descriptron-core 2.0.1__tar.gz

descriptron_core-2.0.1/.gitignore

@@ -0,0 +1,56 @@
+# This tree holds a 116 GB conda installation, a 10 GB tarball, 12 GB of demo
+# imagery and years of run outputs. Exclude everything, then re-include the code.
+*
+
+!.gitignore
+!README.md
+!LICENSE
+!CITATION.cff
+!docs/
+!docs/**
+!docker/
+!docker/**
+!environments/
+!environments/**
+!packages/
+!packages/**
+
+# the Descriptron programs themselves
+!segment-anything-2/
+segment-anything-2/*
+!segment-anything-2/gui/
+segment-anything-2/gui/*
+!segment-anything-2/gui/*.py
+!segment-anything-2/gui/*.sh
+!segment-anything-2/gui/measure/
+segment-anything-2/gui/measure/*
+!segment-anything-2/gui/measure/*.py
+!segment-anything-2/gui/measure/*.sh
+!segment-anything-2/gui/measure/biorag_prompts/
+!segment-anything-2/gui/measure/biorag_prompts/**
+!segment-anything-2/gui/measure/tests/
+!segment-anything-2/gui/measure/tests/*.py
+!segment-anything-2/gui/torchvision_det/
+!segment-anything-2/gui/torchvision_det/**
+!segment-anything-2/gui/detectron2/
+segment-anything-2/gui/detectron2/*
+!segment-anything-2/gui/detectron2/*.py
+!segment-anything-2/gui/icons/
+!segment-anything-2/gui/icons/**
+!segment-anything-2/gui/marmot.jpg
+
+# never, whatever the rules above say
+**/__pycache__/
+**/*.pyc
+**/*.bak*
+**/.ipynb_checkpoints/
+**/*.pth
+**/*.pt
+**/*.ckpt
+**/*.onnx
+**/*.log
+**/dist/
+**/build/
+**/*.egg-info/
+packages/*/src/*/tools/
+packages/*/src/*/data/

descriptron_core-2.0.1/LICENSE

@@ -0,0 +1,201 @@
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descriptron_core-2.0.1/NOTICE

@@ -0,0 +1,52 @@
+Descriptron
+Copyright 2024-2026 Alex R. Van Dam (ORCID 0000-0002-1966-0338)
+
+This product includes software developed by Alex R. Van Dam
+https://github.com/alexrvandam/Descriptron
+
+Licensed under the Apache License, Version 2.0 (see LICENSE). Under Section
+4(d) of that licence, this NOTICE file must be included with any
+redistribution of this software or of any work derived from it.
+
+REQUIRED CITATION
+-----------------
+Anyone who uses Descriptron, or any software derived from it (including
+descriptron-core, descriptron-vision, descriptron-gui and descriptron-mcp), in
+work that is published, presented or distributed must cite:
+
+  1. The software (Descriptron v2):
+     Van Dam, A. R. Descriptron (version used). GitHub repository.
+     https://github.com/alexrvandam/Descriptron
+
+  2. The first Descriptron paper:
+     Van Dam, A. R. & Štarhová Serbina, L. (2026). Descriptron: Artificial
+     intelligence for automating taxonomic species descriptions with a
+     user-friendly software package. Systematic Entomology, 51(1), e70005.
+     https://doi.org/10.1111/syen.70005
+
+  3. Once it is published, the Descriptron v2 paper as well. Its reference
+     will be added here and in CITATION.cff on publication.
+
+BibTeX:
+
+@misc{vandam_descriptron_software,
+  author       = {Van Dam, Alex R.},
+  title        = {Descriptron},
+  howpublished = {GitHub repository},
+  url          = {https://github.com/alexrvandam/Descriptron}
+}
+
+@article{vandam2026descriptron,
+  author  = {Van Dam, Alex R. and Štarhová Serbina, Liliya},
+  title   = {Descriptron: Artificial intelligence for automating taxonomic species
+             descriptions with a user-friendly software package},
+  journal = {Systematic Entomology},
+  volume  = {51},
+  number  = {1},
+  pages   = {e70005},
+  year    = {2026},
+  doi     = {10.1111/syen.70005}
+}
+
+The same information is in CITATION.cff, which GitHub shows as
+"Cite this repository".

descriptron_core-2.0.1/PKG-INFO

@@ -0,0 +1,83 @@
+Metadata-Version: 2.5
+Name: descriptron-core
+Version: 2.0.1
+Summary: Evidence-tiered species descriptions, keys and audits from phenomic matrices
+Project-URL: Homepage, https://github.com/alexrvandam/Descriptron
+Project-URL: Repository, https://github.com/alexrvandam/Descriptron
+Project-URL: Issues, https://github.com/alexrvandam/Descriptron/issues
+Author: Alex R. Van Dam
+License: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: COCO,morphometrics,phenomics,species description,taxonomy
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.9
+Requires-Dist: biopython>=1.81
+Requires-Dist: lxml>=4.9
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: networkx>=3
+Requires-Dist: numpy>=1.23
+Requires-Dist: opencv-python-headless>=4.7
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: pandas>=1.5
+Requires-Dist: pillow>=9
+Requires-Dist: pycocotools>=2.0.6
+Requires-Dist: pyefd>=1.6
+Requires-Dist: python-docx>=1.0
+Requires-Dist: pyyaml>=6
+Requires-Dist: scikit-image>=0.20
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scikit-posthocs>=0.7
+Requires-Dist: scipy>=1.9
+Requires-Dist: seaborn>=0.12
+Requires-Dist: statsmodels>=0.14
+Requires-Dist: umap-learn>=0.5
+Provides-Extra: dev
+Requires-Dist: build>=1; extra == 'dev'
+Requires-Dist: pytest>=7; extra == 'dev'
+Requires-Dist: twine>=5; extra == 'dev'
+Provides-Extra: llm
+Requires-Dist: anthropic>=0.40; extra == 'llm'
+Provides-Extra: rag
+Requires-Dist: pdfplumber>=0.10; extra == 'rag'
+Requires-Dist: requests>=2.28; extra == 'rag'
+Provides-Extra: rag-embeddings
+Requires-Dist: faiss-cpu>=1.7; extra == 'rag-embeddings'
+Requires-Dist: pdfplumber>=0.10; extra == 'rag-embeddings'
+Requires-Dist: requests>=2.28; extra == 'rag-embeddings'
+Requires-Dist: sentence-transformers>=2.2; extra == 'rag-embeddings'
+Description-Content-Type: text/markdown
+
+# descriptron-core
+
+Evidence-tiered species descriptions, keys and audits from phenomic matrices.
+
+**Pure pip: no torch, no CUDA, no compiler.** Installs in about a minute on
+Linux, macOS and Windows. With the deposited COCO files it reproduces every
+analysis in the methods paper without a model of any kind — the audit, key,
+matrix, novelty scoring and delimitation are all deterministic.
+
+```bash
+pip install descriptron-core
+descriptron --list                 # the 62 programs in this package
+descriptron biorag_key_builder_v1 --help
+biorag-audit --help
+```
+
+Writing treatments is the only step that calls a language model:
+
+```bash
+pip install "descriptron-core[llm]"
+```
+
+For mask prediction, landmark transfer and scale-bar reading, add
+[`descriptron-vision`](https://pypi.org/project/descriptron-vision/); for the
+annotation GUI, [`descriptron-gui`](https://pypi.org/project/descriptron-gui/).
+
+The programs are shipped as data and executed with `runpy`, exactly as they run
+from a shell, so packaging cannot quietly change what they do.

descriptron_core-2.0.1/README.md

@@ -0,0 +1,28 @@
+# descriptron-core
+
+Evidence-tiered species descriptions, keys and audits from phenomic matrices.
+
+**Pure pip: no torch, no CUDA, no compiler.** Installs in about a minute on
+Linux, macOS and Windows. With the deposited COCO files it reproduces every
+analysis in the methods paper without a model of any kind — the audit, key,
+matrix, novelty scoring and delimitation are all deterministic.
+
+```bash
+pip install descriptron-core
+descriptron --list                 # the 62 programs in this package
+descriptron biorag_key_builder_v1 --help
+biorag-audit --help
+```
+
+Writing treatments is the only step that calls a language model:
+
+```bash
+pip install "descriptron-core[llm]"
+```
+
+For mask prediction, landmark transfer and scale-bar reading, add
+[`descriptron-vision`](https://pypi.org/project/descriptron-vision/); for the
+annotation GUI, [`descriptron-gui`](https://pypi.org/project/descriptron-gui/).
+
+The programs are shipped as data and executed with `runpy`, exactly as they run
+from a shell, so packaging cannot quietly change what they do.

descriptron_core-2.0.1/pyproject.toml

@@ -0,0 +1,81 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "descriptron-core"
+version = "2.0.1"
+description = "Evidence-tiered species descriptions, keys and audits from phenomic matrices"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+authors = [{ name = "Alex R. Van Dam" }]
+keywords = ["taxonomy", "morphometrics", "phenomics", "species description", "COCO"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Image Processing",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Operating System :: OS Independent",
+]
+
+# Derived from the imports of the 62 programs in this package, not from memory:
+# `python -m descriptron_core.cli --list` names them. No torch, no CUDA, no
+# compiler — this installs in about a minute on Linux, macOS and Windows, and
+# with the deposited COCO files it reproduces every analysis in the methods paper.
+dependencies = [
+  "numpy>=1.23",
+  "pandas>=1.5",
+  "scipy>=1.9",
+  "matplotlib>=3.6",
+  "scikit-learn>=1.2",
+  "scikit-image>=0.20",
+  "opencv-python-headless>=4.7",   # headless: the analysis half never opens a window
+  "pillow>=9",
+  "pycocotools>=2.0.6",
+  "seaborn>=0.12",
+  "statsmodels>=0.14",
+  "scikit-posthocs>=0.7",
+  "umap-learn>=0.5",
+  "networkx>=3",
+  "pyefd>=1.6",
+  "biopython>=1.81",
+  "PyYAML>=6",
+  "lxml>=4.9",
+  "openpyxl>=3.1",
+  "python-docx>=1.0",              # treatment and monograph .docx export
+]
+
+[project.optional-dependencies]
+# Only needed to *write* treatments. The audit, key, matrix, novelty scoring and
+# delimitation are all deterministic and need no model at all.
+llm = ["anthropic>=0.40"]
+# literature retrieval (the RAG in BioRAG): BioSysLit treatments from Zenodo and your
+# own PDFs. Keyword retrieval needs only the first two; sentence-embedding retrieval
+# (`index --embeddings`) also needs sentence-transformers + faiss-cpu, which pull in torch.
+rag = ["requests>=2.28", "pdfplumber>=0.10"]
+rag-embeddings = ["requests>=2.28", "pdfplumber>=0.10", "sentence-transformers>=2.2", "faiss-cpu>=1.7"]
+dev = ["pytest>=7", "build>=1", "twine>=5"]
+
+[project.scripts]
+descriptron        = "descriptron_core.cli:main"
+biorag-pipeline    = "descriptron_core.cli:run_pipeline"
+biorag-key         = "descriptron_core.cli:run_key_builder"
+biorag-audit       = "descriptron_core.cli:run_confabulation_checker"
+biorag-novelty     = "descriptron_core.cli:run_novelty_score"
+biorag-calibrate   = "descriptron_core.cli:run_calibrate"
+
+[project.urls]
+Homepage = "https://github.com/alexrvandam/Descriptron"
+Repository = "https://github.com/alexrvandam/Descriptron"
+Issues = "https://github.com/alexrvandam/Descriptron/issues"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/descriptron_core"]
+
+# tools/ and data/ sit inside the package directory, so `packages` already ships
+# them; a force-include here would add every file a second time and the build
+# fails with "a second file is being added to the wheel archive at the same path".
+[tool.hatch.build]
+artifacts = ["src/descriptron_core/tools/**", "src/descriptron_core/data/**"]

descriptron_core-2.0.1/src/descriptron_core/cli.py

@@ -0,0 +1,98 @@
+"""
+descriptron_core.cli — one entry point for the analysis programs
+================================================================
+
+The 62 programs in this package are run with `runpy` exactly as they are run
+from a shell, rather than being imported as modules. That is deliberate: they
+were written as scripts, they use `if __name__ == "__main__"`, and several
+import their siblings by plain name. Executing them as `__main__` with their own
+directory on `sys.path` preserves that behaviour exactly, so packaging cannot
+quietly change what a program does — which matters when the output is a
+published species description.
+
+    descriptron --list
+    descriptron biorag_key_builder_v1 --help
+    biorag-audit --help
+"""
+from __future__ import annotations
+
+import os
+import runpy
+import sys
+from importlib.resources import files
+from pathlib import Path
+
+__all__ = ["main", "tools_dir", "data_path", "available"]
+
+
+def tools_dir() -> Path:
+    return Path(str(files("descriptron_core") / "tools"))
+
+
+def data_path(*parts: str) -> Path:
+    """Prompts, taxon profiles, ontology releases and schemas that ship with the package."""
+    return Path(str(files("descriptron_core") / "data")).joinpath(*parts)
+
+
+def available() -> list[str]:
+    d = tools_dir()
+    if not d.exists():
+        return []
+    return sorted(p.stem for p in d.iterdir()
+                  if p.suffix in (".py", ".sh") and not p.name.startswith("_"))
+
+
+def _resolve(name: str) -> Path:
+    d = tools_dir()
+    for candidate in (d / name, d / f"{name}.py", d / f"{name}.sh"):
+        if candidate.exists():
+            return candidate
+    matches = [t for t in available() if t.startswith(name)]
+    if len(matches) == 1:
+        return _resolve(matches[0])
+    if matches:
+        raise SystemExit(f"'{name}' is ambiguous: {', '.join(matches)}")
+    raise SystemExit(f"unknown program '{name}'. `descriptron --list` shows them all.")
+
+
+def run(name: str, argv: list[str] | None = None) -> None:
+    path = _resolve(name)
+    argv = list(sys.argv[1:] if argv is None else argv)
+    # the programs' own directory goes on sys.path so a script that imports a
+    # sibling by plain name keeps working, and the packaged prompts and ontology
+    # releases are findable without anyone passing a path
+    sys.path.insert(0, str(path.parent))
+    os.environ.setdefault("DESCRIPTRON_DATA", str(data_path()))
+    if path.suffix == ".sh":
+        os.execvp("bash", ["bash", str(path), *argv])
+    sys.argv = [str(path), *argv]
+    runpy.run_path(str(path), run_name="__main__")
+
+
+def main(argv: list[str] | None = None) -> None:
+    args = list(sys.argv[1:] if argv is None else argv)
+    if not args or args[0] in ("-h", "--help", "help"):
+        print(__doc__.strip())
+        print(f"\n{len(available())} programs available; --list shows them.")
+        return
+    if args[0] in ("--list", "list"):
+        for name in available():
+            print(name)
+        return
+    if args[0] in ("--where", "where"):
+        print(f"tools: {tools_dir()}\ndata:  {data_path()}")
+        return
+    run(args[0], args[1:])
+
+
+def _fixed(script: str):
+    def entry() -> None:
+        run(script, sys.argv[1:])
+    return entry
+
+
+run_pipeline = _fixed("run_full_pipeline_v2")
+run_key_builder = _fixed("biorag_key_builder_v1")
+run_confabulation_checker = _fixed("biorag_confabulation_checker_v2")
+run_novelty_score = _fixed("biorag_novelty_score_v1")
+run_calibrate = _fixed("biorag_calibrate_v1")