Fails to install

[rbf22]

The installation fails to complete, even with a clean conda installation. Problems include resp and psi4 not being available for the modern version of python aka > 3.6

[hesther]

Hi, which operation system are you on? There is currently no Psi4 version for the new Apple chips, so if you have a new MacBook for example, the standard installation won't work. Unfortuntaly, this needs to be fixed by the Psi4 developers, and there is nothing I can currently do about that.

You can safely delete the resp and psi4 lines from environment.yml, and still run ESPsim, but without Psi4 calculations. The rest will still work (it doesn't depend on these packages if you do not call the respective options)

[rbf22]

installing on an intel Mac

conda env create -f environment.yml
Collecting package metadata (repodata.json): done Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed -
Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed \

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libpng conflicts for: matplotlib -> freetype=2.6 -> libpng[version='1.6.*|>=1.6.21,<1.7|>=1.6.32,<1.6.35'] matplotlib -> libpng[version='>=1.6.23,<1.7|>=1.6.37,<1.7.0a0|>=1.6.36,<1.7.0a0|>=1.6.35,<1.7.0a0|>=1.6.34,<1.7.0a0|>=1.6.32,<1.7.0a0']

Package numpy conflicts for: matplotlib -> matplotlib-base[version='>=3.5.3,<3.5.4.0a0'] -> numpy[version='>=1.11.3,<2.0a0|>=1.15.4,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17|>=1.19.5,<2.0a0|>=1.21.6,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.19.2,<2.0a0|>=1.21.2,<2.0a0|>=1.17.5,<2.0a0|>=1.19.4,<2.0a0|>=1.9.3,<2.0a0'] scikit-learn -> scipy -> numpy[version='>=1.11|>=1.18.1,<2.0a0|>=1.21,<1.23.0|>=1.19,<1.23.0|>=1.15.1,<2.0a0'] scipy -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.9.3,<2.0a0|>=1.9|>=1.21,<1.23.0|>=1.19,<1.23.0|>=1.21.2,<2.0a0|>=1.15.1,<2.0a0'] scikit-learn -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.9.3,<2.0a0|>=1.9|>=1.21.2,<2.0a0'] rdkit -> pandas -> numpy[version='1.12.|1.13.|>=1.11.|>=1.12.1,<2.0a0|>=1.15.4,<2.0a0|>=1.21.4,<2.0a0|>=1.21.5,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.9.|>=1.9|>=1.8|>=1.7|>=1.21.2,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.11.3,<2.0a0|>=1.9.3,<1.10.0a0|>=1.17'] pytorch -> numpy[version='1.19.|>=1.19|>=1.11|>=1.19.5,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.18.5,<2.0a0|>=1.17.5,<2.0a0|>=1.16.6,<2.0a0|>=1.19.4,<2.0a0|>=1.21.2,<2.0a0|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0'] rdkit -> numpy[version='1.10.|1.11.|>=1.12|1.9.|>=1.21.6,<2.0a0|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.17.5,<2.0a0|>=1.16.6,<2.0a0|>=1.16.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.14.6,<2.0a0|>=1.9.3,<2.0a0|>=1.11'] numpy matplotlib -> numpy[version='1.10.|1.11.|>=1.14.6,<2.0a0']

Package importlib-metadata conflicts for: rdkit -> sqlalchemy -> importlib-metadata jupyter -> ipykernel -> importlib-metadata[version='<4|<5']

Package certifi conflicts for: pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] pytorch -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] joblib -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] matplotlib -> matplotlib-base[version='>=3.5.3,<3.5.4.0a0'] -> certifi[version='>=2016.09|>=2016.9.26|>=2020.06.20'] rdkit -> matplotlib-base -> certifi[version='>=2020.06.20']

Package tornado conflicts for: jupyter -> ipykernel -> tornado[version='!=6.0.0,!=6.0.1,!=6.0.2|>=4|>=4,<6|>=4.0|>=4.2|>=4.2,<7.0|>=5.0,<7.0|>=6.1|>=5.0|>=5.0,<7|>=4.1,<7|>=6.1.0'] rdkit -> matplotlib-base -> tornado matplotlib -> tornado

Package packaging conflicts for: matplotlib -> matplotlib-base[version='>=3.5.3,<3.5.4.0a0'] -> packaging[version='>=20.0'] pip -> wheel -> packaging[version='>=20.2'] rdkit -> matplotlib-base -> packaging[version='>=20.0'] jupyter -> ipykernel -> packaging

Package joblib conflicts for: joblib scikit-learn -> joblib[version='>=0.11|>=1.0.0']

Package pyparsing conflicts for: matplotlib -> matplotlib-base[version='>=3.5.3,<3.5.4.0a0'] -> pyparsing[version='>=2.0.3,!=2.0.4,!=2.1.2,!=2.1.6|>=2.2.1'] matplotlib -> pyparsing

Package blis conflicts for: scipy -> libblas[version='>=3.9.0,<4.0a0'] -> blis[version='0.5.1.|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0|>=0.9.0,<0.9.1.0a0'] numpy -> libblas[version='>=3.9.0,<4.0a0'] -> blis[version='0.5.1.|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0|>=0.9.0,<0.9.1.0a0'] pytorch -> libblas[version='>=3.9.0,<4.0a0'] -> blis[version='0.5.1.*|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0|>=0.9.0,<0.9.1.0a0']

Package expat conflicts for: jupyter -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0'] scipy -> pypy3.8[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.2.9,<3.0.0a0'] numpy -> pypy3.9[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.4.7,<3.0a0|>=2.2.9,<3.0.0a0'] scikit-learn -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0'] matplotlib -> pypy3.8[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.2.9,<3.0.0a0']

Package kiwisolver conflicts for: matplotlib -> kiwisolver matplotlib -> matplotlib-base[version='>=3.5.3,<3.5.4.0a0'] -> kiwisolver[version='>=1.0.1']

Package freetype conflicts for: matplotlib -> matplotlib-base[version='>=3.5.3,<3.5.4.0a0'] -> freetype[version='>=2.10.2,<3.0a0|>=2.10.4,<3.0a0|>=2.12.1,<3.0a0|>=2.11.0,<3.0a0|>=2.3'] matplotlib -> freetype[version='2.6.*|>=2.9.1,<3.0a0|>=2.8,<2.9.0a0']

Package pip conflicts for: rdkit -> python[version='>=3.6,<3.7.0a0'] -> pip tqdm -> python[version='>=2.7'] -> pip pytorch -> python[version='>=3.8,<3.9.0a0'] -> pip joblib -> python[version='>=3.6'] -> pip scipy -> python[version='>=3.9,<3.10.0a0'] -> pip py3dmol -> python[version='>=3.6'] -> pip matplotlib -> python[version='>=3.8,<3.9.0a0'] -> pip pip numpy -> python[version='>=3.9,<3.10.0a0'] -> pip scikit-learn -> python[version='>=3.9,<3.10.0a0'] -> pip

Package setuptools conflicts for: pip -> setuptools pytorch -> setuptools[version='<59.6'] jupyter -> ipykernel -> setuptools[version='>=60'] rdkit -> pandas -> setuptools[version='<60.0.0'] scikit-learn -> joblib[version='>=1.0.0'] -> setuptools matplotlib -> setuptools joblib -> setuptools

Package llvm-openmp conflicts for: pytorch -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4'] pytorch -> mkl[version='>=2018'] -> llvm-openmp[version='>=9.0.1']

Package futures conflicts for: jupyter -> jupyterlab -> futures matplotlib -> tornado -> futures

Package typing_extensions conflicts for: pytorch -> typing-extensions -> typing_extensions[version='3.10.0.0|3.10.0.0|3.10.0.1|3.10.0.2|4.0.0|4.0.1|4.1.1|4.2.0|4.2.0|4.3.0|3.7.4.3|3.7.4.2|3.7.4.1|3.7.4.1|3.7.4.1|3.7.4.1|3.7.4|3.7.2|3.7.2|3.6.6|3.6.6|3.6.5|4.3.0|4.3.0|4.3.0|4.3.0|4.1.1|3.10.0.2|3.7.4.3|3.7.4.1|3.7.4',build='py27_0|py38_0|pyh06a4308_0|pyh06a4308_0|pyh06a4308_0|py310hecd8cb5_0|py38hecd8cb5_0|py37hecd8cb5_0|py27_0|py27_0|py27_1000|py27_1001|py37hc8dfbb8_2|pyha770c72_0|pyha770c72_0|pyha770c72_0|pyha770c72_0|pyha770c72_0|pyha770c72_0|pyha770c72_0|pyha770c72_1|pyha770c72_0|py_0|py_0|py36hc560c46_3|py37hc8dfbb8_1|py37_0|py37_0|py27_1000|py39hecd8cb5_0|pyh06a4308_0'] pytorch -> typing_extensions matplotlib -> kiwisolver -> typing_extensions

Package libgcc conflicts for: numpy -> openblas[version='>=0.2.15'] -> libgcc scikit-learn -> scipy -> libgcc scipy -> libgcc

Package blas-devel conflicts for: pytorch -> blas=[build=mkl] -> blas-devel==3.9.0[build='8_mkl|9_mkl|11_osx64_mkl|12_osx64_mkl|13_osx64_mkl|14_osx64_mkl|16_osx64_mkl|15_osx64_mkl|10_mkl|7_mkl'] scikit-learn -> blas=[build=openblas] -> blas-devel==3.9.0[build='7_mkl|8_mkl|13_osx64_mkl|14_osx64_mkl|8_openblas|9_openblas|10_openblas|12_osx64_openblas|15_osx64_openblas|16_osx64_openblas|14_osx64_openblas|13_osx64_openblas|11_osx64_openblas|7_openblas|16_osx64_mkl|15_osx64_mkl|12_osx64_mkl|11_osx64_mkl|10_mkl|9_mkl'] scipy -> blas=[build=openblas] -> blas-devel==3.9.0[build='7_mkl|8_mkl|13_osx64_mkl|14_osx64_mkl|8_openblas|9_openblas|10_openblas|12_osx64_openblas|15_osx64_openblas|16_osx64_openblas|14_osx64_openblas|13_osx64_openblas|11_osx64_openblas|7_openblas|16_osx64_mkl|15_osx64_mkl|12_osx64_mkl|11_osx64_mkl|10_mkl|9_mkl'] numpy -> blas=[build=openblas] -> blas-devel==3.9.0[build='7_mkl|8_mkl|13_osx64_mkl|14_osx64_mkl|8_openblas|9_openblas|10_openblas|12_osx64_openblas|15_osx64_openblas|16_osx64_openblas|14_osx64_openblas|13_osx64_openblas|11_osx64_openblas|7_openblas|16_osx64_mkl|15_osx64_mkl|12_osx64_mkl|11_osx64_mkl|10_mkl|9_mkl']

Package intel-openmp conflicts for: pytorch -> intel-openmp pytorch -> mkl[version='>=2018'] -> intel-openmp[version='2018.0.3.|2019.|2021.|2022.']

Package matplotlib-base conflicts for: matplotlib -> matplotlib-base[version='2.1.2|2.1.2|2.1.2|2.2.3|2.2.3|2.2.3|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|3.0.1|3.0.2|3.0.2|3.0.2|3.0.2|3.0.2|3.0.3|3.0.3|3.0.3|3.0.3|3.1.0|3.1.0|3.1.0|3.1.0|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.2|3.1.2|3.1.2|3.1.2|3.1.2|3.1.2|3.1.3|3.1.3|3.1.3|>=3.2.0,<3.2.1.0a0|>=3.2.1,<3.2.2.0a0|>=3.2.2,<3.2.3.0a0|>=3.3.0,<3.3.1.0a0|>=3.3.1,<3.3.2.0a0|>=3.3.2,<3.3.3.0a0|>=3.3.3,<3.3.4.0a0|>=3.3.4,<3.3.5.0a0|>=3.4.1,<3.4.2.0a0|>=3.4.2,<3.4.3.0a0|>=3.4.3,<3.4.4.0a0|>=3.5.0,<3.5.1.0a0|>=3.5.1,<3.5.2.0a0|>=3.5.2,<3.5.3.0a0|>=3.5.3,<3.5.4.0a0|>=2.2.5,<2.2.6.0a0|3.1.3|3.1.3|3.1.3|3.1.2|3.1.2|3.1.2',build='py36h9aa3819_1|py38h9aa3819_1|py38h9aa3819_0|py37h9aa3819_0|py36h31f9439_1|py27hd64abcd_1|py37hd64abcd_1|py37h3a684a6_0|py27h3a684a6_0|py37h31f9439_1|py36hf043ca5_1002|py37hf043ca5_1002|py37hf043ca5_0|py36habd5b94_1|py37habd5b94_1|py37habd5b94_0|py36habd5b94_0|py37h3a684a6_0|py37h3a684a6_1|py36h11da6c2_2|py37h11da6c2_0|py38h11da6c2_0|py36h11da6c2_1|py38h11da6c2_1|py37h11da6c2_0|py36h11da6c2_0|py38h11da6c2_0|py37h11da6c2_1|py36h11da6c2_0|py38h11da6c2_2|py37h11da6c2_2|py38h11da6c2_1|py36h3a684a6_1|py36h3a684a6_0|py36h3a684a6_1|py37h3a684a6_1|py36hf043ca5_0|py36hf043ca5_1001|py37hf043ca5_1001|py36hf043ca5_1000|py36hebca740_1001|py27h11da6c2_2|py36h11da6c2_2|py38h11da6c2_2|py37h11da6c2_2|py36h31f9439_1|py27h31f9439_1|py36h3a684a6_0|py36hd64abcd_1|py37h31f9439_1|py27h31f9439_1|py36h9aa3819_0|py37h9aa3819_1'] rdkit -> matplotlib-base

Package jupyter conflicts for: py3dmol -> jupyter jupyter

Package python-dateutil conflicts for: matplotlib -> python-dateutil matplotlib -> matplotlib-base[version='>=3.5.3,<3.5.4.0a0'] -> python-dateutil[version='>=2.1|>=2.7']

Package scipy conflicts for: scikit-learn -> scipy[version='>=0.19.1|>=1.1.0|>=1.3.2'] scipyThe following specifications were found to be incompatible with your system:

• feature:/osx-64::__osx==10.16=0
• feature:|@/osx-64::__osx==10.16=0
• jupyter -> ipykernel -> __win
• pytorch -> __osx[version='>=10.9']

Your installed version is: not available

Note that strict channel priority may have removed packages required for satisfiability.

[hesther]

Thanks, that’s interesting! It works fine with my old Intel Mac though, so have to do some digging (might also depend on the conda version). I can create a file with compatible version numbers tomorrow. Until then, you could try to create an environment and install only a couple of packages at a time.

[hesther]

I unfortunately couldn't recreate the error you reported on my old Intel Mac, but noticed that conda takes way too long to solve the environment, as reported in #19. After trying a few things, I found that specifying the python version is enough to get an acceptable timing for solving the environment (a few seconds), and I had no problem installing psi4 or resp, too. Would you be willing to try again after updating to the newest version of this repo?