Refactor

[RiesBen]

This branch shall lead to package v1.0 . It will not change anything on the implementations, but refactor the code.

• [x] Readme Improvements.
• [x] src:
  • [x] Code style
  • [x] Typing
  • [x] Docsstrings
  • [x] Added JCS like in publication
  • [x] Add Test for JCS

[pep8speaks]

Hello @RiesBen! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2023-11-10 23:18:39 UTC

[codecov[bot]]

Codecov Report

Attention: 9 lines in your changes are missing coverage. Please review.

Comparison is base (ea612b1) 92.91% compared to head (5cc521e) 96.50%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #17 +/- ## ========================================== + Coverage 92.91% 96.50% +3.59% ========================================== Files 12 13 +1 Lines 536 572 +36 ========================================== + Hits 498 552 +54 + Misses 38 20 -18 ``` | [Files](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy) | Coverage Δ | | |---|---|---| | [src/kartograf/\_\_init\_\_.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9fX2luaXRfXy5weQ==) | `100.00% <100.00%> (ø)` | | | [src/kartograf/atom\_aligner.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9hdG9tX2FsaWduZXIucHk=) | `100.00% <100.00%> (ø)` | | | [src/kartograf/atom\_mapping\_scorer.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9hdG9tX21hcHBpbmdfc2NvcmVyLnB5) | `100.00% <100.00%> (ø)` | | | [src/kartograf/filters/element\_change.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9maWx0ZXJzL2VsZW1lbnRfY2hhbmdlLnB5) | `100.00% <100.00%> (ø)` | | | [src/kartograf/filters/ring\_changes.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9maWx0ZXJzL3JpbmdfY2hhbmdlcy5weQ==) | `100.00% <100.00%> (ø)` | | | [src/kartograf/mapping\_metrics/\_\_init\_\_.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9tYXBwaW5nX21ldHJpY3MvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [src/kartograf/mapping\_metrics/\_abstract\_scorer.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9tYXBwaW5nX21ldHJpY3MvX2Fic3RyYWN0X3Njb3Jlci5weQ==) | `93.33% <100.00%> (ø)` | | | [...c/kartograf/mapping\_metrics/metric\_mapping\_rmsd.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9tYXBwaW5nX21ldHJpY3MvbWV0cmljX21hcHBpbmdfcm1zZC5weQ==) | `100.00% <100.00%> (ø)` | | | [...c/kartograf/mapping\_metrics/metric\_volume\_ratio.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9tYXBwaW5nX21ldHJpY3MvbWV0cmljX3ZvbHVtZV9yYXRpby5weQ==) | `97.05% <100.00%> (ø)` | | | [...raf/mapping\_metrics/metrics\_mapping\_comparisons.py](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#diff-c3JjL2thcnRvZ3JhZi9tYXBwaW5nX21ldHJpY3MvbWV0cmljc19tYXBwaW5nX2NvbXBhcmlzb25zLnB5) | `100.00% <100.00%> (ø)` | | | ... and [2 more](https://app.codecov.io/gh/OpenFreeEnergy/kartograf/pull/17?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy) | |

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[RiesBen]

@richardjgowers Hej, I did some refactoring that I think was quite necessary! Do you have additional points ? :) Maybe we can put additional points in another PR .