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Prep for 1.7.0 release #292

Merged
merged 4 commits into from
Apr 7, 2023
Merged

Prep for 1.7.0 release #292

merged 4 commits into from
Apr 7, 2023

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a-r-j
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@a-r-j a-r-j commented Mar 31, 2023

Reference Issues/PRs

What does this implement/fix? Explain your changes

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

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)
  • 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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Codecov Report

Patch coverage: 39.87% and project coverage change: +3.60 🎉

Comparison is base (8123f42) 40.27% compared to head (1b13ab4) 43.87%.

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Additional details and impacted files
@@            Coverage Diff             @@
##           master     #292      +/-   ##
==========================================
+ Coverage   40.27%   43.87%   +3.60%     
==========================================
  Files          48      113      +65     
  Lines        2811     7718    +4907     
==========================================
+ Hits         1132     3386    +2254     
- Misses       1679     4332    +2653     
Impacted Files Coverage Δ
graphein/ml/datasets/foldcomp_dataset.py 0.00% <0.00%> (ø)
graphein/ml/diffusion.py 0.00% <0.00%> (ø)
graphein/ml/metrics/__init__.py 0.00% <0.00%> (ø)
graphein/ml/metrics/gdt.py 0.00% <0.00%> (ø)
graphein/ml/metrics/tm_score.py 0.00% <0.00%> (ø)
graphein/ppi/graph_metadata.py 0.00% <0.00%> (ø)
graphein/ppi/visualisation.py 0.00% <0.00%> (ø)
graphein/protein/analysis.py 0.00% <0.00%> (ø)
graphein/protein/features/utils.py 27.77% <0.00%> (ø)
graphein/protein/folding_utils.py 0.00% <0.00%> (ø)
... and 95 more

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sonarcloud bot commented Apr 3, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@a-r-j a-r-j merged commit c1628a9 into master Apr 7, 2023
amorehead pushed a commit to amorehead/graphein that referenced this pull request Apr 18, 2023
* update version string

* update readme

* update doc version

* update changelog
a-r-j added a commit that referenced this pull request Apr 22, 2023
…st PDB model, and merging-in latest updates from `master` (#309)

* Fix graph sequence (atomistic graphs in `initialise_graph_with_metadata` had duplicated residues)  (#268)

* Fix param name typo in function docstring

* fix: atomistic graph only has sequence residues for CA atom in `initialise_graph_with_metadata`

* fix: avoid changing dataframe when extracting rows

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* add: test sequence feature in graphs

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* fix graph sequence feature (#268)

* fix matplotlib deprecation

* fix test bug

* change build to ubuntu-latest

* remove unecessary selection

---------

Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Arian Jamasb <arjamasb@gmail.com>

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* After fixing merge conflicts, add more filters and add time-based splits

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* clean up unused files and move docs from root (#276)

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* Switch to miniconda for build (#278)

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* Improve altloc handling (#263)

* Fix bug in `add_k_nn_edges`.

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Co-authored-by: Arian Jamasb <arjamasb@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Df processing #216 (#222)

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Co-authored-by: Cam <73625486+kamurani@users.noreply.github.com>
Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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a-r-j added a commit that referenced this pull request Apr 28, 2023
…st PDB model, and merging-in latest updates from `master` (#311)

* add PDB manager #270

* add download method

* add clustering utilities

* `PDBManager` - Bug fixes, adding necessary changes to export only first PDB model, and merging-in latest updates from `master` (#309)

* Fix graph sequence (atomistic graphs in `initialise_graph_with_metadata` had duplicated residues)  (#268)

* Fix param name typo in function docstring

* fix: atomistic graph only has sequence residues for CA atom in `initialise_graph_with_metadata`

* fix: avoid changing dataframe when extracting rows

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix matplotlib deprecation

* fix test bug

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* remove unecessary selection

---------

Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Arian Jamasb <arjamasb@gmail.com>

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