Upgraded to Python 3.9

[de-code]

part of https://github.com/elifesciences/data-hub-issues/issues/1036

[de-code]

Error:

11:19:06 copying thinc/extra/search.cpp -> build/lib.linux-x86_64-3.9/thinc/extra
11:19:06 running build_ext
11:19:06 building 'thinc.linalg' extension
11:19:06 creating build/temp.linux-x86_64-3.9
11:19:06 creating build/temp.linux-x86_64-3.9/thinc
11:19:06 gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include/python3.9 -I/tmp/pip-install-68kot0nj/thinc_62178600c5254ccdbdb77fa6b0c4b75b/include -I/usr/local/include/python3.9 -c thinc/linalg.cpp -o build/temp.linux-x86_64-3.9/thinc/linalg.o -O3 -Wno-strict-prototypes -Wno-unused-function
11:19:06 error: command 'gcc' failed: No such file or directory
11:19:06 [end of output]
11:19:06
11:19:06 note: This error originates from a subprocess, and is likely not a problem with pip.
11:19:06 ERROR: Failed building wheel for thinc
11:19:06 Running setup.py clean for thinc
11:19:06 Building wheel for blis (setup.py): started
11:19:06 Building wheel for blis (setup.py): finished with status 'error'
11:19:06 error: subprocess-exited-with-error
11:19:06
11:19:06 × python setup.py bdist_wheel did not run successfully.
11:19:06 │ exit code: 1
11:19:06 ╰─> [25 lines of output]
11:19:06 BLIS_COMPILER? None
11:19:06 running bdist_wheel
11:19:06 running build
11:19:06 running build_py
11:19:06 creating build
11:19:06 creating build/lib.linux-x86_64-3.9
11:19:06 creating build/lib.linux-x86_64-3.9/blis
11:19:06 copying blis/about.py -> build/lib.linux-x86_64-3.9/blis
11:19:06 copying blis/init.py -> build/lib.linux-x86_64-3.9/blis
11:19:06 copying blis/benchmark.py -> build/lib.linux-x86_64-3.9/blis
11:19:06 creating build/lib.linux-x86_64-3.9/blis/tests
11:19:06 copying blis/tests/test_gemm.py -> build/lib.linux-x86_64-3.9/blis/tests
11:19:06 copying blis/tests/test_dotv.py -> build/lib.linux-x86_64-3.9/blis/tests
11:19:06 copying blis/tests/common.py -> build/lib.linux-x86_64-3.9/blis/tests
11:19:06 copying blis/tests/init.py -> build/lib.linux-x86_64-3.9/blis/tests
11:19:06 copying blis/py.pyx -> build/lib.linux-x86_64-3.9/blis
11:19:06 copying blis/cy.pyx -> build/lib.linux-x86_64-3.9/blis
11:19:06 copying blis/cy.pxd -> build/lib.linux-x86_64-3.9/blis
11:19:06 copying blis/init.pxd -> build/lib.linux-x86_64-3.9/blis
11:19:06 running build_ext
11:19:06 unix
11:19:06 py_compiler gcc
11:19:06 {'BLIS_ARCH': 'generic', 'HOSTNAME': 'aa9d42588791', 'SSL_CERT_FILE': '/opt/internal/certs.pem', 'TERM': 'xterm', 'OLDPWD': '/usr/local/repos/cython-blis', 'LD_LIBRARY_PATH': '/opt/rh/devtoolset-2/root/usr/lib64:/opt/rh/devtoolset-2/root/usr/lib:/usr/local/lib64:/usr/local/lib', 'LS_COLORS': 'no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=00;32:.cmd=00;32:.exe=00;32:.com=00;32:.btm=00;32:.bat=00;32:.sh=00;32:.csh=00;32:.tar=00;31:.tgz=00;31:.arj=00;31:.taz=00;31:.lzh=00;31:.zip=00;31:.z=00;31:.Z=00;31:.gz=00;31:.bz2=00;31:.bz=00;31:.tz=00;31:.rpm=00;31:.cpio=00;31:.jpg=00;35:.gif=00;35:.bmp=00;35:.xbm=00;35:.xpm=00;35:.png=00;35:.tif=00;35:', 'VIRTUAL_ENV': '/usr/local/repos/cython-blis/env3.6', 'PATH': '/usr/local/repos/cython-blis/env3.6/bin:/opt/rh/devtoolset-2/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PWD': '/usr/local/repos/cython-blis/flame-blis', 'BLIS_ARCh': 'generic', 'LANG': 'en_US.UTF-8', 'HOME': '/root', 'SHLVL': '2', 'LANGUAGE': 'en_US.UTF-8', 'BLIS_ARC': 'generic', 'AUDITWHEEL_PLAT': 'manylinux1_x86_64', 'PKG_CONFIG_PATH': '/usr/local/lib/pkgconfig', 'LESSOPEN': '|/usr/bin/lesspipe.sh %s', 'G_BROKEN_FILENAMES': '1', '': '/usr/local/repos/cython-blis/env3.6/bin/python'}
11:19:06 gcc -c /tmp/pip-install-68kot0nj/blis_a8be362388cf4ae0af320a2724c84538/blis/_src/config/generic/bli_cntx_init_generic.c -o /tmp/tmpjccsnc3r/bli_cntx_init_generic.o -O3 -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.1" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/linux-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/tmp/pip-install-68kot0nj/blis_a8be362388cf4ae0af320a2724c84538/blis/_src/include/linux-x86_64
11:19:06 error: [Errno 2] No such file or directory: 'gcc'
11:19:06 [end of output]
11:19:06
11:19:06 note: This error originates from a subprocess, and is likely not a problem with pip.
11:19:06 ERROR: Failed building wheel for blis
11:19:06 Running setup.py clean for blis
11:19:06 Failed to build thinc blis
11:19:06 ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (thinc, blis)
11:19:06 [end of output]
11:19:06
11:19:06 note: This error originates from a subprocess, and is likely not a problem with pip.
11:19:06 �[0m�[91merror: subprocess-exited-with-error

[de-code]

Error:

gcc: fatal error: cannot execute ‘cc1plus’: execvp: No such file or directory

[de-code]

Error:

11:52:37 Collecting spacy==2.2.4 (from -r requirements.spacy.txt (line 1))
11:52:37 Downloading spacy-2.2.4.tar.gz (6.1 MB)
11:52:37 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.1/6.1 MB 287.3 MB/s eta 0:00:00
11:52:38 Installing build dependencies: started
11:54:00 Installing build dependencies: still running...
11:55:08 Installing build dependencies: still running...
11:56:17 Installing build dependencies: still running...
11:57:25 Installing build dependencies: still running...
11:58:22 Installing build dependencies: still running...
11:59:19 Installing build dependencies: still running...
12:00:41 Installing build dependencies: still running...
12:00:41 Installing build dependencies: finished with status 'done'
12:00:41 Getting requirements to build wheel: started
12:00:41 Getting requirements to build wheel: finished with status 'error'
12:00:41 �[91m error: subprocess-exited-with-error
12:00:41
12:00:41 × Getting requirements to build wheel did not run successfully.
12:00:41 │ exit code: 1
12:00:41 ╰─> [15 lines of output]
12:00:41 Traceback (most recent call last):
12:00:41 File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
12:00:41 main()
12:00:41 File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
12:00:41 json_out['return_val'] = hook(**hook_input['kwargs'])
12:00:41 File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
12:00:41 return hook(config_settings)
12:00:41 File "/tmp/pip-build-env-1ph47fp0/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
12:00:41 return self._get_build_requires(config_settings, requirements=[])
12:00:41 File "/tmp/pip-build-env-1ph47fp0/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
12:00:41 self.run_setup()
12:00:41 File "/tmp/pip-build-env-1ph47fp0/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 320, in run_setup
12:00:41 exec(code, locals())
12:00:41 File "", line 11, in
12:00:41 ImportError: cannot import name 'msvccompiler' from 'distutils' (/tmp/pip-build-env-1ph47fp0/overlay/lib/python3.9/site-packages/setuptools/_distutils/init.py)
12:00:41 [end of output]

[de-code]

Error:

12:23:58 �[0mRemoving intermediate container c8382715fd86
12:23:58 ---> 3c5dcefa8526
12:23:58 Step 11/21 : RUN python -m spacy download en_core_web_lg
12:23:58 ---> Running in 66854ae5e479
12:23:58 �[91mTraceback (most recent call last):
12:23:58 File "/usr/local/lib/python3.9/runpy.py", line 188, in _run_module_as_main
12:23:58 �[0m�[91m mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
12:23:58 File "/usr/local/lib/python3.9/runpy.py", line 147, in _get_module_details
12:23:58 �[0m�[91m return _get_module_details(pkg_main_name, error)
12:23:58 File "/usr/local/lib/python3.9/runpy.py", line 111, in _get_module_details
12:23:58 �[0m�[91m import(pkg_name)
12:23:58 File "/usr/local/lib/python3.9/site-packages/spacy/init.py", line 10, in
12:23:58 �[0m�[91m from thinc.neural.util import prefer_gpu, require_gpu
12:23:58 File "/usr/local/lib/python3.9/site-packages/thinc/neural/init.py", line 4, in
12:23:58 �[0m�[91m from ._classes.model import Model # noqa: F401
12:23:58 File "/usr/local/lib/python3.9/site-packages/thinc/neural/_classes/model.py", line 11, in
12:23:58 �[0m�[91m from ..train import Trainer
12:23:58 File "/usr/local/lib/python3.9/site-packages/thinc/neural/train.py", line 7, in
12:23:58 �[0m�[91m from .optimizers import Adam, linear_decay
12:23:58 File "thinc/neural/optimizers.pyx", line 14, in init thinc.neural.optimizers
12:23:58 �[0m�[91m File "thinc/neural/ops.pyx", line 1, in init thinc.neural.ops
12:23:58 �[0m�[91mValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
12:23:58 �[0mService 'peerscout-dags-dev' failed to build: The command '/bin/sh -c python -m spacy download en_core_web_lg' returned a non-zero code: 1
12:23:58 make[1]: *** [Makefile:91: build-dev] Error 1

[de-code]

Now the Spacy related unit tests are failing