sawnergy 1.0.0__tar.gz → 1.0.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (31) hide show
  1. {sawnergy-1.0.0/sawnergy.egg-info → sawnergy-1.0.2}/PKG-INFO +7 -20
  2. {sawnergy-1.0.0 → sawnergy-1.0.2}/README.md +6 -19
  3. {sawnergy-1.0.0 → sawnergy-1.0.2/sawnergy.egg-info}/PKG-INFO +7 -20
  4. {sawnergy-1.0.0 → sawnergy-1.0.2}/LICENSE +0 -0
  5. {sawnergy-1.0.0 → sawnergy-1.0.2}/NOTICE +0 -0
  6. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/__init__.py +0 -0
  7. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/embedding/SGNS_pml.py +0 -0
  8. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/embedding/SGNS_torch.py +0 -0
  9. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/embedding/__init__.py +0 -0
  10. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/embedding/embedder.py +0 -0
  11. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/logging_util.py +0 -0
  12. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/rin/__init__.py +0 -0
  13. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/rin/rin_builder.py +0 -0
  14. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/rin/rin_util.py +0 -0
  15. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/sawnergy_util.py +0 -0
  16. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/visual/__init__.py +0 -0
  17. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/visual/visualizer.py +0 -0
  18. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/visual/visualizer_util.py +0 -0
  19. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/walks/__init__.py +0 -0
  20. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/walks/walker.py +0 -0
  21. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/walks/walker_util.py +0 -0
  22. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy.egg-info/SOURCES.txt +0 -0
  23. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy.egg-info/dependency_links.txt +0 -0
  24. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy.egg-info/requires.txt +0 -0
  25. {sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy.egg-info/top_level.txt +0 -0
  26. {sawnergy-1.0.0 → sawnergy-1.0.2}/setup.cfg +0 -0
  27. {sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_embedding.py +0 -0
  28. {sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_rin.py +0 -0
  29. {sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_storage.py +0 -0
  30. {sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_visual.py +0 -0
  31. {sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_walks.py +0 -0
{sawnergy-1.0.0/sawnergy.egg-info → sawnergy-1.0.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: sawnergy
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- Version: 1.0.0
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+ Version: 1.0.2
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  Summary: Toolkit for transforming molecular dynamics (MD) trajectories into rich graph representations
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  Home-page: https://github.com/Yehor-Mishchyriak/SAWNERGY
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  Author: Yehor Mishchyriak
@@ -71,6 +71,12 @@ node indexing, and RNG seeds stay consistent across the toolchain.
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  ---
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+ ## Small visual example (constructed fully from trajectory and topology files)
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+ ![rin](https://github.com/Yehor-Mishchyriak/SAWNERGY/blob/main/assets/rin.png)
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+ ![embedding](https://github.com/Yehor-Mishchyriak/SAWNERGY/blob/main/assets/embedding.png)
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+
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+ ---
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  ## Core Components
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  ### `sawnergy.rin.RINBuilder`
@@ -249,24 +255,6 @@ v.build_frame(1,
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  ---
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- ## Testing & Quality Assurance
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-
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- The automated test suite (`pytest`) synthesises deterministic cpptraj outputs and exercises the entire workflow:
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-
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- - RIN parsing, residue aggregation, and metadata verification.
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- - Random/self-avoiding walk sampling and probability consistency with the RIN.
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- - Embedding orchestration, frame ordering, SGNS pair generation property tests.
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- - PureML and PyTorch SGNS smoke tests verifying finite weights and decreasing loss.
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- - Visualiser smoke tests that cover data loading and artist updates.
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-
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- Run the suite (inside the project virtualenv):
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-
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- ```bash
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- python -m pytest
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- ```
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-
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- ---
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-
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  ## Project Structure
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  ```
@@ -277,7 +265,6 @@ python -m pytest
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  │ ├── visual/ # Visualizer and palette utilities
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  │ ├── logging_util.py
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  │ └── sawnergy_util.py
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- ├── tests/ # Synthetic end-to-end tests (pytest)
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  │
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  └── README.md
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  ```
{sawnergy-1.0.0 → sawnergy-1.0.2}/README.md RENAMED
@@ -40,6 +40,12 @@ node indexing, and RNG seeds stay consistent across the toolchain.
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  ---
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+ ## Small visual example (constructed fully from trajectory and topology files)
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+ ![rin](https://github.com/Yehor-Mishchyriak/SAWNERGY/blob/main/assets/rin.png)
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+ ![embedding](https://github.com/Yehor-Mishchyriak/SAWNERGY/blob/main/assets/embedding.png)
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+
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+ ---
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+
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  ## Core Components
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  ### `sawnergy.rin.RINBuilder`
@@ -218,24 +224,6 @@ v.build_frame(1,
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  ---
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- ## Testing & Quality Assurance
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-
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- The automated test suite (`pytest`) synthesises deterministic cpptraj outputs and exercises the entire workflow:
224
-
225
- - RIN parsing, residue aggregation, and metadata verification.
226
- - Random/self-avoiding walk sampling and probability consistency with the RIN.
227
- - Embedding orchestration, frame ordering, SGNS pair generation property tests.
228
- - PureML and PyTorch SGNS smoke tests verifying finite weights and decreasing loss.
229
- - Visualiser smoke tests that cover data loading and artist updates.
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-
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- Run the suite (inside the project virtualenv):
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-
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- ```bash
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- python -m pytest
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- ```
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-
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- ---
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-
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  ## Project Structure
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  ```
@@ -246,7 +234,6 @@ python -m pytest
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  │ ├── visual/ # Visualizer and palette utilities
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  │ ├── logging_util.py
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  │ └── sawnergy_util.py
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- ├── tests/ # Synthetic end-to-end tests (pytest)
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  │
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  └── README.md
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  ```
{sawnergy-1.0.0 → sawnergy-1.0.2/sawnergy.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: sawnergy
3
- Version: 1.0.0
3
+ Version: 1.0.2
4
4
  Summary: Toolkit for transforming molecular dynamics (MD) trajectories into rich graph representations
5
5
  Home-page: https://github.com/Yehor-Mishchyriak/SAWNERGY
6
6
  Author: Yehor Mishchyriak
@@ -71,6 +71,12 @@ node indexing, and RNG seeds stay consistent across the toolchain.
71
71
 
72
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  ---
73
73
 
74
+ ## Small visual example (constructed fully from trajectory and topology files)
75
+ ![rin](https://github.com/Yehor-Mishchyriak/SAWNERGY/blob/main/assets/rin.png)
76
+ ![embedding](https://github.com/Yehor-Mishchyriak/SAWNERGY/blob/main/assets/embedding.png)
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+
78
+ ---
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+
74
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  ## Core Components
75
81
 
76
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  ### `sawnergy.rin.RINBuilder`
@@ -249,24 +255,6 @@ v.build_frame(1,
249
255
 
250
256
  ---
251
257
 
252
- ## Testing & Quality Assurance
253
-
254
- The automated test suite (`pytest`) synthesises deterministic cpptraj outputs and exercises the entire workflow:
255
-
256
- - RIN parsing, residue aggregation, and metadata verification.
257
- - Random/self-avoiding walk sampling and probability consistency with the RIN.
258
- - Embedding orchestration, frame ordering, SGNS pair generation property tests.
259
- - PureML and PyTorch SGNS smoke tests verifying finite weights and decreasing loss.
260
- - Visualiser smoke tests that cover data loading and artist updates.
261
-
262
- Run the suite (inside the project virtualenv):
263
-
264
- ```bash
265
- python -m pytest
266
- ```
267
-
268
- ---
269
-
270
258
  ## Project Structure
271
259
 
272
260
  ```
@@ -277,7 +265,6 @@ python -m pytest
277
265
  │ ├── visual/ # Visualizer and palette utilities
278
266
  │ ├── logging_util.py
279
267
  │ └── sawnergy_util.py
280
- ├── tests/ # Synthetic end-to-end tests (pytest)
281
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  │
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  └── README.md
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  ```
{sawnergy-1.0.0 → sawnergy-1.0.2}/LICENSE RENAMED
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{sawnergy-1.0.0 → sawnergy-1.0.2}/NOTICE RENAMED
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{sawnergy-1.0.0 → sawnergy-1.0.2}/sawnergy/__init__.py RENAMED
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{sawnergy-1.0.0 → sawnergy-1.0.2}/setup.cfg RENAMED
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{sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_rin.py RENAMED
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{sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_storage.py RENAMED
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{sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_visual.py RENAMED
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{sawnergy-1.0.0 → sawnergy-1.0.2}/tests/test_walks.py RENAMED
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