Cannot install the latest package

[const7]

Summary

The installation stuck in looking for compatible requirements.

Problem

I tried both installation commands

pip install timecorr

and

pip install --upgrade git+https://github.com/ContextLab/timecorr.git

Here is the output log:

Collecting timecorr
  Using cached timecorr-0.1.6-py3-none-any.whl (14 kB)
Collecting nose==1.3.7
  Using cached nose-1.3.7-py3-none-any.whl (154 kB)
Collecting numpy==1.16.2
  Using cached numpy-1.16.2-cp37-cp37m-manylinux1_x86_64.whl (17.3 MB)
Collecting hypertools==0.7.0
  Using cached hypertools-0.7.0-py3-none-any.whl (59 kB)
Collecting seaborn==0.9.0
  Using cached seaborn-0.9.0-py3-none-any.whl (208 kB)
Collecting scikit-learn==0.19.2
  Using cached scikit_learn-0.19.2-cp37-cp37m-manylinux1_x86_64.whl (4.9 MB)
Collecting pandas==0.24.2
  Using cached pandas-0.24.2-cp37-cp37m-manylinux1_x86_64.whl (10.1 MB)
Collecting duecredit==0.7.0
  Using cached duecredit-0.7.0.tar.gz (66 kB)
Collecting sphinx==2.0.0
  Using cached Sphinx-2.0.0-py2.py3-none-any.whl (3.2 MB)
Collecting matplotlib==3.0.3
  Using cached matplotlib-3.0.3-cp37-cp37m-manylinux1_x86_64.whl (13.0 MB)
Collecting scipy==1.2.1
  Using cached scipy-1.2.1-cp37-cp37m-manylinux1_x86_64.whl (24.8 MB)
Requirement already satisfied: requests in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from duecredit==0.7.0->timecorr) (2.27.1)
Collecting citeproc-py>=0.4
  Using cached citeproc_py-0.6.0-py3-none-any.whl (179 kB)
Requirement already satisfied: six in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from duecredit==0.7.0->timecorr) (1.16.0)
Collecting deepdish
  Using cached deepdish-0.3.7-py2.py3-none-any.whl (37 kB)
Requirement already satisfied: PPCA>=0.0.2 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from hypertools==0.7.0->timecorr) (0.0.4)
Collecting future
  Using cached future-0.18.2.tar.gz (829 kB)
Requirement already satisfied: umap-learn>=0.4.6 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from hypertools==0.7.0->timecorr) (0.5.3)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from matplotlib==3.0.3->timecorr) (3.0.4)
Requirement already satisfied: cycler>=0.10 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from matplotlib==3.0.3->timecorr) (0.11.0)
Requirement already satisfied: python-dateutil>=2.1 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from matplotlib==3.0.3->timecorr) (2.8.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from matplotlib==3.0.3->timecorr) (1.3.2)
Requirement already satisfied: pytz>=2011k in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from pandas==0.24.2->timecorr) (2021.3)
Collecting sphinxcontrib-htmlhelp
  Using cached sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB)
Collecting sphinxcontrib-devhelp
  Using cached sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting babel!=2.0,>=1.3
  Using cached Babel-2.10.1-py3-none-any.whl (9.5 MB)
Collecting imagesize
  Using cached imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB)
Requirement already satisfied: packaging in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from sphinx==2.0.0->timecorr) (21.3)
Collecting sphinxcontrib-serializinghtml
  Using cached sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
Collecting Jinja2>=2.3
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     |████████████████████████████████| 133 kB 5.2 MB/s 
Collecting sphinxcontrib-qthelp
  Using cached sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Collecting docutils>=0.12
  Using cached docutils-0.18.1-py2.py3-none-any.whl (570 kB)
Collecting snowballstemmer>=1.1
  Using cached snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.12.0-py3-none-any.whl (1.1 MB)
     |████████████████████████████████| 1.1 MB 5.0 MB/s 
Collecting alabaster<0.8,>=0.7
  Using cached alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Requirement already satisfied: setuptools in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from sphinx==2.0.0->timecorr) (61.2.0)
Collecting sphinxcontrib-jsmath
  Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-applehelp
  Using cached sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Collecting lxml
  Using cached lxml-4.8.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (6.4 MB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from requests->duecredit==0.7.0->timecorr) (1.26.9)
Requirement already satisfied: idna<4,>=2.5 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from requests->duecredit==0.7.0->timecorr) (3.3)
Requirement already satisfied: certifi>=2017.4.17 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from requests->duecredit==0.7.0->timecorr) (2021.10.8)
Requirement already satisfied: charset-normalizer~=2.0.0 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from requests->duecredit==0.7.0->timecorr) (2.0.12)
Requirement already satisfied: numba>=0.49 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from umap-learn>=0.4.6->hypertools==0.7.0->timecorr) (0.55.1)
Requirement already satisfied: pynndescent>=0.5 in /home/haiyanwu/miniconda3/envs/test/lib/python3.7/site-packages (from umap-learn>=0.4.6->hypertools==0.7.0->timecorr) (0.5.6)
Collecting umap-learn>=0.4.6
  Using cached umap-learn-0.5.2.tar.gz (86 kB)
  Using cached umap-learn-0.5.1.tar.gz (80 kB)
  Using cached umap-learn-0.5.0.tar.gz (81 kB)
  Using cached umap-learn-0.4.6.tar.gz (69 kB)
INFO: pip is looking at multiple versions of snowballstemmer to determine which version is compatible with other requirements. This could take a while.
Collecting snowballstemmer>=1.1
  Using cached snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB)
  Using cached snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB)
  Using cached snowballstemmer-1.9.1.tar.gz (82 kB)
  Using cached snowballstemmer-1.9.0.tar.gz (76 kB)
  Using cached snowballstemmer-1.2.1-py2.py3-none-any.whl (64 kB)
  Using cached snowballstemmer-1.2.0.tar.gz (49 kB)
  Using cached snowballstemmer-1.1.0.tar.gz (50 kB)
INFO: pip is looking at multiple versions of snowballstemmer to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of six to determine which version is compatible with other requirements. This could take a while.
Collecting six
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. If you want to abort this run, you can press Ctrl + C to do so. To improve how pip performs, tell us what happened here: https://pip.pypa.io/surveys/backtracking
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
  Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)
  Using cached six-1.13.0-py2.py3-none-any.whl (10 kB)
  Using cached six-1.12.0-py2.py3-none-any.whl (10 kB)
  Using cached six-1.11.0-py2.py3-none-any.whl (10 kB)
  Using cached six-1.10.0-py2.py3-none-any.whl (10 kB)
INFO: pip is looking at multiple versions of six to determine which version is compatible with other requirements. This could take a while.
  Using cached six-1.9.0-py2.py3-none-any.whl (10 kB)
  Using cached six-1.8.0-py2.py3-none-any.whl (9.7 kB)
  Using cached six-1.7.3-py2.py3-none-any.whl (9.5 kB)
  Using cached six-1.7.2-py2.py3-none-any.whl (9.6 kB)
  Using cached six-1.7.1-py2.py3-none-any.whl (9.6 kB)
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. If you want to abort this run, you can press Ctrl + C to do so. To improve how pip performs, tell us what happened here: https://pip.pypa.io/surveys/backtracking
  Using cached six-1.7.0-py2.py3-none-any.whl (9.3 kB)
  Using cached six-1.6.1-py2.py3-none-any.whl (8.6 kB)
  Using cached six-1.6.0-py2.py3-none-any.whl (8.5 kB)
  Using cached six-1.5.2-py2.py3-none-any.whl (8.4 kB)
  Using cached six-1.5.1-py2.py3-none-any.whl (8.4 kB)
  Using cached six-1.5.0-py2.py3-none-any.whl (8.2 kB)
INFO: pip is looking at multiple versions of idna to determine which version is compatible with other requirements. This could take a while.
Collecting idna<4,>=2.5
  Using cached idna-3.3-py3-none-any.whl (61 kB)
  Using cached idna-3.2-py3-none-any.whl (59 kB)
  Using cached idna-3.1-py3-none-any.whl (58 kB)
  Using cached idna-3.0-py2.py3-none-any.whl (58 kB)
  Using cached idna-2.10-py2.py3-none-any.whl (58 kB)
  Using cached idna-2.9-py2.py3-none-any.whl (58 kB)
  Using cached idna-2.8-py2.py3-none-any.whl (58 kB)
INFO: pip is looking at multiple versions of idna to determine which version is compatible with other requirements. This could take a while.
  Using cached idna-2.7-py2.py3-none-any.whl (58 kB)
  Using cached idna-2.6-py2.py3-none-any.whl (56 kB)
  Using cached idna-2.5-py2.py3-none-any.whl (55 kB)
INFO: pip is looking at multiple versions of charset-normalizer to determine which version is compatible with other requirements. This could take a while.
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. If you want to abort this run, you can press Ctrl + C to do so. To improve how pip performs, tell us what happened here: https://pip.pypa.io/surveys/backtracking
  Using cached charset_normalizer-2.0.11-py3-none-any.whl (39 kB)
  Using cached charset_normalizer-2.0.10-py3-none-any.whl (39 kB)
  Using cached charset_normalizer-2.0.9-py3-none-any.whl (39 kB)
  Using cached charset_normalizer-2.0.8-py3-none-any.whl (39 kB)
  Using cached charset_normalizer-2.0.7-py3-none-any.whl (38 kB)
  Using cached charset_normalizer-2.0.6-py3-none-any.whl (37 kB)
INFO: pip is looking at multiple versions of charset-normalizer to determine which version is compatible with other requirements. This could take a while.
  Using cached charset_normalizer-2.0.5-py3-none-any.whl (37 kB)

Other information

os version: Ubuntu 20.04
python version: 3.7.13

I also tried to install it in a clean virtual environment and still got the same output.

[jeremymanning]

Hi @const7, thanks for your bug report! I'll keep this issue open until I have a chance to explore in more detail. But in the meantime, I verified that I was able to get timecorr up and running in a conda environment built from the following environment:

name: tc
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.9
  - numpy=1.22.1
  - pandas=1.4.0
  - scipy=1.7.3
  - matplotlib=3.5.1
  - seaborn=0.11.2
  - scikit-learn=0.23.2
  - umap-learn=0.5.2
  - requests=2.27.1
  - deepdish=0.3.7
  - nose=1.3.7
  - sphinx=4.4.0
  - ca-certificates=2021.10.8
  - openssl
  - pip:
    - duecredit==0.9.1
    - future==0.18.2
    - ppca==0.0.4
    - hypertools==0.7.0
    - sphinx==4.4.0
    - timecorr==0.1.5

If you copy that text into a file named "environment.yml", then you can create a new conda environment using conda env create -f environment.yml. To use it, run conda activate tc.

[const7]

It worked. Thanks you!

I also tried to install timecorr on a new machine using different python versions (3.7 and 3.9) with different installation approaches (pip, conda + pip, or environment.yml). All installations under python 3.7 failed with the above problem and everything worked fine under python 3.9. So there may be some compatibility issues with the older python version.

[jeremymanning]

Thanks for the information! I've updated the README to note that only Python 3.9+ is supported for now. I'll leave this issue open until I can explore further and debug.