Add openproblems-cli test instructions

[scottgigante]

@LuckyMD want to try these instructions out and let me know how you do?

[codecov]

Codecov Report

Base: 94.20% // Head: 94.72% // Increases project coverage by +0.51% 🎉

Coverage data is based on head (50ee4d4) compared to base (23cdfe5).
Patch has no changes to coverable lines.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #557      +/-   ##
==========================================
+ Coverage   94.20%   94.72%   +0.51%     
==========================================
  Files         116      142      +26     
  Lines        3018     3618     +600     
  Branches      157      188      +31     
==========================================
+ Hits         2843     3427     +584     
- Misses        119      126       +7     
- Partials       56       65       +9     

Flag	Coverage Δ
unittests	94.72% <ø> (+0.51%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
openproblems/data/sample.py	100.00% <0.00%> (ø)
openproblems/tools/normalize.py	100.00% <0.00%> (ø)
openproblems/data/immune_cells.py	100.00% <0.00%> (ø)
openproblems/tasks/label_projection/api.py	100.00% <0.00%> (ø)
openproblems/tasks/denoising/methods/magic.py	100.00% <0.00%> (ø)
openproblems/tasks/spatial_decomposition/api.py	100.00% <0.00%> (ø)
...lems/tasks/spatial_decomposition/datasets/utils.py	96.07% <0.00%> (ø)
...ks/label_projection/datasets/tabula_muris_senis.py	100.00% <0.00%> (ø)
.../_batch_integration/batch_integration_graph/api.py	100.00% <0.00%> (ø)
...integration/batch_integration_graph/methods/mnn.py	100.00% <0.00%> (ø)
... and 36 more

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[scottgigante-immunai]

cc @mxposed

[mxposed]

A few things I ran into when testing for the Seurat branch:

1. AWS cli can accommodate different credentials/settings via --profile option. Should I add it's use to the instructions?
2. I am on zsh and the run-instances command needed some patching to run: escape newlines, and different syntax for OWNER_NAME substitution. How best to handle this?
3. Inside the image, pip install -e . didn't finish successfully, with this kind of error. I ended up installing python3-venv, creating a virtualenv and installing openproblems inside it. Is this a know problem or sideeffect?

[scottgigante-immunai]

1. AWS cli can accommodate different credentials/settings via --profile option. Should I add it's use to the instructions?

Yes please!

2. I am on zsh and the run-instances command needed some patching to run: escape newlines, and different syntax for OWNER_NAME substitution. How best to handle this?

Easiest thing is probably just to switch to bash :) Maybe just add a note to the README explaining that these commands are designed for bash.

3. Inside the image, pip install -e . didn't finish successfully, with this kind of error. I ended up installing python3-venv, creating a virtualenv and installing openproblems inside it. Is this a know problem or sideeffect?

You shouldn't need a venv... can you share the full command and logs with me so I can try to replicate?

[mxposed]

1. AWS cli can accommodate different credentials/settings via --profile option. Should I add it's use to the instructions?

Yes please!

I don't think I can push directly to this pull request, so I created another one: scottgigante-immunai#4

2. I am on zsh and the run-instances command needed some patching to run: escape newlines, and different syntax for OWNER_NAME substitution. How best to handle this?

Easiest thing is probably just to switch to bash :) Maybe just add a note to the README explaining that these commands are designed for bash.

Added this to EC2.md

3. Inside the image, pip install -e . didn't finish successfully, with this kind of error. I ended up installing python3-venv, creating a virtualenv an
   d installing openproblems inside it. Is this a know problem or sideeffect?

You shouldn't need a venv... can you share the full command and logs with me so I can try to replicate?

Just tested, the problem still persists for me, please see the attached log. I'm not sure what is the source of the problem, but I suspect some bad interaction between pip and setuptools?
log.txt

[scottgigante-immunai]

log.txt

Ah! You need to be inside a docker image. I updated the instructions.

[mxposed]

log.txt

Ah! You need to be inside a docker image. I updated the instructions.

Great, thanks!

[scottgigante-immunai]

Happy for me to merge?