kit-mbs/pydca

Direct coupling analysis software for protein and RNA sequences

pydca's Issues

pip install fails with "file format not recognized"

Hello,

Attempting to pip install pydca into freshly created conda environment fails on Linux due to

build/temp.linux-x86_64-3.5/pydca/plmdca/lbfgs/lib/lbfgs.o: file not recognized: file format not recognized
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1

I have gcc 10.1.0-2.

python 3.5 is a bit old

Is it possible to update to a newer python? At this point it is hard to even create a python 3.5 enviornment with the required numba, llvmlite versions...

llvmlite version not working

Hello there!
I am trying to install th pydca package with pip3 on Ubuntu 20.04.3, python 3.8.10. Everytime I run pip3 install pydca I get the same error with installing package llvmlite. I assume, there is a problem with the version of llvmlite, because running pip3 install llvmlie=0.30.0 led to the same error.
See the error from pip3 install pydca below:

Collecting pydca
  Using cached pydca-1.23-cp38-cp38-linux_x86_64.whl
Requirement already satisfied: scipy==1.3.1 in /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages (from pydca) (1.3.1)
Collecting requests>=2.22.0
  Using cached requests-2.27.1-py2.py3-none-any.whl (63 kB)
Requirement already satisfied: biopython==1.74 in /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages (from pydca) (1.74)
Collecting numba==0.46.0
  Using cached numba-0.46.0-cp38-cp38-linux_x86_64.whl
Collecting llvmlite==0.30.0
  Using cached llvmlite-0.30.0.tar.gz (110 kB)
  Preparing metadata (setup.py) ... done
Collecting matplotlib==3.0.0
  Using cached matplotlib-3.0.0-cp38-cp38-linux_x86_64.whl
Requirement already satisfied: numpy<=1.15.4,>=1.13.3 in /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages (from pydca) (1.15.4)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Using cached pyparsing-3.0.7-py3-none-any.whl (98 kB)
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting cycler>=0.10
  Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.3.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB)
Collecting certifi>=2017.4.17
  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting idna<4,>=2.5
  Using cached idna-3.3-py3-none-any.whl (61 kB)
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting urllib3<1.27,>=1.21.1
  Using cached urllib3-1.26.8-py2.py3-none-any.whl (138 kB)
Collecting six>=1.5
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: llvmlite
  Building wheel for llvmlite (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [26 lines of output]
      running bdist_wheel
      /projects/myb-domain/pyDCAenv2/bin/python3 /tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py
      LLVM version... Traceback (most recent call last):
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 105, in main_posix
          out = subprocess.check_output([llvm_config, '--version'])
        File "/usr/lib/python3.8/subprocess.py", line 415, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
        File "/usr/lib/python3.8/subprocess.py", line 493, in run
          with Popen(*popenargs, **kwargs) as process:
        File "/usr/lib/python3.8/subprocess.py", line 858, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "/usr/lib/python3.8/subprocess.py", line 1704, in _execute_child
          raise child_exception_type(errno_num, err_msg, err_filename)
      FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'
      
      During handling of the above exception, another exception occurred:
      
      Traceback (most recent call last):
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 168, in <module>
          main()
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 158, in main
          main_posix('linux', '.so')
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 107, in main_posix
          raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
      RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
      error: command '/projects/myb-domain/pyDCAenv2/bin/python3' failed with exit status 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for llvmlite
  Running setup.py clean for llvmlite
Failed to build llvmlite
Installing collected packages: llvmlite, certifi, urllib3, six, pyparsing, numba, kiwisolver, idna, cycler, charset-normalizer, requests, python-dateutil, matplotlib, pydca
  Attempting uninstall: llvmlite
    Found existing installation: llvmlite 0.31.0
    Uninstalling llvmlite-0.31.0:
      Successfully uninstalled llvmlite-0.31.0
  Running setup.py install for llvmlite ... error
  error: subprocess-exited-with-error
  
  × Running setup.py install for llvmlite did not run successfully.
  │ exit code: 1
  ╰─> [29 lines of output]
      running install
      running build
      got version from file /tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/llvmlite/_version.py {'version': '0.30.0', 'full': '3cad106e2f727bc400f1b426ce306b1e30e34b72'}
      running build_ext
      /projects/myb-domain/pyDCAenv2/bin/python3 /tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py
      LLVM version... Traceback (most recent call last):
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 105, in main_posix
          out = subprocess.check_output([llvm_config, '--version'])
        File "/usr/lib/python3.8/subprocess.py", line 415, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
        File "/usr/lib/python3.8/subprocess.py", line 493, in run
          with Popen(*popenargs, **kwargs) as process:
        File "/usr/lib/python3.8/subprocess.py", line 858, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "/usr/lib/python3.8/subprocess.py", line 1704, in _execute_child
          raise child_exception_type(errno_num, err_msg, err_filename)
      FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'
      
      During handling of the above exception, another exception occurred:
      
      Traceback (most recent call last):
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 168, in <module>
          main()
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 158, in main
          main_posix('linux', '.so')
        File "/tmp/pip-install-msb9y2yn/llvmlite_c45ea5246f3345099cbb7435333f0d3f/ffi/build.py", line 107, in main_posix
          raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
      RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
      error: command '/projects/myb-domain/pyDCAenv2/bin/python3' failed with exit status 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  WARNING: No metadata found in /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages
  Rolling back uninstall of llvmlite
  Moving to /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages/llvmlite-0.31.0.dist-info/
   from /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages/~lvmlite-0.31.0.dist-info
  Moving to /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages/llvmlite/
   from /projects/myb-domain/pyDCAenv2/lib/python3.8/site-packages/~lvmlite
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> llvmlite


note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Wouldn't it be maybe possible to upgrade the required version of llvmlite? Thank you in advance for your help.

Example for protein DCA analysis

Hi Team,
Thanks for sharing the code.
Could you please kindly provide an runable example for protein analysis? the pydca_demo.py file does not work:

1. it has typos (in L19, it should be plmdca.PlmDCA(protein_msa_file, 'protein', not plmdca.PlmDCA'protein', msa_file, .
2. when run at L27, it throws out error: terminate called after throwing an instance of 'std::out_of_range' what(): _Map_base::at
3. the code does not finish. No DCAVisualizer (needs pdb file). Could you provide instructions how to get pdb file for protein analysis.

Thank you for your help!

Single thread

Hi,

is it possible to force "meanfield_dca.MeanFieldDCA" function only use a single core/thread?
It always gives errors when i try to run it on clusters(Sungrid engine).

Below is error messeage:
/var/spool/gridengine/execd/vn-29/job_scripts/880175: line 12: 1489 Segmentation fault

Many thanks!

Nan in Frobenius Norm Average Product Correction

score_apc = score - av_score_sites[i] * (av_score_sites[j]/av_all_scores)

This formula will result in Nan when the av_all_scores is zero so it's better to an epsilon value to it to avoid undesirable results.

segmentation fault for all command line utilities

I can not run the command line implementation for pydca, neither can I run any command to read the man e.g.
pydca --help

This returns:
Segmentation fault (core dumped)

pip install fails in python 3.10

Hi , I'm trying to install pydca. Unfortunately I'm not getting very far. It's missing a platform attribute (linux_distribution). From other threads I figured that this was predicated and removed in python3.8. I'm on Ubuntu 22.04 and python 3.10. Would it be possible to fix that.

Thanks a lot.

pip install pydca
Defaulting to user installation because normal site-packages is not writeable
Collecting pydca
Using cached pydca-1.23.tar.gz (98 kB)
Preparing metadata (setup.py) ... done
Collecting biopython==1.74
Using cached biopython-1.74.tar.gz (16.1 MB)
Preparing metadata (setup.py) ... done
Collecting llvmlite==0.30.0
Using cached llvmlite-0.30.0.tar.gz (110 kB)
Preparing metadata (setup.py) ... done
Collecting matplotlib==3.0.0
Using cached matplotlib-3.0.0.tar.gz (36.3 MB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [48 lines of output]
Traceback (most recent call last):
File "", line 2, in
File "", line 34, in
File "/tmp/pip-install-r1mrjqrf/matplotlib_fd3102cdcdaa4566b6c139e937eac207/setup.py", line 170, in
msg = pkg.install_help_msg()
File "/tmp/pip-install-r1mrjqrf/matplotlib_fd3102cdcdaa4566b6c139e937eac207/setupext.py", line 539, in install_help_msg
release = platform.linux_distribution()[0].lower()
AttributeError: module 'platform' has no attribute 'linux_distribution'
============================================================================
Edit setup.cfg to change the build options

  BUILDING MATPLOTLIB
              matplotlib: yes [3.0.0]
                  python: yes [3.10.6 (main, Nov 14 2022, 16:10:14) [GCC
                          11.3.0]]
                platform: yes [linux]
  
  REQUIRED DEPENDENCIES AND EXTENSIONS
                   numpy: yes [version 1.23.4]
        install_requires: yes [handled by setuptools]
                  libagg: yes [pkg-config information for 'libagg' could not
                          be found. Using local copy.]
                freetype: no  [The C/C++ header for freetype2 (ft2build.h)
                          could not be found.  You may need to install the
                          development package.]
                     png: yes [version 1.6.37]
                   qhull: yes [pkg-config information for 'libqhull' could not
                          be found. Using local copy.]
  
  OPTIONAL SUBPACKAGES
             sample_data: yes [installing]
                toolkits: yes [installing]
                   tests: no  [skipping due to configuration]
          toolkits_tests: no  [skipping due to configuration]
  
  OPTIONAL BACKEND EXTENSIONS
                     agg: yes [installing]
                   tkagg: yes [installing; run-time loading from Python Tcl /
                          Tk]
                  macosx: no  [Mac OS-X only]
               windowing: no  [Microsoft Windows only]
  
  OPTIONAL PACKAGE DATA
                    dlls: no  [skipping due to configuration]
  
  ============================================================================
                          * The following required packages can not be built:
                          * freetype
  [end of output]

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

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.