PyAtomDB installation problems in Windows 10 with Anaconda

[MonVigo]

Hi Adam,

I have been trying these days to install PyAtomDB on my Windows 10 on Anaconda with the command 'pip install pyatomdb' and I get the following error:

Collecting pyatomdb
Using cached pyatomdb-0.10.8.tar.gz (19.4 MB)
Requirement already satisfied: requests in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (2.27.1)
Requirement already satisfied: wget in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (3.2)
Requirement already satisfied: numpy>=1.9.0 in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (1.21.5)
Requirement already satisfied: scipy>=1.4.0 in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (1.7.3)
Requirement already satisfied: joblib in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (1.1.0)
Requirement already satisfied: mock in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (4.0.3)
Requirement already satisfied: astropy in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (5.0.4)
Requirement already satisfied: pycurl in c:\users\ramon\anaconda3\lib\site-packages (from pyatomdb) (7.44.1)
Requirement already satisfied: PyYAML>=3.13 in c:\users\ramon\anaconda3\lib\site-packages (from astropy->pyatomdb) (6.0)
Requirement already satisfied: pyerfa>=2.0 in c:\users\ramon\anaconda3\lib\site-packages (from astropy->pyatomdb) (2.0.0)
Requirement already satisfied: packaging>=19.0 in c:\users\ramon\anaconda3\lib\site-packages (from astropy->pyatomdb) (21.3)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\users\ramon\anaconda3\lib\site-packages (from packaging>=19.0->astropy->pyatomdb) (3.0.4)
Requirement already satisfied: idna<4,>=2.5 in c:\users\ramon\anaconda3\lib\site-packages (from requests->pyatomdb) (3.3)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\ramon\anaconda3\lib\site-packages (from requests->pyatomdb) (1.26.9)
Requirement already satisfied: certifi>=2017.4.17 in c:\users\ramon\anaconda3\lib\site-packages (from requests->pyatomdb) (2021.10.8)
Requirement already satisfied: charset-normalizer~=2.0.0 in c:\users\ramon\anaconda3\lib\site-packages (from requests->pyatomdb) (2.0.4)
Building wheels for collected packages: pyatomdb
Building wheel for pyatomdb (setup.py): started
Building wheel for pyatomdb (setup.py): finished with status 'error'
Running setup.py clean for pyatomdb
Failed to build pyatomdb
Installing collected packages: pyatomdb
Running setup.py install for pyatomdb: started
Running setup.py install for pyatomdb: finished with status 'error'
Note: you may need to restart the kernel to use updated packages.
ERROR: Command errored out with exit status 1:
command: 'C:\Users\Ramon\anaconda3\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f\setup.py'"'"'; file='"'"'C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\Ramon\AppData\Local\Temp\pip-wheel-km4q961w'
cwd: C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f
Complete output (27 lines):
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-3.9
creating build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\apec.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\atomdb.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\atomic.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\const.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\spectrum.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\test_dep.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\util.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb_init_.py -> build\lib.win-amd64-3.9\pyatomdb
creating build\lib.win-amd64-3.9\tests
copying tests\test1.py -> build\lib.win-amd64-3.9\tests
copying tests_init_.py -> build\lib.win-amd64-3.9\tests
running build_ext
building 'linear_approx' extension
creating build\temp.win-amd64-3.9
creating build\temp.win-amd64-3.9\Release
"C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -DMAJOR_VERSION=1 -DMINOR_VERSION=0 -IC:\Users\Ramon\anaconda3\include -IC:\Users\Ramon\anaconda3\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt" /Tclinear_approx.c /Fobuild\temp.win-amd64-3.9\Release\linear_approx.obj
linear_approx.c
"C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\link.exe" /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\Users\Ramon\anaconda3\libs /LIBPATH:C:\Users\Ramon\anaconda3 /LIBPATH:C:\Users\Ramon\anaconda3\PCbuild\amd64 "/LIBPATH:C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\lib\x64" "/LIBPATH:C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\lib\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\ucrt\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\um\x64" /EXPORT:PyInit_linear_approx build\temp.win-amd64-3.9\Release\linear_approx.obj /OUT:build\lib.win-amd64-3.9\linear_approx.cp39-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.9\Release\linear_approx.cp39-win_amd64.lib
LINK : error LNK2001: símbolo externo PyInit_linear_approx sin resolver
build\temp.win-amd64-3.9\Release\linear_approx.cp39-win_amd64.lib : fatal error LNK1120: 1 externos sin resolver
error: command 'C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\link.exe' failed with exit code 1120

ERROR: Failed building wheel for pyatomdb
ERROR: Command errored out with exit status 1:
command: 'C:\Users\Ramon\anaconda3\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f\setup.py'"'"'; file='"'"'C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\Ramon\AppData\Local\Temp\pip-record-hq7ghhmu\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\Ramon\anaconda3\Include\pyatomdb'
cwd: C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f
Complete output (29 lines):
running install
C:\Users\Ramon\anaconda3\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build\lib.win-amd64-3.9
creating build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\apec.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\atomdb.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\atomic.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\const.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\spectrum.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\test_dep.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb\util.py -> build\lib.win-amd64-3.9\pyatomdb
copying pyatomdb_init_.py -> build\lib.win-amd64-3.9\pyatomdb
creating build\lib.win-amd64-3.9\tests
copying tests\test1.py -> build\lib.win-amd64-3.9\tests
copying tests_init_.py -> build\lib.win-amd64-3.9\tests
running build_ext
building 'linear_approx' extension
creating build\temp.win-amd64-3.9
creating build\temp.win-amd64-3.9\Release
"C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -DMAJOR_VERSION=1 -DMINOR_VERSION=0 -IC:\Users\Ramon\anaconda3\include -IC:\Users\Ramon\anaconda3\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt" /Tclinear_approx.c /Fobuild\temp.win-amd64-3.9\Release\linear_approx.obj
linear_approx.c
"C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\link.exe" /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\Users\Ramon\anaconda3\libs /LIBPATH:C:\Users\Ramon\anaconda3 /LIBPATH:C:\Users\Ramon\anaconda3\PCbuild\amd64 "/LIBPATH:C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\lib\x64" "/LIBPATH:C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\lib\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\ucrt\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\um\x64" /EXPORT:PyInit_linear_approx build\temp.win-amd64-3.9\Release\linear_approx.obj /OUT:build\lib.win-amd64-3.9\linear_approx.cp39-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.9\Release\linear_approx.cp39-win_amd64.lib
LINK : error LNK2001: símbolo externo PyInit_linear_approx sin resolver
build\temp.win-amd64-3.9\Release\linear_approx.cp39-win_amd64.lib : fatal error LNK1120: 1 externos sin resolver
error: command 'C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\link.exe' failed with exit code 1120
----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\Ramon\anaconda3\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f\setup.py'"'"'; file='"'"'C:\Users\Ramon\AppData\Local\Temp\pip-install-osod6ots\pyatomdb_b7587e93d9a0439a8e5e5c5cb003308f\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\Ramon\AppData\Local\Temp\pip-record-hq7ghhmu\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\Ramon\anaconda3\Include\pyatomdb' Check the logs for full command output.

[MonVigo]

I attach a PDF file with the error to make it easier to read
error.pdf
:

[MonVigo]

I also have tried to download the source with 'git clone https://github.com/AtomDB/pyatomdb.git' and then use python 'setup.py develop' but this is the error that I have obtained in this case:

C:\Users\Ramon\pyatomdb\pyatomdb>python setup.py develop --user
running develop
running egg_info
creating pyatomdb.egg-info
writing pyatomdb.egg-info\PKG-INFO
writing dependency_links to pyatomdb.egg-info\dependency_links.txt
writing requirements to pyatomdb.egg-info\requires.txt
writing top-level names to pyatomdb.egg-info\top_level.txt
writing manifest file 'pyatomdb.egg-info\SOURCES.txt'
reading manifest file 'pyatomdb.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'COPYING.txt'
writing manifest file 'pyatomdb.egg-info\SOURCES.txt'
running build_ext
building 'linear_approx' extension
creating build
creating build\temp.win-amd64-3.9
creating build\temp.win-amd64-3.9\Release
C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -DMAJOR_VERSION=1 -DMINOR_VERSION=0 -IC:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.3312.0_x64__qbz5n2kfra8p0\include -IC:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.3312.0_x64__qbz5n2kfra8p0\include -IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\include -IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\include -IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared -IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um -IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt /Tclinear_approx.c /Fobuild\temp.win-amd64-3.9\Release\linear_approx.obj
linear_approx.c
creating C:\Users\Ramon\pyatomdb\pyatomdb\build\lib.win-amd64-3.9
C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.3312.0_x64__qbz5n2kfra8p0\libs /LIBPATH:C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.3312.0_x64__qbz5n2kfra8p0\PCbuild\amd64 /LIBPATH:C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\lib\x64 /LIBPATH:C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\lib\x64 /LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\ucrt\x64 /LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\um\x64 /EXPORT:PyInit_linear_approx build\temp.win-amd64-3.9\Release\linear_approx.obj /OUT:build\lib.win-amd64-3.9\linear_approx.cp39-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.9\Release\linear_approx.cp39-win_amd64.lib
LINK : error LNK2001: símbolo externo PyInit_linear_approx sin resolver
build\temp.win-amd64-3.9\Release\linear_approx.cp39-win_amd64.lib : fatal error LNK1120: 1 externos sin resolver
error: command 'C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\link.exe' failed with exit code 1120

[jagophile]

Hi.

Thanks for raising the issue. Pyatomdb doesn't currently work with Windows - it isn't developed to do so. I have long term plans to make it work on Windows but it's not there yet. Currently Linux and MacOS are supported.

Do you have access to a remote Linux/MacOS machine?

I will file this as a feature request, and will update as/if/when I make it work, but I'm afraid I can't promise it any time soon.

[MonVigo]

Hi,

thanks for your answer. I did not know that Pyatomdb was not working with Windows. I have changed to a Linux machine and currently it works without problems.

Best Regards