ImagingDataCommons/idc-index

pip install from the source tree does not work

Closed this issue · 3 comments

fedorov commented 
!git clone https://github.com/ImagingDataCommons/idc-index
!cd idc-index && git checkout 0.2.6
!python -m pip install -e ./idc-index


from idc_index import index

client = index.IDCClient()

This results in the import error

image

I would think it should work?

Demo notebook (I deleted and reconnected to VM between the two experiments): https://colab.research.google.com/drive/1OdLfAAxmSYFJAZ63_L0W6fvVFw2KbiJX?usp=sharing

vkt1414 commented

!git clone https://github.com/ImagingDataCommons/idc-index
!cd idc-index && git checkout 0.2.6

pip install .

get out of the idc-index directory to force importing from python paths rather than local directory..
and then importing and initializing clients worked for me.

image

jcfr commented

This can be closed. Following the integration of #32, the following test is successful:

$ mkvirtualenv -p python3.9  test-install-from-source
$ git clone https://github.com/ImagingDataCommons/idc-index.git /tmp/idc-index
$ pip install idc-index
$ python -c "from idc_index import index; client = index.IDCClient()"

Index file not found. Downloading latest version of the index file. This will take a minute or so.
Index file downloaded.
NAME:
   s5cmd - Blazing fast S3 and local filesystem execution tool

USAGE:
   s5cmd [global options] command [command options] [arguments...]

COMMANDS:
   ls              list buckets and objects
   cp              copy objects
   rm              remove objects
...

Note that in the example above, the -e is not specified. This is on purpose as creating a editable install would work to disable build isolation as described at https://scikit-build-core.readthedocs.io/en/latest/configuration.html#editable-installs

Last, in the context of notebook and tutorials, I now recommend to simply install the wheel.

jcfr commented

While running the test described above in #15 (comment), I also noticed that the output of s5cmd --help was always displayed.

This is now fixed in:

  • 👍1