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Converted paste into a command #68

Merged
merged 13 commits into from
Oct 22, 2024
Merged

Converted paste into a command #68

merged 13 commits into from
Oct 22, 2024

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anushka255
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@anushka255 anushka255 commented Oct 17, 2024

  • Converted paste to a command
  • Added io submodule to process input files
  • Added test cases for added helper functions
  • Added new test files (slice*.h5ad1). Each of these files hold the same information as slice*.csv and slice*_coor.csv. This was just added to ensure that files that hold same information but are of different types provide same computational results

@anushka255 anushka255 marked this pull request as draft October 17, 2024 16:46
@anushka255 anushka255 changed the title Aa/api Converted paste into command line argument Oct 22, 2024
@anushka255 anushka255 marked this pull request as ready for review October 22, 2024 16:23
@anushka255 anushka255 changed the title Converted paste into command line argument Converted paste into a command Oct 22, 2024
@@ -51,7 +51,7 @@ jobs:
- name: Pytest with coverage
if: matrix.os == 'ubuntu-latest'
# Note: Use of pytest -n .. (pytest-xdist) does not work with coverage
run: coverage run --source=src/paste3 -m pytest
run: coverage run --source=src/paste3 --omit="*/__main__.py" -m pytest
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can we just add a test to check the execution of the main function in __main__.py (or even just if {sys.executable} paste3 --version will work? In any case, let's not make exceptions like this (let coverage go down if it must).

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Added a test to check version number and got rid of the --omit....

@vineetbansal
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vineetbansal commented Oct 22, 2024

We have some .h5ad files in tests/data/input already. Can we rename these and have the new tests pass? (modifying old tests if we need to). I'm a bit wary of introducing more binary files in the data folder than we already have in there (especially if the purpose is simply to make sure that the new api picks up the files based on their names).

@anushka255 anushka255 merged commit 7b298ed into main Oct 22, 2024
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2 participants