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RNA-FRETools / fretraj

PyMOL plugin to calculate accessible contact volumes on PDB structures
https://RNA-FRETools.github.io/fretraj/
GNU General Public License v3.0
9 stars 2 forks source link

pip install not working on GNU/Linux Debian #2

Closed Synthaze closed 3 years ago

Synthaze commented 3 years ago

With python3.7.3, pip3.7 on GNU/Linux Debian 10

python -m venv fretraj
source fretraj/bin/activate
pip install --upgrade pip setuptools wheel
pip install fretraj

Full logs below:


Collecting fretraj
  Using cached fretraj-0.2.1.tar.gz (4.1 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting importlib-metadata<4.0.0,>=3.7.2
  Downloading importlib_metadata-3.10.1-py3-none-any.whl (14 kB)
Collecting astunparse==1.6.2
  Using cached astunparse-1.6.2-py2.py3-none-any.whl (12 kB)
Collecting nglview<3.0.0,>=2.7.7
  Using cached nglview-2.7.7-py3-none-any.whl
Collecting jsonschema<4.0.0,>=3.2.0
  Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
     |████████████████████████████████| 56 kB 209 kB/s 
Collecting numpy<1.20.0
  Using cached numpy-1.19.5-cp37-cp37m-manylinux2010_x86_64.whl (14.8 MB)
Collecting pandas<2.0.0,>=1.2.2
  Using cached pandas-1.2.4-cp37-cp37m-manylinux1_x86_64.whl (9.9 MB)
Collecting PyQt5<6.0.0,>=5.12.3
  Using cached PyQt5-5.15.4-cp36.cp37.cp38.cp39-abi3-manylinux2014_x86_64.whl (8.3 MB)
Collecting pybind11<3.0.0,>=2.6.2
  Using cached pybind11-2.6.2-py2.py3-none-any.whl (191 kB)
Collecting tqdm<5.0.0,>=4.59.0
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     |████████████████████████████████| 75 kB 312 kB/s 
Collecting numba<=0.50.1
  Downloading numba-0.50.1-cp37-cp37m-manylinux2014_x86_64.whl (3.6 MB)
     |████████████████████████████████| 3.6 MB 93 kB/s 
Collecting mdtraj<2.0.0,>=1.9.5
  Using cached mdtraj-1.9.5-cp37-cp37m-manylinux1_x86_64.whl (6.1 MB)
Collecting six<2.0,>=1.6.1
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Requirement already satisfied: wheel<1.0,>=0.23.0 in ./fretraj/lib/python3.7/site-packages (from astunparse==1.6.2->fretraj) (0.36.2)
Collecting zipp>=0.5
  Using cached zipp-3.4.1-py3-none-any.whl (5.2 kB)
Collecting typing-extensions>=3.6.4
  Using cached typing_extensions-3.10.0.0-py3-none-any.whl (26 kB)
Requirement already satisfied: setuptools in ./fretraj/lib/python3.7/site-packages (from jsonschema<4.0.0,>=3.2.0->fretraj) (57.0.0)
Collecting attrs>=17.4.0
  Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB)
     |████████████████████████████████| 53 kB 237 kB/s 
Collecting pyrsistent>=0.14.0
  Downloading pyrsistent-0.17.3.tar.gz (106 kB)
     |████████████████████████████████| 106 kB 14.9 MB/s 
Collecting scipy
  Using cached scipy-1.6.3-cp37-cp37m-manylinux1_x86_64.whl (27.4 MB)
Collecting pyparsing
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting ipywidgets>=7
  Downloading ipywidgets-7.6.3-py2.py3-none-any.whl (121 kB)
     |████████████████████████████████| 121 kB 13.5 MB/s 
Collecting jupyterlab-widgets>=1.0.0
  Downloading jupyterlab_widgets-1.0.0-py3-none-any.whl (243 kB)
     |████████████████████████████████| 243 kB 20.1 MB/s 
Collecting ipykernel>=4.5.1
  Downloading ipykernel-5.5.5-py3-none-any.whl (120 kB)
     |████████████████████████████████| 120 kB 17.5 MB/s 
Collecting nbformat>=4.2.0
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     |████████████████████████████████| 178 kB 21.5 MB/s 
Collecting ipython>=4.0.0
  Downloading ipython-7.23.1-py3-none-any.whl (785 kB)
     |████████████████████████████████| 785 kB 15.3 MB/s 
Collecting widgetsnbextension~=3.5.0
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     |████████████████████████████████| 2.2 MB 15.6 MB/s 
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     |████████████████████████████████| 100 kB 807 kB/s 
Collecting tornado>=4.2
  Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB)
     |████████████████████████████████| 428 kB 21.0 MB/s 
Collecting jupyter-client
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     |████████████████████████████████| 112 kB 18.9 MB/s 
Collecting pexpect>4.3
  Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Collecting pygments
  Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB)
     |████████████████████████████████| 1.0 MB 19.7 MB/s 
Collecting decorator
  Downloading decorator-5.0.9-py3-none-any.whl (8.9 kB)
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
  Downloading prompt_toolkit-3.0.18-py3-none-any.whl (367 kB)
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Collecting matplotlib-inline
  Downloading matplotlib_inline-0.1.2-py3-none-any.whl (8.2 kB)
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Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting backcall
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Collecting parso<0.9.0,>=0.8.0
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Collecting jupyter-core
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Collecting ipython-genutils
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting llvmlite<0.34,>=0.33.0.dev0
  Downloading llvmlite-0.33.0-cp37-cp37m-manylinux1_x86_64.whl (18.3 MB)
     |████████████████████████████████| 18.3 MB 39 kB/s 
Collecting pytz>=2017.3
  Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB)
     |████████████████████████████████| 510 kB 15.3 MB/s 
Collecting python-dateutil>=2.7.3
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting ptyprocess>=0.5
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Collecting wcwidth
  Using cached wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
Collecting PyQt5-sip<13,>=12.8
  Using cached PyQt5_sip-12.9.0-cp37-cp37m-manylinux1_x86_64.whl (317 kB)
Collecting PyQt5-Qt5>=5.15
  Using cached PyQt5_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl (59.9 MB)
Collecting notebook>=4.4.1
  Downloading notebook-6.4.0-py3-none-any.whl (9.5 MB)
     |████████████████████████████████| 9.5 MB 21.4 MB/s 
Collecting nbconvert
  Downloading nbconvert-6.0.7-py3-none-any.whl (552 kB)
     |████████████████████████████████| 552 kB 13.4 MB/s 
Collecting prometheus-client
  Downloading prometheus_client-0.10.1-py2.py3-none-any.whl (55 kB)
     |████████████████████████████████| 55 kB 398 kB/s 
Collecting pyzmq>=17
  Downloading pyzmq-22.1.0-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB)
     |████████████████████████████████| 1.1 MB 10.5 MB/s 
Collecting terminado>=0.8.3
  Downloading terminado-0.10.0-py3-none-any.whl (14 kB)
Collecting Send2Trash>=1.5.0
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Collecting argon2-cffi
  Downloading argon2_cffi-20.1.0-cp35-abi3-manylinux1_x86_64.whl (97 kB)
     |████████████████████████████████| 97 kB 598 kB/s 
Collecting jinja2
  Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB)
     |████████████████████████████████| 133 kB 21.2 MB/s 
Collecting cffi>=1.0.0
  Downloading cffi-1.14.5-cp37-cp37m-manylinux1_x86_64.whl (402 kB)
     |████████████████████████████████| 402 kB 16.0 MB/s 
Collecting pycparser
  Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux2010_x86_64.whl (31 kB)
Collecting bleach
  Downloading bleach-3.3.0-py2.py3-none-any.whl (283 kB)
     |████████████████████████████████| 283 kB 25.1 MB/s 
Collecting testpath
  Downloading testpath-0.5.0-py3-none-any.whl (84 kB)
     |████████████████████████████████| 84 kB 89 kB/s 
Collecting nbclient<0.6.0,>=0.5.0
  Downloading nbclient-0.5.3-py3-none-any.whl (82 kB)
     |████████████████████████████████| 82 kB 61 kB/s 
Collecting entrypoints>=0.2.2
  Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB)
Collecting mistune<2,>=0.8.1
  Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting pandocfilters>=1.4.1
  Downloading pandocfilters-1.4.3.tar.gz (16 kB)
Collecting jupyterlab-pygments
  Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB)
Collecting defusedxml
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Collecting async-generator
  Downloading async_generator-1.10-py3-none-any.whl (18 kB)
Collecting nest-asyncio
  Downloading nest_asyncio-1.5.1-py3-none-any.whl (5.0 kB)
Collecting webencodings
  Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting packaging
  Downloading packaging-20.9-py2.py3-none-any.whl (40 kB)
     |████████████████████████████████| 40 kB 292 kB/s 
Building wheels for collected packages: fretraj, pyrsistent, pandocfilters
  Building wheel for fretraj (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/synthase/genMess/fretraj/bin/python3 /home/synthase/genMess/fretraj/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpmo9v6q4i
       cwd: /tmp/pip-install-2w__b54z/fretraj_9a720deebf0e42e898bfb99cdea4887a
  Complete output (25 lines):
  A setup.py file already exists. Using it.
  Traceback (most recent call last):
    File "/tmp/pip-install-2w__b54z/fretraj_9a720deebf0e42e898bfb99cdea4887a/setup.py", line 2, in <module>
      from setuptools import setup
  ModuleNotFoundError: No module named 'setuptools'
  Traceback (most recent call last):
    File "/home/synthase/genMess/fretraj/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 280, in <module>
      main()
    File "/home/synthase/genMess/fretraj/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 263, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/synthase/genMess/fretraj/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 205, in build_wheel
      metadata_directory)
    File "/tmp/pip-build-env-pgthixbk/overlay/lib/python3.7/site-packages/poetry/core/masonry/api.py", line 69, in build_wheel
      return WheelBuilder.make_in(poetry, Path(wheel_directory))
    File "/tmp/pip-build-env-pgthixbk/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 77, in make_in
      wb.build()
    File "/tmp/pip-build-env-pgthixbk/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 108, in build
      self._build(zip_file)
    File "/tmp/pip-build-env-pgthixbk/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 141, in _build
      self._run_build_command(setup)
    File "/tmp/pip-build-env-pgthixbk/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 185, in _run_build_command
      str(self._path / "build"),
    File "/usr/lib/python3.7/subprocess.py", line 347, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['/home/synthase/genMess/fretraj/bin/python3', '/tmp/pip-install-2w__b54z/fretraj_9a720deebf0e42e898bfb99cdea4887a/setup.py', 'build', '-b', '/tmp/pip-install-2w__b54z/fretraj_9a720deebf0e42e898bfb99cdea4887a/build']' returned non-zero exit status 1.
  ----------------------------------------
  ERROR: Failed building wheel for fretraj
  Building wheel for pyrsistent (setup.py) ... done
  Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=104242 sha256=4cc56a4f466f98eeb2c42bc6c3cabcb756f075b6e52c50fb8d57b582e44b4f7b
  Stored in directory: /home/synthase/.cache/pip/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5
  Building wheel for pandocfilters (setup.py) ... done
  Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=8006 sha256=84a5b76d49d3555014f8429543e803a55b43ab2124df5ce04c5b9ee864f8b0c1
  Stored in directory: /home/synthase/.cache/pip/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000
Successfully built pyrsistent pandocfilters
Failed to build fretraj
ERROR: Could not build wheels for fretraj which use PEP 517 and cannot be installed directly

If this problem comes from your side, please fix it quick! ;)

If you think this is coming from my side, please let me know and I'll investigate.

Thanks.

fdsteffen commented 3 years ago

Thanks for reporting the issue. I could reproduce the error with pip<20.3. Updating pip to version >=20.3 fixed the error for me, as pip then picks up the wheel files from PyPI (available for py3.7 and py3.8) and not the source dist (which results in incompatibilities with PEP 517). If this should not solve the issue for you, you may consider installing FRETraj with conda 

conda install fretraj -c rna-fretools -c conda-forge

as also outlined here.

Synthaze commented 3 years ago

Thanks for your answer. With pip 21.1.2, traceback below:

  Building wheel for fretraj (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 /home/synthase/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpajherh1w
       cwd: /tmp/pip-install-fgap1fvl/fretraj_e8c415353b254ed7aacf08c9cdfeb0e8
  Complete output (25 lines):
  A setup.py file already exists. Using it.
  Traceback (most recent call last):
    File "/tmp/pip-install-fgap1fvl/fretraj_e8c415353b254ed7aacf08c9cdfeb0e8/setup.py", line 2, in <module>
      from setuptools import setup
  ModuleNotFoundError: No module named 'setuptools'
  Traceback (most recent call last):
    File "/home/synthase/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 280, in <module>
      main()
    File "/home/synthase/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 263, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/synthase/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 205, in build_wheel
      metadata_directory)
    File "/tmp/pip-build-env-iw3zw9rz/overlay/lib/python3.7/site-packages/poetry/core/masonry/api.py", line 69, in build_wheel
      return WheelBuilder.make_in(poetry, Path(wheel_directory))
    File "/tmp/pip-build-env-iw3zw9rz/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 77, in make_in
      wb.build()
    File "/tmp/pip-build-env-iw3zw9rz/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 108, in build
      self._build(zip_file)
    File "/tmp/pip-build-env-iw3zw9rz/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 141, in _build
      self._run_build_command(setup)
    File "/tmp/pip-build-env-iw3zw9rz/overlay/lib/python3.7/site-packages/poetry/core/masonry/builders/wheel.py", line 185, in _run_build_command
      str(self._path / "build"),
    File "/usr/lib/python3.7/subprocess.py", line 347, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['/usr/bin/python3', '/tmp/pip-install-fgap1fvl/fretraj_e8c415353b254ed7aacf08c9cdfeb0e8/setup.py', 'build', '-b', '/tmp/pip-install-fgap1fvl/fretraj_e8c415353b254ed7aacf08c9cdfeb0e8/build']' returned non-zero exit status 1.
  ----------------------------------------
  ERROR: Failed building wheel for fretraj
Failed to build fretraj
ERROR: Could not build wheels for fretraj which use PEP 517 and cannot be installed directly

In the meantime, I tried the poetry install which went smoothly but nothing happened when running fretraj --path as stated in your docs (I am not a poetry user at all however, I may have missed something trivial here). Upon successful install, redoing a poetry install does not rise any flag:


Installing dependencies from lock file

No dependencies to install or update

Installing the current project: fretraj (0.2.1)

Then fretraj --path

bash: fretraj: command not found

Well, friendly saying that conda is the last thing I want to be running on my Linux, I still installed and configured it (conda 4.9.2) and I ran the command you indicated. Unfortunately, it is neither working. Traceback below:


Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
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
fdsteffen commented 3 years ago

Was FRETraj installed into a fresh conda environment as there were some conflicts? Below is an environment which includes FRETraj and all dependencies and should be readily recreated with

conda env create -f environment.yml
environment.yml ``` name: fretraj channels: - rna-fretools - conda-forge - defaults dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=1_gnu - alsa-lib=1.2.3=h516909a_0 - argon2-cffi=20.1.0=py37h5e8e339_2 - astunparse=1.6.2=py_0 - async_generator=1.10=py_0 - attrs=21.2.0=pyhd8ed1ab_0 - backcall=0.2.0=pyh9f0ad1d_0 - backports=1.0=py_2 - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0 - bleach=3.3.0=pyh44b312d_0 - blosc=1.21.0=h9c3ff4c_0 - bzip2=1.0.8=h7f98852_4 - c-ares=1.17.1=h7f98852_1 - ca-certificates=2020.12.5=ha878542_0 - certifi=2020.12.5=py37h89c1867_1 - cffi=1.14.5=py37hc58025e_0 - dbus=1.13.6=h48d8840_2 - decorator=5.0.9=pyhd8ed1ab_0 - defusedxml=0.7.1=pyhd8ed1ab_0 - entrypoints=0.3=pyhd8ed1ab_1003 - expat=2.4.1=h9c3ff4c_0 - fontconfig=2.13.1=hba837de_1005 - freetype=2.10.4=h0708190_1 - fretraj=0.2.1=py_0 - gettext=0.19.8.1=h0b5b191_1005 - glib=2.68.2=h9c3ff4c_0 - glib-tools=2.68.2=h9c3ff4c_0 - gst-plugins-base=1.18.4=hf529b03_2 - gstreamer=1.18.4=h76c114f_2 - hdf5=1.10.6=nompi_h6a2412b_1114 - icu=68.1=h58526e2_0 - importlib-metadata=3.10.1=py37h89c1867_0 - ipykernel=5.5.5=py37h085eea5_0 - ipython=7.23.1=py37h085eea5_0 - ipython_genutils=0.2.0=py_1 - ipywidgets=7.6.3=pyhd3deb0d_0 - jedi=0.18.0=py37h89c1867_2 - jinja2=3.0.1=pyhd8ed1ab_0 - jpeg=9d=h36c2ea0_0 - jsonschema=3.2.0=pyhd8ed1ab_3 - jupyter_client=6.1.12=pyhd8ed1ab_0 - jupyter_core=4.7.1=py37h89c1867_0 - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0 - jupyterlab_widgets=1.0.0=pyhd8ed1ab_1 - krb5=1.19.1=hcc1bbae_0 - ld_impl_linux-64=2.33.1=h53a641e_7 - libblas=3.9.0=9_openblas - libcblas=3.9.0=9_openblas - libclang=11.1.0=default_ha53f305_1 - libcurl=7.77.0=h2574ce0_0 - libedit=3.1.20191231=he28a2e2_2 - libev=4.33=h516909a_1 - libevent=2.1.10=hcdb4288_3 - libffi=3.3=he6710b0_2 - libgcc-ng=9.3.0=h2828fa1_19 - libgfortran-ng=9.3.0=hff62375_19 - libgfortran5=9.3.0=hff62375_19 - libglib=2.68.2=h3e27bee_0 - libgomp=9.3.0=h2828fa1_19 - libiconv=1.16=h516909a_0 - liblapack=3.9.0=9_openblas - libllvm11=11.1.0=hf817b99_2 - libllvm9=9.0.1=hf817b99_2 - libnghttp2=1.43.0=h812cca2_0 - libogg=1.3.4=h7f98852_1 - libopenblas=0.3.15=pthreads_h8fe5266_1 - libopus=1.3.1=h7f98852_1 - libpng=1.6.37=h21135ba_2 - libpq=13.3=hd57d9b9_0 - libsodium=1.0.18=h36c2ea0_1 - libssh2=1.9.0=ha56f1ee_6 - libstdcxx-ng=9.3.0=h6de172a_19 - libuuid=2.32.1=h7f98852_1000 - libvorbis=1.3.7=h9c3ff4c_0 - libxcb=1.13=h7f98852_1003 - libxkbcommon=1.0.3=he3ba5ed_0 - libxml2=2.9.12=h72842e0_0 - llvmlite=0.33.0=py37h5202443_1 - lz4-c=1.9.3=h9c3ff4c_0 - lzo=2.10=h516909a_1000 - markupsafe=2.0.1=py37h5e8e339_0 - matplotlib-inline=0.1.2=pyhd8ed1ab_2 - mdtraj=1.9.5=py37hd0d7e5a_1 - mistune=0.8.4=py37h5e8e339_1003 - mock=4.0.3=py37h89c1867_1 - mysql-common=8.0.23=ha770c72_2 - mysql-libs=8.0.23=h935591d_2 - nbclient=0.5.3=pyhd8ed1ab_0 - nbconvert=6.0.7=py37h89c1867_3 - nbformat=5.1.3=pyhd8ed1ab_0 - ncurses=6.2=he6710b0_1 - nest-asyncio=1.5.1=pyhd8ed1ab_0 - nglview=2.7.8=pyh59e0f4d_0 - notebook=6.4.0=pyha770c72_0 - nspr=4.30=h9c3ff4c_0 - nss=3.64=hb5efdd6_0 - numba=0.50.1=py37h0da4684_1 - numexpr=2.7.3=py37hdc94413_0 - numpy=1.19.5=py37haa41c4c_1 - openssl=1.1.1k=h7f98852_0 - packaging=20.9=pyh44b312d_0 - pandas=1.2.4=py37h219a48f_0 - pandoc=2.13=h7f98852_0 - pandocfilters=1.4.2=py_1 - parso=0.8.2=pyhd8ed1ab_0 - pcre=8.44=he1b5a44_0 - pexpect=4.8.0=pyh9f0ad1d_2 - pickleshare=0.7.5=py_1003 - pip=21.1.1=py37h06a4308_0 - prometheus_client=0.10.1=pyhd8ed1ab_0 - prompt-toolkit=3.0.18=pyha770c72_0 - pthread-stubs=0.4=h36c2ea0_1001 - ptyprocess=0.7.0=pyhd3deb0d_0 - pybind11=2.6.2=py37h2527ec5_0 - pybind11-global=2.6.2=py37h2527ec5_0 - pycparser=2.20=pyh9f0ad1d_2 - pygments=2.9.0=pyhd8ed1ab_0 - pyparsing=2.4.7=pyh9f0ad1d_0 - pyqt=5.12.3=py37h89c1867_7 - pyqt-impl=5.12.3=py37he336c9b_7 - pyqt5-sip=4.19.18=py37hcd2ae1e_7 - pyqtchart=5.12=py37he336c9b_7 - pyqtwebengine=5.12.1=py37he336c9b_7 - pyrsistent=0.17.3=py37h5e8e339_2 - pytables=3.6.1=py37h0c4f3e0_3 - python=3.7.10=hdb3f193_0 - python-dateutil=2.8.1=py_0 - python_abi=3.7=1_cp37m - pytz=2021.1=pyhd8ed1ab_0 - pyzmq=22.1.0=py37h336d617_0 - qt=5.12.9=hda022c4_4 - readline=8.1=h27cfd23_0 - scipy=1.6.3=py37h29e03ee_0 - send2trash=1.5.0=py_0 - setuptools=52.0.0=py37h06a4308_0 - six=1.16.0=pyh6c4a22f_0 - snappy=1.1.8=he1b5a44_3 - sqlite=3.35.4=hdfb4753_0 - terminado=0.10.0=py37h89c1867_0 - testpath=0.5.0=pyhd8ed1ab_0 - tk=8.6.10=hbc83047_0 - tornado=6.1=py37h5e8e339_1 - tqdm=4.61.0=pyhd8ed1ab_0 - traitlets=5.0.5=py_0 - typing_extensions=3.7.4.3=py_0 - wcwidth=0.2.5=pyh9f0ad1d_2 - webencodings=0.5.1=py_1 - wheel=0.36.2=pyhd3eb1b0_0 - widgetsnbextension=3.5.1=py37h89c1867_4 - xorg-libxau=1.0.9=h7f98852_0 - xorg-libxdmcp=1.1.3=h7f98852_0 - xz=5.2.5=h7b6447c_0 - zeromq=4.3.4=h9c3ff4c_0 - zipp=3.4.1=pyhd8ed1ab_0 - zlib=1.2.11=h7b6447c_3 - zstd=1.4.9=ha95c52a_0 - pip: - nglview-js-widgets==2.7.7 ```

Installing from source with Poetry seems to have worked. Is the module found after reinitiating the shell?

Synthaze commented 3 years ago

For the poetry install. After reinitiating the shell, poetry show yield all dependencies installed for fretraj, but not fretraj itself:

alabaster                     0.7.12    A configurable sidebar-enabled Sphinx theme
argon2-cffi                   20.1.0    The secure Argon2 password hashing algorithm.
astunparse                    1.6.2     An AST unparser for Python
async-generator               1.10      Async generators and context managers for Python 3.5+
attrs                         20.3.0    Classes Without Boilerplate
babel                         2.9.0     Internationalization utilities
backcall                      0.2.0     Specifications for callback functions passed in to an API
beautifulsoup4                4.9.3     Screen-scraping library
bleach                        3.3.0     An easy safelist-based HTML-sanitizing tool.
certifi                       2020.12.5 Python package for providing Mozilla's CA Bundle.
cffi                          1.14.5    Foreign Function Interface for Python calling C code.
chardet                       4.0.0     Universal encoding detector for Python 2 and 3
click                         7.1.2     Composable command line interface toolkit
colorama                      0.4.4     Cross-platform colored terminal text.
coverage                      5.5       Code coverage measurement for Python
cycler                        0.10.0    Composable style cycles
decorator                     4.4.2     Decorators for Humans
defusedxml                    0.7.1     XML bomb protection for Python stdlib modules
docutils                      0.16      Docutils -- Python Documentation Utilities
entrypoints                   0.3       Discover and load entry points from installed packages.
gitdb                         4.0.5     Git Object Database
gitpython                     3.1.14    Python Git Library
idna                          2.10      Internationalized Domain Names in Applications (IDNA)
imagesize                     1.2.0     Getting image size from png/jpeg/jpeg2000/gif file
importlib-metadata            3.7.2     Read metadata from Python packages
iniconfig                     1.1.1     iniconfig: brain-dead simple config-ini parsing
ipykernel                     5.5.0     IPython Kernel for Jupyter
ipython                       7.21.0    IPython: Productive Interactive Computing
ipython-genutils              0.2.0     Vestigial utilities from IPython
ipywidgets                    7.6.3     IPython HTML widgets for Jupyter
jedi                          0.18.0    An autocompletion tool for Python that can be used for text editors.
jinja2                        2.11.3    A very fast and expressive template engine.
jsonschema                    3.2.0     An implementation of JSON Schema validation for Python
jupyter-book                  0.10.1    Jupyter Book: Create an online book with Jupyter Notebooks
jupyter-cache                 0.4.2     A defined interface for working with a cache of jupyter notebooks.
jupyter-client                6.1.11    Jupyter protocol implementation and client libraries
jupyter-core                  4.7.1     Jupyter core package. A base package on which Jupyter projects rely.
jupyter-sphinx                0.3.1     Jupyter Sphinx Extensions
jupyterlab-widgets            1.0.0     A JupyterLab extension.
jupytext                      1.10.3    Jupyter notebooks as Markdown documents, Julia, Python or R scripts
kiwisolver                    1.3.1     A fast implementation of the Cassowary constraint solver
latexcodec                    2.0.1     A lexer and codec to work with LaTeX code in Python.
linkify-it-py                 1.0.1     Links recognition library with FULL unicode support.
llvmlite                      0.33.0    lightweight wrapper around basic LLVM functionality
markdown-it-py                0.6.2     Python port of markdown-it. Markdown parsing, done right!
markupsafe                    1.1.1     Safely add untrusted strings to HTML/XML markup.
matplotlib                    3.3.4     Python plotting package
mdit-py-plugins               0.2.5     Collection of plugins for markdown-it-py
mdtraj                        1.9.5     MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
mistune                       0.8.4     The fastest markdown parser in pure Python
myst-nb                       0.12.0    A Jupyter Notebook Sphinx reader built on top of the MyST markdown parser.
myst-parser                   0.13.5    An extended commonmark compliant parser, with bridges to docutils & sphinx.
nbclient                      0.5.3     A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor.
nbconvert                     5.6.1     Converting Jupyter Notebooks
nbdime                        2.1.0     Diff and merge of Jupyter Notebooks
nbformat                      5.1.2     The Jupyter Notebook format
nest-asyncio                  1.5.1     Patch asyncio to allow nested event loops
nested-lookup                 0.2.22    Python functions for working with deeply nested documents (lists and dicts)
nglview                       2.7.7     IPython widget to interactively view molecular structures and trajectories.
notebook                      6.2.0     A web-based notebook environment for interactive computing
numba                         0.50.1    compiling Python code using LLVM
numpy                         1.19.5    NumPy is the fundamental package for array computing with Python.
packaging                     20.9      Core utilities for Python packages
pandas                        1.2.3     Powerful data structures for data analysis, time series, and statistics
pandocfilters                 1.4.3     Utilities for writing pandoc filters in python
parso                         0.8.1     A Python Parser
pexpect                       4.8.0     Pexpect allows easy control of interactive console applications.
pickleshare                   0.7.5     Tiny 'shelve'-like database with concurrency support
pillow                        8.1.2     Python Imaging Library (Fork)
pluggy                        0.13.1    plugin and hook calling mechanisms for python
prometheus-client             0.9.0     Python client for the Prometheus monitoring system.
prompt-toolkit                3.0.16    Library for building powerful interactive command lines in Python
ptyprocess                    0.7.0     Run a subprocess in a pseudo terminal
py                            1.10.0    library with cross-python path, ini-parsing, io, code, log facilities
pybind11                      2.6.2     Seamless operability between C++11 and Python
pybtex                        0.24.0    A BibTeX-compatible bibliography processor in Python
pybtex-docutils               1.0.0     A docutils backend for pybtex.
pycparser                     2.20      C parser in Python
pydata-sphinx-theme           0.4.3     Bootstrap-based Sphinx theme from the PyData community
pygments                      2.8.1     Pygments is a syntax highlighting package written in Python.
pyparsing                     2.4.7     Python parsing module
pyqt5                         5.15.3    Python bindings for the Qt cross platform application toolkit
pyqt5-qt                      5.15.2    The subset of a Qt installation needed by PyQt5.
pyqt5-sip                     12.8.1    The sip module support for PyQt5
pyrsistent                    0.17.3    Persistent/Functional/Immutable data structures
pytest                        6.2.2     pytest: simple powerful testing with Python
pytest-cov                    2.11.1    Pytest plugin for measuring coverage.
pytest-mock                   3.5.1     Thin-wrapper around the mock package for easier use with pytest
python-dateutil               2.8.1     Extensions to the standard Python datetime module
pytz                          2021.1    World timezone definitions, modern and historical
pyyaml                        5.4.1     YAML parser and emitter for Python
pyzmq                         22.0.3    Python bindings for 0MQ
requests                      2.25.1    Python HTTP for Humans.
scipy                         1.6.1     SciPy: Scientific Library for Python
seaborn                       0.11.1    seaborn: statistical data visualization
send2trash                    1.5.0     Send file to trash natively under Mac OS X, Windows and Linux.
six                           1.15.0    Python 2 and 3 compatibility utilities
smmap                         3.0.5     A pure Python implementation of a sliding window memory map manager
snowballstemmer               2.1.0     This package provides 29 stemmers for 28 languages generated from Snowball algorithms.
soupsieve                     2.2       A modern CSS selector implementation for Beautiful Soup.
sphinx                        3.5.2     Python documentation generator
sphinx-book-theme             0.0.40    Jupyter Book: Create an online book with Jupyter Notebooks
sphinx-comments               0.0.3     Add comments and annotation to your documentation.
sphinx-copybutton             0.3.1     Add a copy button to each of your code cells.
sphinx-panels                 0.5.2     A sphinx extension for creating panels in a grid layout.
sphinx-thebe                  0.0.8     Integrate interactive code blocks into your documentation with Thebe and Binder.
sphinx-togglebutton           0.2.3     Toggle page content and collapse admonitions in Sphinx.
sphinxcontrib-applehelp       1.0.2     sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books
sphinxcontrib-bibtex          2.1.4     Sphinx extension for BibTeX style citations.
sphinxcontrib-devhelp         1.0.2     sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document.
sphinxcontrib-htmlhelp        1.0.3     sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files
sphinxcontrib-jsmath          1.0.1     A sphinx extension which renders display math in HTML via JavaScript
sphinxcontrib-qthelp          1.0.3     sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document.
sphinxcontrib-serializinghtml 1.1.4     sphinxcontrib-serializinghtml is a sphinx extension which outputs "serialized" HTML files (json and pickle).
sqlalchemy                    1.3.23    Database Abstraction Library
terminado                     0.9.2     Tornado websocket backend for the Xterm.js Javascript terminal emulator library.
testpath                      0.4.4     Test utilities for code working with files and commands
toml                          0.10.2    Python Library for Tom's Obvious, Minimal Language
tornado                       6.1       Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed.
tqdm                          4.59.0    Fast, Extensible Progress Meter
traitlets                     5.0.5     Traitlets Python configuration system
typing-extensions             3.7.4.3   Backported and Experimental Type Hints for Python 3.5+
uc-micro-py                   1.0.1     Micro subset of unicode data files for linkify-it-py projects.
urllib3                       1.26.3    HTTP library with thread-safe connection pooling, file post, and more.
wcwidth                       0.2.5     Measures the displayed width of unicode strings in a terminal
webencodings                  0.5.1     Character encoding aliases for legacy web content
widgetsnbextension            3.5.1     IPython HTML widgets for Jupyter
zipp                          3.4.1     Backport of pathlib-compatible object wrapper for zip files

For conda, it was a fresh install and the conda install fretraj -c rna-fretools -c conda-forge was executed inside a miniconda3 (base) default/fresh environment.

I investigate the conda way and let you know asap.

Synthaze commented 3 years ago

Well thanks! Saving the content of environment.yml in a directory, cd to this directory and doing the following works:

conda env create -f environment.yml
conda activate fretraj
conda install fretraj -c rna-fretools -c conda-forge

Then:

fretraj --path

Yields:

Note: the LabelLib module is not installed. 
ACV calculations will use a Python-only algorithm

package directory: /home/synthase/miniconda3/envs/fretraj/lib/python3.7/site-
packages/fretraj

Which is great.

Maybe think about adding this environment.ymlin the root dir of the package ;)

fdsteffen commented 3 years ago

FRETraj is now available on conda-forge. Installing with conda install fretraj -c conda-forge should solve the environment.