_t int2enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:602:35: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return enum_int_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, 1)
cdef herr_t int2enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:602:49: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return enum_int_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, 1)
cdef herr_t int2enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:604:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
buf_i, bkg_i, dxpl, 0)
# =============================================================================
# ndarray to VLEN routines
cdef herr_t vlen2ndarray(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:611:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
buf_i, bkg_i, dxpl, 0)
# =============================================================================
# ndarray to VLEN routines
cdef herr_t vlen2ndarray(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:611:25: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
buf_i, bkg_i, dxpl, 0)
# =============================================================================
# ndarray to VLEN routines
cdef herr_t vlen2ndarray(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:611:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
buf_i, bkg_i, dxpl, 0)
# =============================================================================
# ndarray to VLEN routines
cdef herr_t vlen2ndarray(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:611:53: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# =============================================================================
# ndarray to VLEN routines
cdef herr_t vlen2ndarray(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:613:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef struct vlen_t:
size_t len
void* ptr
cdef int conv_vlen2ndarray(void* ipt, void* opt, np.dtype elem_dtype,
TypeID intype, TypeID outtype) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:677:8: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef struct vlen_t:
size_t len
void* ptr
cdef int conv_vlen2ndarray(void* ipt, void* opt, np.dtype elem_dtype,
TypeID intype, TypeID outtype) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:677:23: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
in_vlen0.ptr = NULL
memcpy(buf_obj, &ndarray_obj, sizeof(ndarray_obj))
return 0
cdef herr_t ndarray2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:709:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
in_vlen0.ptr = NULL
memcpy(buf_obj, &ndarray_obj, sizeof(ndarray_obj))
return 0
cdef herr_t ndarray2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:709:25: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
in_vlen0.ptr = NULL
memcpy(buf_obj, &ndarray_obj, sizeof(ndarray_obj))
return 0
cdef herr_t ndarray2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:709:39: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
in_vlen0.ptr = NULL
memcpy(buf_obj, &ndarray_obj, sizeof(ndarray_obj))
return 0
cdef herr_t ndarray2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
^
------------------------------------------------------------
h5py/_conv.pyx:709:53: 'H5T_cdata_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef herr_t ndarray2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:711:33: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef int conv_ndarray2vlen(void* ipt, void* opt,
TypeID intype, TypeID outtype) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:780:8: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef int conv_ndarray2vlen(void* ipt, void* opt,
TypeID intype, TypeID outtype) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:780:23: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# HDF5 references to Python instances of h5r.Reference
cdef int conv_objref2pyref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>opt
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>ipt
^
------------------------------------------------------------
h5py/_conv.pyx:349:9: 'hobj_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int conv_objref2pyref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>opt
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>ipt
cdef Reference ref = Reference()
^
------------------------------------------------------------
h5py/_conv.pyx:351:9: 'Reference' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef int conv_pyref2objref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>ipt
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>opt
^
------------------------------------------------------------
h5py/_conv.pyx:368:9: 'hobj_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject** buf_obj = <PyObject**>ipt
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>opt
cdef object obj
cdef Reference ref
^
------------------------------------------------------------
h5py/_conv.pyx:371:9: 'Reference' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int conv_regref2pyref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>opt
cdef PyObject** bkg_obj = <PyObject**>bkg
cdef hdset_reg_ref_t* buf_ref = <hdset_reg_ref_t*>ipt
^
------------------------------------------------------------
h5py/_conv.pyx:392:9: 'hdset_reg_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject** buf_obj = <PyObject**>opt
cdef PyObject** bkg_obj = <PyObject**>bkg
cdef hdset_reg_ref_t* buf_ref = <hdset_reg_ref_t*>ipt
cdef RegionReference ref = RegionReference()
^
------------------------------------------------------------
h5py/_conv.pyx:394:9: 'RegionReference' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef int conv_pyref2regref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>ipt
cdef hdset_reg_ref_t* buf_ref = <hdset_reg_ref_t*>opt
^
------------------------------------------------------------
h5py/_conv.pyx:416:9: 'hdset_reg_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject** buf_obj = <PyObject**>ipt
cdef hdset_reg_ref_t* buf_ref = <hdset_reg_ref_t*>opt
cdef object obj
cdef RegionReference ref
^
------------------------------------------------------------
h5py/_conv.pyx:419:9: 'RegionReference' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef size_t nalloc
cdef int i
cdef char* cbuf = NULL
cdef char* buf = <char*>buf_i
cdef int identical
cdef hid_t supertype = -1
^
------------------------------------------------------------
h5py/_conv.pyx:521:9: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
cdef int command = cdata[0].command
cdef size_t src_size, dst_size
cdef TypeID supertype
^
------------------------------------------------------------
h5py/_conv.pyx:617:9: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
void *bkg_i, hid_t dxpl) except -1:
cdef int command = cdata[0].command
cdef size_t src_size, dst_size
cdef TypeID supertype
cdef TypeID outtype
^
------------------------------------------------------------
h5py/_conv.pyx:618:9: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
cdef int command = cdata[0].command
cdef size_t src_size, dst_size
cdef TypeID supertype
^
------------------------------------------------------------
h5py/_conv.pyx:715:9: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
void *bkg_i, hid_t dxpl) except -1:
cdef int command = cdata[0].command
cdef size_t src_size, dst_size
cdef TypeID supertype
cdef TypeID outtype
^
------------------------------------------------------------
h5py/_conv.pyx:716:9: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# =============================================================================
cpdef int register_converters() except -1:
cdef hid_t vlstring
^
------------------------------------------------------------
h5py/_conv.pyx:811:9: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# =============================================================================
cpdef int register_converters() except -1:
cdef hid_t vlstring
cdef hid_t vlentype
^
------------------------------------------------------------
h5py/_conv.pyx:812:9: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cpdef int register_converters() except -1:
cdef hid_t vlstring
cdef hid_t vlentype
cdef hid_t pyobj
^
------------------------------------------------------------
h5py/_conv.pyx:813:9: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cpdef int register_converters() except -1:
cdef hid_t vlstring
cdef hid_t vlentype
cdef hid_t pyobj
cdef hid_t enum
^
------------------------------------------------------------
h5py/_conv.pyx:814:9: 'hid_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int i
cdef char* buf = <char*>buf_i
cdef char* bkg = <char*>bkg_i
if command == H5T_CONV_INIT:
^
------------------------------------------------------------
h5py/_conv.pyx:84:18: undeclared name not builtin: H5T_CONV_INIT
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* bkg = <char*>bkg_i
if command == H5T_CONV_INIT:
cdata[0].need_bkg = need_bkg
return initop(src_id, dst_id, &(cdata[0].priv))
^
------------------------------------------------------------
h5py/_conv.pyx:87:38: Cannot take address of Python object attribute 'priv'
Error compiling Cython file:
------------------------------------------------------------
...
if command == H5T_CONV_INIT:
cdata[0].need_bkg = need_bkg
return initop(src_id, dst_id, &(cdata[0].priv))
elif command == H5T_CONV_FREE:
^
------------------------------------------------------------
h5py/_conv.pyx:89:20: undeclared name not builtin: H5T_CONV_FREE
Error compiling Cython file:
------------------------------------------------------------
...
cdata[0].need_bkg = need_bkg
return initop(src_id, dst_id, &(cdata[0].priv))
elif command == H5T_CONV_FREE:
free(cdata[0].priv)
^
------------------------------------------------------------
h5py/_conv.pyx:91:8: undeclared name not builtin: free
Error compiling Cython file:
------------------------------------------------------------
...
return initop(src_id, dst_id, &(cdata[0].priv))
elif command == H5T_CONV_FREE:
free(cdata[0].priv)
cdata[0].priv = NULL
^
------------------------------------------------------------
h5py/_conv.pyx:92:24: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_FREE:
free(cdata[0].priv)
cdata[0].priv = NULL
elif command == H5T_CONV_CONV:
^
------------------------------------------------------------
h5py/_conv.pyx:94:20: undeclared name not builtin: H5T_CONV_CONV
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_CONV:
sizes = <conv_size_t*>cdata[0].priv
if H5Tis_variable_str(src_id):
^
------------------------------------------------------------
h5py/_conv.pyx:98:11: undeclared name not builtin: H5Tis_variable_str
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_CONV:
sizes = <conv_size_t*>cdata[0].priv
if H5Tis_variable_str(src_id):
sizes.cset = H5Tget_cset(src_id)
^
------------------------------------------------------------
h5py/_conv.pyx:99:25: undeclared name not builtin: H5Tget_cset
Error compiling Cython file:
------------------------------------------------------------
...
if sizes[0].src_size >= sizes[0].dst_size:
for i from 0<=i<nl:
op( buf + (i*sizes[0].src_size), # input pointer
buf + (i*sizes[0].dst_size), # output pointer
bkg + (i*bkg_stride), # backing buffer
cdata[0].priv) # conversion context
^
------------------------------------------------------------
h5py/_conv.pyx:116:32: Cannot convert Python object to 'void *'
Error compiling Cython file:
------------------------------------------------------------
...
else:
for i from nl>i>=0:
op( buf + (i*sizes[0].src_size),
buf + (i*sizes[0].dst_size),
bkg + (i*bkg_stride),
cdata[0].priv)
^
------------------------------------------------------------
h5py/_conv.pyx:122:32: Cannot convert Python object to 'void *'
Error compiling Cython file:
------------------------------------------------------------
...
# offsets exclusively.
for i from 0<=i<nl:
op( buf + (i*buf_stride),
buf + (i*buf_stride), # note this is the same!
bkg + (i*bkg_stride),
cdata[0].priv)
^
------------------------------------------------------------
h5py/_conv.pyx:131:28: Cannot convert Python object to 'void *'
Error compiling Cython file:
------------------------------------------------------------
...
int cset
cdef herr_t init_generic(hid_t src, hid_t dst, void** priv) except -1:
cdef conv_size_t *sizes
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
^
------------------------------------------------------------
h5py/_conv.pyx:148:26: undeclared name not builtin: malloc
Error compiling Cython file:
------------------------------------------------------------
...
int cset
cdef herr_t init_generic(hid_t src, hid_t dst, void** priv) except -1:
cdef conv_size_t *sizes
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
^
------------------------------------------------------------
h5py/_conv.pyx:148:12: Casting temporary Python object to non-numeric non-Python type
Error compiling Cython file:
------------------------------------------------------------
...
int cset
cdef herr_t init_generic(hid_t src, hid_t dst, void** priv) except -1:
cdef conv_size_t *sizes
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
^
------------------------------------------------------------
h5py/_conv.pyx:148:12: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
cdef herr_t init_generic(hid_t src, hid_t dst, void** priv) except -1:
cdef conv_size_t *sizes
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
priv[0] = sizes
sizes[0].src_size = H5Tget_size(src)
^
------------------------------------------------------------
h5py/_conv.pyx:150:24: undeclared name not builtin: H5Tget_size
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject* temp_obj = NULL
cdef conv_size_t *sizes = <conv_size_t*>priv
cdef PyObject* bkg_obj0
cdef char* buf_cstring0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0))
^
------------------------------------------------------------
h5py/_conv.pyx:168:4: undeclared name not builtin: memcpy
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject* temp_obj = NULL
cdef conv_size_t *sizes = <conv_size_t*>priv
cdef PyObject* bkg_obj0
cdef char* buf_cstring0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0))
^
------------------------------------------------------------
h5py/_conv.pyx:168:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject* temp_obj = NULL
cdef conv_size_t *sizes = <conv_size_t*>priv
cdef PyObject* bkg_obj0
cdef char* buf_cstring0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0))
^
------------------------------------------------------------
h5py/_conv.pyx:168:22: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef conv_size_t *sizes = <conv_size_t*>priv
cdef PyObject* bkg_obj0
cdef char* buf_cstring0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0))
memcpy(&buf_cstring0, buf_cstring, sizeof(buf_cstring0))
^
------------------------------------------------------------
h5py/_conv.pyx:169:11: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef conv_size_t *sizes = <conv_size_t*>priv
cdef PyObject* bkg_obj0
cdef char* buf_cstring0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0))
memcpy(&buf_cstring0, buf_cstring, sizeof(buf_cstring0))
^
------------------------------------------------------------
h5py/_conv.pyx:169:26: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0))
memcpy(&buf_cstring0, buf_cstring, sizeof(buf_cstring0))
# When reading we identify H5T_CSET_ASCII as a byte string and
# H5T_CSET_UTF8 as a utf8-encoded unicode string
if sizes.cset == H5T_CSET_ASCII:
^
------------------------------------------------------------
h5py/_conv.pyx:173:21: undeclared name not builtin: H5T_CSET_ASCII
Error compiling Cython file:
------------------------------------------------------------
...
if sizes.cset == H5T_CSET_ASCII:
if buf_cstring0 == NULL:
temp_obj = PyBytes_FromString("")
else:
temp_obj = PyBytes_FromString(buf_cstring0)
elif sizes.cset == H5T_CSET_UTF8:
^
------------------------------------------------------------
h5py/_conv.pyx:178:23: undeclared name not builtin: H5T_CSET_UTF8
Error compiling Cython file:
------------------------------------------------------------
...
temp_obj = PyBytes_FromString(buf_cstring0)
elif sizes.cset == H5T_CSET_UTF8:
if buf_cstring0 == NULL:
temp_obj = PyUnicode_DecodeUTF8("", 0, NULL)
else:
temp_obj = PyUnicode_DecodeUTF8(buf_cstring0, strlen(buf_cstring0), NULL)
^
------------------------------------------------------------
h5py/_conv.pyx:182:58: undeclared name not builtin: strlen
Error compiling Cython file:
------------------------------------------------------------
...
# HDF5 will eventually overwrite this target location, so we
# make sure to decref the object there.
Py_XDECREF(bkg_obj0)
# Write the new string object to the buffer in-place
memcpy(buf_obj, &temp_obj, sizeof(temp_obj));
^
------------------------------------------------------------
h5py/_conv.pyx:193:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
# HDF5 will eventually overwrite this target location, so we
# make sure to decref the object there.
Py_XDECREF(bkg_obj0)
# Write the new string object to the buffer in-place
memcpy(buf_obj, &temp_obj, sizeof(temp_obj));
^
------------------------------------------------------------
h5py/_conv.pyx:193:20: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef size_t temp_string_len = 0 # Not including null term
cdef PyObject* buf_obj0
cdef char* buf_cstring0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0))
^
------------------------------------------------------------
h5py/_conv.pyx:212:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef size_t temp_string_len = 0 # Not including null term
cdef PyObject* buf_obj0
cdef char* buf_cstring0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0))
^
------------------------------------------------------------
h5py/_conv.pyx:212:22: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
raise TypeError("Unrecognized dataset encoding")
if strlen(temp_string) != temp_string_len:
raise ValueError("VLEN strings do not support embedded NULLs")
buf_cstring0 = <char*>malloc(temp_string_len+1)
^
------------------------------------------------------------
h5py/_conv.pyx:261:23: Casting temporary Python object to non-numeric non-Python type
Error compiling Cython file:
------------------------------------------------------------
...
raise TypeError("Unrecognized dataset encoding")
if strlen(temp_string) != temp_string_len:
raise ValueError("VLEN strings do not support embedded NULLs")
buf_cstring0 = <char*>malloc(temp_string_len+1)
^
------------------------------------------------------------
h5py/_conv.pyx:261:23: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
if strlen(temp_string) != temp_string_len:
raise ValueError("VLEN strings do not support embedded NULLs")
buf_cstring0 = <char*>malloc(temp_string_len+1)
memcpy(buf_cstring0, temp_string, temp_string_len+1)
memcpy(buf_cstring, &buf_cstring0, sizeof(buf_cstring0));
^
------------------------------------------------------------
h5py/_conv.pyx:263:15: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if strlen(temp_string) != temp_string_len:
raise ValueError("VLEN strings do not support embedded NULLs")
buf_cstring0 = <char*>malloc(temp_string_len+1)
memcpy(buf_cstring0, temp_string, temp_string_len+1)
memcpy(buf_cstring, &buf_cstring0, sizeof(buf_cstring0));
^
------------------------------------------------------------
h5py/_conv.pyx:263:28: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef conv_size_t *sizes
if not (H5Tis_variable_str(src) and (not H5Tis_variable_str(dst))):
return -2
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
^
------------------------------------------------------------
h5py/_conv.pyx:280:12: Casting temporary Python object to non-numeric non-Python type
Error compiling Cython file:
------------------------------------------------------------
...
cdef conv_size_t *sizes
if not (H5Tis_variable_str(src) and (not H5Tis_variable_str(dst))):
return -2
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
^
------------------------------------------------------------
h5py/_conv.pyx:280:12: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
cdef conv_size_t *sizes
if not (H5Tis_variable_str(dst) and (not H5Tis_variable_str(src))):
return -2
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
^
------------------------------------------------------------
h5py/_conv.pyx:294:12: Casting temporary Python object to non-numeric non-Python type
Error compiling Cython file:
------------------------------------------------------------
...
cdef conv_size_t *sizes
if not (H5Tis_variable_str(dst) and (not H5Tis_variable_str(src))):
return -2
sizes = <conv_size_t*>malloc(sizeof(conv_size_t))
^
------------------------------------------------------------
h5py/_conv.pyx:294:12: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* temp_string = NULL
cdef size_t temp_string_len = 0 # Without null term
cdef conv_size_t *sizes = <conv_size_t*>priv
cdef char* buf_vlen0
memcpy(&buf_vlen0, buf_vlen, sizeof(buf_vlen0));
^
------------------------------------------------------------
h5py/_conv.pyx:310:11: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* temp_string = NULL
cdef size_t temp_string_len = 0 # Without null term
cdef conv_size_t *sizes = <conv_size_t*>priv
cdef char* buf_vlen0
memcpy(&buf_vlen0, buf_vlen, sizeof(buf_vlen0));
^
------------------------------------------------------------
h5py/_conv.pyx:310:23: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
temp_string_len = strlen(temp_string)
if temp_string_len <= sizes[0].dst_size:
# Pad with zeros
memcpy(buf_fixed, temp_string, temp_string_len)
memset(buf_fixed + temp_string_len, c'\0', sizes[0].dst_size - temp_string_len)
^
------------------------------------------------------------
h5py/_conv.pyx:319:12: undeclared name not builtin: memset
Error compiling Cython file:
------------------------------------------------------------
...
cdef char** buf_vlen = <char**>opt
cdef char* buf_fixed = <char*>ipt
cdef char* temp_string = NULL
cdef conv_size_t *sizes = <conv_size_t*>priv
temp_string = <char*>malloc(sizes[0].src_size+1)
^
------------------------------------------------------------
h5py/_conv.pyx:335:18: Casting temporary Python object to non-numeric non-Python type
Error compiling Cython file:
------------------------------------------------------------
...
cdef char** buf_vlen = <char**>opt
cdef char* buf_fixed = <char*>ipt
cdef char* temp_string = NULL
cdef conv_size_t *sizes = <conv_size_t*>priv
temp_string = <char*>malloc(sizes[0].src_size+1)
^
------------------------------------------------------------
h5py/_conv.pyx:335:18: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
temp_string = <char*>malloc(sizes[0].src_size+1)
memcpy(temp_string, buf_fixed, sizes[0].src_size)
temp_string[sizes[0].src_size] = c'\0'
memcpy(buf_vlen, &temp_string, sizeof(temp_string));
^
------------------------------------------------------------
h5py/_conv.pyx:339:11: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
temp_string = <char*>malloc(sizes[0].src_size+1)
memcpy(temp_string, buf_fixed, sizes[0].src_size)
temp_string[sizes[0].src_size] = c'\0'
memcpy(buf_vlen, &temp_string, sizeof(temp_string));
^
------------------------------------------------------------
h5py/_conv.pyx:339:21: Cannot convert 'char **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
# HDF5 references to Python instances of h5r.Reference
cdef int conv_objref2pyref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>opt
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>ipt
^
------------------------------------------------------------
h5py/_conv.pyx:349:32: 'hobj_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int conv_objref2pyref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>opt
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>ipt
cdef Reference ref = Reference()
^
------------------------------------------------------------
h5py/_conv.pyx:351:25: 'Reference' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>ipt
cdef Reference ref = Reference()
cdef PyObject* ref_ptr = NULL
memcpy(&ref.ref.obj_ref, buf_ref, sizeof(ref.ref.obj_ref))
^
------------------------------------------------------------
h5py/_conv.pyx:354:11: Cannot take address of Python object attribute 'obj_ref'
Error compiling Cython file:
------------------------------------------------------------
...
cdef Reference ref = Reference()
cdef PyObject* ref_ptr = NULL
memcpy(&ref.ref.obj_ref, buf_ref, sizeof(ref.ref.obj_ref))
ref.typecode = H5R_OBJECT
^
------------------------------------------------------------
h5py/_conv.pyx:355:19: undeclared name not builtin: H5R_OBJECT
Error compiling Cython file:
------------------------------------------------------------
...
ref_ptr = <PyObject*>ref
Py_INCREF(ref_ptr) # because Cython discards its reference when the
# function exits
memcpy(buf_obj, &ref_ptr, sizeof(ref_ptr))
^
------------------------------------------------------------
h5py/_conv.pyx:361:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
ref_ptr = <PyObject*>ref
Py_INCREF(ref_ptr) # because Cython discards its reference when the
# function exits
memcpy(buf_obj, &ref_ptr, sizeof(ref_ptr))
^
------------------------------------------------------------
h5py/_conv.pyx:361:20: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef int conv_pyref2objref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>ipt
cdef hobj_ref_t* buf_ref = <hobj_ref_t*>opt
^
------------------------------------------------------------
h5py/_conv.pyx:368:32: 'hobj_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef object obj
cdef Reference ref
cdef PyObject* buf_obj0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0));
^
------------------------------------------------------------
h5py/_conv.pyx:375:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef object obj
cdef Reference ref
cdef PyObject* buf_obj0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0));
^
------------------------------------------------------------
h5py/_conv.pyx:375:22: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0));
if buf_obj0 != NULL and buf_obj0 != Py_None:
obj = <object>(buf_obj0)
if not isinstance(obj, Reference):
^
------------------------------------------------------------
h5py/_conv.pyx:379:31: 'Reference' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
if buf_obj0 != NULL and buf_obj0 != Py_None:
obj = <object>(buf_obj0)
if not isinstance(obj, Reference):
raise TypeError("Can't convert incompatible object to HDF5 object reference")
ref = <Reference>(buf_obj0)
^
------------------------------------------------------------
h5py/_conv.pyx:381:15: 'Reference' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
if buf_obj0 != NULL and buf_obj0 != Py_None:
obj = <object>(buf_obj0)
if not isinstance(obj, Reference):
raise TypeError("Can't convert incompatible object to HDF5 object reference")
ref = <Reference>(buf_obj0)
memcpy(buf_ref, &ref.ref.obj_ref, sizeof(ref.ref.obj_ref))
^
------------------------------------------------------------
h5py/_conv.pyx:382:24: Cannot take address of Python object attribute 'obj_ref'
Error compiling Cython file:
------------------------------------------------------------
...
if not isinstance(obj, Reference):
raise TypeError("Can't convert incompatible object to HDF5 object reference")
ref = <Reference>(buf_obj0)
memcpy(buf_ref, &ref.ref.obj_ref, sizeof(ref.ref.obj_ref))
else:
memset(buf_ref, c'\0', sizeof(hobj_ref_t))
^
------------------------------------------------------------
h5py/_conv.pyx:384:38: 'hobj_ref_t' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int conv_regref2pyref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>opt
cdef PyObject** bkg_obj = <PyObject**>bkg
cdef hdset_reg_ref_t* buf_ref = <hdset_reg_ref_t*>ipt
^
------------------------------------------------------------
h5py/_conv.pyx:392:37: 'hdset_reg_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject** buf_obj = <PyObject**>opt
cdef PyObject** bkg_obj = <PyObject**>bkg
cdef hdset_reg_ref_t* buf_ref = <hdset_reg_ref_t*>ipt
cdef RegionReference ref = RegionReference()
^
------------------------------------------------------------
h5py/_conv.pyx:394:31: 'RegionReference' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef RegionReference ref = RegionReference()
cdef PyObject* ref_ptr = NULL
cdef PyObject* bkg_obj0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0));
^
------------------------------------------------------------
h5py/_conv.pyx:399:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef RegionReference ref = RegionReference()
cdef PyObject* ref_ptr = NULL
cdef PyObject* bkg_obj0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0));
^
------------------------------------------------------------
h5py/_conv.pyx:399:22: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject* ref_ptr = NULL
cdef PyObject* bkg_obj0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0));
memcpy(ref.ref.reg_ref, buf_ref, sizeof(hdset_reg_ref_t))
^
------------------------------------------------------------
h5py/_conv.pyx:400:44: 'hdset_reg_ref_t' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef PyObject* bkg_obj0
memcpy(&bkg_obj0, bkg_obj, sizeof(bkg_obj0));
memcpy(ref.ref.reg_ref, buf_ref, sizeof(hdset_reg_ref_t))
ref.typecode = H5R_DATASET_REGION
^
------------------------------------------------------------
h5py/_conv.pyx:402:19: undeclared name not builtin: H5R_DATASET_REGION
Error compiling Cython file:
------------------------------------------------------------
...
ref_ptr = <PyObject*>ref
Py_INCREF(ref_ptr) # because Cython discards its reference when the
# function exits
Py_XDECREF(bkg_obj0)
memcpy(buf_obj, &ref_ptr, sizeof(ref_ptr))
^
------------------------------------------------------------
h5py/_conv.pyx:409:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
ref_ptr = <PyObject*>ref
Py_INCREF(ref_ptr) # because Cython discards its reference when the
# function exits
Py_XDECREF(bkg_obj0)
memcpy(buf_obj, &ref_ptr, sizeof(ref_ptr))
^
------------------------------------------------------------
h5py/_conv.pyx:409:20: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef int conv_pyref2regref(void* ipt, void* opt, void* bkg, void* priv) except -1:
cdef PyObject** buf_obj = <PyObject**>ipt
cdef hdset_reg_ref_t* buf_ref = <hdset_reg_ref_t*>opt
^
------------------------------------------------------------
h5py/_conv.pyx:416:37: 'hdset_reg_ref_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef object obj
cdef RegionReference ref
cdef PyObject* buf_obj0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0));
^
------------------------------------------------------------
h5py/_conv.pyx:423:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef object obj
cdef RegionReference ref
cdef PyObject* buf_obj0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0));
^
------------------------------------------------------------
h5py/_conv.pyx:423:22: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0));
if buf_obj0 != NULL and buf_obj0 != Py_None:
obj = <object>(buf_obj0)
if not isinstance(obj, RegionReference):
^
------------------------------------------------------------
h5py/_conv.pyx:427:31: 'RegionReference' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
if buf_obj0 != NULL and buf_obj0 != Py_None:
obj = <object>(buf_obj0)
if not isinstance(obj, RegionReference):
raise TypeError("Can't convert incompatible object to HDF5 region reference")
ref = <RegionReference>(buf_obj0)
^
------------------------------------------------------------
h5py/_conv.pyx:429:15: 'RegionReference' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
if buf_obj0 != NULL and buf_obj0 != Py_None:
obj = <object>(buf_obj0)
if not isinstance(obj, RegionReference):
raise TypeError("Can't convert incompatible object to HDF5 region reference")
ref = <RegionReference>(buf_obj0)
memcpy(buf_ref, ref.ref.reg_ref, sizeof(hdset_reg_ref_t))
^
------------------------------------------------------------
h5py/_conv.pyx:430:48: 'hdset_reg_ref_t' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
if not isinstance(obj, RegionReference):
raise TypeError("Can't convert incompatible object to HDF5 region reference")
ref = <RegionReference>(buf_obj0)
memcpy(buf_ref, ref.ref.reg_ref, sizeof(hdset_reg_ref_t))
else:
memset(buf_ref, c'\0', sizeof(hdset_reg_ref_t))
^
------------------------------------------------------------
h5py/_conv.pyx:432:38: 'hdset_reg_ref_t' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef herr_t vlen2str(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_vlen2str, init_generic, H5T_BKG_YES)
^
------------------------------------------------------------
h5py/_conv.pyx:444:63: undeclared name not builtin: H5T_BKG_YES
Error compiling Cython file:
------------------------------------------------------------
...
cdef herr_t str2vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
void *bkg_i, hid_t dxpl) except -1:
return generic_converter(src_id, dst_id, cdata, nl, buf_stride, bkg_stride,
buf_i, bkg_i, dxpl, conv_str2vlen, init_generic, H5T_BKG_NO)
^
------------------------------------------------------------
h5py/_conv.pyx:450:62: undeclared name not builtin: H5T_BKG_NO
Error compiling Cython file:
------------------------------------------------------------
...
cdef int enum_int_converter_init(hid_t src, hid_t dst,
H5T_cdata_t *cdata, int forward) except -1 with gil:
cdef conv_enum_t *info
cdata[0].need_bkg = H5T_BKG_NO
cdata[0].priv = info = <conv_enum_t*>malloc(sizeof(conv_enum_t))
^
------------------------------------------------------------
h5py/_conv.pyx:500:27: Casting temporary Python object to non-numeric non-Python type
Error compiling Cython file:
------------------------------------------------------------
...
cdef int enum_int_converter_init(hid_t src, hid_t dst,
H5T_cdata_t *cdata, int forward) except -1 with gil:
cdef conv_enum_t *info
cdata[0].need_bkg = H5T_BKG_NO
cdata[0].priv = info = <conv_enum_t*>malloc(sizeof(conv_enum_t))
^
------------------------------------------------------------
h5py/_conv.pyx:500:27: Cannot convert 'conv_enum_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef void enum_int_converter_free(H5T_cdata_t *cdata):
cdef conv_enum_t *info
info = <conv_enum_t*>cdata[0].priv
free(info)
^
------------------------------------------------------------
h5py/_conv.pyx:508:9: Cannot convert 'conv_enum_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef void enum_int_converter_free(H5T_cdata_t *cdata):
cdef conv_enum_t *info
info = <conv_enum_t*>cdata[0].priv
free(info)
cdata[0].priv = NULL
^
------------------------------------------------------------
h5py/_conv.pyx:509:20: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
info = <conv_enum_t*>cdata[0].priv
try:
if forward:
supertype = H5Tget_super(src)
^
------------------------------------------------------------
h5py/_conv.pyx:527:24: undeclared name not builtin: H5Tget_super
Error compiling Cython file:
------------------------------------------------------------
...
info = <conv_enum_t*>cdata[0].priv
try:
if forward:
supertype = H5Tget_super(src)
identical = H5Tequal(supertype, dst)
^
------------------------------------------------------------
h5py/_conv.pyx:528:24: undeclared name not builtin: H5Tequal
Error compiling Cython file:
------------------------------------------------------------
...
return 0
if buf_stride == 0:
# Contiguous case: call H5Tconvert directly
if forward:
H5Tconvert(supertype, dst, nl, buf, NULL, dxpl)
^
------------------------------------------------------------
h5py/_conv.pyx:540:16: undeclared name not builtin: H5Tconvert
Error compiling Cython file:
------------------------------------------------------------
...
return 0
if buf_stride == 0:
# Contiguous case: call H5Tconvert directly
if forward:
H5Tconvert(supertype, dst, nl, buf, NULL, dxpl)
^
------------------------------------------------------------
h5py/_conv.pyx:540:52: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if buf_stride == 0:
# Contiguous case: call H5Tconvert directly
if forward:
H5Tconvert(supertype, dst, nl, buf, NULL, dxpl)
else:
H5Tconvert(src, supertype, nl, buf, NULL, dxpl)
^
------------------------------------------------------------
h5py/_conv.pyx:542:52: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if info[0].src_size > info[0].dst_size:
nalloc = info[0].src_size*nl
else:
nalloc = info[0].dst_size*nl
cbuf = <char*>malloc(nalloc)
^
------------------------------------------------------------
h5py/_conv.pyx:550:19: Casting temporary Python object to non-numeric non-Python type
Error compiling Cython file:
------------------------------------------------------------
...
if info[0].src_size > info[0].dst_size:
nalloc = info[0].src_size*nl
else:
nalloc = info[0].dst_size*nl
cbuf = <char*>malloc(nalloc)
^
------------------------------------------------------------
h5py/_conv.pyx:550:19: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
for i from 0<=i<nl:
memcpy(cbuf + (i*info[0].src_size), buf + (i*buf_stride),
info[0].src_size)
if forward:
H5Tconvert(supertype, dst, nl, cbuf, NULL, dxpl)
^
------------------------------------------------------------
h5py/_conv.pyx:559:53: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
info[0].src_size)
if forward:
H5Tconvert(supertype, dst, nl, cbuf, NULL, dxpl)
else:
H5Tconvert(src, supertype, nl, cbuf, NULL, dxpl)
^
------------------------------------------------------------
h5py/_conv.pyx:561:53: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
finally:
free(cbuf)
cbuf = NULL
if supertype > 0:
H5Tclose(supertype)
^
------------------------------------------------------------
h5py/_conv.pyx:571:12: undeclared name not builtin: H5Tclose
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* buf = <char*>buf_i
if command == H5T_CONV_INIT:
cdata[0].need_bkg = H5T_BKG_NO
if H5Tget_class(src_id) != H5T_VLEN or H5Tget_class(dst_id) != H5T_OPAQUE:
^
------------------------------------------------------------
h5py/_conv.pyx:627:11: undeclared name not builtin: H5Tget_class
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* buf = <char*>buf_i
if command == H5T_CONV_INIT:
cdata[0].need_bkg = H5T_BKG_NO
if H5Tget_class(src_id) != H5T_VLEN or H5Tget_class(dst_id) != H5T_OPAQUE:
^
------------------------------------------------------------
h5py/_conv.pyx:627:35: undeclared name not builtin: H5T_VLEN
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* buf = <char*>buf_i
if command == H5T_CONV_INIT:
cdata[0].need_bkg = H5T_BKG_NO
if H5Tget_class(src_id) != H5T_VLEN or H5Tget_class(dst_id) != H5T_OPAQUE:
^
------------------------------------------------------------
h5py/_conv.pyx:627:71: undeclared name not builtin: H5T_OPAQUE
Error compiling Cython file:
------------------------------------------------------------
...
pass
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
supertype = typewrap(H5Tget_super(src_id))
^
------------------------------------------------------------
h5py/_conv.pyx:637:20: 'typewrap' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
supertype = typewrap(H5Tget_super(src_id))
dt = supertype.dtype
outtype = py_create(dt)
^
------------------------------------------------------------
h5py/_conv.pyx:639:18: 'py_create' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef void* data
cdef np.ndarray ndarray
cdef PyObject* ndarray_obj
cdef vlen_t in_vlen0
memcpy(&in_vlen0, in_vlen, sizeof(in_vlen0))
^
------------------------------------------------------------
h5py/_conv.pyx:688:11: Cannot convert 'vlen_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef void* data
cdef np.ndarray ndarray
cdef PyObject* ndarray_obj
cdef vlen_t in_vlen0
memcpy(&in_vlen0, in_vlen, sizeof(in_vlen0))
^
------------------------------------------------------------
h5py/_conv.pyx:688:22: Cannot convert 'vlen_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
dims[0] = in_vlen0.len
data = in_vlen0.ptr
if outtype.get_size() > intype.get_size():
data = realloc(data, outtype.get_size() * in_vlen0.len)
H5Tconvert(intype.id, outtype.id, in_vlen0.len, data, NULL, H5P_DEFAULT)
^
------------------------------------------------------------
h5py/_conv.pyx:694:64: undeclared name not builtin: H5P_DEFAULT
Error compiling Cython file:
------------------------------------------------------------
...
dims[0] = in_vlen0.len
data = in_vlen0.ptr
if outtype.get_size() > intype.get_size():
data = realloc(data, outtype.get_size() * in_vlen0.len)
H5Tconvert(intype.id, outtype.id, in_vlen0.len, data, NULL, H5P_DEFAULT)
^
------------------------------------------------------------
h5py/_conv.pyx:694:52: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
dims[0] = in_vlen0.len
data = in_vlen0.ptr
if outtype.get_size() > intype.get_size():
data = realloc(data, outtype.get_size() * in_vlen0.len)
H5Tconvert(intype.id, outtype.id, in_vlen0.len, data, NULL, H5P_DEFAULT)
^
------------------------------------------------------------
h5py/_conv.pyx:694:58: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
ndarray_obj = <PyObject*>ndarray
Py_INCREF(ndarray_obj)
# Write the new object to the buffer in-place
in_vlen0.ptr = NULL
memcpy(buf_obj, &ndarray_obj, sizeof(ndarray_obj))
^
------------------------------------------------------------
h5py/_conv.pyx:705:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
ndarray_obj = <PyObject*>ndarray
Py_INCREF(ndarray_obj)
# Write the new object to the buffer in-place
in_vlen0.ptr = NULL
memcpy(buf_obj, &ndarray_obj, sizeof(ndarray_obj))
^
------------------------------------------------------------
h5py/_conv.pyx:705:20: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* buf = <char*>buf_i
if command == H5T_CONV_INIT:
cdata[0].need_bkg = H5T_BKG_NO
if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
^
------------------------------------------------------------
h5py/_conv.pyx:727:32: 'H5PY_OBJ' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
if command == H5T_CONV_INIT:
cdata[0].need_bkg = H5T_BKG_NO
if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
return -2
supertype = typewrap(H5Tget_super(dst_id))
^
------------------------------------------------------------
h5py/_conv.pyx:729:20: 'typewrap' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdata[0].need_bkg = H5T_BKG_NO
if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
return -2
supertype = typewrap(H5Tget_super(dst_id))
for i from 0 <= i < nl:
memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem))
^
------------------------------------------------------------
h5py/_conv.pyx:731:19: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdata[0].need_bkg = H5T_BKG_NO
if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
return -2
supertype = typewrap(H5Tget_super(dst_id))
for i from 0 <= i < nl:
memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem))
^
------------------------------------------------------------
h5py/_conv.pyx:731:37: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
return -2
supertype = typewrap(H5Tget_super(dst_id))
for i from 0 <= i < nl:
memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem))
if supertype != py_create((<np.ndarray> pdata_elem).dtype, 1):
^
------------------------------------------------------------
h5py/_conv.pyx:732:28: 'py_create' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
pass
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
^
------------------------------------------------------------
h5py/_conv.pyx:744:15: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
pass
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
^
------------------------------------------------------------
h5py/_conv.pyx:744:28: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
supertype = py_create((<np.ndarray> pdata_elem).dtype)
^
------------------------------------------------------------
h5py/_conv.pyx:745:20: 'py_create' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
supertype = py_create((<np.ndarray> pdata_elem).dtype)
outtype = typewrap(H5Tget_super(dst_id))
^
------------------------------------------------------------
h5py/_conv.pyx:746:18: 'typewrap' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef void* data
cdef np.ndarray ndarray
cdef size_t len
cdef PyObject* buf_obj0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0))
^
------------------------------------------------------------
h5py/_conv.pyx:791:11: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef void* data
cdef np.ndarray ndarray
cdef size_t len
cdef PyObject* buf_obj0
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0))
^
------------------------------------------------------------
h5py/_conv.pyx:791:22: Cannot convert 'PyObject **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0))
ndarray = <np.ndarray> buf_obj0
len = ndarray.shape[0]
if outtype.get_size() > intype.get_size():
data = malloc(outtype.get_size() * len)
^
------------------------------------------------------------
h5py/_conv.pyx:796:21: Cannot convert Python object to 'void *'
Error compiling Cython file:
------------------------------------------------------------
...
memcpy(&buf_obj0, buf_obj, sizeof(buf_obj0))
ndarray = <np.ndarray> buf_obj0
len = ndarray.shape[0]
if outtype.get_size() > intype.get_size():
data = malloc(outtype.get_size() * len)
^
------------------------------------------------------------
h5py/_conv.pyx:796:21: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
len = ndarray.shape[0]
if outtype.get_size() > intype.get_size():
data = malloc(outtype.get_size() * len)
else:
data = malloc(intype.get_size() * len)
^
------------------------------------------------------------
h5py/_conv.pyx:798:21: Cannot convert Python object to 'void *'
Error compiling Cython file:
------------------------------------------------------------
...
len = ndarray.shape[0]
if outtype.get_size() > intype.get_size():
data = malloc(outtype.get_size() * len)
else:
data = malloc(intype.get_size() * len)
^
------------------------------------------------------------
h5py/_conv.pyx:798:21: Storing unsafe C derivative of temporary Python reference
Error compiling Cython file:
------------------------------------------------------------
...
if outtype.get_size() > intype.get_size():
data = malloc(outtype.get_size() * len)
else:
data = malloc(intype.get_size() * len)
memcpy(data, ndarray.data, intype.get_size() * len)
^
------------------------------------------------------------
h5py/_conv.pyx:799:11: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if outtype.get_size() > intype.get_size():
data = malloc(outtype.get_size() * len)
else:
data = malloc(intype.get_size() * len)
memcpy(data, ndarray.data, intype.get_size() * len)
H5Tconvert(intype.id, outtype.id, len, data, NULL, H5P_DEFAULT)
^
------------------------------------------------------------
h5py/_conv.pyx:800:43: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if outtype.get_size() > intype.get_size():
data = malloc(outtype.get_size() * len)
else:
data = malloc(intype.get_size() * len)
memcpy(data, ndarray.data, intype.get_size() * len)
H5Tconvert(intype.id, outtype.id, len, data, NULL, H5P_DEFAULT)
^
------------------------------------------------------------
h5py/_conv.pyx:800:49: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
else:
data = malloc(intype.get_size() * len)
memcpy(data, ndarray.data, intype.get_size() * len)
H5Tconvert(intype.id, outtype.id, len, data, NULL, H5P_DEFAULT)
memcpy(&in_vlen[0].len, &len, sizeof(len))
^
------------------------------------------------------------
h5py/_conv.pyx:802:11: Cannot convert 'size_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
else:
data = malloc(intype.get_size() * len)
memcpy(data, ndarray.data, intype.get_size() * len)
H5Tconvert(intype.id, outtype.id, len, data, NULL, H5P_DEFAULT)
memcpy(&in_vlen[0].len, &len, sizeof(len))
^
------------------------------------------------------------
h5py/_conv.pyx:802:28: Cannot convert 'size_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
data = malloc(intype.get_size() * len)
memcpy(data, ndarray.data, intype.get_size() * len)
H5Tconvert(intype.id, outtype.id, len, data, NULL, H5P_DEFAULT)
memcpy(&in_vlen[0].len, &len, sizeof(len))
memcpy(&in_vlen[0].ptr, &data, sizeof(data))
^
------------------------------------------------------------
h5py/_conv.pyx:803:11: Cannot convert 'void **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
data = malloc(intype.get_size() * len)
memcpy(data, ndarray.data, intype.get_size() * len)
H5Tconvert(intype.id, outtype.id, len, data, NULL, H5P_DEFAULT)
memcpy(&in_vlen[0].len, &len, sizeof(len))
memcpy(&in_vlen[0].ptr, &data, sizeof(data))
^
------------------------------------------------------------
h5py/_conv.pyx:803:28: Cannot convert 'void **' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef hid_t vlstring
cdef hid_t vlentype
cdef hid_t pyobj
cdef hid_t enum
vlstring = H5Tcopy(H5T_C_S1)
^
------------------------------------------------------------
h5py/_conv.pyx:816:15: undeclared name not builtin: H5Tcopy
Error compiling Cython file:
------------------------------------------------------------
...
cdef hid_t vlstring
cdef hid_t vlentype
cdef hid_t pyobj
cdef hid_t enum
vlstring = H5Tcopy(H5T_C_S1)
^
------------------------------------------------------------
h5py/_conv.pyx:816:23: undeclared name not builtin: H5T_C_S1
Error compiling Cython file:
------------------------------------------------------------
...
cdef hid_t vlentype
cdef hid_t pyobj
cdef hid_t enum
vlstring = H5Tcopy(H5T_C_S1)
H5Tset_size(vlstring, H5T_VARIABLE)
^
------------------------------------------------------------
h5py/_conv.pyx:817:4: undeclared name not builtin: H5Tset_size
Error compiling Cython file:
------------------------------------------------------------
...
cdef hid_t vlentype
cdef hid_t pyobj
cdef hid_t enum
vlstring = H5Tcopy(H5T_C_S1)
H5Tset_size(vlstring, H5T_VARIABLE)
^
------------------------------------------------------------
h5py/_conv.pyx:817:26: undeclared name not builtin: H5T_VARIABLE
Error compiling Cython file:
------------------------------------------------------------
...
cdef hid_t enum
vlstring = H5Tcopy(H5T_C_S1)
H5Tset_size(vlstring, H5T_VARIABLE)
enum = H5Tenum_create(H5T_STD_I32LE)
^
------------------------------------------------------------
h5py/_conv.pyx:819:11: undeclared name not builtin: H5Tenum_create
Error compiling Cython file:
------------------------------------------------------------
...
cdef hid_t enum
vlstring = H5Tcopy(H5T_C_S1)
H5Tset_size(vlstring, H5T_VARIABLE)
enum = H5Tenum_create(H5T_STD_I32LE)
^
------------------------------------------------------------
h5py/_conv.pyx:819:26: undeclared name not builtin: H5T_STD_I32LE
Error compiling Cython file:
------------------------------------------------------------
...
vlstring = H5Tcopy(H5T_C_S1)
H5Tset_size(vlstring, H5T_VARIABLE)
enum = H5Tenum_create(H5T_STD_I32LE)
vlentype = H5Tvlen_create(H5T_STD_I32LE)
^
------------------------------------------------------------
h5py/_conv.pyx:821:15: undeclared name not builtin: H5Tvlen_create
Error compiling Cython file:
------------------------------------------------------------
...
enum = H5Tenum_create(H5T_STD_I32LE)
vlentype = H5Tvlen_create(H5T_STD_I32LE)
pyobj = H5PY_OBJ
^
------------------------------------------------------------
h5py/_conv.pyx:823:12: 'H5PY_OBJ' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
vlentype = H5Tvlen_create(H5T_STD_I32LE)
pyobj = H5PY_OBJ
H5Tregister(H5T_PERS_HARD, "vlen2str", vlstring, pyobj, vlen2str)
^
------------------------------------------------------------
h5py/_conv.pyx:825:4: undeclared name not builtin: H5Tregister
Error compiling Cython file:
------------------------------------------------------------
...
vlentype = H5Tvlen_create(H5T_STD_I32LE)
pyobj = H5PY_OBJ
H5Tregister(H5T_PERS_HARD, "vlen2str", vlstring, pyobj, vlen2str)
^
------------------------------------------------------------
h5py/_conv.pyx:825:16: undeclared name not builtin: H5T_PERS_HARD
Error compiling Cython file:
------------------------------------------------------------
...
vlentype = H5Tvlen_create(H5T_STD_I32LE)
pyobj = H5PY_OBJ
H5Tregister(H5T_PERS_HARD, "vlen2str", vlstring, pyobj, vlen2str)
^
------------------------------------------------------------
h5py/_conv.pyx:825:60: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
vlentype = H5Tvlen_create(H5T_STD_I32LE)
pyobj = H5PY_OBJ
H5Tregister(H5T_PERS_HARD, "vlen2str", vlstring, pyobj, vlen2str)
H5Tregister(H5T_PERS_HARD, "str2vlen", pyobj, vlstring, str2vlen)
^
------------------------------------------------------------
h5py/_conv.pyx:826:60: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
pyobj = H5PY_OBJ
H5Tregister(H5T_PERS_HARD, "vlen2str", vlstring, pyobj, vlen2str)
H5Tregister(H5T_PERS_HARD, "str2vlen", pyobj, vlstring, str2vlen)
H5Tregister(H5T_PERS_SOFT, "vlen2fixed", vlstring, H5T_C_S1, vlen2fixed)
^
------------------------------------------------------------
h5py/_conv.pyx:828:16: undeclared name not builtin: H5T_PERS_SOFT
Error compiling Cython file:
------------------------------------------------------------
...
pyobj = H5PY_OBJ
H5Tregister(H5T_PERS_HARD, "vlen2str", vlstring, pyobj, vlen2str)
H5Tregister(H5T_PERS_HARD, "str2vlen", pyobj, vlstring, str2vlen)
H5Tregister(H5T_PERS_SOFT, "vlen2fixed", vlstring, H5T_C_S1, vlen2fixed)
^
------------------------------------------------------------
h5py/_conv.pyx:828:65: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_HARD, "vlen2str", vlstring, pyobj, vlen2str)
H5Tregister(H5T_PERS_HARD, "str2vlen", pyobj, vlstring, str2vlen)
H5Tregister(H5T_PERS_SOFT, "vlen2fixed", vlstring, H5T_C_S1, vlen2fixed)
H5Tregister(H5T_PERS_SOFT, "fixed2vlen", H5T_C_S1, vlstring, fixed2vlen)
^
------------------------------------------------------------
h5py/_conv.pyx:829:65: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_HARD, "str2vlen", pyobj, vlstring, str2vlen)
H5Tregister(H5T_PERS_SOFT, "vlen2fixed", vlstring, H5T_C_S1, vlen2fixed)
H5Tregister(H5T_PERS_SOFT, "fixed2vlen", H5T_C_S1, vlstring, fixed2vlen)
H5Tregister(H5T_PERS_HARD, "objref2pyref", H5T_STD_REF_OBJ, pyobj, objref2pyref)
^
------------------------------------------------------------
h5py/_conv.pyx:831:47: undeclared name not builtin: H5T_STD_REF_OBJ
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_HARD, "str2vlen", pyobj, vlstring, str2vlen)
H5Tregister(H5T_PERS_SOFT, "vlen2fixed", vlstring, H5T_C_S1, vlen2fixed)
H5Tregister(H5T_PERS_SOFT, "fixed2vlen", H5T_C_S1, vlstring, fixed2vlen)
H5Tregister(H5T_PERS_HARD, "objref2pyref", H5T_STD_REF_OBJ, pyobj, objref2pyref)
^
------------------------------------------------------------
h5py/_conv.pyx:831:71: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_SOFT, "vlen2fixed", vlstring, H5T_C_S1, vlen2fixed)
H5Tregister(H5T_PERS_SOFT, "fixed2vlen", H5T_C_S1, vlstring, fixed2vlen)
H5Tregister(H5T_PERS_HARD, "objref2pyref", H5T_STD_REF_OBJ, pyobj, objref2pyref)
H5Tregister(H5T_PERS_HARD, "pyref2objref", pyobj, H5T_STD_REF_OBJ, pyref2objref)
^
------------------------------------------------------------
h5py/_conv.pyx:832:71: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_SOFT, "fixed2vlen", H5T_C_S1, vlstring, fixed2vlen)
H5Tregister(H5T_PERS_HARD, "objref2pyref", H5T_STD_REF_OBJ, pyobj, objref2pyref)
H5Tregister(H5T_PERS_HARD, "pyref2objref", pyobj, H5T_STD_REF_OBJ, pyref2objref)
H5Tregister(H5T_PERS_HARD, "regref2pyref", H5T_STD_REF_DSETREG, pyobj, regref2pyref)
^
------------------------------------------------------------
h5py/_conv.pyx:834:47: undeclared name not builtin: H5T_STD_REF_DSETREG
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_SOFT, "fixed2vlen", H5T_C_S1, vlstring, fixed2vlen)
H5Tregister(H5T_PERS_HARD, "objref2pyref", H5T_STD_REF_OBJ, pyobj, objref2pyref)
H5Tregister(H5T_PERS_HARD, "pyref2objref", pyobj, H5T_STD_REF_OBJ, pyref2objref)
H5Tregister(H5T_PERS_HARD, "regref2pyref", H5T_STD_REF_DSETREG, pyobj, regref2pyref)
^
------------------------------------------------------------
h5py/_conv.pyx:834:75: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_HARD, "objref2pyref", H5T_STD_REF_OBJ, pyobj, objref2pyref)
H5Tregister(H5T_PERS_HARD, "pyref2objref", pyobj, H5T_STD_REF_OBJ, pyref2objref)
H5Tregister(H5T_PERS_HARD, "regref2pyref", H5T_STD_REF_DSETREG, pyobj, regref2pyref)
H5Tregister(H5T_PERS_HARD, "pyref2regref", pyobj, H5T_STD_REF_DSETREG, pyref2regref)
^
------------------------------------------------------------
h5py/_conv.pyx:835:75: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_HARD, "pyref2objref", pyobj, H5T_STD_REF_OBJ, pyref2objref)
H5Tregister(H5T_PERS_HARD, "regref2pyref", H5T_STD_REF_DSETREG, pyobj, regref2pyref)
H5Tregister(H5T_PERS_HARD, "pyref2regref", pyobj, H5T_STD_REF_DSETREG, pyref2regref)
H5Tregister(H5T_PERS_SOFT, "enum2int", enum, H5T_STD_I32LE, enum2int)
^
------------------------------------------------------------
h5py/_conv.pyx:837:64: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_HARD, "regref2pyref", H5T_STD_REF_DSETREG, pyobj, regref2pyref)
H5Tregister(H5T_PERS_HARD, "pyref2regref", pyobj, H5T_STD_REF_DSETREG, pyref2regref)
H5Tregister(H5T_PERS_SOFT, "enum2int", enum, H5T_STD_I32LE, enum2int)
H5Tregister(H5T_PERS_SOFT, "int2enum", H5T_STD_I32LE, enum, int2enum)
^
------------------------------------------------------------
h5py/_conv.pyx:838:64: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_HARD, "pyref2regref", pyobj, H5T_STD_REF_DSETREG, pyref2regref)
H5Tregister(H5T_PERS_SOFT, "enum2int", enum, H5T_STD_I32LE, enum2int)
H5Tregister(H5T_PERS_SOFT, "int2enum", H5T_STD_I32LE, enum, int2enum)
H5Tregister(H5T_PERS_SOFT, "vlen2ndarray", vlentype, pyobj, vlen2ndarray)
^
------------------------------------------------------------
h5py/_conv.pyx:840:64: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tregister(H5T_PERS_SOFT, "enum2int", enum, H5T_STD_I32LE, enum2int)
H5Tregister(H5T_PERS_SOFT, "int2enum", H5T_STD_I32LE, enum, int2enum)
H5Tregister(H5T_PERS_SOFT, "vlen2ndarray", vlentype, pyobj, vlen2ndarray)
H5Tregister(H5T_PERS_SOFT, "ndarray2vlen", pyobj, vlentype, ndarray2vlen)
^
------------------------------------------------------------
h5py/_conv.pyx:841:64: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cpdef int unregister_converters() except -1:
H5Tunregister(H5T_PERS_HARD, "vlen2str", -1, -1, vlen2str)
^
------------------------------------------------------------
h5py/_conv.pyx:851:4: undeclared name not builtin: H5Tunregister
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cpdef int unregister_converters() except -1:
H5Tunregister(H5T_PERS_HARD, "vlen2str", -1, -1, vlen2str)
^
------------------------------------------------------------
h5py/_conv.pyx:851:53: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cpdef int unregister_converters() except -1:
H5Tunregister(H5T_PERS_HARD, "vlen2str", -1, -1, vlen2str)
H5Tunregister(H5T_PERS_HARD, "str2vlen", -1, -1, str2vlen)
^
------------------------------------------------------------
h5py/_conv.pyx:852:53: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cpdef int unregister_converters() except -1:
H5Tunregister(H5T_PERS_HARD, "vlen2str", -1, -1, vlen2str)
H5Tunregister(H5T_PERS_HARD, "str2vlen", -1, -1, str2vlen)
H5Tunregister(H5T_PERS_SOFT, "vlen2fixed", -1, -1, vlen2fixed)
^
------------------------------------------------------------
h5py/_conv.pyx:854:55: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_HARD, "vlen2str", -1, -1, vlen2str)
H5Tunregister(H5T_PERS_HARD, "str2vlen", -1, -1, str2vlen)
H5Tunregister(H5T_PERS_SOFT, "vlen2fixed", -1, -1, vlen2fixed)
H5Tunregister(H5T_PERS_SOFT, "fixed2vlen", -1, -1, fixed2vlen)
^
------------------------------------------------------------
h5py/_conv.pyx:855:55: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_HARD, "str2vlen", -1, -1, str2vlen)
H5Tunregister(H5T_PERS_SOFT, "vlen2fixed", -1, -1, vlen2fixed)
H5Tunregister(H5T_PERS_SOFT, "fixed2vlen", -1, -1, fixed2vlen)
H5Tunregister(H5T_PERS_HARD, "objref2pyref", -1, -1, objref2pyref)
^
------------------------------------------------------------
h5py/_conv.pyx:857:57: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_SOFT, "vlen2fixed", -1, -1, vlen2fixed)
H5Tunregister(H5T_PERS_SOFT, "fixed2vlen", -1, -1, fixed2vlen)
H5Tunregister(H5T_PERS_HARD, "objref2pyref", -1, -1, objref2pyref)
H5Tunregister(H5T_PERS_HARD, "pyref2objref", -1, -1, pyref2objref)
^
------------------------------------------------------------
h5py/_conv.pyx:858:57: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_SOFT, "fixed2vlen", -1, -1, fixed2vlen)
H5Tunregister(H5T_PERS_HARD, "objref2pyref", -1, -1, objref2pyref)
H5Tunregister(H5T_PERS_HARD, "pyref2objref", -1, -1, pyref2objref)
H5Tunregister(H5T_PERS_HARD, "regref2pyref", -1, -1, regref2pyref)
^
------------------------------------------------------------
h5py/_conv.pyx:860:57: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_HARD, "objref2pyref", -1, -1, objref2pyref)
H5Tunregister(H5T_PERS_HARD, "pyref2objref", -1, -1, pyref2objref)
H5Tunregister(H5T_PERS_HARD, "regref2pyref", -1, -1, regref2pyref)
H5Tunregister(H5T_PERS_HARD, "pyref2regref", -1, -1, pyref2regref)
^
------------------------------------------------------------
h5py/_conv.pyx:861:57: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_HARD, "pyref2objref", -1, -1, pyref2objref)
H5Tunregister(H5T_PERS_HARD, "regref2pyref", -1, -1, regref2pyref)
H5Tunregister(H5T_PERS_HARD, "pyref2regref", -1, -1, pyref2regref)
H5Tunregister(H5T_PERS_SOFT, "enum2int", -1, -1, enum2int)
^
------------------------------------------------------------
h5py/_conv.pyx:863:53: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_HARD, "regref2pyref", -1, -1, regref2pyref)
H5Tunregister(H5T_PERS_HARD, "pyref2regref", -1, -1, pyref2regref)
H5Tunregister(H5T_PERS_SOFT, "enum2int", -1, -1, enum2int)
H5Tunregister(H5T_PERS_SOFT, "int2enum", -1, -1, int2enum)
^
------------------------------------------------------------
h5py/_conv.pyx:864:53: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_HARD, "pyref2regref", -1, -1, pyref2regref)
H5Tunregister(H5T_PERS_SOFT, "enum2int", -1, -1, enum2int)
H5Tunregister(H5T_PERS_SOFT, "int2enum", -1, -1, int2enum)
H5Tunregister(H5T_PERS_SOFT, "vlen2ndarray", -1, -1, vlen2ndarray)
^
------------------------------------------------------------
h5py/_conv.pyx:866:57: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
H5Tunregister(H5T_PERS_SOFT, "enum2int", -1, -1, enum2int)
H5Tunregister(H5T_PERS_SOFT, "int2enum", -1, -1, int2enum)
H5Tunregister(H5T_PERS_SOFT, "vlen2ndarray", -1, -1, vlen2ndarray)
H5Tunregister(H5T_PERS_SOFT, "ndarray2vlen", -1, -1, ndarray2vlen)
^
------------------------------------------------------------
h5py/_conv.pyx:867:57: Cannot convert '<error>' to Python object
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-990qh8xu/h5py_447ed218a500438085f3341266b7d4cd/setup.py", line 150, in <module>
setup(
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/__init__.py", line 107, in setup
return distutils.core.setup(**attrs)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 346, in run
self.run_command("build")
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-install-990qh8xu/h5py_447ed218a500438085f3341266b7d4cd/setup_build.py", line 202, in run
self.extensions = cythonize(self._make_extensions(config),
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "/opt/anaconda3/envs/anvio-dev/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /tmp/pip-install-990qh8xu/h5py_447ed218a500438085f3341266b7d4cd/h5py/_conv.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for h5py
Running setup.py clean for h5py
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects
Config Error: According to the exit code ('1'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less.Thanks @dgslos, but these outputs don't help :) We know things will fail. Someone needs to fix each of those issues and start putting together a PR for Python 3.10 upgrade, if it is possible at all.
The need
Anvi'o currently requires Python 3.6. Which is ancient .. and no longer supported.
The solution
The upgrade to Python 3.10 is not as simple as simply changing the Python version while setting up the conda environment for anvi'o. We have been stuck with Python 3.6 due to pandas and snakemake dependencies (newer versions of Python required newer versions of pandas and snakemake, but our codebase was not ready to work with the newer versions of pandas and snakemake).
The solution is to bite the bullet, start a new conda environment the following way,
And then,
requirements.txtrequirements.txt.Beneficiaries
Everyone everywhere. But especially Richard Fox at the MBL.