spatialrna 0.3.0.dev0__tar.gz → 0.3.0.dev2__tar.gz

spatialrna-0.3.0.dev2/PKG-INFO

@@ -0,0 +1,57 @@
+Metadata-Version: 2.4
+Name: spatialrna
+Version: 0.3.0.dev2
+Summary: A package for spatial RNA graph data processing and analysis.
+Author: Ruqian Lyu
+Author-email: Anne Pan <anne.pan@svi.edu.au>
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: zarr>=3
+Requires-Dist: numcodecs
+Requires-Dist: tqdm
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Provides-Extra: gnn
+Requires-Dist: torch; extra == "gnn"
+Requires-Dist: torch_geometric; extra == "gnn"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+
+# spatialrna
+
+A package that provides an easier interface for building graph data from spatial transcriptomics data.
+
+
+## Prerequisites
+
+Create a conda environment with Python >= 3.10:
+
+```bash
+conda create -n spatialrna python=3.10
+conda activate spatialrna
+```
+
+To use the graphs with GNN models, also install PyTorch and PyTorch Geometric matching your CUDA version (see the PyTorch and PyG installation guides).
+
+## Installation
+
+```bash
+pip install spatialrna
+```
+
+Development pre-release (0.3.x):
+
+```bash
+pip install --pre spatialrna
+```
+
+## Documentation
+
+Documentation is available at https://ruqianl.github.io/spatialrna_docs/

spatialrna-0.3.0.dev2/README.md

@@ -0,0 +1,31 @@
+# spatialrna
+
+A package that provides an easier interface for building graph data from spatial transcriptomics data.
+
+
+## Prerequisites
+
+Create a conda environment with Python >= 3.10:
+
+```bash
+conda create -n spatialrna python=3.10
+conda activate spatialrna
+```
+
+To use the graphs with GNN models, also install PyTorch and PyTorch Geometric matching your CUDA version (see the PyTorch and PyG installation guides).
+
+## Installation
+
+```bash
+pip install spatialrna
+```
+
+Development pre-release (0.3.x):
+
+```bash
+pip install --pre spatialrna
+```
+
+## Documentation
+
+Documentation is available at https://ruqianl.github.io/spatialrna_docs/

{spatialrna-0.3.0.dev0 → spatialrna-0.3.0.dev2}/pyproject.toml

@@ -3,18 +3,18 @@ requires = ["setuptools>=68"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "spatialrna"
-version = "0.3.0.dev0"
-description = "Spatial RNA graph data processing and analysis for single-molecule spatial transcriptomics (Xenium / Atera): graphs, GNN training / embedding, clustering, spatial maps."
+name="spatialrna"
+description = "A package for spatial RNA graph data processing and analysis."
 readme = "README.md"
+version = "0.3.0.dev2"
+authors = [{ name = "Anne Pan", email = "anne.pan@svi.edu.au" },{ name = "Ruqian Lyu" }]
+license = { text = "MIT" }
 requires-python = ">=3.10"
-authors = [{ name = "Anne Pan", email = "anne.pan@svi.edu.au" }]
 classifiers = [
     "Programming Language :: Python :: 3",
     "Operating System :: OS Independent",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-# Core: readers, graph builders, clustering, maps. No torch needed.
 dependencies = [
     "numpy",
     "pandas",
@@ -26,6 +26,7 @@ dependencies = [
     "matplotlib",
 ]
 
+
 [project.optional-dependencies]
 # SpatialRNA dataset, datasets, train_val. Install torch and the PyG wheels matching
 # your CUDA first -- see README.

spatialrna-0.3.0.dev2/src/spatialrna.egg-info/PKG-INFO

@@ -0,0 +1,57 @@
+Metadata-Version: 2.4
+Name: spatialrna
+Version: 0.3.0.dev2
+Summary: A package for spatial RNA graph data processing and analysis.
+Author: Ruqian Lyu
+Author-email: Anne Pan <anne.pan@svi.edu.au>
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: zarr>=3
+Requires-Dist: numcodecs
+Requires-Dist: tqdm
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Provides-Extra: gnn
+Requires-Dist: torch; extra == "gnn"
+Requires-Dist: torch_geometric; extra == "gnn"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+
+# spatialrna
+
+A package that provides an easier interface for building graph data from spatial transcriptomics data.
+
+
+## Prerequisites
+
+Create a conda environment with Python >= 3.10:
+
+```bash
+conda create -n spatialrna python=3.10
+conda activate spatialrna
+```
+
+To use the graphs with GNN models, also install PyTorch and PyTorch Geometric matching your CUDA version (see the PyTorch and PyG installation guides).
+
+## Installation
+
+```bash
+pip install spatialrna
+```
+
+Development pre-release (0.3.x):
+
+```bash
+pip install --pre spatialrna
+```
+
+## Documentation
+
+Documentation is available at https://ruqianl.github.io/spatialrna_docs/

spatialrna-0.3.0.dev0/PKG-INFO

@@ -1,102 +0,0 @@
-Metadata-Version: 2.4
-Name: spatialrna
-Version: 0.3.0.dev0
-Summary: Spatial RNA graph data processing and analysis for single-molecule spatial transcriptomics (Xenium / Atera): graphs, GNN training / embedding, clustering, spatial maps.
-Author-email: Anne Pan <anne.pan@svi.edu.au>
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: OS Independent
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: scipy
-Requires-Dist: zarr>=3
-Requires-Dist: numcodecs
-Requires-Dist: tqdm
-Requires-Dist: scikit-learn
-Requires-Dist: matplotlib
-Provides-Extra: gnn
-Requires-Dist: torch; extra == "gnn"
-Requires-Dist: torch_geometric; extra == "gnn"
-Provides-Extra: dev
-Requires-Dist: pytest; extra == "dev"
-
-# spatialrna
-
-Spatial RNA graph data processing and analysis for single-molecule spatial
-transcriptomics (10x Xenium and Atera): transcripts → tile graphs and subgraphs →
-any graph neural network (train / validate / embed) → clusters → spatial maps.
-
-This continues the lab's `spatialrna` 0.2 (Ruqian Lyu) with the same scope and adds
-reading of raw Xenium / Atera outputs, zarr storage, a fast KD-tree graph builder,
-balanced grid tiling for large sections, and GPU Gaussian mixtures. The ISTIST
-pipeline builds on it with its own model (CrossSampleGAT), transcript-level
-annotation, statistics and an HTML report.
-
-## Install
-
-```bash
-pip install -e .                 # readers, graph builders, clustering, maps (no torch)
-pip install -e ".[gnn]"          # + SpatialRNA dataset, datasets, train_val
-                                 #   (install torch + PyG for your CUDA first)
-```
-
-Python >= 3.10, zarr-python >= 3.
-
-## Modules
-
-| module | what it does | 0.2 equivalent | needs torch |
-|---|---|---|---|
-| `readers` | Xenium / Atera `transcripts.zarr.zip` → transcripts (layout auto-detected) | – | no |
-| `graph_build` | KD-tree radius graphs, subgraph sampling, `plan_tiles` (grid tiling) | – | no |
-| `graph_zarr_io` | `SpatialRNA`: tiles (strips or grid) + padding → radius graphs → subgraphs, zarr I/O | `spatialrna.py` | yes |
-| `datasets` | `ZarrGraphDataset` over many tile / subgraph stores | `spatialrna_ondisk.py` | yes |
-| `train_val` | model-agnostic link-prediction training / validation, `embed_tile` | `train_val.py` | yes |
-| `cluster` | `gmm` (GPU or numpy EM), `kmeans` | `run_kmeans.py` | optional |
-| `viz` | `pixel_map`, two-panel overviews, one panel per label | `viz.py` | no |
-
-## Quick start
-
-```python
-import numpy as np, torch
-import spatialrna as sr
-
-df = sr.readers.load_transcripts("/path/to/output")          # x, y, z, qv, gene
-print(sr.readers.describe("/path/to/output"))
-
-# tile graphs (here: 100 near-square tiles with equal transcript counts)
-# SpatialRNA(root="data/S01.zarr", sample_name="S01", cohort_zarr_path="data/cohort.zarr",
-#            num_tiles=100, tile_mode="grid", one_hot_encoding=enc, ...)
-
-# train any model(x, edge_index) on the tiles / subgraphs
-from spatialrna import train_val as tv
-from spatialrna.datasets import ZarrGraphDataset
-graphs = ZarrGraphDataset.from_sample_store("data/S01.zarr", kind="subgraphs")
-opt = torch.optim.Adam(model.parameters(), lr=1e-3)
-loss, acc = tv.train_link_prediction(model, graphs, opt, device, num_genes)
-emb, tx_id = tv.embed_tile(model, graphs[0], device, num_genes)
-
-# clusters and a map
-labels, gmm = sr.cluster.gmm(emb.numpy(), 12)
-fig = sr.viz.pixel_map(x, y, labels)
-```
-
-## Tiling
-
-`SpatialRNA(tile_mode="strips")` (default, as in 0.2) cuts `num_tiles` equal-width
-bands along `tile_by_dim`. `tile_mode="grid"` cuts near-square tiles with equal
-transcript counts: no empty tiles in irregular tissue and little padding with many
-tiles (~5–7 % at 500 tiles, vs ~40 % for 500 strips).
-
-## Tests
-
-```bash
-pip install -e ".[dev]"
-pytest              # test_zarr_roundtrip needs the [gnn] extra
-```
-
-## Note on the name
-
-`spatialrna` 0.1–0.2 on PyPI is maintained by Ruqian Lyu; this is 0.3.0.dev0.
-Coordinate with her before uploading to PyPI under the same name.

spatialrna-0.3.0.dev0/README.md

@@ -1,78 +0,0 @@
-# spatialrna
-
-Spatial RNA graph data processing and analysis for single-molecule spatial
-transcriptomics (10x Xenium and Atera): transcripts → tile graphs and subgraphs →
-any graph neural network (train / validate / embed) → clusters → spatial maps.
-
-This continues the lab's `spatialrna` 0.2 (Ruqian Lyu) with the same scope and adds
-reading of raw Xenium / Atera outputs, zarr storage, a fast KD-tree graph builder,
-balanced grid tiling for large sections, and GPU Gaussian mixtures. The ISTIST
-pipeline builds on it with its own model (CrossSampleGAT), transcript-level
-annotation, statistics and an HTML report.
-
-## Install
-
-```bash
-pip install -e .                 # readers, graph builders, clustering, maps (no torch)
-pip install -e ".[gnn]"          # + SpatialRNA dataset, datasets, train_val
-                                 #   (install torch + PyG for your CUDA first)
-```
-
-Python >= 3.10, zarr-python >= 3.
-
-## Modules
-
-| module | what it does | 0.2 equivalent | needs torch |
-|---|---|---|---|
-| `readers` | Xenium / Atera `transcripts.zarr.zip` → transcripts (layout auto-detected) | – | no |
-| `graph_build` | KD-tree radius graphs, subgraph sampling, `plan_tiles` (grid tiling) | – | no |
-| `graph_zarr_io` | `SpatialRNA`: tiles (strips or grid) + padding → radius graphs → subgraphs, zarr I/O | `spatialrna.py` | yes |
-| `datasets` | `ZarrGraphDataset` over many tile / subgraph stores | `spatialrna_ondisk.py` | yes |
-| `train_val` | model-agnostic link-prediction training / validation, `embed_tile` | `train_val.py` | yes |
-| `cluster` | `gmm` (GPU or numpy EM), `kmeans` | `run_kmeans.py` | optional |
-| `viz` | `pixel_map`, two-panel overviews, one panel per label | `viz.py` | no |
-
-## Quick start
-
-```python
-import numpy as np, torch
-import spatialrna as sr
-
-df = sr.readers.load_transcripts("/path/to/output")          # x, y, z, qv, gene
-print(sr.readers.describe("/path/to/output"))
-
-# tile graphs (here: 100 near-square tiles with equal transcript counts)
-# SpatialRNA(root="data/S01.zarr", sample_name="S01", cohort_zarr_path="data/cohort.zarr",
-#            num_tiles=100, tile_mode="grid", one_hot_encoding=enc, ...)
-
-# train any model(x, edge_index) on the tiles / subgraphs
-from spatialrna import train_val as tv
-from spatialrna.datasets import ZarrGraphDataset
-graphs = ZarrGraphDataset.from_sample_store("data/S01.zarr", kind="subgraphs")
-opt = torch.optim.Adam(model.parameters(), lr=1e-3)
-loss, acc = tv.train_link_prediction(model, graphs, opt, device, num_genes)
-emb, tx_id = tv.embed_tile(model, graphs[0], device, num_genes)
-
-# clusters and a map
-labels, gmm = sr.cluster.gmm(emb.numpy(), 12)
-fig = sr.viz.pixel_map(x, y, labels)
-```
-
-## Tiling
-
-`SpatialRNA(tile_mode="strips")` (default, as in 0.2) cuts `num_tiles` equal-width
-bands along `tile_by_dim`. `tile_mode="grid"` cuts near-square tiles with equal
-transcript counts: no empty tiles in irregular tissue and little padding with many
-tiles (~5–7 % at 500 tiles, vs ~40 % for 500 strips).
-
-## Tests
-
-```bash
-pip install -e ".[dev]"
-pytest              # test_zarr_roundtrip needs the [gnn] extra
-```
-
-## Note on the name
-
-`spatialrna` 0.1–0.2 on PyPI is maintained by Ruqian Lyu; this is 0.3.0.dev0.
-Coordinate with her before uploading to PyPI under the same name.

spatialrna-0.3.0.dev0/src/spatialrna.egg-info/PKG-INFO

@@ -1,102 +0,0 @@
-Metadata-Version: 2.4
-Name: spatialrna
-Version: 0.3.0.dev0
-Summary: Spatial RNA graph data processing and analysis for single-molecule spatial transcriptomics (Xenium / Atera): graphs, GNN training / embedding, clustering, spatial maps.
-Author-email: Anne Pan <anne.pan@svi.edu.au>
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: OS Independent
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: scipy
-Requires-Dist: zarr>=3
-Requires-Dist: numcodecs
-Requires-Dist: tqdm
-Requires-Dist: scikit-learn
-Requires-Dist: matplotlib
-Provides-Extra: gnn
-Requires-Dist: torch; extra == "gnn"
-Requires-Dist: torch_geometric; extra == "gnn"
-Provides-Extra: dev
-Requires-Dist: pytest; extra == "dev"
-
-# spatialrna
-
-Spatial RNA graph data processing and analysis for single-molecule spatial
-transcriptomics (10x Xenium and Atera): transcripts → tile graphs and subgraphs →
-any graph neural network (train / validate / embed) → clusters → spatial maps.
-
-This continues the lab's `spatialrna` 0.2 (Ruqian Lyu) with the same scope and adds
-reading of raw Xenium / Atera outputs, zarr storage, a fast KD-tree graph builder,
-balanced grid tiling for large sections, and GPU Gaussian mixtures. The ISTIST
-pipeline builds on it with its own model (CrossSampleGAT), transcript-level
-annotation, statistics and an HTML report.
-
-## Install
-
-```bash
-pip install -e .                 # readers, graph builders, clustering, maps (no torch)
-pip install -e ".[gnn]"          # + SpatialRNA dataset, datasets, train_val
-                                 #   (install torch + PyG for your CUDA first)
-```
-
-Python >= 3.10, zarr-python >= 3.
-
-## Modules
-
-| module | what it does | 0.2 equivalent | needs torch |
-|---|---|---|---|
-| `readers` | Xenium / Atera `transcripts.zarr.zip` → transcripts (layout auto-detected) | – | no |
-| `graph_build` | KD-tree radius graphs, subgraph sampling, `plan_tiles` (grid tiling) | – | no |
-| `graph_zarr_io` | `SpatialRNA`: tiles (strips or grid) + padding → radius graphs → subgraphs, zarr I/O | `spatialrna.py` | yes |
-| `datasets` | `ZarrGraphDataset` over many tile / subgraph stores | `spatialrna_ondisk.py` | yes |
-| `train_val` | model-agnostic link-prediction training / validation, `embed_tile` | `train_val.py` | yes |
-| `cluster` | `gmm` (GPU or numpy EM), `kmeans` | `run_kmeans.py` | optional |
-| `viz` | `pixel_map`, two-panel overviews, one panel per label | `viz.py` | no |
-
-## Quick start
-
-```python
-import numpy as np, torch
-import spatialrna as sr
-
-df = sr.readers.load_transcripts("/path/to/output")          # x, y, z, qv, gene
-print(sr.readers.describe("/path/to/output"))
-
-# tile graphs (here: 100 near-square tiles with equal transcript counts)
-# SpatialRNA(root="data/S01.zarr", sample_name="S01", cohort_zarr_path="data/cohort.zarr",
-#            num_tiles=100, tile_mode="grid", one_hot_encoding=enc, ...)
-
-# train any model(x, edge_index) on the tiles / subgraphs
-from spatialrna import train_val as tv
-from spatialrna.datasets import ZarrGraphDataset
-graphs = ZarrGraphDataset.from_sample_store("data/S01.zarr", kind="subgraphs")
-opt = torch.optim.Adam(model.parameters(), lr=1e-3)
-loss, acc = tv.train_link_prediction(model, graphs, opt, device, num_genes)
-emb, tx_id = tv.embed_tile(model, graphs[0], device, num_genes)
-
-# clusters and a map
-labels, gmm = sr.cluster.gmm(emb.numpy(), 12)
-fig = sr.viz.pixel_map(x, y, labels)
-```
-
-## Tiling
-
-`SpatialRNA(tile_mode="strips")` (default, as in 0.2) cuts `num_tiles` equal-width
-bands along `tile_by_dim`. `tile_mode="grid"` cuts near-square tiles with equal
-transcript counts: no empty tiles in irregular tissue and little padding with many
-tiles (~5–7 % at 500 tiles, vs ~40 % for 500 strips).
-
-## Tests
-
-```bash
-pip install -e ".[dev]"
-pytest              # test_zarr_roundtrip needs the [gnn] extra
-```
-
-## Note on the name
-
-`spatialrna` 0.1–0.2 on PyPI is maintained by Ruqian Lyu; this is 0.3.0.dev0.
-Coordinate with her before uploading to PyPI under the same name.