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CryPTSys / PharmaPy

A numerical platform for the digital design of pharmaceutical processes
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trouble installing #90

Open WernerHerzog opened 1 year ago

WernerHerzog commented 1 year ago

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

(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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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 https://github.com/cython/cython/issues/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

(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

djlaky commented 1 year ago

We are aware of installation issues and are currently working on a pull request that should be available in the master branch soon. Sorry for the inconvenience! Keep an eye on https://github.com/CryPTSys/PharmaPy/pull/91