Installation error in conda env (MacOS)

[nityasagarjena]

  -- Configuring incomplete, errors occurred!
  --
  -------
  ------------
  -----------------
  ----------------------
  ---------------------------
  --------------------------------
  -- Trying 'Unix Makefiles' generator - failure
  --------------------------------------------------------------------------------
  
                  ********************************************************************************
                  scikit-build could not get a working generator for your system. Aborting build.
  
                  Building MacOSX wheels for Python 3.10 requires XCode.
  Get it here:
  
    https://developer.apple.com/xcode/
  
                  ********************************************************************************
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pylada
Failed to build p2ptrans pylada
ERROR: Could not build wheels for p2ptrans, pylada, which is required to install pyproject.toml-based projects

[ftherrien]

Hi! Thanks for your question, I will need the full error output in order to help you

[nityasagarjena]

(base) mac01099:~ nitje08$ pip install git+https://github.com/ftherrien/p2ptrans
Collecting git+https://github.com/ftherrien/p2ptrans
Cloning https://github.com/ftherrien/p2ptrans to /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-req-build-11wx1iq6
error: subprocess-exited-with-error

× git version did not run successfully.
│ exit code: 69
╰─> [2 lines of output]
You have not agreed to the Xcode license agreements. Please run 'sudo xcodebuild -license' from within a Terminal window to review and agree to the Xcode and Apple SDKs license.
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git version did not run successfully.
│ exit code: 69
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
(base) mac01099:~ nitje08$

[ftherrien]

"You have not agreed to the Xcode license agreements. Please run 'sudo xcodebuild -license' from within a Terminal window to review and agree to the Xcode and Apple SDKs license."

That seems to be your issue

[nityasagarjena]

  collect2: error: ld returned 1 exit status
  error: Command "/opt/homebrew/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.9-x86_64-cpython-310/build/src.macosx-10.9-x86_64-3.10/p2ptrans/fmodulesmodule.o build/temp.macosx-10.9-x86_64-cpython-310/build/src.macosx-10.9-x86_64-3.10/build/src.macosx-10.9-x86_64-3.10/p2ptrans/fortranobject.o build/temp.macosx-10.9-x86_64-cpython-310/source/lap.o build/temp.macosx-10.9-x86_64-cpython-310/source/utils.o build/temp.macosx-10.9-x86_64-cpython-310/source/tiling.o build/temp.macosx-10.9-x86_64-cpython-310/source/potential.o build/temp.macosx-10.9-x86_64-cpython-310/source/transform.o build/temp.macosx-10.9-x86_64-cpython-310/build/src.macosx-10.9-x86_64-3.10/p2ptrans/fmodules-f2pywrappers2.o -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13 -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13/../../.. -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13/../../.. -lgfortran -o build/lib.macosx-10.9-x86_64-cpython-310/p2ptrans/fmodules.cpython-310-darwin.so -lgomp" failed with exit status 1
  INFO:
  ########### EXT COMPILER OPTIMIZATION ###########
  INFO: Platform      :
    Architecture: x64
    Compiler    : clang
  
  CPU baseline  :
    Requested   : 'min'
    Enabled     : SSE SSE2 SSE3
    Flags       : -msse -msse2 -msse3
    Extra checks: none
  
  CPU dispatch  :
    Requested   : 'max -xop -fma4'
    Enabled     : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL
    Generated   : none
  INFO: CCompilerOpt.cache_flush[863] : write cache to path -> /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-req-build-07n55ere/build/temp.macosx-10.9-x86_64-cpython-310/ccompiler_opt_cache_ext.py
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for p2ptrans
Building wheel for pylada (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for pylada (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [164 lines of output]

  --------------------------------------------------------------------------------
  -- Trying 'Ninja' generator
  --------------------------------
  ---------------------------
  ----------------------
  -----------------
  ------------
  -------
  --
  CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
  
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
  
  Not searching for unused variables given on the command line.
  
  -- The CXX compiler identification is AppleClang 15.0.0.15000040
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- The Fortran compiler identification is GNU 13.2.0
  -- Checking whether Fortran compiler has -isysroot
  -- Checking whether Fortran compiler has -isysroot - yes
  -- Checking whether Fortran compiler supports OSX deployment target flag
  -- Checking whether Fortran compiler supports OSX deployment target flag - yes
  -- Detecting Fortran compiler ABI info
  -- Detecting Fortran compiler ABI info - failed
  -- Check for working Fortran compiler: /opt/homebrew/bin/gfortran
  -- Check for working Fortran compiler: /opt/homebrew/bin/gfortran - broken
  CMake Error at /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-build-env-kjlppao6/overlay/lib/python3.10/site-packages/cmake/data/share/cmake-3.27/Modules/CMakeTestFortranCompiler.cmake:59 (message):
    The Fortran compiler
  
      "/opt/homebrew/bin/gfortran"
  
    is not able to compile a simple test program.
  
    It fails with the following output:
  
      Change Dir: '/private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-install-jjit615u/pylada_ed6dce0d4a4f47d3bc70ac39b3a265e6/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-578D6V'
  
      Run Build Command(s): /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-build-env-kjlppao6/overlay/lib/python3.10/site-packages/ninja/data/bin/ninja -v cmTC_8b83f
      [1/4] /opt/homebrew/bin/gfortran -cpp   -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=10.9 -E /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-install-jjit615u/pylada_ed6dce0d4a4f47d3bc70ac39b3a265e6/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-578D6V/testFortranCompiler.f -o CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f-pp.f && /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-build-env-kjlppao6/overlay/lib/python3.10/site-packages/cmake/data/bin/cmake -E cmake_ninja_depends --tdi=CMakeFiles/cmTC_8b83f.dir/FortranDependInfo.json --lang=Fortran --src=CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f-pp.f --out=CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f-pp.f --dep=CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f-pp.f.d --obj=CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f.o --ddi=CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f.o.ddi
      [2/4] /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-build-env-kjlppao6/overlay/lib/python3.10/site-packages/cmake/data/bin/cmake -E cmake_ninja_dyndep --tdi=CMakeFiles/cmTC_8b83f.dir/FortranDependInfo.json --lang=Fortran --dd=CMakeFiles/cmTC_8b83f.dir/Fortran.dd @CMakeFiles/cmTC_8b83f.dir/Fortran.dd.rsp
      [3/4] /opt/homebrew/bin/gfortran -I/private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-install-jjit615u/pylada_ed6dce0d4a4f47d3bc70ac39b3a265e6/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-578D6V -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=10.9 -fpreprocessed -c CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f-pp.f -o CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f.o
      [4/4] : && /opt/homebrew/bin/gfortran  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=10.9 CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f.o -o cmTC_8b83f   && :
      FAILED: cmTC_8b83f
      : && /opt/homebrew/bin/gfortran  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=10.9 CMakeFiles/cmTC_8b83f.dir/testFortranCompiler.f.o -o cmTC_8b83f   && :
      ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/lib/libSystem.tbd' for architecture arm64
      collect2: error: ld returned 1 exit status
      ninja: build stopped: subcommand failed.
  
  
  
  
  
    CMake will not be able to correctly generate this project.
  Call Stack (most recent call first):
    CMakeLists.txt:4 (ENABLE_LANGUAGE)
  
  
  -- Configuring incomplete, errors occurred!
  --
  -------
  ------------
  -----------------
  ----------------------
  ---------------------------
  --------------------------------
  -- Trying 'Ninja' generator - failure
  --------------------------------------------------------------------------------
  
  
  
  --------------------------------------------------------------------------------
  -- Trying 'Unix Makefiles' generator
  --------------------------------
  ---------------------------
  ----------------------
  -----------------
  ------------
  -------
  --
  CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
  
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
  
  Not searching for unused variables given on the command line.
  
  -- The CXX compiler identification is AppleClang 15.0.0.15000040
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- The Fortran compiler identification is GNU 13.2.0
  -- Checking whether Fortran compiler has -isysroot
  -- Checking whether Fortran compiler has -isysroot - yes
  -- Checking whether Fortran compiler supports OSX deployment target flag
  -- Checking whether Fortran compiler supports OSX deployment target flag - yes
  -- Detecting Fortran compiler ABI info
  -- Detecting Fortran compiler ABI info - failed
  -- Check for working Fortran compiler: /opt/homebrew/bin/gfortran
  -- Check for working Fortran compiler: /opt/homebrew/bin/gfortran - broken
  CMake Error at /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-build-env-kjlppao6/overlay/lib/python3.10/site-packages/cmake/data/share/cmake-3.27/Modules/CMakeTestFortranCompiler.cmake:59 (message):
    The Fortran compiler
  
      "/opt/homebrew/bin/gfortran"
  
    is not able to compile a simple test program.
  
    It fails with the following output:
  
      Change Dir: '/private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-install-jjit615u/pylada_ed6dce0d4a4f47d3bc70ac39b3a265e6/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-ihsZgo'
  
      Run Build Command(s): /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-build-env-kjlppao6/overlay/lib/python3.10/site-packages/cmake/data/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_4c06e/fast
      /Applications/Xcode.app/Contents/Developer/usr/bin/make  -f CMakeFiles/cmTC_4c06e.dir/build.make CMakeFiles/cmTC_4c06e.dir/build
      Building Fortran object CMakeFiles/cmTC_4c06e.dir/testFortranCompiler.f.o
      /opt/homebrew/bin/gfortran   -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=10.9 -c /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-install-jjit615u/pylada_ed6dce0d4a4f47d3bc70ac39b3a265e6/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-ihsZgo/testFortranCompiler.f -o CMakeFiles/cmTC_4c06e.dir/testFortranCompiler.f.o
      Linking Fortran executable cmTC_4c06e
      /private/var/folders/rg/cmkgtzsd4dq4xtn_fzrhgw3h00zv6h/T/pip-build-env-kjlppao6/overlay/lib/python3.10/site-packages/cmake/data/bin/cmake -E cmake_link_script CMakeFiles/cmTC_4c06e.dir/link.txt --verbose=1
      /opt/homebrew/bin/gfortran  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=10.9 CMakeFiles/cmTC_4c06e.dir/testFortranCompiler.f.o -o cmTC_4c06e
      ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/lib/libSystem.tbd' for architecture arm64
      collect2: error: ld returned 1 exit status
      make[1]: *** [cmTC_4c06e] Error 1
      make: *** [cmTC_4c06e/fast] Error 2
  
  
  
  
  
    CMake will not be able to correctly generate this project.
  Call Stack (most recent call first):
    CMakeLists.txt:4 (ENABLE_LANGUAGE)
  
  
  -- Configuring incomplete, errors occurred!
  --
  -------
  ------------
  -----------------
  ----------------------
  ---------------------------
  --------------------------------
  -- Trying 'Unix Makefiles' generator - failure
  --------------------------------------------------------------------------------
  
                  ********************************************************************************
                  scikit-build could not get a working generator for your system. Aborting build.
  
                  Building MacOSX wheels for Python 3.10 requires XCode.
  Get it here:
  
    https://developer.apple.com/xcode/
  
                  ********************************************************************************
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pylada
Failed to build p2ptrans pylada
ERROR: Could not build wheels for p2ptrans, pylada, which is required to install pyproject.toml-based projects
(base) mac01099:~ nitje08$

[ftherrien]

Hi, I can't really help you if you keep dumping parts of error messages without explaining what you tried and what system you are using.

I am gathering that you are trying to install on MacOS. Do you have GCC installed? Are you installing in a virtual environment? What is your version of python? What command do you use to install?

[nityasagarjena]

Hi, I got it installed in my HPC account, but the following command gives the error,

(myenv) [x_nitje@tetralith2 ~]$ p2ptrans --help
Traceback (most recent call last):
File "/home/x_nitje/.conda/envs/myenv/bin/p2ptrans", line 6, in
from p2ptrans import *
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/p2ptrans/init.py", line 4, in
from . import display
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/p2ptrans/display.py", line 4, in
from .config import *
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/p2ptrans/config.py", line 1, in
from pylada.crystal import Structure, primitive, gruber, read, write, supercell, space_group, into_cell
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/pylada/init.py", line 127, in
from . import error, crystal, physics, misc, tools, ewald, decorations, periodic_table, vasp,
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/pylada/espresso/init.py", line 35, in
from .structure_handling import read_structure
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/pylada/espresso/structure_handling.py", line 240
%(atom.type, atom.pos[0],atom.pos[1], atom.pos[2],
^
SyntaxError: invalid syntax
(myenv) [x_nitje@tetralith2 ~]$

[nityasagarjena]

(myenv) [x_nitje@tetralith2 ~]$ python --version
Python 3.8.15
(myenv) [x_nitje@tetralith2 ~]$

[nityasagarjena]

This went successfully in my HPC conda env, and got the p2ptrans, but having the error with p2ptrans --help

pip install git+https://github.com/ftherrien/p2ptrans
Collecting git+https://github.com/ftherrien/p2ptrans
Cloning https://github.com/ftherrien/p2ptrans to /tmp/pip-req-build-uxk0f2zi
Running command git clone --filter=blob:none --quiet https://github.com/ftherrien/p2ptrans /tmp/pip-req-build-uxk0f2zi
Resolved https://github.com/ftherrien/p2ptrans to commit 3cae692
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting pylada@ git+https://github.com/pylada/pylada-light#egg=pylada (from p2ptrans==2.1.0)
Cloning https://github.com/pylada/pylada-light to /tmp/pip-install-wqz_4f5t/pylada_f1effe403c744136b9b539d6ccdb330f
Running command git clone --filter=blob:none --quiet https://github.com/pylada/pylada-light /tmp/pip-install-wqz_4f5t/pylada_f1effe403c744136b9b539d6ccdb330f
Resolved https://github.com/pylada/pylada-light to commit 1516ea5be1cb1e8aad3bb03e6a32b2965e78d4da
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in ./.conda/envs/myenv/lib/python3.8/site-packages (from p2ptrans==2.1.0) (1.24.4)
Requirement already satisfied: matplotlib in ./.conda/envs/myenv/lib/python3.8/site-packages (from p2ptrans==2.1.0) (3.6.2)
Requirement already satisfied: spglib in ./.conda/envs/myenv/lib/python3.8/site-packages (from p2ptrans==2.1.0) (2.0.2)
Requirement already satisfied: contourpy>=1.0.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from matplotlib->p2ptrans==2.1.0) (1.0.5)
Requirement already satisfied: cycler>=0.10 in ./.conda/envs/myenv/lib/python3.8/site-packages (from matplotlib->p2ptrans==2.1.0) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in ./.conda/envs/myenv/lib/python3.8/site-packages/fonttools-4.38.0-py3.8.egg (from matplotlib->p2ptrans==2.1.0) (4.38.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from matplotlib->p2ptrans==2.1.0) (1.4.4)
Requirement already satisfied: packaging>=20.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from matplotlib->p2ptrans==2.1.0) (23.2)
Requirement already satisfied: pillow>=6.2.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from matplotlib->p2ptrans==2.1.0) (9.3.0)
Requirement already satisfied: pyparsing>=2.2.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from matplotlib->p2ptrans==2.1.0) (3.0.9)
Requirement already satisfied: python-dateutil>=2.7 in ./.conda/envs/myenv/lib/python3.8/site-packages (from matplotlib->p2ptrans==2.1.0) (2.8.2)
Requirement already satisfied: py in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.11.0)
Requirement already satisfied: scipy in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.9.3)
Requirement already satisfied: quantities in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.14.1)
Requirement already satisfied: cython in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (3.0.2)
Requirement already satisfied: six in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.16.0)
Requirement already satisfied: traitlets in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (5.9.0)
Requirement already satisfied: f90nml>=1.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.4.3)
Requirement already satisfied: nbconvert in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (7.2.9)
Requirement already satisfied: nbformat in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (5.7.3)
Requirement already satisfied: ipykernel in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (6.21.2)
Requirement already satisfied: IPython in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (8.10.0)
Requirement already satisfied: black in ./.conda/envs/myenv/lib/python3.8/site-packages (from pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (23.9.1)
Requirement already satisfied: click>=8.0.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from black->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (8.1.3)
Requirement already satisfied: mypy-extensions>=0.4.3 in ./.conda/envs/myenv/lib/python3.8/site-packages (from black->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.0.0)
Requirement already satisfied: pathspec>=0.9.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from black->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.11.2)
Requirement already satisfied: platformdirs>=2 in ./.conda/envs/myenv/lib/python3.8/site-packages (from black->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (3.0.0)
Requirement already satisfied: tomli>=1.1.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from black->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (2.0.1)
Requirement already satisfied: typing-extensions>=4.0.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from black->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (4.4.0)
Requirement already satisfied: comm>=0.1.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.1.2)
Requirement already satisfied: debugpy>=1.6.5 in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.6.6)
Requirement already satisfied: jupyter-client>=6.1.12 in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (8.0.3)
Requirement already satisfied: jupyter-core!=5.0.*,>=4.12 in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (5.2.0)
Requirement already satisfied: matplotlib-inline>=0.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.1.6)
Requirement already satisfied: nest-asyncio in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.5.6)
Requirement already satisfied: psutil in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (5.9.4)
Requirement already satisfied: pyzmq>=20 in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (25.0.0)
Requirement already satisfied: tornado>=6.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from ipykernel->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (6.2)
Requirement already satisfied: backcall in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.2.0)
Requirement already satisfied: decorator in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (5.1.1)
Requirement already satisfied: jedi>=0.16 in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.18.2)
Requirement already satisfied: pickleshare in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.7.5)
Requirement already satisfied: prompt-toolkit<3.1.0,>=3.0.30 in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (3.0.36)
Requirement already satisfied: pygments>=2.4.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (2.14.0)
Requirement already satisfied: stack-data in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.6.2)
Requirement already satisfied: pexpect>4.3 in ./.conda/envs/myenv/lib/python3.8/site-packages (from IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (4.8.0)
Requirement already satisfied: beautifulsoup4 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (4.11.2)
Requirement already satisfied: bleach in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (6.0.0)
Requirement already satisfied: defusedxml in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.7.1)
Requirement already satisfied: importlib-metadata>=3.6 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (6.0.0)
Requirement already satisfied: jinja2>=3.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (3.1.2)
Requirement already satisfied: jupyterlab-pygments in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.2.2)
Requirement already satisfied: markupsafe>=2.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (2.1.2)
Requirement already satisfied: mistune<3,>=2.0.3 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (2.0.5)
Requirement already satisfied: nbclient>=0.5.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.7.2)
Requirement already satisfied: pandocfilters>=1.4.1 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.5.0)
Requirement already satisfied: tinycss2 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.2.1)
Requirement already satisfied: fastjsonschema in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbformat->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (2.16.2)
Requirement already satisfied: jsonschema>=2.6 in ./.conda/envs/myenv/lib/python3.8/site-packages (from nbformat->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (4.17.3)
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Requirement already satisfied: parso<0.9.0,>=0.8.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from jedi>=0.16->IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.8.3)
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Requirement already satisfied: soupsieve>1.2 in ./.conda/envs/myenv/lib/python3.8/site-packages (from beautifulsoup4->nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (2.4)
Requirement already satisfied: webencodings in ./.conda/envs/myenv/lib/python3.8/site-packages (from bleach->nbconvert->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.5.1)
Requirement already satisfied: executing>=1.2.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from stack-data->IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (1.2.0)
Requirement already satisfied: asttokens>=2.1.0 in ./.conda/envs/myenv/lib/python3.8/site-packages (from stack-data->IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (2.2.1)
Requirement already satisfied: pure-eval in ./.conda/envs/myenv/lib/python3.8/site-packages (from stack-data->IPython->pylada@ git+https://github.com/pylada/pylada-light#egg=pylada->p2ptrans==2.1.0) (0.2.2)
(myenv) [x_nitje@tetralith2 ~]$

(myenv) [x_nitje@tetralith2 ~]$ p2ptrans --help
Traceback (most recent call last):
File "/home/x_nitje/.conda/envs/myenv/bin/p2ptrans", line 6, in
from p2ptrans import *
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/p2ptrans/init.py", line 4, in
from . import display
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/p2ptrans/display.py", line 4, in
from .config import *
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/p2ptrans/config.py", line 1, in
from pylada.crystal import Structure, primitive, gruber, read, write, supercell, space_group, into_cell
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/pylada/init.py", line 127, in
from . import error, crystal, physics, misc, tools, ewald, decorations, periodic_table, vasp,
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/pylada/espresso/init.py", line 35, in
from .structure_handling import read_structure
File "/home/x_nitje/.conda/envs/myenv/lib/python3.8/site-packages/pylada/espresso/structure_handling.py", line 240
%(atom.type, atom.pos[0],atom.pos[1], atom.pos[2],
^
SyntaxError: invalid syntax
(myenv) [x_nitje@tetralith2 ~]$

[ftherrien]

@nityasagarjena it should work now if you reinstall pylada