Installation issues with cyvcf2 on Ubuntu 16.04 LTS

I was trying to install this on Ubuntu 16.04

pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt

I got the following issues:

1. curl.h missing

    htslib/hfile_s3_write.c:86:23: fatal error: curl/curl.h: No such file or directory
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------

This was fixed with: (we install this in CI)

sudo apt install -y libcurl4-openssl-dev

2. bzlib.h missing

...
    htslib/cram/cram_io.c:53:19: fatal error: bzlib.h: No such file or directory
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------

This was fixed with:

sudo apt-get install libbz2-dev

Then this:

3. lzma.h missing

...
    htslib/cram/cram_io.c:57:18: fatal error: lzma.h: No such file or directory
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------

This was fixed with:

apt-get install liblzma-dev

I guess, we don’t see this in the CI, because these are already present, also we have Ubuntu 18.04 in the CI:

Although these are linux specific, I think, we can probably worth mentioning these in the docs and also we install libcurl4-openssl-dev in the CI: https://github.com/pystatgen/sgkit/blob/162447e20e6b680f35730047f0d28a7064d079bc/.github/workflows/build.yml#L22

its not mentioned in the contributing docs either: https://pystatgen.github.io/sgkit/contributing.html#install

[horta]

Right now cyvcf2 wheel is being built against ssl 1.1.x on Linux (although the wheels are not in test pypi yet, explained in the above link), which should work in machines with both 1.0.x and 1.1.x as far as I tested. So the problem is not exactly the difference in ssl version but linking it against deprecated ssl 1.0.x version (I think Python 3.5 dropped its support of ssl 1.0.x).

In summary, the problem seems to be solved, I just can’t try it on Travis CI because I have no OSS credits anymore for this month.

[horta]

@jeromekelleher is correct in that cibuildwheel already takes care of that. In fact, libss, libcurl, alongside with htslib are included in the wheels. I’ve just updated the issue https://github.com/brentp/cyvcf2/pull/175 with some findings and (it seems so) the solution.