Binder fails to compile pygraphviz

Binder repo help
1

Perhaps some more experienced folk know why Binder fails to build my repository of jupyter notebooks

my requirements.txt file reads:

rdflib>=5.0.0
networkx>=2.6.1
jupyter
graphviz
pygraphviz==1.7

My naive reading of the “Build Logs” (which, frustratingly, can’t be copy/pasted or otherwise stored) suggests that the following are relevant lines:

The build appears to successfully find and obtain pygraphviz;

Collecting pygraphviz--1.7
  Downloading pygraphviz-1.7.zip (118 kB)

however, I note that it is a zip file, not a .whl file like the other requirements are once found. For example:

Collecting rdflib>=5.0.0
  Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)

Once the build process gets around to building pygraphviz, it fails saying:

Building wheel for pygraphviz (setup.py): finished with status 'error'
ERROR: Command errored out with exit status 1:

followed by the log of the attempt to build pygraphviz …
ending thus:

error: command 'gcc' failed with exit status 1
----------------------------------------------
ERROR: Failed building wheel for pygraphviz

Is there anything I can do to persuade Binder to successfully compile this python module?

2

mybinder.org uses repodocker to build images. You can install and run that tool locally to debug your build.

That means pygraphviz isn’t available as a precompiled package for your platform, so instead a zip containing the source for that module is downloaded and compiled.

3

I just tried running %pip install pygraphviz in a running Binder session and saw a couple things.

By default it wanted to get version 1.6.

The install failed and among the errors the following:

Package libcgraph was not found in the pkg-config search path.

This makes me think you need some additional apt packages added. Usually I use the configuration file apt.txt to add these. See here about use of apt.txt.

Try adding apt.txt with the following content based on python - pip install pygraphviz: No package 'libcgraph' found - Stack Overflow

graphviz
libgraphviz-dev
pkg-config
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4

It required a few more adjustments to the requirements.txt file, but adding apt.txt to the repo, exactly as suggested, worked exactly as hoped. Many thanks!

5

A few notes:

  • all of those packages are available on conda-forge
    • all work on all of the conda-forge platforms (including windows and MacOS ARM/M1) out of the box… without invoking a compiler at install time
      • like it or lump it, on MyBinder you’re already running in a conda environment, unless you write your own Dockerfile
  • basically never install jupyter, it brings in mountains of stuff (like qt) that will not improve your binder experience
    • usually, just jupyterlab or notebook are sufficient… and probably with a full minimum version so you don’t get… whatever is installed on binder (by mamba during the repo2docker build)

So a notional environment.yml would be:

channels:
  - conda-forge
dependencies:
  - jupyterlab >=3.0.16,<4 # or `notebook >=6.4,<7` if that's your thing
  - networkx >=2.6.1
  - python-graphviz        # this is the equivalent of pip's `graphviz`
  - pygraphviz ==1.7
  - rdflib >=5.0.0

This would do one mamba solve (instead of apt’s solver, then pip’s solver, then invoking gcc). This is going to be faster/have better cache characteristics than apt.txt + requirements.txt… and have been verified to work by the conda-forge maintainers… and very possibly be faster at runtime because of compiler tuning.

can’t be copy/pasted

If you select some rows, Ctrl+Shift+C will copy the selection, as will Ctrl+Right Click to get the context menu. But I agree, having a “download log” button would be swell. Heck, that could be done entirely in the browser without any server changes.

2 Likes