eca-pp 0.4.0__tar.gz

eca_pp-0.4.0/PKG-INFO

@@ -0,0 +1,281 @@
+Metadata-Version: 2.4
+Name: eca-pp
+Version: 0.4.0
+Summary: Standardized single-cell preprocessing for the Ensemble Cell Atlas ecosystem
+Project-URL: Repository, https://github.com/chansigit/eca-pp
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.22
+Requires-Dist: scipy>=1.7
+Requires-Dist: h5py>=3.8
+Requires-Dist: anndata>=0.8
+Requires-Dist: stancounts>=0.3
+Requires-Dist: stangene>=0.5
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Provides-Extra: llm
+Requires-Dist: deepseek-harness-sdk>=0.1.2a3; extra == "llm"
+Requires-Dist: mcp>=1.27; extra == "llm"
+Requires-Dist: PyYAML>=6; extra == "llm"
+Requires-Dist: uvicorn>=0.30; extra == "llm"
+Requires-Dist: anyio>=4.0; extra == "llm"
+Provides-Extra: probe
+Requires-Dist: scanpy>=1.10; extra == "probe"
+Requires-Dist: harmonypy<0.3,>=0.0.9; extra == "probe"
+Requires-Dist: scikit-learn>=1.1; extra == "probe"
+Requires-Dist: leidenalg>=0.10; extra == "probe"
+Provides-Extra: agent
+Requires-Dist: openai-agents<1,>=0.22; extra == "agent"
+Requires-Dist: deepseek-harness-sdk>=0.1.2a3; extra == "agent"
+Requires-Dist: mcp>=1.27; extra == "agent"
+Requires-Dist: PyYAML>=6; extra == "agent"
+Requires-Dist: uvicorn>=0.30; extra == "agent"
+Requires-Dist: anyio>=4.0; extra == "agent"
+Provides-Extra: claude
+Requires-Dist: claude-agent-sdk>=0.2.152; extra == "claude"
+Requires-Dist: anyio>=4.0; extra == "claude"
+Provides-Extra: openai
+Requires-Dist: openai-agents<1,>=0.22; extra == "openai"
+Requires-Dist: anyio>=4.0; extra == "openai"
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/chansigit/eca-pp/main/assets/eca-pp-logo.svg" alt="ECA-PP logo: scattered cells organized into a consistent atlas" width="160" height="160">
+</p>
+
+<h1 align="center">ECA-PP: Standardized Single-Cell Preprocessing</h1>
+
+<p align="center">
+  <strong>Give real-world single-cell data a consistent starting point.</strong>
+</p>
+
+<p align="center">
+  <a href="pyproject.toml"><img src="https://img.shields.io/badge/Version-0.4.0-258B81?style=flat" alt="Project version 0.4.0"></a>
+  <a href="pyproject.toml"><img src="https://img.shields.io/badge/Python-3.10%2B-3776AB?style=flat&amp;logo=python&amp;logoColor=white" alt="Python 3.10 or newer"></a>
+  <a href="#where-it-fits"><img src="https://img.shields.io/badge/Input-H5AD-64748B?style=flat" alt="Starts from H5AD data"></a>
+  <a href="https://github.com/chansigit/eca-rsi"><img src="https://img.shields.io/badge/Ecosystem-Ensemble_Cell_Atlas-258B81?style=flat" alt="Part of the Ensemble Cell Atlas ecosystem"></a>
+</p>
+
+<p align="center">
+  <a href="#why-standardize-before-analysis">🔬 Why ECA-PP?</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#what-you-get">What you get</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#try-it">🚀 Try it</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#faq">FAQ</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#further-reading">📖 Further reading</a>
+</p>
+
+<br>
+
+ECA-PP prepares published single-cell RNA sequencing datasets for reuse. Starting
+from an **H5AD file**, it finds expression counts, standardizes gene names,
+calculates quality-control measurements, and identifies useful batch and
+cell-type metadata. You get prepared data and a record of the evidence behind
+each decision.
+
+ECA-PP belongs to the **Ensemble Cell Atlas (ECA)** ecosystem. It handles routine
+preprocessing for **[ECA-RSI](https://github.com/chansigit/eca-rsi)**
+(Recursive Self-Improvement), ECA's automated data governance system, so that
+system can focus on quality assessment, annotation, and iterative refinement.
+You can also use ECA-PP independently in your own pipeline.
+
+<br>
+
+## Why standardize before analysis?
+
+Public single-cell data reflects the choices of many different authors.
+Expression matrices arrive as text tables, sparse matrix files, Seurat objects,
+or H5AD files, often with metadata in separate supplements. Converting them into
+one format solves only part of the problem.
+
+Inside an H5AD file, expression values may be raw, normalized, or scaled. Gene
+names may mix old symbols and Ensembl IDs. Sample and cell-type columns may use
+unfamiliar names, duplicate one another, or contain missing values. Even existing
+QC measurements may have been calculated using different gene sets.
+
+ECA-PP gives these recurring problems a shared treatment:
+
+- **Consistent preprocessing across studies.** Counts checks, gene mapping, and
+  QC use a common implementation. QC and normalized expression are calculated
+  on the same final gene set.
+
+- **Metadata choices supported by data.** Small integration trials test batch
+  candidates for improved mixing and preservation of cell-type structure.
+  Technical and donor factors take priority over biological conditions.
+
+- **Automation you can inspect.** Model suggestions pass programmatic checks;
+  built-in rules keep column identification moving when a model is unavailable.
+  Decisions, changes, and unresolved questions are recorded for review.
+
+<br>
+
+## What you get
+
+- **A standardized dataset.** An H5AD with counts, normalized expression,
+  standardized gene names, QC measurements, and preserved author metadata.
+
+- **Guidance for downstream analysis.** Proposed batch and existing cell-type
+  columns, evidence for each selection, and an assessment of whether batch
+  correction is needed.
+
+- **A record of what happened.** Each step writes a `result.json` describing its
+  outcome, changes, and issues that need attention. Your source file stays unchanged.
+
+<br>
+
+## Where it fits
+
+General-purpose agents can usually download files, unpack archives, and script
+conversions into `.h5ad`, the AnnData format used by Scanpy. **ECA-PP starts at
+H5AD**, where decisions about counts, gene identity, QC, and batch structure need
+domain-specific standards applied consistently across studies.
+
+| Stage | Responsibility |
+| --- | --- |
+| Upstream tools or agents | Gather published files and convert them into H5AD. |
+| ECA-PP | Standardize the data and evaluate metadata using shared rules and recorded evidence. |
+| ECA-RSI | Coordinate subsequent quality review, annotation, and iterative refinement. |
+
+ECA-PP currently prepares data and evaluates metadata. It does not assign new
+biological cell-type labels, filter individual low-quality cells or doublets,
+or produce a final integrated atlas.
+
+Follow the main path below; the lower branches show required review, dataset
+rejection, and the trial loop used to evaluate metadata. Click the diagram for
+an interactive version with search, zoom, and guided views.
+
+<p align="center">
+  <a href="https://raw.githack.com/chansigit/eca-pp/main/docs/workflow.html">
+    <picture>
+      <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/chansigit/eca-pp/main/assets/eca-pp-workflow-dark.svg">
+      <img src="https://raw.githubusercontent.com/chansigit/eca-pp/main/assets/eca-pp-workflow-light.svg" alt="ECA-PP workflow: input H5AD, standardization, prepared data, metadata identification with integration trials, recorded decisions, and handoff to ECA-RSI. Unresolved standardization choices need review; unsuitable inputs are rejected." width="1100">
+    </picture>
+  </a>
+</p>
+
+<br>
+
+## Try it
+
+### 1. Install
+
+Use Python 3.10 or newer, preferably in a dedicated environment. ECA-PP runs on CPUs.
+
+```bash
+pip install "eca-pp[probe,openai]==0.4.0"
+```
+
+This also installs `stancounts` and `stangene`, the counts-recovery and gene-mapping
+dependencies. To work on ECA-PP itself, clone this repository and use
+`pip install ".[probe,openai]"` instead.
+
+### 2. Standardize your dataset
+
+Replace `your-data.h5ad` with your input file:
+
+```bash
+eca-pp-standardize your-data.h5ad -o results/standardize
+```
+
+Open **`results/standardize/result.json`** to check the outcome. A successful run
+produces `standardized.h5ad`. If a required choice is unresolved, such as the
+species, the report explains what needs clarification before you continue.
+
+<details>
+<summary>Dataset size checks and gene filtering</summary>
+
+The default checks require at least **100 cells and 5,000 detected genes across
+the whole dataset**. A gene is detected if it has a nonzero count in at least one
+cell. **This is not a requirement for each cell to express 5,000 genes.**
+
+By default, features that cannot be mapped to a canonical gene are removed from
+the output. Use `--keep-unmapped` to retain them. The dataset-level gene threshold
+is checked again after gene mapping and filtering.
+
+See the [tutorial's options](https://github.com/chansigit/eca-pp/blob/main/docs/tutorial.md#4-常用参数) for adjusting size checks
+or specifying the species and counts layer.
+
+</details>
+
+### 3. Identify batch and cell-type columns
+
+After successful standardization, run:
+
+```bash
+eca-pp-identify-columns results/standardize/standardized.h5ad \
+  -o results/columns
+```
+
+For AI-assisted decisions, set `ARK_API_KEY` in your environment before running
+this command. The default uses Doubao Turbo through the OpenAI Agents SDK.
+Without model credentials, ECA-PP uses built-in rules and integration trials.
+
+Read **`results/columns/result.json`** for the selected columns and supporting
+evidence. For example, ECA-PP may identify a sequencing channel as the batch but
+conclude that the cells are already sufficiently mixed and correction is unnecessary.
+
+<details>
+<summary>Find the output files</summary>
+
+| File | Contents |
+| --- | --- |
+| `results/standardize/standardized.h5ad` | Prepared expression data, gene identifiers, and QC measurements. |
+| `results/standardize/result.json` | Input checks, counts source, species, gene changes, and review notes. |
+| `results/columns/result.json` | Selected metadata, correction assessment, decisions, and trial results. |
+| `results/columns/batch.tsv` | Batch labels when the selected grouping is derived from barcodes or multiple columns; created only when needed. |
+
+</details>
+
+<br>
+
+## FAQ
+
+### Does ECA-PP change my original data?
+
+The source file stays unchanged. ECA-PP writes a separate dataset, preserves
+author metadata, and backs up fields it replaces. Gene mapping and filtering
+changes are recorded. Standardization may reject a whole dataset that fails its
+checks, but does not remove individual cells from an accepted dataset.
+
+### What does an empty batch or cell-type result mean?
+
+`null` means no suitable column was selected. This can be a valid outcome when
+evidence is insufficient. A selected batch with `correction: "unnecessary"`
+means the evidence did not support correcting it. Neither conclusion should be
+confused with an execution error; check the outcome and reasons in `result.json`.
+
+### Do I need an AI model?
+
+Standardization runs locally by default; optional AI assistance is available for
+unresolved species inference. Column identification uses a model when configured
+and falls back to built-in rules when it is unavailable. See the
+[model configuration guide](https://github.com/chansigit/eca-pp/blob/main/docs/tutorial.md#8-识别批次列--细胞类型列identify-columns)
+for backend and model choices.
+
+### Can I recover counts from normalized data?
+
+ECA-PP uses [stancounts](https://github.com/chansigit/stancounts) to recover counts
+from supported transformed inputs when possible. Recovery depends on the data;
+unsupported or ambiguous cases are reported rather than silently treated as raw counts.
+
+<br>
+
+## Further reading
+
+**For users:** the [hands-on tutorial](https://github.com/chansigit/eca-pp/blob/main/docs/tutorial.md) walks through a real
+mouse dataset, result interpretation, common options, model setup, and reruns.
+The tutorial is currently in Chinese. Each command also provides `--help`.
+
+**For developers:** the [standardization specification](https://github.com/chansigit/eca-pp/blob/main/docs/standardize-spec.md)
+and [column-identification specification](https://github.com/chansigit/eca-pp/blob/main/docs/identify-columns-spec.md) describe
+methods, interfaces, and tests. Download the
+[interactive architecture diagram](https://github.com/chansigit/eca-pp/blob/main/docs/architecture.html) to open it in a browser.
+
+**Continue in the ECA ecosystem:** [ECA-RSI](https://github.com/chansigit/eca-rsi)
+coordinates downstream analysis, including sample-level QC and annotation with
+[OSP](https://github.com/chansigit/osp).
+
+For questions, unexpected results, or feature requests,
+[open an issue](https://github.com/chansigit/eca-pp/issues).

eca_pp-0.4.0/README.md

@@ -0,0 +1,241 @@
+<p align="center">
+  <img src="https://raw.githubusercontent.com/chansigit/eca-pp/main/assets/eca-pp-logo.svg" alt="ECA-PP logo: scattered cells organized into a consistent atlas" width="160" height="160">
+</p>
+
+<h1 align="center">ECA-PP: Standardized Single-Cell Preprocessing</h1>
+
+<p align="center">
+  <strong>Give real-world single-cell data a consistent starting point.</strong>
+</p>
+
+<p align="center">
+  <a href="pyproject.toml"><img src="https://img.shields.io/badge/Version-0.4.0-258B81?style=flat" alt="Project version 0.4.0"></a>
+  <a href="pyproject.toml"><img src="https://img.shields.io/badge/Python-3.10%2B-3776AB?style=flat&amp;logo=python&amp;logoColor=white" alt="Python 3.10 or newer"></a>
+  <a href="#where-it-fits"><img src="https://img.shields.io/badge/Input-H5AD-64748B?style=flat" alt="Starts from H5AD data"></a>
+  <a href="https://github.com/chansigit/eca-rsi"><img src="https://img.shields.io/badge/Ecosystem-Ensemble_Cell_Atlas-258B81?style=flat" alt="Part of the Ensemble Cell Atlas ecosystem"></a>
+</p>
+
+<p align="center">
+  <a href="#why-standardize-before-analysis">🔬 Why ECA-PP?</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#what-you-get">What you get</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#try-it">🚀 Try it</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#faq">FAQ</a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="#further-reading">📖 Further reading</a>
+</p>
+
+<br>
+
+ECA-PP prepares published single-cell RNA sequencing datasets for reuse. Starting
+from an **H5AD file**, it finds expression counts, standardizes gene names,
+calculates quality-control measurements, and identifies useful batch and
+cell-type metadata. You get prepared data and a record of the evidence behind
+each decision.
+
+ECA-PP belongs to the **Ensemble Cell Atlas (ECA)** ecosystem. It handles routine
+preprocessing for **[ECA-RSI](https://github.com/chansigit/eca-rsi)**
+(Recursive Self-Improvement), ECA's automated data governance system, so that
+system can focus on quality assessment, annotation, and iterative refinement.
+You can also use ECA-PP independently in your own pipeline.
+
+<br>
+
+## Why standardize before analysis?
+
+Public single-cell data reflects the choices of many different authors.
+Expression matrices arrive as text tables, sparse matrix files, Seurat objects,
+or H5AD files, often with metadata in separate supplements. Converting them into
+one format solves only part of the problem.
+
+Inside an H5AD file, expression values may be raw, normalized, or scaled. Gene
+names may mix old symbols and Ensembl IDs. Sample and cell-type columns may use
+unfamiliar names, duplicate one another, or contain missing values. Even existing
+QC measurements may have been calculated using different gene sets.
+
+ECA-PP gives these recurring problems a shared treatment:
+
+- **Consistent preprocessing across studies.** Counts checks, gene mapping, and
+  QC use a common implementation. QC and normalized expression are calculated
+  on the same final gene set.
+
+- **Metadata choices supported by data.** Small integration trials test batch
+  candidates for improved mixing and preservation of cell-type structure.
+  Technical and donor factors take priority over biological conditions.
+
+- **Automation you can inspect.** Model suggestions pass programmatic checks;
+  built-in rules keep column identification moving when a model is unavailable.
+  Decisions, changes, and unresolved questions are recorded for review.
+
+<br>
+
+## What you get
+
+- **A standardized dataset.** An H5AD with counts, normalized expression,
+  standardized gene names, QC measurements, and preserved author metadata.
+
+- **Guidance for downstream analysis.** Proposed batch and existing cell-type
+  columns, evidence for each selection, and an assessment of whether batch
+  correction is needed.
+
+- **A record of what happened.** Each step writes a `result.json` describing its
+  outcome, changes, and issues that need attention. Your source file stays unchanged.
+
+<br>
+
+## Where it fits
+
+General-purpose agents can usually download files, unpack archives, and script
+conversions into `.h5ad`, the AnnData format used by Scanpy. **ECA-PP starts at
+H5AD**, where decisions about counts, gene identity, QC, and batch structure need
+domain-specific standards applied consistently across studies.
+
+| Stage | Responsibility |
+| --- | --- |
+| Upstream tools or agents | Gather published files and convert them into H5AD. |
+| ECA-PP | Standardize the data and evaluate metadata using shared rules and recorded evidence. |
+| ECA-RSI | Coordinate subsequent quality review, annotation, and iterative refinement. |
+
+ECA-PP currently prepares data and evaluates metadata. It does not assign new
+biological cell-type labels, filter individual low-quality cells or doublets,
+or produce a final integrated atlas.
+
+Follow the main path below; the lower branches show required review, dataset
+rejection, and the trial loop used to evaluate metadata. Click the diagram for
+an interactive version with search, zoom, and guided views.
+
+<p align="center">
+  <a href="https://raw.githack.com/chansigit/eca-pp/main/docs/workflow.html">
+    <picture>
+      <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/chansigit/eca-pp/main/assets/eca-pp-workflow-dark.svg">
+      <img src="https://raw.githubusercontent.com/chansigit/eca-pp/main/assets/eca-pp-workflow-light.svg" alt="ECA-PP workflow: input H5AD, standardization, prepared data, metadata identification with integration trials, recorded decisions, and handoff to ECA-RSI. Unresolved standardization choices need review; unsuitable inputs are rejected." width="1100">
+    </picture>
+  </a>
+</p>
+
+<br>
+
+## Try it
+
+### 1. Install
+
+Use Python 3.10 or newer, preferably in a dedicated environment. ECA-PP runs on CPUs.
+
+```bash
+pip install "eca-pp[probe,openai]==0.4.0"
+```
+
+This also installs `stancounts` and `stangene`, the counts-recovery and gene-mapping
+dependencies. To work on ECA-PP itself, clone this repository and use
+`pip install ".[probe,openai]"` instead.
+
+### 2. Standardize your dataset
+
+Replace `your-data.h5ad` with your input file:
+
+```bash
+eca-pp-standardize your-data.h5ad -o results/standardize
+```
+
+Open **`results/standardize/result.json`** to check the outcome. A successful run
+produces `standardized.h5ad`. If a required choice is unresolved, such as the
+species, the report explains what needs clarification before you continue.
+
+<details>
+<summary>Dataset size checks and gene filtering</summary>
+
+The default checks require at least **100 cells and 5,000 detected genes across
+the whole dataset**. A gene is detected if it has a nonzero count in at least one
+cell. **This is not a requirement for each cell to express 5,000 genes.**
+
+By default, features that cannot be mapped to a canonical gene are removed from
+the output. Use `--keep-unmapped` to retain them. The dataset-level gene threshold
+is checked again after gene mapping and filtering.
+
+See the [tutorial's options](https://github.com/chansigit/eca-pp/blob/main/docs/tutorial.md#4-常用参数) for adjusting size checks
+or specifying the species and counts layer.
+
+</details>
+
+### 3. Identify batch and cell-type columns
+
+After successful standardization, run:
+
+```bash
+eca-pp-identify-columns results/standardize/standardized.h5ad \
+  -o results/columns
+```
+
+For AI-assisted decisions, set `ARK_API_KEY` in your environment before running
+this command. The default uses Doubao Turbo through the OpenAI Agents SDK.
+Without model credentials, ECA-PP uses built-in rules and integration trials.
+
+Read **`results/columns/result.json`** for the selected columns and supporting
+evidence. For example, ECA-PP may identify a sequencing channel as the batch but
+conclude that the cells are already sufficiently mixed and correction is unnecessary.
+
+<details>
+<summary>Find the output files</summary>
+
+| File | Contents |
+| --- | --- |
+| `results/standardize/standardized.h5ad` | Prepared expression data, gene identifiers, and QC measurements. |
+| `results/standardize/result.json` | Input checks, counts source, species, gene changes, and review notes. |
+| `results/columns/result.json` | Selected metadata, correction assessment, decisions, and trial results. |
+| `results/columns/batch.tsv` | Batch labels when the selected grouping is derived from barcodes or multiple columns; created only when needed. |
+
+</details>
+
+<br>
+
+## FAQ
+
+### Does ECA-PP change my original data?
+
+The source file stays unchanged. ECA-PP writes a separate dataset, preserves
+author metadata, and backs up fields it replaces. Gene mapping and filtering
+changes are recorded. Standardization may reject a whole dataset that fails its
+checks, but does not remove individual cells from an accepted dataset.
+
+### What does an empty batch or cell-type result mean?
+
+`null` means no suitable column was selected. This can be a valid outcome when
+evidence is insufficient. A selected batch with `correction: "unnecessary"`
+means the evidence did not support correcting it. Neither conclusion should be
+confused with an execution error; check the outcome and reasons in `result.json`.
+
+### Do I need an AI model?
+
+Standardization runs locally by default; optional AI assistance is available for
+unresolved species inference. Column identification uses a model when configured
+and falls back to built-in rules when it is unavailable. See the
+[model configuration guide](https://github.com/chansigit/eca-pp/blob/main/docs/tutorial.md#8-识别批次列--细胞类型列identify-columns)
+for backend and model choices.
+
+### Can I recover counts from normalized data?
+
+ECA-PP uses [stancounts](https://github.com/chansigit/stancounts) to recover counts
+from supported transformed inputs when possible. Recovery depends on the data;
+unsupported or ambiguous cases are reported rather than silently treated as raw counts.
+
+<br>
+
+## Further reading
+
+**For users:** the [hands-on tutorial](https://github.com/chansigit/eca-pp/blob/main/docs/tutorial.md) walks through a real
+mouse dataset, result interpretation, common options, model setup, and reruns.
+The tutorial is currently in Chinese. Each command also provides `--help`.
+
+**For developers:** the [standardization specification](https://github.com/chansigit/eca-pp/blob/main/docs/standardize-spec.md)
+and [column-identification specification](https://github.com/chansigit/eca-pp/blob/main/docs/identify-columns-spec.md) describe
+methods, interfaces, and tests. Download the
+[interactive architecture diagram](https://github.com/chansigit/eca-pp/blob/main/docs/architecture.html) to open it in a browser.
+
+**Continue in the ECA ecosystem:** [ECA-RSI](https://github.com/chansigit/eca-rsi)
+coordinates downstream analysis, including sample-level QC and annotation with
+[OSP](https://github.com/chansigit/osp).
+
+For questions, unexpected results, or feature requests,
+[open an issue](https://github.com/chansigit/eca-pp/issues).

eca_pp-0.4.0/pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools>=68"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "eca-pp"
+version = "0.4.0"
+description = "Standardized single-cell preprocessing for the Ensemble Cell Atlas ecosystem"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "numpy>=1.22",
+    "scipy>=1.7",
+    "h5py>=3.8",
+    "anndata>=0.8",
+    "stancounts>=0.3",
+    "stangene>=0.5",
+]
+
+[project.optional-dependencies]
+test = ["pytest>=7.0"]
+llm = ["deepseek-harness-sdk>=0.1.2a3", "mcp>=1.27", "PyYAML>=6", "uvicorn>=0.30", "anyio>=4.0"]
+probe = ["scanpy>=1.10", "harmonypy>=0.0.9,<0.3", "scikit-learn>=1.1",
+         "leidenalg>=0.10"]
+agent = ["openai-agents>=0.22,<1", "deepseek-harness-sdk>=0.1.2a3",
+         "mcp>=1.27", "PyYAML>=6", "uvicorn>=0.30", "anyio>=4.0"]
+claude = ["claude-agent-sdk>=0.2.152", "anyio>=4.0"]
+openai = ["openai-agents>=0.22,<1", "anyio>=4.0"]
+# 下期: doublets = ["scrublet"], gpu = ["scvi-tools"] …
+
+[project.scripts]
+eca-pp-standardize = "eca_pp.standardize.cli:cli"
+eca-pp-integration-probe = "eca_pp.probe.cli:cli"
+eca-pp-identify-columns = "eca_pp.identify_columns.cli:cli"
+
+[project.urls]
+Repository = "https://github.com/chansigit/eca-pp"
+
+[tool.setuptools.packages.find]
+where = ["src"]

eca_pp-0.4.0/setup.cfg

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

eca_pp-0.4.0/src/eca_pp/__init__.py

@@ -0,0 +1,3 @@
+"""Standalone, orchestrator-free curation steps (spec: docs/standardize-spec.md)."""
+
+__version__ = "0.4.0"