1511878618 commented 2 years ago

Reference Issues/PRs

Fixes #210

What does this implement/fix? Explain your changes

support for loading both local and downloading pdb files, and save at self.raw_dir

What testing did you do to verify the changes in this PR?

Currently, none of this, just test on dataset loader doc notebook.

More changes and complements will be done at tomorrow morning.........

Pull Request Checklist

[ ] Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
[ ] Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
[x] Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
[ ] Ran python -m py.test tests/ and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., python -m py.test tests/protein/test_graphs.py)
[ ] Checked for style issues by running black . and isort .

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a-r-j commented 2 years ago

Awesome work, thanks @1511878618 ! If you merge into #213 the CI pipeline should be much faster & I can push a release to PyPI tonight :)

1511878618 commented 2 years ago

Awesome work, thanks @1511878618 ! If you merge into #213 the CI pipeline should be much faster & I can push a release to PyPI tonight :)

I'm not sure about how to change into #213, and i see master branch is associated with #213. Or, maybe you can help me?

Also, I'm not sure whether are there some potential bugs in it~

codecov-commenter commented 2 years ago

Codecov Report

Base: 40.27% // Head: 48.00% // Increases project coverage by +7.73% :tada:

Coverage data is based on head (07cd92a) compared to base (8123f42). Patch coverage: 51.68% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #214 +/- ## ========================================== + Coverage 40.27% 48.00% +7.73% ========================================== Files 48 86 +38 Lines 2811 5458 +2647 ========================================== + Hits 1132 2620 +1488 - Misses 1679 2838 +1159 ``` | [Impacted Files](https://codecov.io/gh/a-r-j/graphein/pull/214?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | Coverage Δ | | |---|---|---| | [graphein/grn/parse\_trrust.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vZ3JuL3BhcnNlX3RycnVzdC5weQ==) | `37.77% <ø> (ø)` | | | [graphein/ml/diffusion.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvZGlmZnVzaW9uLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ml/transform.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvdHJhbnNmb3JtLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ppi/edges.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL2VkZ2VzLnB5) | `100.00% <ø> (ø)` | | | [graphein/ppi/graph\_metadata.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL2dyYXBoX21ldGFkYXRhLnB5) | `0.00% <ø> (ø)` | | | [graphein/ppi/graphs.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL2dyYXBocy5weQ==) | `54.34% <ø> (ø)` | | | [graphein/ppi/parse\_biogrid.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL3BhcnNlX2Jpb2dyaWQucHk=) | `75.00% <ø> (ø)` | | | [graphein/ppi/visualisation.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL3Zpc3VhbGlzYXRpb24ucHk=) | `0.00% <0.00%> (ø)` | | | [graphein/protein/analysis.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9hbmFseXNpcy5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/protein/edges/intramolecular.py](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9lZGdlcy9pbnRyYW1vbGVjdWxhci5weQ==) | `22.68% <0.00%> (ø)` | | | ... and [79 more](https://codecov.io/gh/a-r-j/graphein/pull/214/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb)

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