andrey-core 0.1.0__tar.gz

andrey_core-0.1.0/.gitignore

@@ -0,0 +1,60 @@
+__pycache__/
+*.py[cod]
+*.so
+.pytest_cache/
+.ruff_cache/
+
+*.egg-info/
+build/
+dist/
+
+.venv*/
+venv/
+# The bench venv is built by benchmarks/start.sh, which pins competitor versions there.
+# Its lockfile is an artifact of that build, and travels with a batch's results, not the repo.
+benchmarks/uv.lock
+# The R package library benchmarks/start_r.sh builds for the R lane, beside the venv.
+benchmarks/.r-lib-bench/
+env/
+
+.vscode/
+.idea/
+*.swp
+*.code-workspace
+.DS_Store
+Thumbs.db
+
+.env
+.envrc
+
+*.log
+*.out
+tmp/
+temp/
+.cache/
+
+# Local job scripts (e.g., SLURM submit scripts).
+jobs/
+
+outputs/
+
+.claude/*
+!.claude/CLAUDE.md
+!.claude/commands
+!.claude/skills
+
+
+docs/PR/
+
+# docs site: generated build artifacts (never committed, never shipped in the wheel)
+docs/_build/
+docs/_generated/
+docs/docs/examples/*.ipynb
+docs/docs/code/generated/
+docs/_static/andrey-tokens.css
+docs/_static/graph-comparison.html
+docs/_static/graph-types-*.html
+
+.ipynb_checkpoints/
+apps/live-discovery/brand/
+apps/live-discovery/data/

andrey_core-0.1.0/LICENSE

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andrey_core-0.1.0/PKG-INFO

@@ -0,0 +1,224 @@
+Metadata-Version: 2.5
+Name: andrey-core
+Version: 0.1.0
+Summary: Andrey, a very fast causal discovery package
+Project-URL: Homepage, https://andrey.abel.ai
+Project-URL: Documentation, https://andrey.abel.ai/docs/
+Project-URL: Source, https://github.com/Abel-ai-lab/andrey
+Project-URL: Issues, https://github.com/Abel-ai-lab/andrey/issues
+Project-URL: Changelog, https://andrey.abel.ai/docs/changelog.html
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.11
+Requires-Dist: networkx>=3
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.2
+Requires-Dist: pydantic>=2
+Requires-Dist: pyyaml>=6
+Requires-Dist: scikit-learn>=1.5
+Requires-Dist: scipy>=1.13
+Requires-Dist: statsmodels>=0.14
+Requires-Dist: threadpoolctl>=3
+Requires-Dist: typer>=0.12
+Provides-Extra: all
+Requires-Dist: matplotlib>=3.7; extra == 'all'
+Requires-Dist: numba>=0.61; extra == 'all'
+Requires-Dist: pygraphviz>=2; extra == 'all'
+Requires-Dist: safetensors>=0.4; extra == 'all'
+Requires-Dist: torch>=2.2; extra == 'all'
+Provides-Extra: data
+Requires-Dist: safetensors>=0.4; extra == 'data'
+Provides-Extra: numba
+Requires-Dist: numba>=0.61; extra == 'numba'
+Provides-Extra: torch
+Requires-Dist: torch>=2.2; extra == 'torch'
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.7; extra == 'viz'
+Requires-Dist: pygraphviz>=2; extra == 'viz'
+Description-Content-Type: text/markdown
+
+<!-- One image on its own dark ground reads on both GitHub themes; PyPI keeps a plain <img>. -->
+<p align="center">
+  <img alt="Andrey, a very fast causal discovery package"
+    src="https://raw.githubusercontent.com/Abel-ai-lab/andrey/v0.1.0/.github/readme/banner.svg" width="830">
+</p>
+
+<p align="center">
+  <a href="https://github.com/Abel-ai-lab/andrey/actions/workflows/ci.yml"><img alt="CI status"
+    src="https://img.shields.io/github/actions/workflow/status/Abel-ai-lab/andrey/ci.yml?branch=main&amp;label=CI"></a>
+  <img alt="Python 3.11, 3.12, 3.13, 3.14"
+    src="https://img.shields.io/badge/python-3.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-3b5bdb">
+  <a href="https://github.com/Abel-ai-lab/andrey/blob/main/LICENSE"><img alt="License: Apache 2.0"
+    src="https://img.shields.io/badge/license-Apache%202.0-3b5bdb"></a>
+</p>
+
+Andrey is a causal discovery package for Python.
+
+<!-- PITCH:START -->
+<!-- Generated by apps/build_launch.py; do not edit. -->
+
+- **Fast**: Over 100x faster on PC, and faster on most other supported methods.
+- **Just as accurate**: the same errors or fewer in 38 of 42 comparisons with other packages.
+- **One API**: 18 methods, each one function call.
+- **Agent-ready**: a command line that answers in JSON, and a skill for coding agents.
+
+<!-- PITCH:END -->
+
+```shell
+uv add andrey-core
+```
+
+- **With pip**: `pip install andrey-core`
+- **Optional extras**: `andrey-core[numba]` for compiled CPU code, `andrey-core[torch]` for GPUs
+- **Development version**: `uv add git+https://github.com/Abel-ai-lab/andrey`
+- **[Installation guide](https://andrey.abel.ai/docs/guides/getting-started.html#install)**: the
+  extras, a PyTorch build for your GPU, and building Andrey from source
+
+<!-- CHART:START -->
+<!-- Generated from summary.json by apps/build_launch.py; do not edit. -->
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)"
+      srcset="https://raw.githubusercontent.com/Abel-ai-lab/andrey/v0.1.0/.github/readme/benchmark-chart-dark.svg">
+    <img alt="Andrey's speedup over the slowest package on the same data: PC 941x at 400 variables,
+      FCI 8.7x at 800 variables, GES 4.3x at 150 variables, BOSS 3.4x at 800 variables, GRaSP
+      1.4x at 400 variables, DirectLiNGAM 3.3x at 200 variables"
+      src="https://raw.githubusercontent.com/Abel-ai-lab/andrey/v0.1.0/.github/readme/benchmark-chart-light.svg" width="100%">
+  </picture>
+</p>
+
+<p align="center"><a href="https://andrey.abel.ai/docs/benchmarks.html">Benchmark report</a></p>
+
+<!-- CHART:END -->
+
+<!-- WHY_FAST:START -->
+<!-- Generated from site/why_fast.py by apps/build_launch.py; do not edit. -->
+
+Four ideas make it fast; each is animated in
+[a blog post](https://andrey.abel.ai/blog/why-andrey-is-fast.html):
+
+- **Do many things at once**: thousands of independence tests run as one array operation, with the
+  same results.
+- **Never compute twice**: the correlation matrix is computed once and cached; GES memoizes its
+  local scores.
+- **Skip what can't matter**: tests with a closed form settle most edges before any matrix is
+  inverted.
+- **Use the hardware you have**: with the optional extras, Numba compiles GES's path checks and a
+  GPU computes large tables.
+
+<!-- WHY_FAST:END -->
+
+## What's inside
+
+<!-- METHODS:START -->
+<!-- Generated from andrey.spec by apps/build_launch.py; do not edit. -->
+
+| Family | Methods | Returns |
+|---|---|---|
+| Constraint-based | [`pc`](https://andrey.abel.ai/docs/code/generated/andrey.pc.html), [`fci`](https://andrey.abel.ai/docs/code/generated/andrey.fci.html), [`gfci`](https://andrey.abel.ai/docs/code/generated/andrey.gfci.html)\*, [`cdnod`](https://andrey.abel.ai/docs/code/generated/andrey.cdnod.html)\* | CPDAG, PAG |
+| Score-based | [`ges`](https://andrey.abel.ai/docs/code/generated/andrey.ges.html), [`gies`](https://andrey.abel.ai/docs/code/generated/andrey.gies.html)\*, [`hc`](https://andrey.abel.ai/docs/code/generated/andrey.hc.html)\*, [`exact_search`](https://andrey.abel.ai/docs/code/generated/andrey.exact_search.html)\*, [`calm`](https://andrey.abel.ai/docs/code/generated/andrey.calm.html)\* | CPDAG, DAG |
+| Permutation-based | [`boss`](https://andrey.abel.ai/docs/code/generated/andrey.boss.html), [`grasp`](https://andrey.abel.ai/docs/code/generated/andrey.grasp.html) | CPDAG |
+| Linear non-Gaussian | [`direct_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.direct_lingam.html), [`ica_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.ica_lingam.html), [`multi_group_direct_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.multi_group_direct_lingam.html)\* | DAG |
+| Time series | [`varma_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.varma_lingam.html)\*, [`longitudinal_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.longitudinal_lingam.html)\* | Temporal graph |
+| Latent variables | [`gin`](https://andrey.abel.ai/docs/code/generated/andrey.gin.html)\* | DAG |
+| Pairwise direction | [`pnl`](https://andrey.abel.ai/docs/code/generated/andrey.pnl.html)\* | Two-node DAG |
+
+\* [Experimental](https://andrey.abel.ai/docs/code/index.html#experimental-methods):
+no published benchmark yet, and the API may change.
+
+<!-- METHODS:END -->
+
+## Quick start
+
+<!-- QUICKSTART:START -->
+<!-- Generated by apps/build_launch.py, which runs the code; do not edit. -->
+
+Learn the protein-signalling network of Sachs et al. (2005) from 853 cells, and score it against
+the known network:
+
+```python
+import andrey
+from andrey.data import load_dataset
+from andrey.metrics import score
+
+sachs = load_dataset("sachs")  # 853 cells, 11 proteins, and the known network
+out = andrey.pc(sachs.data)    # learn a graph
+print(out)
+
+scores = score(out.structure, sachs.graph)
+print({k: round(scores[k], 2) for k in ("shd", "skeleton_precision", "skeleton_recall")})
+```
+
+```text
+PC  cpdag  |  11 nodes  |  8 edges (6 undirected, 2 directed)
+
+  raf -- mek
+  plc -- pip3
+  pip2 -- pip3
+  erk -- akt
+  erk -- pka
+  akt -- pka
+  p38 -> pkc
+  jnk -> pkc
+{'shd': 11, 'skeleton_precision': 1.0, 'skeleton_recall': 0.47}
+```
+
+PC finds 8 edges, all among the known network's 17. The structural Hamming distance (SHD) counts
+the edges to add, remove, or reorient to reach the known network: 11 here (9 edges are missing, and
+2 are oriented that the known network leaves undirected), and 17 for a graph with no edges.
+
+<!-- QUICKSTART:END -->
+
+For your own data, pass a pandas DataFrame or a NumPy array: one row per sample, one column per
+variable. From a shell or an agent:
+
+```shell
+andrey run pc --data your_data.csv   # JSON when piped, a summary in a terminal
+andrey --skill                       # a guide an agent loads as a skill
+```
+
+## Learn more
+
+- [Documentation](https://andrey.abel.ai/docs/): guides and the API reference.
+- [Examples](https://andrey.abel.ai/docs/examples/): notebooks, one method or task each.
+- [Demos](https://andrey.abel.ai/docs/demos/): step through methods and explore results in your
+  browser.
+- [Benchmarks](https://andrey.abel.ai/docs/benchmarks.html): every size, time, and error count.
+- [Launch post](https://andrey.abel.ai/blog/introducing-andrey.html),
+  [FAQ](https://andrey.abel.ai/docs/faq.html), and
+  [changelog](https://andrey.abel.ai/docs/changelog.html).
+
+Andrey is in alpha: the API may change between releases, so pin the version you use. Linux is fully
+tested; macOS and Windows install and run on the CPU, but the full test suite and the GPU speedups
+(CUDA / MPS) are not tested there yet.
+
+## Citing, license, contributing
+
+If you use Andrey in your work, please cite it, or use the
+[citation file](https://github.com/Abel-ai-lab/andrey/blob/main/CITATION.cff):
+
+```bibtex
+@software{andrey,
+  author = {{Abel AI Lab}},
+  title = {Andrey: A very fast causal discovery package},
+  year = {2026},
+  version = {0.1.0},
+  url = {https://andrey.abel.ai},
+}
+```
+
+Andrey is released under the
+[Apache License 2.0](https://github.com/Abel-ai-lab/andrey/blob/main/LICENSE). Bug reports and pull
+requests are welcome in the [issue tracker](https://github.com/Abel-ai-lab/andrey/issues); the
+[contributing guide](https://github.com/Abel-ai-lab/andrey/blob/main/CONTRIBUTING.md) explains how
+to set up a development environment.
+
+Andrey is inspired by
+[causal-learn](https://github.com/py-why/causal-learn), [pgmpy](https://github.com/pgmpy/pgmpy),
+[Tetrad](https://github.com/cmu-phil/tetrad), and many other causal discovery packages.

andrey_core-0.1.0/README.md

@@ -0,0 +1,180 @@
+<!-- One image on its own dark ground reads on both GitHub themes; PyPI keeps a plain <img>. -->
+<p align="center">
+  <img alt="Andrey, a very fast causal discovery package"
+    src=".github/readme/banner.svg" width="830">
+</p>
+
+<p align="center">
+  <a href="https://github.com/Abel-ai-lab/andrey/actions/workflows/ci.yml"><img alt="CI status"
+    src="https://img.shields.io/github/actions/workflow/status/Abel-ai-lab/andrey/ci.yml?branch=main&amp;label=CI"></a>
+  <img alt="Python 3.11, 3.12, 3.13, 3.14"
+    src="https://img.shields.io/badge/python-3.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-3b5bdb">
+  <a href="https://github.com/Abel-ai-lab/andrey/blob/main/LICENSE"><img alt="License: Apache 2.0"
+    src="https://img.shields.io/badge/license-Apache%202.0-3b5bdb"></a>
+</p>
+
+Andrey is a causal discovery package for Python.
+
+<!-- PITCH:START -->
+<!-- Generated by apps/build_launch.py; do not edit. -->
+
+- **Fast**: Over 100x faster on PC, and faster on most other supported methods.
+- **Just as accurate**: the same errors or fewer in 38 of 42 comparisons with other packages.
+- **One API**: 18 methods, each one function call.
+- **Agent-ready**: a command line that answers in JSON, and a skill for coding agents.
+
+<!-- PITCH:END -->
+
+```shell
+uv add andrey-core
+```
+
+- **With pip**: `pip install andrey-core`
+- **Optional extras**: `andrey-core[numba]` for compiled CPU code, `andrey-core[torch]` for GPUs
+- **Development version**: `uv add git+https://github.com/Abel-ai-lab/andrey`
+- **[Installation guide](https://andrey.abel.ai/docs/guides/getting-started.html#install)**: the
+  extras, a PyTorch build for your GPU, and building Andrey from source
+
+<!-- CHART:START -->
+<!-- Generated from summary.json by apps/build_launch.py; do not edit. -->
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)"
+      srcset=".github/readme/benchmark-chart-dark.svg">
+    <img alt="Andrey's speedup over the slowest package on the same data: PC 941x at 400 variables,
+      FCI 8.7x at 800 variables, GES 4.3x at 150 variables, BOSS 3.4x at 800 variables, GRaSP
+      1.4x at 400 variables, DirectLiNGAM 3.3x at 200 variables"
+      src=".github/readme/benchmark-chart-light.svg" width="100%">
+  </picture>
+</p>
+
+<p align="center"><a href="https://andrey.abel.ai/docs/benchmarks.html">Benchmark report</a></p>
+
+<!-- CHART:END -->
+
+<!-- WHY_FAST:START -->
+<!-- Generated from site/why_fast.py by apps/build_launch.py; do not edit. -->
+
+Four ideas make it fast; each is animated in
+[a blog post](https://andrey.abel.ai/blog/why-andrey-is-fast.html):
+
+- **Do many things at once**: thousands of independence tests run as one array operation, with the
+  same results.
+- **Never compute twice**: the correlation matrix is computed once and cached; GES memoizes its
+  local scores.
+- **Skip what can't matter**: tests with a closed form settle most edges before any matrix is
+  inverted.
+- **Use the hardware you have**: with the optional extras, Numba compiles GES's path checks and a
+  GPU computes large tables.
+
+<!-- WHY_FAST:END -->
+
+## What's inside
+
+<!-- METHODS:START -->
+<!-- Generated from andrey.spec by apps/build_launch.py; do not edit. -->
+
+| Family | Methods | Returns |
+|---|---|---|
+| Constraint-based | [`pc`](https://andrey.abel.ai/docs/code/generated/andrey.pc.html), [`fci`](https://andrey.abel.ai/docs/code/generated/andrey.fci.html), [`gfci`](https://andrey.abel.ai/docs/code/generated/andrey.gfci.html)\*, [`cdnod`](https://andrey.abel.ai/docs/code/generated/andrey.cdnod.html)\* | CPDAG, PAG |
+| Score-based | [`ges`](https://andrey.abel.ai/docs/code/generated/andrey.ges.html), [`gies`](https://andrey.abel.ai/docs/code/generated/andrey.gies.html)\*, [`hc`](https://andrey.abel.ai/docs/code/generated/andrey.hc.html)\*, [`exact_search`](https://andrey.abel.ai/docs/code/generated/andrey.exact_search.html)\*, [`calm`](https://andrey.abel.ai/docs/code/generated/andrey.calm.html)\* | CPDAG, DAG |
+| Permutation-based | [`boss`](https://andrey.abel.ai/docs/code/generated/andrey.boss.html), [`grasp`](https://andrey.abel.ai/docs/code/generated/andrey.grasp.html) | CPDAG |
+| Linear non-Gaussian | [`direct_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.direct_lingam.html), [`ica_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.ica_lingam.html), [`multi_group_direct_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.multi_group_direct_lingam.html)\* | DAG |
+| Time series | [`varma_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.varma_lingam.html)\*, [`longitudinal_lingam`](https://andrey.abel.ai/docs/code/generated/andrey.longitudinal_lingam.html)\* | Temporal graph |
+| Latent variables | [`gin`](https://andrey.abel.ai/docs/code/generated/andrey.gin.html)\* | DAG |
+| Pairwise direction | [`pnl`](https://andrey.abel.ai/docs/code/generated/andrey.pnl.html)\* | Two-node DAG |
+
+\* [Experimental](https://andrey.abel.ai/docs/code/index.html#experimental-methods):
+no published benchmark yet, and the API may change.
+
+<!-- METHODS:END -->
+
+## Quick start
+
+<!-- QUICKSTART:START -->
+<!-- Generated by apps/build_launch.py, which runs the code; do not edit. -->
+
+Learn the protein-signalling network of Sachs et al. (2005) from 853 cells, and score it against
+the known network:
+
+```python
+import andrey
+from andrey.data import load_dataset
+from andrey.metrics import score
+
+sachs = load_dataset("sachs")  # 853 cells, 11 proteins, and the known network
+out = andrey.pc(sachs.data)    # learn a graph
+print(out)
+
+scores = score(out.structure, sachs.graph)
+print({k: round(scores[k], 2) for k in ("shd", "skeleton_precision", "skeleton_recall")})
+```
+
+```text
+PC  cpdag  |  11 nodes  |  8 edges (6 undirected, 2 directed)
+
+  raf -- mek
+  plc -- pip3
+  pip2 -- pip3
+  erk -- akt
+  erk -- pka
+  akt -- pka
+  p38 -> pkc
+  jnk -> pkc
+{'shd': 11, 'skeleton_precision': 1.0, 'skeleton_recall': 0.47}
+```
+
+PC finds 8 edges, all among the known network's 17. The structural Hamming distance (SHD) counts
+the edges to add, remove, or reorient to reach the known network: 11 here (9 edges are missing, and
+2 are oriented that the known network leaves undirected), and 17 for a graph with no edges.
+
+<!-- QUICKSTART:END -->
+
+For your own data, pass a pandas DataFrame or a NumPy array: one row per sample, one column per
+variable. From a shell or an agent:
+
+```shell
+andrey run pc --data your_data.csv   # JSON when piped, a summary in a terminal
+andrey --skill                       # a guide an agent loads as a skill
+```
+
+## Learn more
+
+- [Documentation](https://andrey.abel.ai/docs/): guides and the API reference.
+- [Examples](https://andrey.abel.ai/docs/examples/): notebooks, one method or task each.
+- [Demos](https://andrey.abel.ai/docs/demos/): step through methods and explore results in your
+  browser.
+- [Benchmarks](https://andrey.abel.ai/docs/benchmarks.html): every size, time, and error count.
+- [Launch post](https://andrey.abel.ai/blog/introducing-andrey.html),
+  [FAQ](https://andrey.abel.ai/docs/faq.html), and
+  [changelog](https://andrey.abel.ai/docs/changelog.html).
+
+Andrey is in alpha: the API may change between releases, so pin the version you use. Linux is fully
+tested; macOS and Windows install and run on the CPU, but the full test suite and the GPU speedups
+(CUDA / MPS) are not tested there yet.
+
+## Citing, license, contributing
+
+If you use Andrey in your work, please cite it, or use the
+[citation file](https://github.com/Abel-ai-lab/andrey/blob/main/CITATION.cff):
+
+```bibtex
+@software{andrey,
+  author = {{Abel AI Lab}},
+  title = {Andrey: A very fast causal discovery package},
+  year = {2026},
+  version = {0.1.0},
+  url = {https://andrey.abel.ai},
+}
+```
+
+Andrey is released under the
+[Apache License 2.0](https://github.com/Abel-ai-lab/andrey/blob/main/LICENSE). Bug reports and pull
+requests are welcome in the [issue tracker](https://github.com/Abel-ai-lab/andrey/issues); the
+[contributing guide](https://github.com/Abel-ai-lab/andrey/blob/main/CONTRIBUTING.md) explains how
+to set up a development environment.
+
+Andrey is inspired by
+[causal-learn](https://github.com/py-why/causal-learn), [pgmpy](https://github.com/pgmpy/pgmpy),
+[Tetrad](https://github.com/cmu-phil/tetrad), and many other causal discovery packages.