autosaxs 3.0.0__tar.gz

autosaxs-3.0.0/LICENSE

@@ -0,0 +1,74 @@
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+To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!)  The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives.
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autosaxs-3.0.0/PKG-INFO

@@ -0,0 +1,193 @@
+Metadata-Version: 2.4
+Name: autosaxs
+Version: 3.0.0
+Summary: Interactive SAXS pipeline core: calibration, integration, subtraction, ATSAS descriptors, plots, shape fitting, reports. After install, run `autosaxs --help`: epilog lists get-docs, get-skills, get-default-config (export docs and default config into your workspace).
+Author-email: "Mikhail S. Lifar" <mikhailkulkov11@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/MikhailLifar/autoSAXS
+Project-URL: Repository, https://github.com/MikhailLifar/autoSAXS
+Project-URL: Issues, https://github.com/MikhailLifar/autoSAXS/issues
+Project-URL: Documentation, https://github.com/MikhailLifar/autoSAXS#readme
+Keywords: saxs,small-angle scattering,pyFAI,ATSAS,calibration,integration
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ase
+Requires-Dist: denss>=1.8.0
+Requires-Dist: fabio
+Requires-Dist: matplotlib
+Requires-Dist: mcsas3>=1.0.6
+Requires-Dist: numpy<2.4,>=2.0
+Requires-Dist: pandas
+Requires-Dist: pyFAI
+Requires-Dist: PyYAML
+Requires-Dist: reportlab
+Requires-Dist: sasmodels
+Requires-Dist: scikit-image
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: squarify
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: import-linter; extra == "dev"
+Requires-Dist: pip; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Provides-Extra: gui
+Requires-Dist: customtkinter; extra == "gui"
+Requires-Dist: PyQt5; extra == "gui"
+Requires-Dist: watchdog; extra == "gui"
+Provides-Extra: llm
+Requires-Dist: httpx; extra == "llm"
+Requires-Dist: openai; extra == "llm"
+Requires-Dist: requests; extra == "llm"
+Dynamic: license-file
+
+# autoSAXS
+
+**autoSAXS** is a Python toolkit for reproducible small-angle X-ray scattering (SAXS) pipelines — from detector images to subtracted curves, size distributions, and shape models — usable from a **CLI**, from **Python**, from desktop GUIs or through your favourite AI agent.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/MikhailLifar/autoSAXS/main/readme-assets/hero_model_dam_frequency.gif" alt="model_dam frequency / occupancy map" width="420"/>
+</p>
+
+## Why autoSAXS
+
+- **One skills API for everything** — the same processing steps run as `autosaxs <skill> …` or as Python functions with stable signatures, so scripts, GUIs, and agents share one surface.
+- **Unique algorithms** — **automatic calibration** from calibrant frames and **automatic buffer scaling** for robust sample−buffer subtraction, reducing manual tuning at the beamline.
+- **Flexible inputs** — path expressions (file, directory, or glob) instead of “one file only,” with consistent expansion rules.
+- **Opt-in caching** — re-run interactive work without recomputing unchanged steps.
+- **GUIs when you want them** — `guisaxs-skills` (form-driven skill runner) and `guisaxs-liveview` (watch-folder live processing with optional monodisperse / polydisperse analysis).
+- **Built for automation** — designed for reproducible beamline-to-analysis workflows and LLM/agent-driven runs via the CLI.
+- **Seamless AI integration** — ship a built-in **`saxs-processing`** Cursor/agent skill (`autosaxs get-skills`) so assistants can orchestrate the pipeline from documented procedures.
+
+## Use cases
+
+- Synchrotron or lab SAXS: calibrate geometry, integrate TIFF stacks, average frames, and subtract buffer.
+- Monodisperse analysis: Guinier → pair-distance distribution p(r) → optional ab initio shape recovery, 3d primitives modeling or electron density inference.
+- Polydisperse analysis: Guinier → size distribution D(R) → optional McSAS or ATSAS MIXTURE.
+- Live experiments: watch a folder for new detector images and process them as they arrive.
+- Scripting and agents: drive the full pipeline from Python or `autosaxs` without reimplementing I/O conventions.
+
+## Install
+
+Core + CLI:
+
+```bash
+python -m pip install autosaxs
+autosaxs --help
+```
+
+With desktop GUIs (`guisaxs-skills`, `guisaxs-liveview`):
+
+```bash
+python -m pip install "autosaxs[gui]"
+```
+
+Optional LLM helper stack (`openai` / `httpx` / `requests`):
+
+```bash
+python -m pip install "autosaxs[llm]"
+```
+
+Helper commands (export docs and defaults into a directory):
+
+- `autosaxs get-docs` — write the short `README.md` and detailed `autosaxs-docs/skills_reference.md`
+- `autosaxs get-skills` — write Cursor-style `saxs-processing/` skill
+- `autosaxs get-default-config` — copy bundled `config_base.conf`
+
+From git `main` (development): `python -m pip install "autosaxs @ git+https://github.com/MikhailLifar/autoSAXS.git"` or `autosaxs -U`
+
+## Main features
+
+Pipeline stages exposed as skills: **calibrate → integrate / average → subtract → analyze → model → report**, including Guinier, Kratky, `fit-distances` (p(r)), `fit-sizes` (D(R)), `model-dam`, `model-bodies`, `model-density` (DENSS), `model-dr-mc` (McSAS), `model-mixture`, and reporting helpers.
+
+Apps: 
+**guisaxs-skills** (catalog + forms + isolated CLI runs, beta version)
+**guisaxs-liveview** (queued live integration, buffer subtraction, optional analysis wizards).
+
+Full per-skill documentation: [`autosaxs-docs/skills_reference.md`](autosaxs-docs/skills_reference.md).
+
+## Quick start
+
+Monodisperse protein walkthrough using [`examples/monodisperse_protein/`](examples/monodisperse_protein/) (AgBh calibrant, mask, sample + buffer TIFFs). `--q-min` / `--q-max` are the buffer-matching window in nm⁻¹ — pick them from the sample+buffer overlay; `4.8`–`5.8` fits this example.
+
+### Python
+
+```python
+from pathlib import Path
+from autosaxs.skill import calibrate, integrate, subtract, process_monodisperse
+
+ex = Path("examples/monodisperse_protein")
+
+calibrate(
+    ex / "AgBh700_96.9_calib.tif",
+    output_dir=str(ex / "calibration"),
+    mask=ex / "mask-20260706_133745.txt",
+    wavelength=1.445,
+)
+integrate(
+    f"{ex / 'ihs27_buffer.tif'}, {ex / 'ihs27_sample.tif'}",
+    ex / "calibration" / "integrator",
+    output_dir=str(ex / "integrated"),
+)
+subtract(
+    ex / "integrated" / "int_ihs27_sample.dat",
+    ex / "integrated" / "int_ihs27_buffer.dat",
+    output_dir=str(ex / "subtracted"),
+    q_min=4.8,
+    q_max=5.8,
+)
+process_monodisperse(ex / "subtracted" / "sub_ihs27_sample.dat")
+```
+
+### CLI
+
+```bash
+cd examples/monodisperse_protein
+
+autosaxs calibrate AgBh700_96.9_calib.tif \
+  --mask mask-20260706_133745.txt --wavelength 1.445 -o calibration/
+
+autosaxs integrate "ihs27_buffer.tif, ihs27_sample.tif" \
+  calibration/integrator/ -o integrated/
+
+autosaxs subtract integrated/int_ihs27_sample.dat integrated/int_ihs27_buffer.dat \
+  --q-min 4.8 --q-max 5.8 -o subtracted/
+
+autosaxs process-monodisperse subtracted/sub_ihs27_sample.dat
+```
+
+### Online GUI
+
+```bash
+guisaxs-liveview
+```
+
+## Acknowledgements
+
+autoSAXS builds on the SAXS ecosystem rather than replacing it:
+
+- **[pyFAI](https://pyfai.readthedocs.io/)** — detector geometry, calibration, and 1D integration.
+- **[ATSAS](https://www.embl-hamburg.de/biosaxs/download.html)** — tools such as `autorg`, `datgnom`, `gnom`, `dammif`, `mixture`, and `bodies` (external install; recommended **ATSAS 3.2.1**). Importing autoSAXS **warns** if ATSAS is missing; skills that shell out to ATSAS **raise** immediately when it is unavailable.
+- **[DENSS](https://www.tdgrant.com/denss)** — electron-density reconstruction (`model_density`); pulled in via the `denss` PyPI dependency.
+- **[McSAS](https://github.com/BAMresearch/McSAS) / McSAS3** — Monte Carlo polydisperse sizing (`model_dr_mc`).
+
+## Contacts
+
+- **Mikhail S. Lifar** — `mikhailkulkov11@gmail.com`
+- Affiliation: The Smart Materials Research Institute, Southern Federal University (Rostov-on-Don)
+- Project: [github.com/MikhailLifar/autoSAXS](https://github.com/MikhailLifar/autoSAXS)
+
+## Contributing
+
+Issues and pull requests are welcome on GitHub. Bug reports, clearer docs, and new skill coverage all help. Licensed under the **Apache License 2.0**.

autosaxs-3.0.0/README.md

@@ -0,0 +1,139 @@
+# autoSAXS
+
+**autoSAXS** is a Python toolkit for reproducible small-angle X-ray scattering (SAXS) pipelines — from detector images to subtracted curves, size distributions, and shape models — usable from a **CLI**, from **Python**, from desktop GUIs or through your favourite AI agent.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/MikhailLifar/autoSAXS/main/readme-assets/hero_model_dam_frequency.gif" alt="model_dam frequency / occupancy map" width="420"/>
+</p>
+
+## Why autoSAXS
+
+- **One skills API for everything** — the same processing steps run as `autosaxs <skill> …` or as Python functions with stable signatures, so scripts, GUIs, and agents share one surface.
+- **Unique algorithms** — **automatic calibration** from calibrant frames and **automatic buffer scaling** for robust sample−buffer subtraction, reducing manual tuning at the beamline.
+- **Flexible inputs** — path expressions (file, directory, or glob) instead of “one file only,” with consistent expansion rules.
+- **Opt-in caching** — re-run interactive work without recomputing unchanged steps.
+- **GUIs when you want them** — `guisaxs-skills` (form-driven skill runner) and `guisaxs-liveview` (watch-folder live processing with optional monodisperse / polydisperse analysis).
+- **Built for automation** — designed for reproducible beamline-to-analysis workflows and LLM/agent-driven runs via the CLI.
+- **Seamless AI integration** — ship a built-in **`saxs-processing`** Cursor/agent skill (`autosaxs get-skills`) so assistants can orchestrate the pipeline from documented procedures.
+
+## Use cases
+
+- Synchrotron or lab SAXS: calibrate geometry, integrate TIFF stacks, average frames, and subtract buffer.
+- Monodisperse analysis: Guinier → pair-distance distribution p(r) → optional ab initio shape recovery, 3d primitives modeling or electron density inference.
+- Polydisperse analysis: Guinier → size distribution D(R) → optional McSAS or ATSAS MIXTURE.
+- Live experiments: watch a folder for new detector images and process them as they arrive.
+- Scripting and agents: drive the full pipeline from Python or `autosaxs` without reimplementing I/O conventions.
+
+## Install
+
+Core + CLI:
+
+```bash
+python -m pip install autosaxs
+autosaxs --help
+```
+
+With desktop GUIs (`guisaxs-skills`, `guisaxs-liveview`):
+
+```bash
+python -m pip install "autosaxs[gui]"
+```
+
+Optional LLM helper stack (`openai` / `httpx` / `requests`):
+
+```bash
+python -m pip install "autosaxs[llm]"
+```
+
+Helper commands (export docs and defaults into a directory):
+
+- `autosaxs get-docs` — write the short `README.md` and detailed `autosaxs-docs/skills_reference.md`
+- `autosaxs get-skills` — write Cursor-style `saxs-processing/` skill
+- `autosaxs get-default-config` — copy bundled `config_base.conf`
+
+From git `main` (development): `python -m pip install "autosaxs @ git+https://github.com/MikhailLifar/autoSAXS.git"` or `autosaxs -U`
+
+## Main features
+
+Pipeline stages exposed as skills: **calibrate → integrate / average → subtract → analyze → model → report**, including Guinier, Kratky, `fit-distances` (p(r)), `fit-sizes` (D(R)), `model-dam`, `model-bodies`, `model-density` (DENSS), `model-dr-mc` (McSAS), `model-mixture`, and reporting helpers.
+
+Apps: 
+**guisaxs-skills** (catalog + forms + isolated CLI runs, beta version)
+**guisaxs-liveview** (queued live integration, buffer subtraction, optional analysis wizards).
+
+Full per-skill documentation: [`autosaxs-docs/skills_reference.md`](autosaxs-docs/skills_reference.md).
+
+## Quick start
+
+Monodisperse protein walkthrough using [`examples/monodisperse_protein/`](examples/monodisperse_protein/) (AgBh calibrant, mask, sample + buffer TIFFs). `--q-min` / `--q-max` are the buffer-matching window in nm⁻¹ — pick them from the sample+buffer overlay; `4.8`–`5.8` fits this example.
+
+### Python
+
+```python
+from pathlib import Path
+from autosaxs.skill import calibrate, integrate, subtract, process_monodisperse
+
+ex = Path("examples/monodisperse_protein")
+
+calibrate(
+    ex / "AgBh700_96.9_calib.tif",
+    output_dir=str(ex / "calibration"),
+    mask=ex / "mask-20260706_133745.txt",
+    wavelength=1.445,
+)
+integrate(
+    f"{ex / 'ihs27_buffer.tif'}, {ex / 'ihs27_sample.tif'}",
+    ex / "calibration" / "integrator",
+    output_dir=str(ex / "integrated"),
+)
+subtract(
+    ex / "integrated" / "int_ihs27_sample.dat",
+    ex / "integrated" / "int_ihs27_buffer.dat",
+    output_dir=str(ex / "subtracted"),
+    q_min=4.8,
+    q_max=5.8,
+)
+process_monodisperse(ex / "subtracted" / "sub_ihs27_sample.dat")
+```
+
+### CLI
+
+```bash
+cd examples/monodisperse_protein
+
+autosaxs calibrate AgBh700_96.9_calib.tif \
+  --mask mask-20260706_133745.txt --wavelength 1.445 -o calibration/
+
+autosaxs integrate "ihs27_buffer.tif, ihs27_sample.tif" \
+  calibration/integrator/ -o integrated/
+
+autosaxs subtract integrated/int_ihs27_sample.dat integrated/int_ihs27_buffer.dat \
+  --q-min 4.8 --q-max 5.8 -o subtracted/
+
+autosaxs process-monodisperse subtracted/sub_ihs27_sample.dat
+```
+
+### Online GUI
+
+```bash
+guisaxs-liveview
+```
+
+## Acknowledgements
+
+autoSAXS builds on the SAXS ecosystem rather than replacing it:
+
+- **[pyFAI](https://pyfai.readthedocs.io/)** — detector geometry, calibration, and 1D integration.
+- **[ATSAS](https://www.embl-hamburg.de/biosaxs/download.html)** — tools such as `autorg`, `datgnom`, `gnom`, `dammif`, `mixture`, and `bodies` (external install; recommended **ATSAS 3.2.1**). Importing autoSAXS **warns** if ATSAS is missing; skills that shell out to ATSAS **raise** immediately when it is unavailable.
+- **[DENSS](https://www.tdgrant.com/denss)** — electron-density reconstruction (`model_density`); pulled in via the `denss` PyPI dependency.
+- **[McSAS](https://github.com/BAMresearch/McSAS) / McSAS3** — Monte Carlo polydisperse sizing (`model_dr_mc`).
+
+## Contacts
+
+- **Mikhail S. Lifar** — `mikhailkulkov11@gmail.com`
+- Affiliation: The Smart Materials Research Institute, Southern Federal University (Rostov-on-Don)
+- Project: [github.com/MikhailLifar/autoSAXS](https://github.com/MikhailLifar/autoSAXS)
+
+## Contributing
+
+Issues and pull requests are welcome on GitHub. Bug reports, clearer docs, and new skill coverage all help. Licensed under the **Apache License 2.0**.

autosaxs-3.0.0/pyproject.toml

@@ -0,0 +1,77 @@
+[build-system]
+requires = ["setuptools>=77", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "autosaxs"
+version = "3.0.0"
+description = "Interactive SAXS pipeline core: calibration, integration, subtraction, ATSAS descriptors, plots, shape fitting, reports. After install, run `autosaxs --help`: epilog lists get-docs, get-skills, get-default-config (export docs and default config into your workspace)."
+readme = "README.md"
+requires-python = ">=3.10"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Mikhail S. Lifar", email = "mikhailkulkov11@gmail.com" },
+]
+keywords = ["saxs", "small-angle scattering", "pyFAI", "ATSAS", "calibration", "integration"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "ase",
+    "denss>=1.8.0",
+    "fabio",
+    "matplotlib",
+    "mcsas3>=1.0.6",
+    "numpy>=2.0,<2.4",
+    "pandas",
+    "pyFAI",
+    "PyYAML",
+    "reportlab",
+    "sasmodels",
+    "scikit-image",
+    "scikit-learn",
+    "scipy",
+    "seaborn",
+    "squarify",
+]
+
+[project.urls]
+Homepage = "https://github.com/MikhailLifar/autoSAXS"
+Repository = "https://github.com/MikhailLifar/autoSAXS"
+Issues = "https://github.com/MikhailLifar/autoSAXS/issues"
+Documentation = "https://github.com/MikhailLifar/autoSAXS#readme"
+
+[project.scripts]
+autosaxs = "autosaxs.cli:main"
+guisaxs-skills = "guisaxs_skills.__main__:main"
+guisaxs-liveview = "guisaxs_liveview.__main__:main"
+
+[project.optional-dependencies]
+dev = ["build", "import-linter", "pip", "twine"]
+gui = ["customtkinter", "PyQt5", "watchdog"]
+llm = ["httpx", "openai", "requests"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["autosaxs*", "guisaxs_skills*", "guisaxs_liveview*"]
+
+[tool.setuptools.package-data]
+autosaxs = [
+    "resources/agent_quickstart.txt",
+    "resources/ai_skills/*.md",
+    "resources/config_base.conf",
+    "resources/help/guisaxs_liveview/**/*",
+    "resources/prompts/**/*.txt",
+    "resources/readme/*.md",
+    "resources/readme/images/**/*",
+    "resources/schemas/*.json",
+]

autosaxs-3.0.0/setup.cfg

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

autosaxs-3.0.0/src/autosaxs/__init__.py

@@ -0,0 +1,45 @@
+# autosaxs: interactive SAXS pipeline core (controller, processor, skill, utils, guinier, event_bus, cli, viewer, context, gui, gui_interface, api, polydispfit, report)
+from __future__ import annotations
+
+import logging
+from importlib.metadata import PackageNotFoundError, version as _pkg_version
+
+try:
+    __version__ = _pkg_version("autosaxs")
+except PackageNotFoundError:
+    # Editable/source tree without an installed distribution metadata entry.
+    __version__ = "0.0.0+local"
+
+# pyFAI logs API deprecations (set_wavelength, AzimuthalIntegrator, …) via this
+# logger with full stack traces; keep calling the same APIs but don't spam users.
+logging.getLogger("pyFAI.DEPRECATION").setLevel(logging.ERROR)
+
+from .skill.skill_wrap import warn_atsas_on_import
+
+warn_atsas_on_import()
+
+from .core.event_bus import EventBus, EventType
+from .core.context import Context
+from .pipeline import cli_interface
+from .core import integrator
+from .core import processor
+from .core import utils
+from .core import viewer
+from .pipeline import api
+from . import skill
+from .pipeline.saxs_controller import Controller
+
+__all__ = [
+    "EventBus",
+    "EventType",
+    "Context",
+    "Controller",
+    "cli_interface",
+    "integrator",
+    "processor",
+    "utils",
+    "viewer",
+    "api",
+    "skill",
+    "__version__",
+]

autosaxs-3.0.0/src/autosaxs/cli/__init__.py

@@ -0,0 +1,6 @@
+"""CLI surface: argument parsing and path-expression helpers."""
+
+from .cli import main
+
+__all__ = ["main"]
+