Problems installing tombo via PIP

[lpryszcz]

Hi, lately I'm getting an error while installing tombo via PIP. A few month ago it worked ok. The same happens in docker container and local machines. Conda package seems to be working ok. Any idea?

(base) test@pavilion:~$ pip install ont-tombo
Collecting ont-tombo
  Using cached https://files.pythonhosted.org/packages/34/6d/f3426707cf097d381dee752b73027920353d4a7744d8bdab696012f1bc8f/ont-tombo-1.5.1.tar.gz
ERROR: Files/directories not found in /tmp/pip-install-8rhz6gmv/ont-tombo/pip-egg-info
(base) test@pavilion:~$ pip install https://github.com/nanoporetech/tombo.git
Collecting https://github.com/nanoporetech/tombo.git
  Downloading https://github.com/nanoporetech/tombo.git
     \ 225kB 1.0MB/s
  ERROR: Cannot unpack file /tmp/pip-unpack-x8u5jrfa/tombo.git (downloaded from /tmp/pip-req-build-b3_erpsj, content-type: text/html; charset=utf-8); cannot detect archive format
ERROR: Cannot determine archive format of /tmp/pip-req-build-b3_erpsj
(base) test@pavilion:~$ git clone https://github.com/nanoporetech/tombo
Cloning into 'tombo'...
remote: Enumerating objects: 725, done.
remote: Counting objects: 100% (14/14), done.
remote: Compressing objects: 100% (11/11), done.
remote: Total 725 (delta 6), reused 7 (delta 3), pack-reused 711
Receiving objects: 100% (725/725), 38.69 MiB | 11.39 MiB/s, done.
Resolving deltas: 100% (339/339), done.
(base) test@pavilion:~$ cd tombo
(base) test@pavilion:~/tombo$ pip install -e .
Obtaining file:///home/test/tombo
ERROR: Files/directories not found in /home/test/tombo/

[lpryszcz]

actually, creating empty .cpp files is enough to build the package.

touch tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp
pip install -e .

[marcus1487]

This is likely due to updates in pip recently (I have experienced similar issues as well). pip is moving to separated build systems from the setup.py file. This has impacts on how cython modules are built (e.g. _c_dynamic_programming.pyx and _c_helper.pyx). I think the best bet at the moment would be to find a version of pip that works and stick with that for tombo installs.