sampledisco 0.1.0__tar.gz

sampledisco-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Harry Jiang, Hongkai Ji, and the SampleDisco authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

sampledisco-0.1.0/PKG-INFO

@@ -0,0 +1,254 @@
+Metadata-Version: 2.4
+Name: sampledisco
+Version: 0.1.0
+Summary: Cross-omics, cross-condition sample embedding for single-cell data (RNA + ATAC)
+Author: Hongkai Ji
+Author-email: Harry Jiang <hjiang55@jh.edu>
+License: MIT License
+        
+        Copyright (c) 2026 Harry Jiang, Hongkai Ji, and the SampleDisco authors
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/J041120h/GenoDistance
+Project-URL: Documentation, https://j041120h.github.io/SampleDisco_tutorial/
+Project-URL: Repository, https://github.com/J041120h/GenoDistance
+Keywords: single-cell,sample-embedding,multi-omics,scRNA-seq,scATAC-seq,bioinformatics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=1.5
+Requires-Dist: scipy>=1.9
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scikit-misc>=0.3
+Requires-Dist: statsmodels>=0.13
+Requires-Dist: patsy>=0.5
+Requires-Dist: scanpy>=1.11
+Requires-Dist: anndata>=0.10
+Requires-Dist: muon>=0.1
+Requires-Dist: harmony-pytorch>=0.1
+Requires-Dist: harmonypy>=0.0.9
+Requires-Dist: scglue>=0.3
+Requires-Dist: torch>=2.0
+Requires-Dist: python-igraph>=0.10
+Requires-Dist: leidenalg>=0.9
+Requires-Dist: networkx>=3.0
+Requires-Dist: POT>=0.9
+Requires-Dist: pygam>=0.9
+Requires-Dist: numba>=0.57
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: seaborn>=0.12
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: psutil>=5.9
+Requires-Dist: ruamel.yaml>=0.17
+Requires-Dist: pybedtools>=0.9
+Requires-Dist: pyensembl>=2.3
+Requires-Dist: combat>=0.3
+Requires-Dist: adjustText>=1.0
+Provides-Extra: trees
+Requires-Dist: biopython>=1.80; extra == "trees"
+Requires-Dist: scikit-bio>=0.5; extra == "trees"
+Requires-Dist: dendropy>=4.5; extra == "trees"
+Dynamic: license-file
+
+# SampleDisco
+
+A cross-omics, cross-condition **sample embedding** tool for single-cell data.
+
+SampleDisco takes a cell-level embedding (from any standard scRNA / scATAC / multi-omics integration method) and lifts it to a **sample-level embedding** that captures both cell-type composition and the per-cell-type state of each sample. Every downstream analysis — sample-to-sample distance, clustering, trajectory inference, phenotype association — then runs on that single shared sample embedding, regardless of modality.
+
+Paper draft: [`/users/hjiang/GenoDistance/SampleDisco_Draft-11.pdf`](../SampleDisco_Draft-11.pdf)
+
+---
+
+## What the method does
+
+For each modality (RNA, ATAC, or integrated multi-omics) the pipeline produces two cell-level views:
+
+| Key | Role | Source |
+|---|---|---|
+| **`Z_clust`** | sample-removed embedding — used for clustering and composition blocks | Harmony (single-omics) / Harmony post-pass on scGLUE (multi-omics) |
+| **`Z_cmd`**  | sample-preserved embedding — used for the counterfactual displacement (CMD) block | second Harmony pass (single-omics) / scGLUE primary output (multi-omics) |
+
+It then assembles **four blocks** per sample (or per sample × modality for multi-omics):
+
+1. **A1** — one-hot cell-type composition
+2. **A2** — soft k-means composition at K_med (≈120)
+3. **A3** — soft k-means composition at K_fine (≈300)
+4. **CMD** — leave-one-out cell-type-resolved displacement on `Z_cmd`
+
+The four blocks are inverse-variance weighted, Frobenius-stacked, PCA-reduced to 10 dimensions, and Harmony-corrected at sample level. The result is stored as `adata.uns['X_DR_sample']` and feeds every downstream module.
+
+---
+
+## Repository layout
+
+```
+code/
+├── SampleDisc.py              # CLI entry point (simple or complex mode)
+├── config/                    # 9 YAML configs covering covid / blood / eye / heart / ENCODE / tabula / long_covid / unpaired / default
+├── wrapper/                   # Orchestration
+│   ├── wrapper.py             # Master wrapper; gates RNA + ATAC + multiomics + shared downstream
+│   ├── rna_wrapper.py
+│   ├── atac_wrapper.py
+│   └── multiomics_wrapper.py
+├── preparation/               # Preprocessing
+│   ├── rna_preprocess_{cpu,gpu}.py   # QC → HVG → PCA → dual Harmony → Z_clust + Z_cmd
+│   ├── atac_preprocess_{cpu,gpu}.py  # QC → TF-IDF → HVF → LSI → dual Harmony → Z_clust + Z_cmd
+│   ├── cell_type_{cpu,gpu}.py        # Leiden clustering on Z_clust (RNA or ATAC)
+│   ├── ATAC_cell_type{,_gpu}.py      # ATAC-specific cell typing variants
+│   ├── multi_omics_glue.py           # scGLUE integration (cross-modality VAE + guidance graph)
+│   ├── multi_omics_batch_correction.py # Harmony post-pass on X_glue → Z_clust
+│   ├── multi_omics_merge.py          # post-GLUE merge + per-modality preprocess/slimming
+│   └── multi_omics_cell_type_{cpu,gpu}.py  # RNA-Leiden + k-NN label transfer to ATAC
+├── sample_embedding/          # Core method
+│   ├── blocks.py              # composition, CMD, weighting, Frobenius stack, final PCA + Harmony
+│   ├── sample_embedding.py    # CPU pipeline
+│   └── sample_embedding_gpu.py # GPU pipeline (cuML + cupy)
+├── parameter_selection/
+│   └── autotune.py            # Bayesian GP sweep over CMD α; adaptive proxy ensemble
+├── sample_distance/           # Pairwise sample distances (DR / EMD / chi-square / JS)
+├── sample_clustering/         # Hierarchical (HRA / HRC / NN / UPGMA / consensus), K-means, proportion test, RAISIN
+├── sample_trajectory/         # CCA (supervised) and TSCAN (unsupervised) + GAM-based trajectory DGE
+├── sample_association/        # Per-PC variance explained vs sample-level covariates (permutation FDR)
+├── visualization/             # Embedding plots, dendrograms, DGE volcanos, modality-aware multi-omics scatters
+├── utils/                     # Shared helpers: seed, safe h5ad I/O, limma, TF-IDF, batch regress, Grouping
+├── gene_activity/             # ATAC peak → gene activity inference + RNA-ATAC validation
+└── claude/                    # Active one-off run scripts (rerun launchers, monitored SE, parameter sweeps)
+```
+
+---
+
+## Usage
+
+### Complex mode (recommended) — YAML-driven
+
+```bash
+python SampleDisc.py -m complex --config config/config.yaml
+```
+
+The YAML drives every flag and parameter for all three pipelines:
+
+- **Pipeline gates** (top-level): `run_rna_pipeline`, `run_atac_pipeline`, `run_multiomics_pipeline`
+- **Per-modality phase gates** (Phase 1): `*_preprocessing`, `*_cell_type_cluster`, `*_derive_sample_embedding`
+- **Per-modality downstream gates** (Phase 2): `*_sample_distance_calculation`, `*_trajectory_analysis`, `*_trajectory_dge`, `*_sample_cluster`, `*_proportion_test`, `*_cluster_dge`, `*_visualize_data`, `*_dimension_association_analysis`
+- **Multi-omics-specific**: `multiomics_run_glue_*`, `multiomics_treat_sample_as_batch`, `multiomics_run_glue_twice_for_sample_removal`
+
+The 9 ready-to-use configs in `config/` are point-in-time snapshots for the datasets used in the paper; copy one and adjust paths / column names for your own data.
+
+### Simple mode — one positional file, defaults everywhere
+
+```bash
+python SampleDisc.py -m simple -c <count_data.h5ad> -o <output_dir>
+```
+
+---
+
+## Inputs
+
+A standard scanpy AnnData file with at minimum:
+- `.X` — count matrix (genes for RNA, peaks for ATAC)
+- `.obs['sample']` — sample column (required)
+- Optional: `.obs['batch']`, `.obs['cell_type']`, sample-level metadata file (CSV) to merge
+
+For multi-omics, the pipeline takes two separate h5ads (RNA + ATAC) and integrates them via scGLUE; samples may be **paired** (1:1 cell correspondence) or **unpaired**.
+
+---
+
+## Outputs (under `output_dir`)
+
+```
+<output_dir>/
+├── rna/
+│   ├── preprocess/adata_preprocessed.h5ad
+│   ├── sample_embedding/sample_embedding.csv
+│   ├── Sample_distance/{cosine,correlation}/*
+│   ├── CCA/  or  TSCAN/                       # whichever trajectory mode
+│   ├── trajectoryDEG/
+│   ├── sample_cluster/{kmeans_*,proportion_test/}
+│   ├── sample_association/variance_explained_sample.csv + figures/
+│   └── visualization/*.png
+├── atac/   (parallel structure)
+├── multiomics/
+│   ├── integration/glue/{rna-pp,atac-pp,guidance.graphml.gz}
+│   ├── preprocess/adata_sample.h5ad           # post-GLUE merged adata with Z_clust + Z_cmd
+│   ├── sample_embedding/sample_embedding.csv
+│   └── (same downstream subdirs as single-omics)
+└── sys_log/main_process_status.json           # which stages completed
+```
+
+---
+
+## Installation
+
+SampleDisco is **one package**. The CPU install is pip-only; **GPU acceleration is
+activated simply by installing the GPU libraries separately** — the same package
+detects and uses them at runtime. There is no separate "GPU build" of SampleDisco.
+
+### 1. Core install (CPU)
+
+```bash
+pip install sampledisco          # once published — or `pip install -e .` from a clone
+```
+
+### 2. System prerequisite — bedtools
+
+scGLUE (the multi-omics integrator) calls the `bedtools` binary, which pip cannot
+provide:
+
+```bash
+conda install -c bioconda bedtools
+```
+
+### 3. GPU acceleration (optional, install yourself)
+
+The GPU functions (RAPIDS-accelerated normalization, Harmony, k-means / PCA, Leiden,
+scGLUE training) turn on **only when the RAPIDS stack is present** in your
+environment. RAPIDS is CUDA-driver-specific and conda-only, so you install it
+separately, matching your driver (the pins below target a CUDA-12.5 driver such as
+the cluster's GPU nodes):
+
+```bash
+conda install -c rapidsai -c conda-forge -c nvidia \
+    cuml=24.12 cudf=24.12 cugraph=24.12 rmm=24.12 cuvs=24.12 cupy=13 cuda-version=12.5
+pip install rapids-singlecell==0.13.1 --no-deps
+```
+
+Then set `use_gpu: true` in your config. **You do not reinstall SampleDisco** — once
+those packages are importable the GPU paths activate automatically; if they are
+missing or the driver is too old, SampleDisco falls back to CPU equivalents
+(`harmonypy` / linear regression, scikit-learn k-means, PyTorch CPU).
+
+### One-command environments (recommended)
+
+For a fully reproducible environment (including bedtools), use the provided conda
+files instead of the manual steps above — see `INSTALL.md` for the driver/version
+notes:
+
+```bash
+conda env create -f environment-cpu.yml      # CPU
+conda env create -f environment-gpu.yml      # GPU (RAPIDS 24.12)
+```

sampledisco-0.1.0/README.md

@@ -0,0 +1,178 @@
+# SampleDisco
+
+A cross-omics, cross-condition **sample embedding** tool for single-cell data.
+
+SampleDisco takes a cell-level embedding (from any standard scRNA / scATAC / multi-omics integration method) and lifts it to a **sample-level embedding** that captures both cell-type composition and the per-cell-type state of each sample. Every downstream analysis — sample-to-sample distance, clustering, trajectory inference, phenotype association — then runs on that single shared sample embedding, regardless of modality.
+
+Paper draft: [`/users/hjiang/GenoDistance/SampleDisco_Draft-11.pdf`](../SampleDisco_Draft-11.pdf)
+
+---
+
+## What the method does
+
+For each modality (RNA, ATAC, or integrated multi-omics) the pipeline produces two cell-level views:
+
+| Key | Role | Source |
+|---|---|---|
+| **`Z_clust`** | sample-removed embedding — used for clustering and composition blocks | Harmony (single-omics) / Harmony post-pass on scGLUE (multi-omics) |
+| **`Z_cmd`**  | sample-preserved embedding — used for the counterfactual displacement (CMD) block | second Harmony pass (single-omics) / scGLUE primary output (multi-omics) |
+
+It then assembles **four blocks** per sample (or per sample × modality for multi-omics):
+
+1. **A1** — one-hot cell-type composition
+2. **A2** — soft k-means composition at K_med (≈120)
+3. **A3** — soft k-means composition at K_fine (≈300)
+4. **CMD** — leave-one-out cell-type-resolved displacement on `Z_cmd`
+
+The four blocks are inverse-variance weighted, Frobenius-stacked, PCA-reduced to 10 dimensions, and Harmony-corrected at sample level. The result is stored as `adata.uns['X_DR_sample']` and feeds every downstream module.
+
+---
+
+## Repository layout
+
+```
+code/
+├── SampleDisc.py              # CLI entry point (simple or complex mode)
+├── config/                    # 9 YAML configs covering covid / blood / eye / heart / ENCODE / tabula / long_covid / unpaired / default
+├── wrapper/                   # Orchestration
+│   ├── wrapper.py             # Master wrapper; gates RNA + ATAC + multiomics + shared downstream
+│   ├── rna_wrapper.py
+│   ├── atac_wrapper.py
+│   └── multiomics_wrapper.py
+├── preparation/               # Preprocessing
+│   ├── rna_preprocess_{cpu,gpu}.py   # QC → HVG → PCA → dual Harmony → Z_clust + Z_cmd
+│   ├── atac_preprocess_{cpu,gpu}.py  # QC → TF-IDF → HVF → LSI → dual Harmony → Z_clust + Z_cmd
+│   ├── cell_type_{cpu,gpu}.py        # Leiden clustering on Z_clust (RNA or ATAC)
+│   ├── ATAC_cell_type{,_gpu}.py      # ATAC-specific cell typing variants
+│   ├── multi_omics_glue.py           # scGLUE integration (cross-modality VAE + guidance graph)
+│   ├── multi_omics_batch_correction.py # Harmony post-pass on X_glue → Z_clust
+│   ├── multi_omics_merge.py          # post-GLUE merge + per-modality preprocess/slimming
+│   └── multi_omics_cell_type_{cpu,gpu}.py  # RNA-Leiden + k-NN label transfer to ATAC
+├── sample_embedding/          # Core method
+│   ├── blocks.py              # composition, CMD, weighting, Frobenius stack, final PCA + Harmony
+│   ├── sample_embedding.py    # CPU pipeline
+│   └── sample_embedding_gpu.py # GPU pipeline (cuML + cupy)
+├── parameter_selection/
+│   └── autotune.py            # Bayesian GP sweep over CMD α; adaptive proxy ensemble
+├── sample_distance/           # Pairwise sample distances (DR / EMD / chi-square / JS)
+├── sample_clustering/         # Hierarchical (HRA / HRC / NN / UPGMA / consensus), K-means, proportion test, RAISIN
+├── sample_trajectory/         # CCA (supervised) and TSCAN (unsupervised) + GAM-based trajectory DGE
+├── sample_association/        # Per-PC variance explained vs sample-level covariates (permutation FDR)
+├── visualization/             # Embedding plots, dendrograms, DGE volcanos, modality-aware multi-omics scatters
+├── utils/                     # Shared helpers: seed, safe h5ad I/O, limma, TF-IDF, batch regress, Grouping
+├── gene_activity/             # ATAC peak → gene activity inference + RNA-ATAC validation
+└── claude/                    # Active one-off run scripts (rerun launchers, monitored SE, parameter sweeps)
+```
+
+---
+
+## Usage
+
+### Complex mode (recommended) — YAML-driven
+
+```bash
+python SampleDisc.py -m complex --config config/config.yaml
+```
+
+The YAML drives every flag and parameter for all three pipelines:
+
+- **Pipeline gates** (top-level): `run_rna_pipeline`, `run_atac_pipeline`, `run_multiomics_pipeline`
+- **Per-modality phase gates** (Phase 1): `*_preprocessing`, `*_cell_type_cluster`, `*_derive_sample_embedding`
+- **Per-modality downstream gates** (Phase 2): `*_sample_distance_calculation`, `*_trajectory_analysis`, `*_trajectory_dge`, `*_sample_cluster`, `*_proportion_test`, `*_cluster_dge`, `*_visualize_data`, `*_dimension_association_analysis`
+- **Multi-omics-specific**: `multiomics_run_glue_*`, `multiomics_treat_sample_as_batch`, `multiomics_run_glue_twice_for_sample_removal`
+
+The 9 ready-to-use configs in `config/` are point-in-time snapshots for the datasets used in the paper; copy one and adjust paths / column names for your own data.
+
+### Simple mode — one positional file, defaults everywhere
+
+```bash
+python SampleDisc.py -m simple -c <count_data.h5ad> -o <output_dir>
+```
+
+---
+
+## Inputs
+
+A standard scanpy AnnData file with at minimum:
+- `.X` — count matrix (genes for RNA, peaks for ATAC)
+- `.obs['sample']` — sample column (required)
+- Optional: `.obs['batch']`, `.obs['cell_type']`, sample-level metadata file (CSV) to merge
+
+For multi-omics, the pipeline takes two separate h5ads (RNA + ATAC) and integrates them via scGLUE; samples may be **paired** (1:1 cell correspondence) or **unpaired**.
+
+---
+
+## Outputs (under `output_dir`)
+
+```
+<output_dir>/
+├── rna/
+│   ├── preprocess/adata_preprocessed.h5ad
+│   ├── sample_embedding/sample_embedding.csv
+│   ├── Sample_distance/{cosine,correlation}/*
+│   ├── CCA/  or  TSCAN/                       # whichever trajectory mode
+│   ├── trajectoryDEG/
+│   ├── sample_cluster/{kmeans_*,proportion_test/}
+│   ├── sample_association/variance_explained_sample.csv + figures/
+│   └── visualization/*.png
+├── atac/   (parallel structure)
+├── multiomics/
+│   ├── integration/glue/{rna-pp,atac-pp,guidance.graphml.gz}
+│   ├── preprocess/adata_sample.h5ad           # post-GLUE merged adata with Z_clust + Z_cmd
+│   ├── sample_embedding/sample_embedding.csv
+│   └── (same downstream subdirs as single-omics)
+└── sys_log/main_process_status.json           # which stages completed
+```
+
+---
+
+## Installation
+
+SampleDisco is **one package**. The CPU install is pip-only; **GPU acceleration is
+activated simply by installing the GPU libraries separately** — the same package
+detects and uses them at runtime. There is no separate "GPU build" of SampleDisco.
+
+### 1. Core install (CPU)
+
+```bash
+pip install sampledisco          # once published — or `pip install -e .` from a clone
+```
+
+### 2. System prerequisite — bedtools
+
+scGLUE (the multi-omics integrator) calls the `bedtools` binary, which pip cannot
+provide:
+
+```bash
+conda install -c bioconda bedtools
+```
+
+### 3. GPU acceleration (optional, install yourself)
+
+The GPU functions (RAPIDS-accelerated normalization, Harmony, k-means / PCA, Leiden,
+scGLUE training) turn on **only when the RAPIDS stack is present** in your
+environment. RAPIDS is CUDA-driver-specific and conda-only, so you install it
+separately, matching your driver (the pins below target a CUDA-12.5 driver such as
+the cluster's GPU nodes):
+
+```bash
+conda install -c rapidsai -c conda-forge -c nvidia \
+    cuml=24.12 cudf=24.12 cugraph=24.12 rmm=24.12 cuvs=24.12 cupy=13 cuda-version=12.5
+pip install rapids-singlecell==0.13.1 --no-deps
+```
+
+Then set `use_gpu: true` in your config. **You do not reinstall SampleDisco** — once
+those packages are importable the GPU paths activate automatically; if they are
+missing or the driver is too old, SampleDisco falls back to CPU equivalents
+(`harmonypy` / linear regression, scikit-learn k-means, PyTorch CPU).
+
+### One-command environments (recommended)
+
+For a fully reproducible environment (including bedtools), use the provided conda
+files instead of the manual steps above — see `INSTALL.md` for the driver/version
+notes:
+
+```bash
+conda env create -f environment-cpu.yml      # CPU
+conda env create -f environment-gpu.yml      # GPU (RAPIDS 24.12)
+```

sampledisco-0.1.0/pyproject.toml

@@ -0,0 +1,49 @@
+# Packaging metadata for SampleDisco.
+# Installable as a normal package (src/ layout): `pip install -e .` exposes the
+# `sampledisco` import and the `sampledisco` console command from anywhere — no
+# more `cd code && python SampleDisc.py`. Core deps are declared in
+# requirements.txt; optional GPU acceleration is in requirements-gpu.txt.
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sampledisco"
+version = "0.1.0"
+description = "Cross-omics, cross-condition sample embedding for single-cell data (RNA + ATAC)"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+authors = [
+    { name = "Harry Jiang", email = "hjiang55@jh.edu" },
+    { name = "Hongkai Ji" },
+]
+keywords = ["single-cell", "sample-embedding", "multi-omics", "scRNA-seq", "scATAC-seq", "bioinformatics"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dynamic = ["dependencies"]
+
+[project.urls]
+Homepage = "https://github.com/J041120h/GenoDistance"
+Documentation = "https://j041120h.github.io/SampleDisco_tutorial/"
+Repository = "https://github.com/J041120h/GenoDistance"
+
+[project.scripts]
+sampledisco = "sampledisco.cli:main"
+
+[project.optional-dependencies]
+# Phylogenetic-tree sample clustering (NN / UPGMA / consensus). Off the default
+# wrapper path, so its heavy deps are optional: pip install -e '.[trees]'
+trees = ["biopython>=1.80", "scikit-bio>=0.5", "dendropy>=4.5"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+dependencies = { file = ["requirements.txt"] }

sampledisco-0.1.0/requirements.txt

@@ -0,0 +1,37 @@
+# SampleDisco core (CPU) dependencies.
+# GPU acceleration is optional and environment/driver-specific: see
+# requirements-gpu.txt and .claude/CLAUDE.md.
+numpy>=1.23
+pandas>=1.5
+scipy>=1.9
+scikit-learn>=1.2
+scikit-misc>=0.3
+statsmodels>=0.13
+patsy>=0.5
+scanpy>=1.11
+anndata>=0.10
+muon>=0.1
+harmony-pytorch>=0.1
+harmonypy>=0.0.9
+scglue>=0.3
+torch>=2.0
+python-igraph>=0.10
+leidenalg>=0.9
+networkx>=3.0
+POT>=0.9
+pygam>=0.9
+numba>=0.57
+matplotlib>=3.6
+seaborn>=0.12
+pyyaml>=6.0
+psutil>=5.9
+ruamel.yaml>=0.17
+pybedtools>=0.9
+
+# multi-omics gene annotation (scGLUE path, imported at module top)
+pyensembl>=2.3
+# cluster-DGE (RAISIN) — both on the live downstream path
+combat>=0.3
+adjustText>=1.0
+# NOTE: scGLUE must be installed from PyPI (`pip install scglue`), NOT bioconda —
+# the bioconda recipe caps numpy<1.22 and breaks the rest of the stack.

sampledisco-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

sampledisco-0.1.0/src/sampledisco/__init__.py

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+"""SampleDisco — cross-omics, cross-condition sample embedding for single-cell data.
+
+Public API (imported lazily so ``import sampledisco`` stays light and does not
+pull scanpy / torch / scGLUE until you actually call into the pipeline):
+
+    import sampledisco
+    sampledisco.wrapper(...)                 # full pipeline (RNA / ATAC / multi-omics)
+    sampledisco.compute_sample_embedding(...)  # the core method only
+
+The CLI entry point is ``sampledisco --config <yaml>`` (see ``sampledisco.cli``).
+"""
+from __future__ import annotations
+
+__version__ = "0.1.0"
+
+__all__ = ["wrapper", "compute_sample_embedding"]
+
+
+def __getattr__(name: str):
+    # PEP 562 lazy attribute access — defer heavy imports to first use.
+    if name == "wrapper":
+        from sampledisco.wrapper.wrapper import wrapper
+        return wrapper
+    if name == "compute_sample_embedding":
+        from sampledisco.sample_embedding import compute_sample_embedding
+        return compute_sample_embedding
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

sampledisco-0.1.0/src/sampledisco/cli.py

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+import argparse
+import sys
+import traceback
+import yaml
+import os
+import inspect
+from sampledisco.wrapper.wrapper import wrapper
+
+def parse_args():
+    parser = argparse.ArgumentParser(description="Run the data processing wrapper.")
+
+    parser.add_argument("-m", "--mode", type=str, required=True, choices=["simple", "complex"],
+                        help="Run mode. Choose 'simple' or 'complex'.")
+
+    # Simple mode args
+    parser.add_argument("-c", "--count_data", type=str, help="Path to count data file")
+    parser.add_argument("-s", "--sample_meta_data", type=str, help="(Optional) Path to sample metadata file")
+    parser.add_argument("-o", "--output_directory", type=str, help="Path to output directory")
+
+    # Complex mode args
+    parser.add_argument("--config", type=str, help="Path to YAML config file")
+
+    return parser.parse_args()
+
+def load_config(config_path):
+    if not os.path.exists(config_path):
+        print(f"Error: Config file '{config_path}' does not exist.", file=sys.stderr)
+        sys.exit(1)
+    with open(config_path, 'r') as f:
+        return yaml.safe_load(f)
+
+def validate_config(config, func):
+    valid_params = inspect.signature(func).parameters
+    for key in config:
+        if key not in valid_params:
+            raise ValueError(f"Unexpected parameter in config: '{key}'")
+    for key in valid_params:
+        if key not in config:
+            raise ValueError(f"Missing required parameter in config: '{key}'")
+
+def main():
+    args = parse_args()
+
+    if args.mode == "simple":
+        if not args.count_data or not args.output_directory:
+            print("Error: In 'simple' mode, -c and -o must be provided.", file=sys.stderr)
+            sys.exit(1)
+
+        if args.sample_meta_data:
+            wrapper(args.count_data, args.sample_meta_data, args.output_directory)
+        else:
+            wrapper(args.count_data, output_directory=args.output_directory)
+
+    elif args.mode == "complex":
+        if not args.config:
+            print("Error: In 'complex' mode, --config must be provided.", file=sys.stderr)
+            sys.exit(1)
+
+        config = load_config(args.config)
+
+        try:
+            validate_config(config, wrapper)
+            wrapper(**config)
+        except Exception as e:
+            print(f"Error: {e}", file=sys.stderr)
+            print(traceback.format_exc(), file=sys.stderr)
+            sys.exit(1)
+
+if __name__ == "__main__":
+    main()