spatialrna 0.3.0.dev1__tar.gz → 0.3.0.dev3__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 (24) hide show
  1. spatialrna-0.3.0.dev3/PKG-INFO +57 -0
  2. spatialrna-0.3.0.dev3/README.md +31 -0
  3. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/pyproject.toml +8 -6
  4. spatialrna-0.3.0.dev3/src/spatialrna.egg-info/PKG-INFO +57 -0
  5. spatialrna-0.3.0.dev1/PKG-INFO +0 -34
  6. spatialrna-0.3.0.dev1/README.md +0 -10
  7. spatialrna-0.3.0.dev1/src/spatialrna.egg-info/PKG-INFO +0 -34
  8. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/setup.cfg +0 -0
  9. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/__init__.py +0 -0
  10. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/cluster.py +0 -0
  11. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/datasets.py +0 -0
  12. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/graph_build.py +0 -0
  13. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/graph_zarr_io.py +0 -0
  14. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/readers.py +0 -0
  15. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/train_val.py +0 -0
  16. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna/viz.py +0 -0
  17. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna.egg-info/SOURCES.txt +0 -0
  18. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna.egg-info/dependency_links.txt +0 -0
  19. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna.egg-info/requires.txt +0 -0
  20. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/src/spatialrna.egg-info/top_level.txt +0 -0
  21. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/tests/test_cluster_viz.py +0 -0
  22. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/tests/test_readers.py +0 -0
  23. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/tests/test_tiling.py +0 -0
  24. {spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/tests/test_zarr_roundtrip.py +0 -0
spatialrna-0.3.0.dev3/PKG-INFO ADDED
@@ -0,0 +1,57 @@
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+ Metadata-Version: 2.4
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+ Name: spatialrna
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+ Version: 0.3.0.dev3
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+ Summary: A package for spatial RNA graph data processing and analysis.
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+ Author: Yan Pan, Ruqian Lyu
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+ Maintainer-email: Yan Pan <anne.pan@svi.edu.au>
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+ License: MIT
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ Requires-Dist: numpy
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+ Requires-Dist: pandas
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+ Requires-Dist: scipy
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+ Requires-Dist: zarr>=3
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+ Requires-Dist: numcodecs
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+ Requires-Dist: tqdm
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+ Requires-Dist: scikit-learn
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+ Requires-Dist: matplotlib
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+ Provides-Extra: gnn
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+ Requires-Dist: torch; extra == "gnn"
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+ Requires-Dist: torch_geometric; extra == "gnn"
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+ Provides-Extra: dev
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+ Requires-Dist: pytest; extra == "dev"
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+
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+ # spatialrna
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+
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+ A package that provides an easier interface for building graph data from spatial transcriptomics data.
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+
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+
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+ ## Prerequisites
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+
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+ Create a conda environment with Python >= 3.10:
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+
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+ ```bash
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+ conda create -n spatialrna python=3.10
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+ conda activate spatialrna
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+ ```
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+
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+ To use the graphs with GNN models, also install PyTorch and PyTorch Geometric matching your CUDA version (see the PyTorch and PyG installation guides).
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install spatialrna
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+ ```
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+
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+ Development pre-release (0.3.x):
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+
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+ ```bash
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+ pip install --pre spatialrna
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+ ```
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+
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+ ## Documentation
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+
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+ Documentation is available at https://ruqianl.github.io/spatialrna_docs/
spatialrna-0.3.0.dev3/README.md ADDED
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+ # spatialrna
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+
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+ A package that provides an easier interface for building graph data from spatial transcriptomics data.
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+
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+
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+ ## Prerequisites
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+
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+ Create a conda environment with Python >= 3.10:
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+
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+ ```bash
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+ conda create -n spatialrna python=3.10
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+ conda activate spatialrna
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+ ```
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+
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+ To use the graphs with GNN models, also install PyTorch and PyTorch Geometric matching your CUDA version (see the PyTorch and PyG installation guides).
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install spatialrna
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+ ```
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+
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+ Development pre-release (0.3.x):
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+
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+ ```bash
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+ pip install --pre spatialrna
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+ ```
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+
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+ ## Documentation
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+
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+ Documentation is available at https://ruqianl.github.io/spatialrna_docs/
{spatialrna-0.3.0.dev1 → spatialrna-0.3.0.dev3}/pyproject.toml RENAMED
@@ -3,18 +3,19 @@ requires = ["setuptools>=68"]
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  build-backend = "setuptools.build_meta"
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  [project]
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- name = "spatialrna"
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- version = "0.3.0.dev1"
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- description = "Spatial RNA graph data processing and analysis for iST (Xenium / Atera): graphs, GNN training / embedding, clustering, spatial maps."
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+ name="spatialrna"
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+ description = "A package for spatial RNA graph data processing and analysis."
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  readme = "README.md"
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- requires-python = ">=3.12"
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- authors = [{ name = "Anne Pan", email = "anne.pan@svi.edu.au" }]
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+ version = "0.3.0.dev3"
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+ authors = [{ name = "Yan Pan" }, { name = "Ruqian Lyu" }]
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+ maintainers = [{ name = "Yan Pan", email = "anne.pan@svi.edu.au" }]
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+ license = { text = "MIT" }
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+ requires-python = ">=3.10"
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  classifiers = [
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  "Programming Language :: Python :: 3",
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  "Operating System :: OS Independent",
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  "Topic :: Scientific/Engineering :: Bio-Informatics",
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  ]
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- # Core: readers, graph builders, clustering, maps. No torch needed.
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  dependencies = [
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  "numpy",
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  "pandas",
@@ -26,6 +27,7 @@ dependencies = [
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  "matplotlib",
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  ]
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+
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  [project.optional-dependencies]
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  # SpatialRNA dataset, datasets, train_val. Install torch and the PyG wheels matching
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  # your CUDA first -- see README.
spatialrna-0.3.0.dev3/src/spatialrna.egg-info/PKG-INFO ADDED
@@ -0,0 +1,57 @@
1
+ Metadata-Version: 2.4
2
+ Name: spatialrna
3
+ Version: 0.3.0.dev3
4
+ Summary: A package for spatial RNA graph data processing and analysis.
5
+ Author: Yan Pan, Ruqian Lyu
6
+ Maintainer-email: Yan Pan <anne.pan@svi.edu.au>
7
+ License: MIT
8
+ Classifier: Programming Language :: Python :: 3
9
+ Classifier: Operating System :: OS Independent
10
+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
11
+ Requires-Python: >=3.10
12
+ Description-Content-Type: text/markdown
13
+ Requires-Dist: numpy
14
+ Requires-Dist: pandas
15
+ Requires-Dist: scipy
16
+ Requires-Dist: zarr>=3
17
+ Requires-Dist: numcodecs
18
+ Requires-Dist: tqdm
19
+ Requires-Dist: scikit-learn
20
+ Requires-Dist: matplotlib
21
+ Provides-Extra: gnn
22
+ Requires-Dist: torch; extra == "gnn"
23
+ Requires-Dist: torch_geometric; extra == "gnn"
24
+ Provides-Extra: dev
25
+ Requires-Dist: pytest; extra == "dev"
26
+
27
+ # spatialrna
28
+
29
+ A package that provides an easier interface for building graph data from spatial transcriptomics data.
30
+
31
+
32
+ ## Prerequisites
33
+
34
+ Create a conda environment with Python >= 3.10:
35
+
36
+ ```bash
37
+ conda create -n spatialrna python=3.10
38
+ conda activate spatialrna
39
+ ```
40
+
41
+ To use the graphs with GNN models, also install PyTorch and PyTorch Geometric matching your CUDA version (see the PyTorch and PyG installation guides).
42
+
43
+ ## Installation
44
+
45
+ ```bash
46
+ pip install spatialrna
47
+ ```
48
+
49
+ Development pre-release (0.3.x):
50
+
51
+ ```bash
52
+ pip install --pre spatialrna
53
+ ```
54
+
55
+ ## Documentation
56
+
57
+ Documentation is available at https://ruqianl.github.io/spatialrna_docs/
spatialrna-0.3.0.dev1/PKG-INFO DELETED
@@ -1,34 +0,0 @@
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- Metadata-Version: 2.4
2
- Name: spatialrna
3
- Version: 0.3.0.dev1
4
- Summary: Spatial RNA graph data processing and analysis for iST (Xenium / Atera): graphs, GNN training / embedding, clustering, spatial maps.
5
- Author-email: Anne Pan <anne.pan@svi.edu.au>
6
- Classifier: Programming Language :: Python :: 3
7
- Classifier: Operating System :: OS Independent
8
- Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
9
- Requires-Python: >=3.12
10
- Description-Content-Type: text/markdown
11
- Requires-Dist: numpy
12
- Requires-Dist: pandas
13
- Requires-Dist: scipy
14
- Requires-Dist: zarr>=3
15
- Requires-Dist: numcodecs
16
- Requires-Dist: tqdm
17
- Requires-Dist: scikit-learn
18
- Requires-Dist: matplotlib
19
- Provides-Extra: gnn
20
- Requires-Dist: torch; extra == "gnn"
21
- Requires-Dist: torch_geometric; extra == "gnn"
22
- Provides-Extra: dev
23
- Requires-Dist: pytest; extra == "dev"
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-
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- description = "A package for spatial RNA graph data processing and analysis."
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- readme = "README.md"
27
- version = "0.3.0.dev1"
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- authors = [{ name = "Anne Pan", email = "anne.pan@svi.edu.au" },{ name = "Ruqian Lyu" }]
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- license = { text = "MIT" }
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- requires-python = ">=3.12"
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-
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- [project.urls]
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- Repository = "https://gitlab.svi.edu.au/biocellgen-public/spatialrna_pypi_public"
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- Documentation = "https://ruqianl.github.io/spatialrna_docs/"
spatialrna-0.3.0.dev1/README.md DELETED
@@ -1,10 +0,0 @@
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- description = "A package for spatial RNA graph data processing and analysis."
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- readme = "README.md"
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- version = "0.3.0.dev1"
4
- authors = [{ name = "Anne Pan", email = "anne.pan@svi.edu.au" },{ name = "Ruqian Lyu" }]
5
- license = { text = "MIT" }
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- requires-python = ">=3.12"
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-
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- [project.urls]
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- Repository = "https://gitlab.svi.edu.au/biocellgen-public/spatialrna_pypi_public"
10
- Documentation = "https://ruqianl.github.io/spatialrna_docs/"
spatialrna-0.3.0.dev1/src/spatialrna.egg-info/PKG-INFO DELETED
@@ -1,34 +0,0 @@
1
- Metadata-Version: 2.4
2
- Name: spatialrna
3
- Version: 0.3.0.dev1
4
- Summary: Spatial RNA graph data processing and analysis for iST (Xenium / Atera): graphs, GNN training / embedding, clustering, spatial maps.
5
- Author-email: Anne Pan <anne.pan@svi.edu.au>
6
- Classifier: Programming Language :: Python :: 3
7
- Classifier: Operating System :: OS Independent
8
- Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
9
- Requires-Python: >=3.12
10
- Description-Content-Type: text/markdown
11
- Requires-Dist: numpy
12
- Requires-Dist: pandas
13
- Requires-Dist: scipy
14
- Requires-Dist: zarr>=3
15
- Requires-Dist: numcodecs
16
- Requires-Dist: tqdm
17
- Requires-Dist: scikit-learn
18
- Requires-Dist: matplotlib
19
- Provides-Extra: gnn
20
- Requires-Dist: torch; extra == "gnn"
21
- Requires-Dist: torch_geometric; extra == "gnn"
22
- Provides-Extra: dev
23
- Requires-Dist: pytest; extra == "dev"
24
-
25
- description = "A package for spatial RNA graph data processing and analysis."
26
- readme = "README.md"
27
- version = "0.3.0.dev1"
28
- authors = [{ name = "Anne Pan", email = "anne.pan@svi.edu.au" },{ name = "Ruqian Lyu" }]
29
- license = { text = "MIT" }
30
- requires-python = ">=3.12"
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-
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- [project.urls]
33
- Repository = "https://gitlab.svi.edu.au/biocellgen-public/spatialrna_pypi_public"
34
- Documentation = "https://ruqianl.github.io/spatialrna_docs/"