Installation with newer version of `matplotlib`: "`ValueError: Passing a Normalize instance simultaneously with vmin/vmax is not supported.`"

[kalavattam]

Welcome to the HiCExplorer GitHub repository! Before opening the issue please check that the following requirements are met:

• [x] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below.

  • Issue 764
  • Issue 840

• [x] Paste your HiCExplorer version (hicInfo --version) and your python version (python --version) below.

  
  #  I. Initial environment in which I encountered the bug (described below)
  #  ### Encounter bug ###
  ❯ echo "${CONDA_DEFAULT_ENV}"
  hicexplorer_env

❯ hicexplorer --version hicexplorer 3.7.2

❯ mamba list | grep matplotlib-base matplotlib-base 3.6.2 py310h8d5ebf3_0 conda-forge

❯ mamba list | grep python biopython 1.81 py310h1fa729e_0 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bx-python 0.10.0 py310h551a815_0 bioconda ipython 8.16.0 pyh0d859eb_0 conda-forge msgpack-python 1.0.6 py310hd41b1e2_0 conda-forge python 3.10.12 hd12c33a_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-graphviz 0.20.1 pyh22cad53_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge

II. Test environment with installation per this comment:

https://github.com/deeptools/HiCExplorer/issues/764#issuecomment-985617076

Still encounter bug

❯ echo "${CONDA_DEFAULT_ENV}" hicexplorer_test_env_1

❯ hicexplorer --version hicexplorer 3.7.2

❯ mamba list | grep matplotlib-base matplotlib-base 3.5.3 py37hf395dca_2 conda-forge

❯ mamba list | grep python biopython 1.79 py37h540881e_2 conda-forge bx-python 0.9.0 py37hfa8f21c_1 bioconda ipython 7.33.0 py37h89c1867_0 conda-forge msgpack-python 1.0.4 py37h7cecad7_0 conda-forge python 3.7.12 hf930737_100_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-graphviz 0.20.1 pyh22cad53_0 conda-forge python-lzo 1.14 py37hd06c622_1 conda-forge python_abi 3.7 4_cp37m conda-forge

III. Test environment with installation per this comment:

https://github.com/deeptools/HiCExplorer/issues/764#issuecomment-985631158

No longer encounter bug

❯ echo "${CONDA_DEFAULT_ENV}" hicexplorer_test_env_2

❯ hicexplorer --version hicexplorer 3.7.2

❯ mamba list | grep matplotlib-base matplotlib-base 3.2.2 py37h1d35a4c_1 conda-forge

❯ mamba list | grep python biopython 1.79 py37h540881e_2 conda-forge bx-python 0.9.0 py37hfa8f21c_1 bioconda ipython 7.33.0 py37h89c1867_0 conda-forge msgpack-python 1.0.4 py37h7cecad7_0 conda-forge python 3.7.12 hf930737_100_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-graphviz 0.20.1 pyh22cad53_0 conda-forge python-lzo 1.14 py37hd06c622_1 conda-forge python_abi 3.7 4_cp37m conda-forge

- [x] Have you checked our documentation on [hicexplorer.readthedocs.io](https://hicexplorer.readthedocs.io)?
- [x] Do you use [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html) to install HiCExplorer? 
```bash
#  I. Installation command for initial environment
#  ### Encounter bug ###
mamba create \
    -n hicexplorer_env \
    -c conda-forge -c bioconda \
        hicexplorer=3.7.2=pyhdfd78af_1

#  II. Installation command for initial environment
#  ### Encounter bug ###
mamba create \
    -n hicexplorer_test_env_1 \
    -c bioconda -c conda-forge \
        hicexplorer=3.7.2 \
        python=3.7

#  III. Installation command for initial environment
#  ### No longer encounter bug ###
mamba create \
    -n hicexplorer_test_env_2 \
    -c bioconda -c conda-forge \
        hicexplorer=3.7.2 \
        python=3.7 \
        matplotlib=3.2.2

• [x] Do you use the latest HiCExplorer release? If not, please install it via a conda environment: conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge and activate the environment: conda activate hicexplorer. Retry your command. You can exit a conda environment via conda deactivate. To learn more about conda and environments, please consider the following documentation.

Retry your command, is it solved now? If not please continue with the following:

• [x] Paste the full HiCExplorer command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).

  
  #  Command that gives rise to error message in `hicexplorer_env` and
  #  `hicexplorer_test_env_1`, but works in `hicexplorer_test_env_2`
  dir="path/to/directory/containing/cool/files"
  cool="specific_file.cool"

Working with S. cerevisiae, so chromosomes have roman-numeral names

hicPlotMatrix \ --chromosomeOrder I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI \ --colorMap "PuRd" \ --log \ --vMin 0.0001 \ --vMax 1 \ --matrix "${dir}/${cool}" \ --outFileName "test.pdf"

Bug seems to arise from invocation of --vMin ${value_floor} and --vMax

${value_celing} with the flag --log; however, it's expected that this should

work and, indeed, did work when I used earlier versions of HiCExplorer

- [x] Paste the output printed on screen from the command that produces the issue
  below (ignore if you simply spotted the issue in the code/documentation).
```txt
❯ echo "${CONDA_DEFAULT_ENV}"
hicexplorer_env  # Same error with hicexplorer_test_env_1

❯ hicPlotMatrix \
>     --chromosomeOrder I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI \
>     --colorMap "PuRd" \
>     --log \
>     --vMin 0.0001 \
>     --vMax 1 \
>     --matrix "${dir}/${cool}" \
>     --outFileName "test.pdf"
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:min: 2.0356669271154623e-05, max: 0.32483315613704933

Traceback (most recent call last):
  File "/home/kalavatt/miniconda3/envs/hicexplorer_env/bin/hicPlotMatrix", line 7, in <module>
    main()
  File "/home/kalavatt/miniconda3/envs/hicexplorer_env/lib/python3.10/site-packages/hicexplorer/hicPlotMatrix.py", line 820, in main
    plotHeatmap(matrix, ma.get_chromosome_sizes(), fig, position,
  File "/home/kalavatt/miniconda3/envs/hicexplorer_env/lib/python3.10/site-packages/hicexplorer/hicPlotMatrix.py", line 244, in plotHeatmap
    img3 = axHeat2.pcolormesh(
  File "/home/kalavatt/miniconda3/envs/hicexplorer_env/lib/python3.10/site-packages/matplotlib/__init__.py", line 1423, in inner
    return func(ax, *map(sanitize_sequence, args), **kwargs)
  File "/home/kalavatt/miniconda3/envs/hicexplorer_env/lib/python3.10/site-packages/matplotlib/axes/_axes.py", line 6174, in pcolormesh
    collection._scale_norm(norm, vmin, vmax)
  File "/home/kalavatt/miniconda3/envs/hicexplorer_env/lib/python3.10/site-packages/matplotlib/cm.py", line 436, in _scale_norm
    raise ValueError(
ValueError: Passing a Normalize instance simultaneously with vmin/vmax is not supported.  Please pass vmin/vmax directly to the norm when creating it.

❯ echo "${CONDA_DEFAULT_ENV}"
hicexplorer_test_env_2

❯ hicPlotMatrix \
>     --chromosomeOrder I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI \
>     --colorMap "PuRd" \
>     --log \
>     --vMin 0.0001 \
>     --vMax 1 \
>     --matrix "${dir}/${cool}" \
>     --outFileName "test.pdf"
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:min: 2.0356669271154623e-05, max: 0.32483315613704933

Workaround

When installing hicexplorer via conda or mamba, explicitly specify an older version of matplotlib per the developer comment here: matplotlib >=3.1.1,<=3.2.2

Example installation call to avoid bug

mamba create \
    -n hicexplorer_test_env_2 \
    -c bioconda -c conda-forge \
        hicexplorer=3.7.2 \
        python=3.7 \
        matplotlib=3.2.2

[joachimwolff]

I published today a maintenance update version 3.7.3 which should fix this issue.