Potential dependency conflicts between pyensembl and numpy

[NeolithEra]

Hi, as shown in the following full dependency graph of pyensembl, pyensembl requires numpy >=1.7 ， while the installed version of gtfparse(1.2.0) requires numpy >=1.7,<2.0.

According to Pip's “first found wins” installation strategy, numpy 1.18.0 is the actually installed version.

Although the first found package version numpy 1.18.0 just satisfies the later dependency constraint （numpy >=1.7,<2.0), it will lead to a build failure once developers release a newer version of numpy .

Dependency tree--------

pyensembl - 1.8.4
| +- datacache(install version:1.1.5 version range:>=1.1.4)
| | +- appdirs(install version:1.4.3 version range:>=1.4.0)
| | +- mock(install version:3.0.5 version range:*)
| | +- pandas(install version:0.25.3 version range:>=0.15.2)
| | +- progressbar33(install version:2.4 version range:>=2.4)
| | +- requests(install version:2.22.0 version range:>=2.5.1)
| | | +- certifi(install version:2019.11.28 version range:>=2017.4.17)
| | | +- chardet(install version:3.0.4 version range:<3.1.0,>=3.0.2)
| | | +- idna(install version:2.8 version range:>=2.5,<2.9)
| | | +- urllib3(install version:1.25.7 version range:<1.26,>=1.21.1)
| | +- typechecks(install version:0.1.0 version range:>=0.0.2)
| +- gtfparse(install version:1.2.0 version range:>=1.1.0)
| | +- numpy(install version:1.18.0 version range:>=1.7,<2.0)
| | +- pandas(install version:0.25.3 version range:>=0.15)
| +- memoized-property(install version:1.0.3 version range:>=1.0.2)
| +- numpy(install version:1.18.0 version range:>=1.7)
| +- pandas(install version:0.25.3 version range:>=0.15)
| +- serializable(install version:0.2.1 version range:*)
| +- six(install version:1.13.0 version range:>=1.9.0)
| +- tinytimer(install version:0.0.0 version range:*)
| +- typechecks(install version:0.1.0 version range:>=0.0.2)

Thanks for your attention. Best, Neolith

[NeolithEra]

Suggested Solution

1. Fix your direct dependencies to be numpy<2.0. I have checked this revision will not affect your downstream projects now.
2. Ask your upstream project gtfparse to loose the version range of numpy to be >=1.7.

@iskandr Which solution do you prefer, 1 or 2? Please let me know your choice. May I pull a request to solve this issue?

[iskandr]

Hey @NeolithEra -- thanks for pointing this out. I think either solution works and a PR for either one would be greatly appreciated. Your call on which is best.

[iskandr]

Changed gtfparse to 'numpy>=1.7',.