cryptsys / pharmapy Goto Github PK

Problematic decisions by SUNDIALS when nearing the final point

We should rework the connectivity components of PharmaPy (Connections.py and DynamicInputs). Unit conversion and get_inputs need to be addressed as well.

Hello, it was very complicated for me to install your package, even if I'm quite used to work with python and conda environments!
Ideally, on the long term, if you could make a pip or conda package out of it ...
remarks with the install_instructions: when I hit '\InstallOnWindows.bat, I was alsways lacking one dependency (numpy, cython, ...). Then when all dependencies were install, I had another error "AttributeError: '_thread._local' object has no attribute 'cython_errors_stack'"

I tried with manual installation (as a small remark in 'conda config -- show envs_dirs' there should be no space between -- and show) and always this error 'sphinxcontrib.bibtex does not exist', event when installing the appropriate package

It seems that one of the problem is 'numpy.distutils' which is now deprecated

Hello team,
how about if we consider using a Dependabot to keep the dependencies updated and safe?
https://docs.github.com/en/code-security/getting-started/dependabot-quickstart-guide

Alpha value from the filtration unit and CakePhase alpha are different. Check this mismatch

Invite Varun

When installing on Windows executing InstallOnWindows.bat ends with the following error and the pharmapy environment isn't created.

[1/1] Cythonizing assimulo\solvers\euler.pyx
C:\ProgramData\Anaconda3\lib\site-packages\Cython\Compiler\Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: C:\Users<username>\AppData\Local\Temp\easy_install-s9rd0icw\Assimulo-3.0\assimulo\solvers\euler.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
non-existing path in '': 'assimulo\thirdparty\hairer\dopri5.pyf'
non-existing path in '': 'assimulo\thirdparty\hairer\rodas_decsol.pyf'
non-existing path in '': 'assimulo\thirdparty\hairer\radau_decsol.pyf'
non-existing path in '': 'assimulo\thirdparty\hairer\radar5.pyf'
non-existing path in '': 'assimulo\thirdparty\odepack\odepack.pyf'
non-existing path in '': 'assimulo\thirdparty\odassl\odassl.pyf'
Could not find Blas or Lapack, disabling support for the solver GLIMDA.
target build\src.win-amd64-3.9\assimulo\thirdparty\hairer\dopri5module.c does not exist:
Assuming dopri5module.c was generated with "build_src --inplace" command.
error: Setup script exited with error: 'assimulo\thirdparty\hairer\dopri5module.c' missing
Done!

Hi,
I am having trouble installing PharmaPy. It seems the main issue is related to Cython. Here is the log in case it helps.

(base) PS C:\WINDOWS\system32> cd 'C:\Users\MyName\Desktop\PharmaPy-master\PharmaPy-master'
At line:1 char:3

• Do .\InstallOnWindows.bat
• ~
  Missing statement body in do loop.
  • CategoryInfo : ParserError: (:) [], ParentContainsErrorRecordException
  • FullyQualifiedErrorId : MissingLoopStatement

(base) PS C:\Users\MyName\Desktop\PharmaPy-master\PharmaPy-master> .\InstallOnWindows.bat

Welcome to the PharmaPy installation wizard.

Enter environment name: PharmaPytry

Creating pandas environment...

Collecting package metadata (current_repodata.json): \ DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
| DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/msys2/win-64/current_repodata.json HTTP/1.1" 304 0
/ DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/win-64/current_repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/win-64/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/win-64/current_repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/msys2/noarch/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/noarch/current_repodata.json HTTP/1.1" 200 None
failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/win-64/current_repodata.json
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https//conda.anaconda.org/conda-forge/win-64'

EnvironmentNameNotFound: Could not find conda environment: PharmaPytry
You can list all discoverable environments with conda info --envs.

Installing PharmaPy...

running develop
C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` and ``easy_install``.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://github.com/pypa/setuptools/issues/917 for details.
    ********************************************************************************

!!
easy_install.initialize_options(self)
C:\Users\MyName\anaconda3\Lib\site-packages\setuptools_distutils\cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!!
self.initialize_options()
running egg_info
writing PharmaPy.egg-info\PKG-INFO
writing dependency_links to PharmaPy.egg-info\dependency_links.txt
writing requirements to PharmaPy.egg-info\requires.txt
writing top-level names to PharmaPy.egg-info\top_level.txt
reading manifest file 'PharmaPy.egg-info\SOURCES.txt'
adding license file 'LICENSE.md'
writing manifest file 'PharmaPy.egg-info\SOURCES.txt'
running build_ext
Creating c:\users\MyName\anaconda3\lib\site-packages\PharmaPy.egg-link (link to .)
PharmaPy 0.0.0 is already the active version in easy-install.pth

Installed c:\users\MyName\desktop\pharmapy-master\pharmapy-master
Processing dependencies for PharmaPy==0.0.0
Searching for assimulo
Reading https://pypi.org/simple/assimulo/
Downloading https://files.pythonhosted.org/packages/28/ef/4d8b15a0842410bb4ca8f500dadd5ff76fb3e34559f956a51c19b8a4912b/Assimulo-3.0.tar.gz#sha256=61cdca4562745078c966cc4fab44d8bc0db11a9e6856b45c470ac65c16af9e8a
Best match: Assimulo 3.0
Processing Assimulo-3.0.tar.gz
Writing C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\setup.cfg
Running Assimulo-3.0\setup.py -q bdist_egg --dist-dir C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\egg-dist-tmp-bygjrr4g
C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\setup.py:75: DeprecationWarning:

numpy.distutils is deprecated since NumPy 1.23.0, as a result
of the deprecation of distutils itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use setuptools < 60.0 for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html

import numpy.distutils as nd
No path to BLAS supplied, disabling support. View more information using --log=DEBUG
No path to SuperLU supplied, disabling support. View more information using --log=DEBUG
Could not find Sundials, check the provided path (--sundials-home=) to see that it actually points to Sundials.
No path to LAPACK supplied, disabling support. View more information using --log=DEBUG
Compiling assimulo\algebraic.pyx because it changed.
Compiling assimulo\explicit_ode.pyx because it changed.
Compiling assimulo\implicit_ode.pyx because it changed.
Compiling assimulo\ode.pyx because it changed.
Compiling assimulo\problem.pyx because it changed.
Compiling assimulo\special_systems.pyx because it changed.
Compiling assimulo\support.pyx because it changed.
[1/7] Cythonizing assimulo\algebraic.pyx
C:\Users\MyName\anaconda3\Lib\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: C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\assimulo\algebraic.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: assimulo\constants.pxi:35:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:36:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:37:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:38:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:39:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:49:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:50:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:51:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:52:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:53:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
[2/7] Cythonizing assimulo\explicit_ode.pyx
C:\Users\MyName\anaconda3\Lib\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: C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\assimulo\explicit_ode.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: assimulo\constants.pxi:35:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:36:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:37:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:38:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:39:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:49:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:50:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:51:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:52:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:53:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
[3/7] Cythonizing assimulo\implicit_ode.pyx
C:\Users\MyName\anaconda3\Lib\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: C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\assimulo\implicit_ode.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: assimulo\constants.pxi:35:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:36:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:37:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:38:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:39:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:49:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:50:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:51:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:52:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:53:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
[4/7] Cythonizing assimulo\ode.pyx
C:\Users\MyName\anaconda3\Lib\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: C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\assimulo\ode.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: assimulo\constants.pxi:35:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:36:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:37:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:38:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:39:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:49:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:50:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:51:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:52:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
warning: assimulo\constants.pxi:53:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See cython/cython#4310
Traceback (most recent call last):
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 156, in save_modules
yield saved
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 198, in setup_context
yield
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 259, in run_setup
_execfile(setup_script, ns)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 46, in _execfile
exec(code, globals, locals)
File "C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\setup.py", line 543, in
File "C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\setup.py", line 407, in cython_extensionlists
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Build\Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Build\Dependencies.py", line 1280, in cythonize_one
result = compile_single(pyx_file, options, full_module_name=full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Main.py", line 615, in compile_single
return run_pipeline(source, options, full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Main.py", line 539, in run_pipeline
err, enddata = Pipeline.run_pipeline(pipeline, source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Pipeline.py", line 398, in run_pipeline
data = run(phase, data)
^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Pipeline.py", line 375, in run
return phase(data)
^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Pipeline.py", line 34, in parse
tree = context.parse(source_desc, scope, pxd = 0, full_module_name = full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Main.py", line 381, in parse
tree = Parsing.p_module(s, pxd, full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "Cython\Compiler\Parsing.py", line 3910, in Cython.Compiler.Parsing.p_module
File "Cython\Compiler\Parsing.py", line 3929, in Cython.Compiler.Parsing.p_module
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2389, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 3245, in Cython.Compiler.Parsing.p_cdef_statement
File "Cython\Compiler\Parsing.py", line 3725, in Cython.Compiler.Parsing.p_c_class_definition
File "Cython\Compiler\Parsing.py", line 2483, in Cython.Compiler.Parsing.p_suite_with_docstring
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2389, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 3258, in Cython.Compiler.Parsing.p_cdef_statement
File "Cython\Compiler\Parsing.py", line 3500, in Cython.Compiler.Parsing.p_c_func_or_var_declaration
File "Cython\Compiler\Parsing.py", line 2483, in Cython.Compiler.Parsing.p_suite_with_docstring
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2431, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 1943, in Cython.Compiler.Parsing.p_for_statement
File "Cython\Compiler\Parsing.py", line 2472, in Cython.Compiler.Parsing.p_suite
File "Cython\Compiler\Parsing.py", line 2483, in Cython.Compiler.Parsing.p_suite_with_docstring
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2450, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 2290, in Cython.Compiler.Parsing.p_simple_statement_list
File "Cython\Compiler\Scanning.py", line 537, in Cython.Compiler.Scanning.PyrexScanner.expect_newline
File "Cython\Compiler\Scanning.py", line 506, in Cython.Compiler.Scanning.PyrexScanner.expect
File "Cython\Compiler\Scanning.py", line 516, in Cython.Compiler.Scanning.PyrexScanner.expected
File "Cython\Compiler\Scanning.py", line 493, in Cython.Compiler.Scanning.PyrexScanner.error
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Errors.py", line 181, in error
report_error(err)
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Errors.py", line 149, in report_error
error_stack = threadlocal.cython_errors_stack
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: '_thread._local' object has no attribute 'cython_errors_stack'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\MyName\Desktop\PharmaPy-master\PharmaPy-master\setup.py", line 15, in
setup(name='PharmaPy',
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools_init_.py", line 107, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools_distutils\core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools_distutils\core.py", line 201, in run_commands
dist.run_commands()
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools_distutils\dist.py", line 969, in run_commands
self.run_command(cmd)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\develop.py", line 34, in run
self.install_for_development()
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\develop.py", line 126, in install_for_development
self.process_distribution(None, self.dist, not self.no_deps)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\easy_install.py", line 750, in process_distribution
distros = WorkingSet([]).resolve(
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\pkg_resources_init_.py", line 829, in resolve
dist = self.resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\pkg_resources_init.py", line 865, in resolve_dist
dist = best[req.key] = env.best_match(
^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\pkg_resources_init.py", line 1135, in best_match
return self.obtain(req, installer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\pkg_resources_init_.py", line 1147, in obtain
return installer(requirement)
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\easy_install.py", line 677, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\easy_install.py", line 703, in install_item
dists = self.install_eggs(spec, download, tmpdir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\easy_install.py", line 896, in install_eggs
return self.build_and_install(setup_script, setup_base)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\easy_install.py", line 1170, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\command\easy_install.py", line 1154, in run_setup
run_setup(setup_script, args)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 249, in run_setup
with setup_context(setup_dir):
File "C:\Users\MyName\anaconda3\Lib\contextlib.py", line 155, in exit
self.gen.throw(typ, value, traceback)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 190, in setup_context
with save_modules():
File "C:\Users\MyName\anaconda3\Lib\contextlib.py", line 155, in exit
self.gen.throw(typ, value, traceback)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 169, in save_modules
saved_exc.resume()
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 143, in resume
raise exc.with_traceback(self._tb)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 156, in save_modules
yield saved
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 198, in setup_context
yield
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 259, in run_setup
_execfile(setup_script, ns)
File "C:\Users\MyName\anaconda3\Lib\site-packages\setuptools\sandbox.py", line 46, in _execfile
exec(code, globals, locals)
File "C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\setup.py", line 543, in
File "C:\Users\RyanConner\AppData\Local\Temp\easy_install-531510lj\Assimulo-3.0\setup.py", line 407, in cython_extensionlists
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Build\Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Build\Dependencies.py", line 1280, in cythonize_one
result = compile_single(pyx_file, options, full_module_name=full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Main.py", line 615, in compile_single
return run_pipeline(source, options, full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Main.py", line 539, in run_pipeline
err, enddata = Pipeline.run_pipeline(pipeline, source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Pipeline.py", line 398, in run_pipeline
data = run(phase, data)
^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Pipeline.py", line 375, in run
return phase(data)
^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Pipeline.py", line 34, in parse
tree = context.parse(source_desc, scope, pxd = 0, full_module_name = full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Main.py", line 381, in parse
tree = Parsing.p_module(s, pxd, full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "Cython\Compiler\Parsing.py", line 3910, in Cython.Compiler.Parsing.p_module
File "Cython\Compiler\Parsing.py", line 3929, in Cython.Compiler.Parsing.p_module
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2389, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 3245, in Cython.Compiler.Parsing.p_cdef_statement
File "Cython\Compiler\Parsing.py", line 3725, in Cython.Compiler.Parsing.p_c_class_definition
File "Cython\Compiler\Parsing.py", line 2483, in Cython.Compiler.Parsing.p_suite_with_docstring
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2389, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 3258, in Cython.Compiler.Parsing.p_cdef_statement
File "Cython\Compiler\Parsing.py", line 3500, in Cython.Compiler.Parsing.p_c_func_or_var_declaration
File "Cython\Compiler\Parsing.py", line 2483, in Cython.Compiler.Parsing.p_suite_with_docstring
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2431, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 1943, in Cython.Compiler.Parsing.p_for_statement
File "Cython\Compiler\Parsing.py", line 2472, in Cython.Compiler.Parsing.p_suite
File "Cython\Compiler\Parsing.py", line 2483, in Cython.Compiler.Parsing.p_suite_with_docstring
File "Cython\Compiler\Parsing.py", line 2458, in Cython.Compiler.Parsing.p_statement_list
File "Cython\Compiler\Parsing.py", line 2450, in Cython.Compiler.Parsing.p_statement
File "Cython\Compiler\Parsing.py", line 2290, in Cython.Compiler.Parsing.p_simple_statement_list
File "Cython\Compiler\Scanning.py", line 537, in Cython.Compiler.Scanning.PyrexScanner.expect_newline
File "Cython\Compiler\Scanning.py", line 506, in Cython.Compiler.Scanning.PyrexScanner.expect
File "Cython\Compiler\Scanning.py", line 516, in Cython.Compiler.Scanning.PyrexScanner.expected
File "Cython\Compiler\Scanning.py", line 493, in Cython.Compiler.Scanning.PyrexScanner.error
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Errors.py", line 181, in error
report_error(err)
File "C:\Users\MyName\anaconda3\Lib\site-packages\Cython\Compiler\Errors.py", line 149, in report_error
error_stack = threadlocal.cython_errors_stack
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: '_thread._local' object has no attribute 'cython_errors_stack'
Done!
(base) PS C:\Users\MyName\Desktop\PharmaPy-master\PharmaPy-master> conda activate PharmaPytry

EnvironmentNameNotFound: Could not find conda environment: PharmaPytry
You can list all discoverable environments with conda info --envs.

Invoke-Expression : Cannot bind argument to parameter 'Command' because it is an empty string.
At C:\Users\MyName\anaconda3\shell\condabin\Conda.psm1:76 char:36

•     Invoke-Expression -Command $activateCommand;
  

•                                ~~~~~~~~~~~~~~~~
  

  • CategoryInfo : InvalidData: (:) [Invoke-Expression], ParameterBindingValidationException
  • FullyQualifiedErrorId : ParameterArgumentValidationErrorEmptyStringNotAllowed,Microsoft.PowerShell.Commands.Invo
    keExpressionCommand

(base) PS C:\Users\MyName\Desktop\PharmaPy-master\PharmaPy-master> conda activate PharmaPyTry

EnvironmentNameNotFound: Could not find conda environment: PharmaPyTry
You can list all discoverable environments with conda info --envs.

Invoke-Expression : Cannot bind argument to parameter 'Command' because it is an empty string.
At C:\Users\MyName\anaconda3\shell\condabin\Conda.psm1:76 char:36

•     Invoke-Expression -Command $activateCommand;
  

•                                ~~~~~~~~~~~~~~~~
  

  • CategoryInfo : InvalidData: (:) [Invoke-Expression], ParameterBindingValidationException
  • FullyQualifiedErrorId : ParameterArgumentValidationErrorEmptyStringNotAllowed,Microsoft.PowerShell.Commands.Invo
    keExpressionCommand

Could use google colab if PharmaPy becomes open and we use pip for package management.

Please