Installation issues on MacOS

[plbt5]

I have both python 2.7 as pythn 3.9 installed. Hence, I install by

$ python3 setup.py
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
   or: setup.py --help [cmd1 cmd2 ...]
   or: setup.py --help-commands
   or: setup.py cmd --help

error: no commands supplied

Following the --help page (useful, tx), I apply the install command:

$ python3 setup.py install
running install
running bdist_egg
running egg_info
creating case_utils.egg-info
writing case_utils.egg-info/PKG-INFO
writing dependency_links to case_utils.egg-info/dependency_links.txt
writing entry points to case_utils.egg-info/entry_points.txt
writing requirements to case_utils.egg-info/requires.txt
writing top-level names to case_utils.egg-info/top_level.txt
writing manifest file 'case_utils.egg-info/SOURCES.txt'
reading manifest file 'case_utils.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'case_utils.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-11-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/case_utils
copying case_utils/__init__.py -> build/lib/case_utils
copying case_utils/local_uuid.py -> build/lib/case_utils
creating build/lib/case_utils/case_sparql_select
copying case_utils/case_sparql_select/__init__.py -> build/lib/case_utils/case_sparql_select
creating build/lib/case_utils/case_file
copying case_utils/case_file/__init__.py -> build/lib/case_utils/case_file
creating build/lib/case_utils/case_validate
copying case_utils/case_validate/__init__.py -> build/lib/case_utils/case_validate
creating build/lib/case_utils/ontology
copying case_utils/ontology/version_info.py -> build/lib/case_utils/ontology
copying case_utils/ontology/__init__.py -> build/lib/case_utils/ontology
creating build/lib/case_utils/case_sparql_construct
copying case_utils/case_sparql_construct/__init__.py -> build/lib/case_utils/case_sparql_construct
copying case_utils/py.typed -> build/lib/case_utils
copying case_utils/ontology/case-0.5.0.ttl -> build/lib/case_utils/ontology
copying case_utils/ontology/case-0.5.0-subclasses.ttl -> build/lib/case_utils/ontology
creating build/bdist.macosx-11-x86_64
creating build/bdist.macosx-11-x86_64/egg
creating build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select
copying build/lib/case_utils/case_sparql_select/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_file
copying build/lib/case_utils/case_file/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_file
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_validate
copying build/lib/case_utils/case_validate/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_validate
copying build/lib/case_utils/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/version_info.py -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/case-0.5.0.ttl -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/case-0.5.0-subclasses.ttl -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/local_uuid.py -> build/bdist.macosx-11-x86_64/egg/case_utils
copying build/lib/case_utils/py.typed -> build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct
copying build/lib/case_utils/case_sparql_construct/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_file/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_validate/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/ontology/version_info.py to version_info.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/ontology/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/local_uuid.py to local_uuid.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct/__init__.py to __init__.cpython-39.pyc
creating build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/PKG-INFO -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/SOURCES.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/dependency_links.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/entry_points.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/requires.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/top_level.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
case_utils.case_sparql_construct.__pycache__.__init__.cpython-39: module references __file__
case_utils.case_sparql_select.__pycache__.__init__.cpython-39: module references __file__
case_utils.case_validate.__pycache__.__init__.cpython-39: module references __file__
case_utils.ontology.__pycache__.__init__.cpython-39: module references __file__
creating dist
creating 'dist/case_utils-0.3.0-py3.9.egg' and adding 'build/bdist.macosx-11-x86_64/egg' to it
removing 'build/bdist.macosx-11-x86_64/egg' (and everything under it)
Processing case_utils-0.3.0-py3.9.egg
creating /usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg
Extracting case_utils-0.3.0-py3.9.egg to /usr/local/lib/python3.9/site-packages
Adding case-utils 0.3.0 to easy-install.pth file
Installing case_file script to /usr/local/bin
Installing case_sparql_construct script to /usr/local/bin
Installing case_sparql_select script to /usr/local/bin
Installing case_validate script to /usr/local/bin

Installed /usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg
Processing dependencies for case-utils==0.3.0
Searching for tabulate
Reading https://pypi.org/simple/tabulate/
Downloading https://files.pythonhosted.org/packages/ca/80/7c0cad11bd99985cfe7c09427ee0b4f9bd6b048bd13d4ffb32c6db237dfb/tabulate-0.8.9-py3-none-any.whl#sha256=d7c013fe7abbc5e491394e10fa845f8f32fe54f8dc60c6622c6cf482d25d47e4
Best match: tabulate 0.8.9
Processing tabulate-0.8.9-py3-none-any.whl
Installing tabulate-0.8.9-py3-none-any.whl to /usr/local/lib/python3.9/site-packages
Adding tabulate 0.8.9 to easy-install.pth file
Installing tabulate script to /usr/local/bin

Installed /usr/local/lib/python3.9/site-packages/tabulate-0.8.9-py3.9.egg
Searching for requests
Reading https://pypi.org/simple/requests/
Downloading https://files.pythonhosted.org/packages/92/96/144f70b972a9c0eabbd4391ef93ccd49d0f2747f4f6a2a2738e99e5adc65/requests-2.26.0-py2.py3-none-any.whl#sha256=6c1246513ecd5ecd4528a0906f910e8f0f9c6b8ec72030dc9fd154dc1a6efd24
Best match: requests 2.26.0
Processing requests-2.26.0-py2.py3-none-any.whl
Installing requests-2.26.0-py2.py3-none-any.whl to /usr/local/lib/python3.9/site-packages
Adding requests 2.26.0 to easy-install.pth file

Installed /usr/local/lib/python3.9/site-packages/requests-2.26.0-py3.9.egg
Searching for rdflib>=6.0.2
Reading https://pypi.org/simple/rdflib/
Downloading https://files.pythonhosted.org/packages/34/77/2995c0d4b89607ce2c5e062995f7a26ed61a4d9e20cfc3711f5e8adeaa7e/rdflib-6.0.2-py3-none-any.whl#sha256=b7642daac8cdad1ba157fecb236f5d1b2aa1de64e714dcee80d65e2b794d88a6
Best match: rdflib 6.0.2
Processing rdflib-6.0.2-py3-none-any.whl
Installing rdflib-6.0.2-py3-none-any.whl to /usr/local/lib/python3.9/site-packages
Adding rdflib 6.0.2 to easy-install.pth file
Installing csv2rdf script to /usr/local/bin
Installing rdf2dot script to /usr/local/bin
Installing rdfgraphisomorphism script to /usr/local/bin
Installing rdfpipe script to /usr/local/bin
Installing rdfs2dot script to /usr/local/bin

Installed /usr/local/lib/python3.9/site-packages/rdflib-6.0.2-py3.9.egg
Searching for pyshacl
Reading https://pypi.org/simple/pyshacl/
Downloading https://files.pythonhosted.org/packages/39/62/4a4a03b9daefe1046b976e7cf0ff1238942ca51fa0cfa029fad9af4bcaad/pyshacl-0.17.2-py3-none-any.whl#sha256=ec147758eabadac13d8a981c5b9da9447ac6eb04cc6f013b92902cf24adad373
Best match: pyshacl 0.17.2
Processing pyshacl-0.17.2-py3-none-any.whl
Installing pyshacl-0.17.2-py3-none-any.whl to /usr/local/lib/python3.9/site-packages
Adding pyshacl 0.17.2 to easy-install.pth file
Installing pyshacl script to /usr/local/bin

Installed /usr/local/lib/python3.9/site-packages/pyshacl-0.17.2-py3.9.egg
Searching for pandas
Reading https://pypi.org/simple/pandas/
Downloading https://files.pythonhosted.org/packages/58/58/b729eda34f78060e14cb430c91d4f7ba3cf1e34797976877a3a1125ea5b2/pandas-1.3.4.tar.gz#sha256=a2aa18d3f0b7d538e21932f637fbfe8518d085238b429e4790a35e1e44a96ffc
Best match: pandas 1.3.4
Processing pandas-1.3.4.tar.gz
Writing /var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-nz_zqwp7/pandas-1.3.4/setup.cfg
Running pandas-1.3.4/setup.py -q bdist_egg --dist-dir /var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-nz_zqwp7/pandas-1.3.4/egg-dist-tmp-i8ff599n
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 152, in save_modules
    yield saved
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 254, in run_setup
    _execfile(setup_script, ns)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-nz_zqwp7/pandas-1.3.4/setup.py", line 18, in <module>
ModuleNotFoundError: No module named 'numpy'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/paulbrandt/Workspace/CASE/CASE-Utilities-Python/setup.py", line 17, in <module>
    setuptools.setup()
  File "/usr/local/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
    return distutils.core.setup(**attrs)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run(show_deprecation=False)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 408, in run
    self.easy_install(spec, not self.no_deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 650, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 697, in install_item
    self.process_distribution(spec, dist, deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 744, in process_distribution
    distros = WorkingSet([]).resolve(
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 766, in resolve
    dist = best[req.key] = env.best_match(
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1051, in best_match
    return self.obtain(req, installer)
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1063, in obtain
    return installer(requirement)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 669, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 695, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1162, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1146, in run_setup
    run_setup(setup_script, args)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 257, in run_setup
    raise
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 164, in save_modules
    saved_exc.resume()
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 139, in resume
    raise exc.with_traceback(self._tb)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 152, in save_modules
    yield saved
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 254, in run_setup
    _execfile(setup_script, ns)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-nz_zqwp7/pandas-1.3.4/setup.py", line 18, in <module>
ModuleNotFoundError: No module named 'numpy'

Manually installing numpy:

$ python3 -m pip install numpy
...
Successfully installed numpy-1.21.4

Re-installing, i.e.:

$ python3 setup.py install
running install
running bdist_egg
running egg_info
writing case_utils.egg-info/PKG-INFO
writing dependency_links to case_utils.egg-info/dependency_links.txt
writing entry points to case_utils.egg-info/entry_points.txt
writing requirements to case_utils.egg-info/requires.txt
writing top-level names to case_utils.egg-info/top_level.txt
reading manifest file 'case_utils.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'case_utils.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-11-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-11-x86_64/egg
creating build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select
copying build/lib/case_utils/case_sparql_select/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_file
copying build/lib/case_utils/case_file/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_file
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_validate
copying build/lib/case_utils/case_validate/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_validate
copying build/lib/case_utils/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/version_info.py -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/case-0.5.0.ttl -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/case-0.5.0-subclasses.ttl -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/local_uuid.py -> build/bdist.macosx-11-x86_64/egg/case_utils
copying build/lib/case_utils/py.typed -> build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct
copying build/lib/case_utils/case_sparql_construct/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_file/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_validate/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/ontology/version_info.py to version_info.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/ontology/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/local_uuid.py to local_uuid.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct/__init__.py to __init__.cpython-39.pyc
creating build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/PKG-INFO -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/SOURCES.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/dependency_links.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/entry_points.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/requires.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/top_level.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
case_utils.case_sparql_construct.__pycache__.__init__.cpython-39: module references __file__
case_utils.case_sparql_select.__pycache__.__init__.cpython-39: module references __file__
case_utils.case_validate.__pycache__.__init__.cpython-39: module references __file__
case_utils.ontology.__pycache__.__init__.cpython-39: module references __file__
creating 'dist/case_utils-0.3.0-py3.9.egg' and adding 'build/bdist.macosx-11-x86_64/egg' to it
removing 'build/bdist.macosx-11-x86_64/egg' (and everything under it)
Processing case_utils-0.3.0-py3.9.egg
removing '/usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg' (and everything under it)
creating /usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg
Extracting case_utils-0.3.0-py3.9.egg to /usr/local/lib/python3.9/site-packages
case-utils 0.3.0 is already the active version in easy-install.pth
Installing case_file script to /usr/local/bin
Installing case_sparql_construct script to /usr/local/bin
Installing case_sparql_select script to /usr/local/bin
Installing case_validate script to /usr/local/bin

Installed /usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg
Processing dependencies for case-utils==0.3.0
Searching for pandas
Reading https://pypi.org/simple/pandas/
Downloading https://files.pythonhosted.org/packages/58/58/b729eda34f78060e14cb430c91d4f7ba3cf1e34797976877a3a1125ea5b2/pandas-1.3.4.tar.gz#sha256=a2aa18d3f0b7d538e21932f637fbfe8518d085238b429e4790a35e1e44a96ffc
Best match: pandas 1.3.4
Processing pandas-1.3.4.tar.gz
Writing /var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-eu7avhbg/pandas-1.3.4/setup.cfg
Running pandas-1.3.4/setup.py -q bdist_egg --dist-dir /var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-eu7avhbg/pandas-1.3.4/egg-dist-tmp-kynmrlxf
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 152, in save_modules
    yield saved
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 254, in run_setup
    _execfile(setup_script, ns)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-eu7avhbg/pandas-1.3.4/setup.py", line 650, in <module>
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-eu7avhbg/pandas-1.3.4/setup.py", line 414, in maybe_cythonize
RuntimeError: Cannot cythonize without Cython installed.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/paulbrandt/Workspace/CASE/CASE-Utilities-Python/setup.py", line 17, in <module>
    setuptools.setup()
  File "/usr/local/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
    return distutils.core.setup(**attrs)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run(show_deprecation=False)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 408, in run
    self.easy_install(spec, not self.no_deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 650, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 697, in install_item
    self.process_distribution(spec, dist, deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 744, in process_distribution
    distros = WorkingSet([]).resolve(
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 766, in resolve
    dist = best[req.key] = env.best_match(
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1051, in best_match
    return self.obtain(req, installer)
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1063, in obtain
    return installer(requirement)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 669, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 695, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1162, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1146, in run_setup
    run_setup(setup_script, args)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 257, in run_setup
    raise
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 164, in save_modules
    saved_exc.resume()
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 139, in resume
    raise exc.with_traceback(self._tb)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 152, in save_modules
    yield saved
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 254, in run_setup
    _execfile(setup_script, ns)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-eu7avhbg/pandas-1.3.4/setup.py", line 650, in <module>
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-eu7avhbg/pandas-1.3.4/setup.py", line 414, in maybe_cythonize
RuntimeError: Cannot cythonize without Cython installed.

Hence, installing Cython:

$ python3 -m pip install Cython
...
Successfully installed Cython-0.29.24

Reinstalling:

$ python3 setup.py install
running install
running bdist_egg
running egg_info
writing case_utils.egg-info/PKG-INFO
writing dependency_links to case_utils.egg-info/dependency_links.txt
writing entry points to case_utils.egg-info/entry_points.txt
writing requirements to case_utils.egg-info/requires.txt
writing top-level names to case_utils.egg-info/top_level.txt
reading manifest file 'case_utils.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'case_utils.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-11-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-11-x86_64/egg
creating build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select
copying build/lib/case_utils/case_sparql_select/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_file
copying build/lib/case_utils/case_file/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_file
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_validate
copying build/lib/case_utils/case_validate/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_validate
copying build/lib/case_utils/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/version_info.py -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/case-0.5.0.ttl -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/ontology/case-0.5.0-subclasses.ttl -> build/bdist.macosx-11-x86_64/egg/case_utils/ontology
copying build/lib/case_utils/local_uuid.py -> build/bdist.macosx-11-x86_64/egg/case_utils
copying build/lib/case_utils/py.typed -> build/bdist.macosx-11-x86_64/egg/case_utils
creating build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct
copying build/lib/case_utils/case_sparql_construct/__init__.py -> build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_select/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_file/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_validate/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/ontology/version_info.py to version_info.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/ontology/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/local_uuid.py to local_uuid.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/case_utils/case_sparql_construct/__init__.py to __init__.cpython-39.pyc
creating build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/PKG-INFO -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/SOURCES.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/dependency_links.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/entry_points.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/requires.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying case_utils.egg-info/top_level.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
case_utils.case_sparql_construct.__pycache__.__init__.cpython-39: module references __file__
case_utils.case_sparql_select.__pycache__.__init__.cpython-39: module references __file__
case_utils.case_validate.__pycache__.__init__.cpython-39: module references __file__
case_utils.ontology.__pycache__.__init__.cpython-39: module references __file__
creating 'dist/case_utils-0.3.0-py3.9.egg' and adding 'build/bdist.macosx-11-x86_64/egg' to it
removing 'build/bdist.macosx-11-x86_64/egg' (and everything under it)
Processing case_utils-0.3.0-py3.9.egg
removing '/usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg' (and everything under it)
creating /usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg
Extracting case_utils-0.3.0-py3.9.egg to /usr/local/lib/python3.9/site-packages
case-utils 0.3.0 is already the active version in easy-install.pth
Installing case_file script to /usr/local/bin
Installing case_sparql_construct script to /usr/local/bin
Installing case_sparql_select script to /usr/local/bin
Installing case_validate script to /usr/local/bin

Installed /usr/local/lib/python3.9/site-packages/case_utils-0.3.0-py3.9.egg
Processing dependencies for case-utils==0.3.0
Searching for pandas
Reading https://pypi.org/simple/pandas/
Downloading https://files.pythonhosted.org/packages/58/58/b729eda34f78060e14cb430c91d4f7ba3cf1e34797976877a3a1125ea5b2/pandas-1.3.4.tar.gz#sha256=a2aa18d3f0b7d538e21932f637fbfe8518d085238b429e4790a35e1e44a96ffc
Best match: pandas 1.3.4
Processing pandas-1.3.4.tar.gz
Writing /var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-hhjf5got/pandas-1.3.4/setup.cfg
Running pandas-1.3.4/setup.py -q bdist_egg --dist-dir /var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-hhjf5got/pandas-1.3.4/egg-dist-tmp-cyd2mjd6
Compiling pandas/_libs/algos.pyx because it changed.
Compiling pandas/_libs/arrays.pyx because it changed.
Compiling pandas/_libs/groupby.pyx because it changed.
Compiling pandas/_libs/hashing.pyx because it changed.
Compiling pandas/_libs/hashtable.pyx because it changed.
Compiling pandas/_libs/index.pyx because it changed.
Compiling pandas/_libs/indexing.pyx because it changed.
Compiling pandas/_libs/internals.pyx because it changed.
Compiling pandas/_libs/interval.pyx because it changed.
Compiling pandas/_libs/join.pyx because it changed.
Compiling pandas/_libs/lib.pyx because it changed.
Compiling pandas/_libs/missing.pyx because it changed.
Compiling pandas/_libs/parsers.pyx because it changed.
Compiling pandas/_libs/reduction.pyx because it changed.
Compiling pandas/_libs/ops.pyx because it changed.
Compiling pandas/_libs/ops_dispatch.pyx because it changed.
Compiling pandas/_libs/properties.pyx because it changed.
Compiling pandas/_libs/reshape.pyx because it changed.
Compiling pandas/_libs/sparse.pyx because it changed.
Compiling pandas/_libs/tslib.pyx because it changed.
Compiling pandas/_libs/tslibs/base.pyx because it changed.
Compiling pandas/_libs/tslibs/ccalendar.pyx because it changed.
Compiling pandas/_libs/tslibs/dtypes.pyx because it changed.
Compiling pandas/_libs/tslibs/conversion.pyx because it changed.
Compiling pandas/_libs/tslibs/fields.pyx because it changed.
Compiling pandas/_libs/tslibs/nattype.pyx because it changed.
Compiling pandas/_libs/tslibs/np_datetime.pyx because it changed.
Compiling pandas/_libs/tslibs/offsets.pyx because it changed.
Compiling pandas/_libs/tslibs/parsing.pyx because it changed.
Compiling pandas/_libs/tslibs/period.pyx because it changed.
Compiling pandas/_libs/tslibs/strptime.pyx because it changed.
Compiling pandas/_libs/tslibs/timedeltas.pyx because it changed.
Compiling pandas/_libs/tslibs/timestamps.pyx because it changed.
Compiling pandas/_libs/tslibs/timezones.pyx because it changed.
Compiling pandas/_libs/tslibs/tzconversion.pyx because it changed.
Compiling pandas/_libs/tslibs/vectorized.pyx because it changed.
Compiling pandas/_libs/testing.pyx because it changed.
Compiling pandas/_libs/window/aggregations.pyx because it changed.
Compiling pandas/_libs/window/indexers.pyx because it changed.
Compiling pandas/_libs/writers.pyx because it changed.
Compiling pandas/io/sas/sas.pyx because it changed.
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 152, in save_modules
    yield saved
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 254, in run_setup
    _execfile(setup_script, ns)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-hhjf5got/pandas-1.3.4/setup.py", line 650, in <module>
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-hhjf5got/pandas-1.3.4/setup.py", line 423, in maybe_cythonize
  File "/usr/local/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1078, in cythonize
    pool = multiprocessing.Pool(
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 119, in Pool
    return Pool(processes, initializer, initargs, maxtasksperchild,
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 212, in __init__
    self._repopulate_pool()
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 303, in _repopulate_pool
    return self._repopulate_pool_static(self._ctx, self.Process,
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 326, in _repopulate_pool_static
    w.start()
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
    return Popen(process_obj)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 61, in _launch
    with open(parent_w, 'wb', closefd=False) as f:
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 421, in _open
    if mode not in ('r', 'rt', 'rb', 'rU', 'U') and not self._ok(path):
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 432, in _ok
    realpath = os.path.normcase(os.path.realpath(path))
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py", line 391, in realpath
    filename = os.fspath(filename)
TypeError: expected str, bytes or os.PathLike object, not int

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/paulbrandt/Workspace/CASE/CASE-Utilities-Python/setup.py", line 17, in <module>
    setuptools.setup()
  File "/usr/local/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
    return distutils.core.setup(**attrs)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run(show_deprecation=False)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 408, in run
    self.easy_install(spec, not self.no_deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 650, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 697, in install_item
    self.process_distribution(spec, dist, deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 744, in process_distribution
    distros = WorkingSet([]).resolve(
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 766, in resolve
    dist = best[req.key] = env.best_match(
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1051, in best_match
    return self.obtain(req, installer)
  File "/usr/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1063, in obtain
    return installer(requirement)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 669, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 695, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1162, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/usr/local/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1146, in run_setup
    run_setup(setup_script, args)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 257, in run_setup
    raise
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 164, in save_modules
    saved_exc.resume()
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 139, in resume
    raise exc.with_traceback(self._tb)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 152, in save_modules
    yield saved
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 254, in run_setup
    _execfile(setup_script, ns)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-hhjf5got/pandas-1.3.4/setup.py", line 650, in <module>
  File "/var/folders/0n/9k_3vk4x1lj421lq6wqb1vcr0000gn/T/easy_install-hhjf5got/pandas-1.3.4/setup.py", line 423, in maybe_cythonize
  File "/usr/local/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1078, in cythonize
    pool = multiprocessing.Pool(
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 119, in Pool
    return Pool(processes, initializer, initargs, maxtasksperchild,
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 212, in __init__
    self._repopulate_pool()
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 303, in _repopulate_pool
    return self._repopulate_pool_static(self._ctx, self.Process,
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 326, in _repopulate_pool_static
    w.start()
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
    return Popen(process_obj)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 61, in _launch
    with open(parent_w, 'wb', closefd=False) as f:
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 421, in _open
    if mode not in ('r', 'rt', 'rb', 'rU', 'U') and not self._ok(path):
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 432, in _ok
    realpath = os.path.normcase(os.path.realpath(path))
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py", line 391, in realpath
    filename = os.fspath(filename)
TypeError: expected str, bytes or os.PathLike object, not int
Traceback (most recent call last):
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py", line 201, in main
    cache[rtype].remove(name)
KeyError: '/mp-ir0let60'
Traceback (most recent call last):
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py", line 201, in main
    cache[rtype].remove(name)
KeyError: '/mp-4ngxzdpg'
Traceback (most recent call last):
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py", line 201, in main
    cache[rtype].remove(name)
KeyError: '/mp-r21215g4'
Traceback (most recent call last):
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py", line 201, in main
    cache[rtype].remove(name)
KeyError: '/mp-rlbqp8w6'
Traceback (most recent call last):
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py", line 201, in main
    cache[rtype].remove(name)
KeyError: '/mp-6az3whq7'
Traceback (most recent call last):
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py", line 201, in main
    cache[rtype].remove(name)
KeyError: '/mp-yqk8crjy'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/spawn.py", line 124, in _main
    preparation_data = reduction.pickle.load(from_parent)
EOFError: Ran out of input
Pauls-MacBook-Pro:CASE-Utilities-Python paulbrandt$ /usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 6 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '
/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:229: UserWarning: resource_tracker: '/mp-4ngxzdpg': [Errno 2] No such file or directory
  warnings.warn('resource_tracker: %r: %s' % (name, e))
/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:229: UserWarning: resource_tracker: '/mp-yqk8crjy': [Errno 2] No such file or directory
  warnings.warn('resource_tracker: %r: %s' % (name, e))
/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:229: UserWarning: resource_tracker: '/mp-r21215g4': [Errno 2] No such file or directory
  warnings.warn('resource_tracker: %r: %s' % (name, e))
/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:229: UserWarning: resource_tracker: '/mp-rlbqp8w6': [Errno 2] No such file or directory
  warnings.warn('resource_tracker: %r: %s' % (name, e))
/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:229: UserWarning: resource_tracker: '/mp-6az3whq7': [Errno 2] No such file or directory
  warnings.warn('resource_tracker: %r: %s' % (name, e))
/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:229: UserWarning: resource_tracker: '/mp-ir0let60': [Errno 2] No such file or directory
  warnings.warn('resource_tracker: %r: %s' % (name, e))

I want to make sure that repititively running install is not inducing issues. Hence, I removed everything (not the additionally installed packages) and start with a clean slate. Cloning git, and doing a python3 setup.py install. No intermediate package failures, but when Compiling pandas/io/sas/sas.pyx it halts again with the very same error.

I'm running MacOS Big Sur, v 11.6

[ajnelson-nist]

That was quite an adventure you went on!

The README of this repository documents three installation steps. Step 2 was designated optional, creating a virtual environment. I haven't tested installing this without a virtual environment. @plbt5 , you might want to consider a virtual environment (the way the CI does that is python3 -m venv venv ; source venv/bin/activate, demonstrated here.) instead of installing packages to your system-wide Python instance, though that is ultimately a matter of personal preference.

Meanwhile, I've reproduced the issue, using a virtual environment. python setup.py install stops recursively collecting packages. I don't know why, but it's happening. The documentation needs to be revised to use pip install . instead of python setup.py install. I'll file a PR to close this.

Meanwhile, I came across another long-build behavior that seems to suggest you'll want to run pip install --upgrade pip setuptools wheel. It seems pip <21.0 runs a lengthy build of pandas.

[ajnelson-nist]

@plbt5 , please let me know if the develop branch's README contains satisfactory directions for you.

[plbt5]

@ajnelson-nist I've followed the installation instructions and initiated a make check. The following lines are the last in a long list of tests that have been executed. I assume this proves the resolution of the installation issue that I had.

When you agree you can close this issue.

========================================================================================== test session starts ==========================================================================================
platform darwin -- Python 3.9.12, pytest-7.1.2, pluggy-1.0.0
rootdir: /Users/paulbrandt/Workspace/CASE/CASE-Utilities-Python
collected 17 items                                                                                                                                                                                      

hexbinary/test_hexbinary.py .x..x...xxx.xx..x                                                                                                                                                     [100%]

=========================================================================================== warnings summary ============================================================================================
hexbinary/test_hexbinary.py:61
  /Users/paulbrandt/Workspace/CASE/CASE-Utilities-Python/tests/hexbinary/test_hexbinary.py:61: UserWarning: Code: hexBinaryCanonical is not defined in namespace XSD
    l_hbc_uppercase = rdflib.Literal("AB", datatype=rdflib.XSD.hexBinaryCanonical)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================================================================ 9 passed, 8 xfailed, 1 warning in 0.45s ================================================================================

[ajnelson-nist]

That's good, make did not report an error. Yes, it looks like things work well enough for you now.