mfethuls 0.3.1__tar.gz

mfethuls-0.3.1/LICENSE

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mfethuls-0.3.1/NOTICE

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+mfethuls
+Copyright 2026 Luca Bertossi
+
+This product is licensed under the Apache License, Version 2.0 (see LICENSE).
+Versions released before the change to Apache-2.0 were published under the MIT License.

mfethuls-0.3.1/PKG-INFO

@@ -0,0 +1,166 @@
+Metadata-Version: 2.4
+Name: mfethuls
+Version: 0.3.1
+Summary: From scattered instrument files to analysis-ready data: a Python framework and app that read, clean and organise experimental lab data.
+Author-email: Luca Bertossi <lucabertossi@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/lucaAyt/mfethuls
+Project-URL: Documentation, https://github.com/lucaAyt/mfethuls/tree/master/docs
+Project-URL: Repository, https://github.com/lucaAyt/mfethuls
+Project-URL: Issues, https://github.com/lucaAyt/mfethuls/issues
+Project-URL: Changelog, https://github.com/lucaAyt/mfethuls/releases
+Keywords: laboratory,instrument data,ETL,data management,DSC,TGA,FTIR,UV-Vis,rheology,materials science
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: duckdb>=1.0.0
+Requires-Dist: filelock>=3.12
+Requires-Dist: nmrglue>=0.11
+Requires-Dist: numpy>=1.24.2
+Requires-Dist: openpyxl>=3.1.0
+Requires-Dist: pandas>=1.5.3
+Requires-Dist: pyarrow>=20.0.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: pytz>=2024.1
+Provides-Extra: notebook
+Requires-Dist: notebook>=6.5.3; extra == "notebook"
+Requires-Dist: marimo>=0.9.0; extra == "notebook"
+Requires-Dist: matplotlib>=3.10.1; extra == "notebook"
+Requires-Dist: plotly>=6.0.0; extra == "notebook"
+Requires-Dist: seaborn>=0.13.0; extra == "notebook"
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.10.1; extra == "viz"
+Requires-Dist: kaleido>=1.0.0; extra == "viz"
+Requires-Dist: plotly>=6.0.0; extra == "viz"
+Requires-Dist: streamlit>=1.36.0; extra == "viz"
+Provides-Extra: dev
+Requires-Dist: pytest>=9.0.3; extra == "dev"
+Requires-Dist: ruff>=0.6.0; extra == "dev"
+Dynamic: license-file
+
+# mfethuls
+
+From scattered instrument files to analysis-ready data. mfethuls is a Python framework that reads, cleans and organises experimental data: raw instrument exports are ingested against an experiment registry, normalised to a canonical schema and stored as traceable, queryable Parquet datasets. Use it from the app (`mfethuls-app`, no code needed), from notebooks, or with SQL. Experimentalists get consistent, comparable data and publication-ready figures; data scientists get harmonised data from every instrument to build features and models on.
+
+---
+
+## Instrument support
+
+| Instrument | Models |
+|---|---|
+| DSC | Generic, Mettler Toledo, Perkin Elmer |
+| TGA | Generic |
+| FTIR | Bruker |
+| UV-Vis | Shimadzu, Ocean Optics Flame (in-situ) |
+| NMR | Bruker |
+| Rheometer | Anton Paar |
+| DMA | TA Q800 |
+| SEC | Agilent |
+| SAXS | Anton Paar |
+| MS | Bruker |
+
+Each parser normalises raw exports to a [canonical column schema](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/schema.md) — same column names and units regardless of instrument model.
+
+---
+
+## Install
+
+```shell
+pip install "mfethuls[viz,notebook]"
+```
+
+The latest development version: `pip install "mfethuls[viz,notebook] @ git+https://github.com/lucaAyt/mfethuls.git"`. The extras:
+
+| Extra | Installs | Use when |
+|---|---|---|
+| `viz` | Plotly, Matplotlib, Kaleido, Streamlit | The app or notebook plotting |
+| `notebook` | Jupyter, Marimo, Matplotlib, Plotly, seaborn | Interactive notebooks with plotting |
+
+---
+
+## Getting started
+
+No Docker, no database, no server. Start the app:
+
+```shell
+mfethuls-app
+```
+
+The welcome page offers three ways in:
+
+- **Get started**: choose your data folder (one subfolder per instrument) and your registry (CSV or Excel, one row per experiment; the app can create an empty one or give you an example). They are saved in `~/.mfethuls/settings.json`, so notebooks use the same folders; change them any time under **⚙ Settings**.
+- **Try the example**: explore example DSC, TGA, FTIR and fluorescence data, copied to `~/mfethuls-example`. Your own data is not touched.
+- **Use it from Python**: the tutorial notebook (below).
+
+A getting-started checklist then walks through registering (**Ingest** → **Review & register**), ingesting, selecting and plotting (**Colour by**, **Style by**, axis limits, SVG/HTML export) and cleaning up (**⚙ Settings** → **Clean up**); a compact tracker stays at the top of the sidebar, next to 🏠 (back to the welcome page) and ⚙.
+
+Non-technical users: double-click `launch.bat` (Windows) or run `bash launch.sh`; it needs only [`uv`](https://docs.astral.sh/uv/). See [docs/guides/local_setup.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/local_setup.md). Folders can also come from `.env` (copy `env_example`); folders saved in the app take precedence. `experiments_template.csv` in the repo root has an example row for every supported instrument.
+
+**Python API:** a guided tutorial (a marimo notebook on its own copy of the example data) opens with `mfethuls-tutorial`, or **Use it from Python** on the app's welcome page.
+
+```python
+import mfethuls
+
+# Load one or more experiments
+cs = mfethuls.load_experiments(["exp_001", "exp_002"])
+df = cs.to_dataframe()   # tidy long-format DataFrame
+
+# Load all experiments for a sample
+cs = mfethuls.load_samples(["S001", "S002"])
+```
+
+**Plotting:**
+
+```python
+fig, ax = mfethuls.plot_experiments(cs)                  # publication figure (Matplotlib)
+fig = mfethuls.plot_experiments(cs, backend="plotly")    # interactive, every data point (WebGL)
+mfethuls.set_plot_backend("plotly")                      # make Plotly the default
+```
+
+Each instrument gets a suitable plot, with axis labels and units (*Temperature (°C)*, *Wavenumber (cm⁻¹)*). Experiments that share an x-axis are overlaid, otherwise each gets its own panel, and time-resolved spectra series are coloured by elapsed time. Matplotlib figures use a fixed publication style and save as vector SVG/PDF. See [docs/guides/plotting.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/plotting.md).
+
+---
+
+## For teams
+
+A shared lab server (API, background ingest, Postgres, cloud storage, OneDrive sync and a shared app) is developed separately as **mfethuls-server**, which builds on this package.
+
+---
+
+## Data access for analysis
+
+Three stores, each with a distinct role — see [docs/guides/data_analysis.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/data_analysis.md) for the full guide including DuckDB SQL recipes and model-building patterns.
+
+---
+
+## Docs
+
+| Document | Contents |
+|---|---|
+| [docs/guides/quickstart.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/quickstart.md) | Start here: install, the app's first run, and using mfethuls from Python |
+| [docs/guides/workflow.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/workflow.md) | End-to-end tutorial — registry → ingest → dashboard → notebook |
+| [docs/guides/local_setup.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/local_setup.md) | Non-technical user guide — `uv` + launcher |
+| [docs/guides/data_analysis.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/data_analysis.md) | Notebook access — Python API, DuckDB SQL, model building |
+| [docs/guides/plotting.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/plotting.md) | Built-in plots, Matplotlib/Plotly backends, labels and units, dashboard plotting |
+| [docs/reference/registry.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/registry.md) | Registry format, column reference, measurement profiles |
+| [docs/reference/architecture.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/architecture.md) | System diagrams, ETL pipeline, storage design |
+| [docs/reference/schema.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/schema.md) | Canonical column names, units, normalisation rules |
+
+---
+
+## License
+
+Apache License 2.0 — see [LICENSE](https://github.com/lucaAyt/mfethuls/blob/master/LICENSE) and [NOTICE](https://github.com/lucaAyt/mfethuls/blob/master/NOTICE). Versions released before the change were published under the MIT License.
+
+Contributions are welcome; see [CONTRIBUTING.md](https://github.com/lucaAyt/mfethuls/blob/master/CONTRIBUTING.md). First-time contributors are asked to sign the [Contributor License Agreement](https://github.com/lucaAyt/mfethuls/blob/master/CLA.md).

mfethuls-0.3.1/README.md

@@ -0,0 +1,115 @@
+# mfethuls
+
+From scattered instrument files to analysis-ready data. mfethuls is a Python framework that reads, cleans and organises experimental data: raw instrument exports are ingested against an experiment registry, normalised to a canonical schema and stored as traceable, queryable Parquet datasets. Use it from the app (`mfethuls-app`, no code needed), from notebooks, or with SQL. Experimentalists get consistent, comparable data and publication-ready figures; data scientists get harmonised data from every instrument to build features and models on.
+
+---
+
+## Instrument support
+
+| Instrument | Models |
+|---|---|
+| DSC | Generic, Mettler Toledo, Perkin Elmer |
+| TGA | Generic |
+| FTIR | Bruker |
+| UV-Vis | Shimadzu, Ocean Optics Flame (in-situ) |
+| NMR | Bruker |
+| Rheometer | Anton Paar |
+| DMA | TA Q800 |
+| SEC | Agilent |
+| SAXS | Anton Paar |
+| MS | Bruker |
+
+Each parser normalises raw exports to a [canonical column schema](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/schema.md) — same column names and units regardless of instrument model.
+
+---
+
+## Install
+
+```shell
+pip install "mfethuls[viz,notebook]"
+```
+
+The latest development version: `pip install "mfethuls[viz,notebook] @ git+https://github.com/lucaAyt/mfethuls.git"`. The extras:
+
+| Extra | Installs | Use when |
+|---|---|---|
+| `viz` | Plotly, Matplotlib, Kaleido, Streamlit | The app or notebook plotting |
+| `notebook` | Jupyter, Marimo, Matplotlib, Plotly, seaborn | Interactive notebooks with plotting |
+
+---
+
+## Getting started
+
+No Docker, no database, no server. Start the app:
+
+```shell
+mfethuls-app
+```
+
+The welcome page offers three ways in:
+
+- **Get started**: choose your data folder (one subfolder per instrument) and your registry (CSV or Excel, one row per experiment; the app can create an empty one or give you an example). They are saved in `~/.mfethuls/settings.json`, so notebooks use the same folders; change them any time under **⚙ Settings**.
+- **Try the example**: explore example DSC, TGA, FTIR and fluorescence data, copied to `~/mfethuls-example`. Your own data is not touched.
+- **Use it from Python**: the tutorial notebook (below).
+
+A getting-started checklist then walks through registering (**Ingest** → **Review & register**), ingesting, selecting and plotting (**Colour by**, **Style by**, axis limits, SVG/HTML export) and cleaning up (**⚙ Settings** → **Clean up**); a compact tracker stays at the top of the sidebar, next to 🏠 (back to the welcome page) and ⚙.
+
+Non-technical users: double-click `launch.bat` (Windows) or run `bash launch.sh`; it needs only [`uv`](https://docs.astral.sh/uv/). See [docs/guides/local_setup.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/local_setup.md). Folders can also come from `.env` (copy `env_example`); folders saved in the app take precedence. `experiments_template.csv` in the repo root has an example row for every supported instrument.
+
+**Python API:** a guided tutorial (a marimo notebook on its own copy of the example data) opens with `mfethuls-tutorial`, or **Use it from Python** on the app's welcome page.
+
+```python
+import mfethuls
+
+# Load one or more experiments
+cs = mfethuls.load_experiments(["exp_001", "exp_002"])
+df = cs.to_dataframe()   # tidy long-format DataFrame
+
+# Load all experiments for a sample
+cs = mfethuls.load_samples(["S001", "S002"])
+```
+
+**Plotting:**
+
+```python
+fig, ax = mfethuls.plot_experiments(cs)                  # publication figure (Matplotlib)
+fig = mfethuls.plot_experiments(cs, backend="plotly")    # interactive, every data point (WebGL)
+mfethuls.set_plot_backend("plotly")                      # make Plotly the default
+```
+
+Each instrument gets a suitable plot, with axis labels and units (*Temperature (°C)*, *Wavenumber (cm⁻¹)*). Experiments that share an x-axis are overlaid, otherwise each gets its own panel, and time-resolved spectra series are coloured by elapsed time. Matplotlib figures use a fixed publication style and save as vector SVG/PDF. See [docs/guides/plotting.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/plotting.md).
+
+---
+
+## For teams
+
+A shared lab server (API, background ingest, Postgres, cloud storage, OneDrive sync and a shared app) is developed separately as **mfethuls-server**, which builds on this package.
+
+---
+
+## Data access for analysis
+
+Three stores, each with a distinct role — see [docs/guides/data_analysis.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/data_analysis.md) for the full guide including DuckDB SQL recipes and model-building patterns.
+
+---
+
+## Docs
+
+| Document | Contents |
+|---|---|
+| [docs/guides/quickstart.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/quickstart.md) | Start here: install, the app's first run, and using mfethuls from Python |
+| [docs/guides/workflow.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/workflow.md) | End-to-end tutorial — registry → ingest → dashboard → notebook |
+| [docs/guides/local_setup.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/local_setup.md) | Non-technical user guide — `uv` + launcher |
+| [docs/guides/data_analysis.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/data_analysis.md) | Notebook access — Python API, DuckDB SQL, model building |
+| [docs/guides/plotting.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/guides/plotting.md) | Built-in plots, Matplotlib/Plotly backends, labels and units, dashboard plotting |
+| [docs/reference/registry.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/registry.md) | Registry format, column reference, measurement profiles |
+| [docs/reference/architecture.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/architecture.md) | System diagrams, ETL pipeline, storage design |
+| [docs/reference/schema.md](https://github.com/lucaAyt/mfethuls/blob/master/docs/reference/schema.md) | Canonical column names, units, normalisation rules |
+
+---
+
+## License
+
+Apache License 2.0 — see [LICENSE](https://github.com/lucaAyt/mfethuls/blob/master/LICENSE) and [NOTICE](https://github.com/lucaAyt/mfethuls/blob/master/NOTICE). Versions released before the change were published under the MIT License.
+
+Contributions are welcome; see [CONTRIBUTING.md](https://github.com/lucaAyt/mfethuls/blob/master/CONTRIBUTING.md). First-time contributors are asked to sign the [Contributor License Agreement](https://github.com/lucaAyt/mfethuls/blob/master/CLA.md).

mfethuls-0.3.1/pyproject.toml

@@ -0,0 +1,85 @@
+[project]
+name = "mfethuls"
+version = "0.3.1"
+description = "From scattered instrument files to analysis-ready data: a Python framework and app that read, clean and organise experimental lab data."
+authors = [{name = "Luca Bertossi", email = "lucabertossi@gmail.com"}]
+readme = "README.md"
+license = "Apache-2.0"
+license-files = ["LICENSE", "NOTICE"]
+requires-python = ">=3.11"
+keywords = ["laboratory", "instrument data", "ETL", "data management", "DSC", "TGA", "FTIR", "UV-Vis", "rheology", "materials science"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+]
+dependencies = [
+    "duckdb>=1.0.0",
+    "filelock>=3.12",
+    "nmrglue>=0.11",
+    "numpy>=1.24.2",
+    "openpyxl>=3.1.0",
+    "pandas>=1.5.3",
+    "pyarrow>=20.0.0",
+    "python-dotenv>=1.0.0",
+    "pytz>=2024.1",
+]
+
+[project.optional-dependencies]
+notebook = [
+    "notebook>=6.5.3",
+    "marimo>=0.9.0",
+    "matplotlib>=3.10.1",
+    "plotly>=6.0.0",
+    "seaborn>=0.13.0",
+]
+viz = [
+    "matplotlib>=3.10.1",
+    "kaleido>=1.0.0",
+    "plotly>=6.0.0",
+    "streamlit>=1.36.0",
+]
+dev = [
+    "pytest>=9.0.3",
+    "ruff>=0.6.0",
+]
+
+[tool.ruff]
+line-length = 120
+extend-exclude = ["notebooks", "__marimo__"]
+
+[tool.ruff.lint]
+# Errors only (syntax, undefined names, unused imports); no style rules.
+select = ["E4", "E7", "E9", "F"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+mfethuls = ["py.typed"]
+"mfethuls.config" = ["*.json", "schemas/*.json"]
+"mfethuls.examples" = ["experiments_registry.csv", "data/**/*"]
+"mfethuls.tutorials" = ["*.py"]
+
+[build-system]
+requires = ["setuptools>=77.0"]  # SPDX license expression and license-files (PEP 639)
+build-backend = "setuptools.build_meta"
+
+[project.urls]
+Homepage = "https://github.com/lucaAyt/mfethuls"
+Documentation = "https://github.com/lucaAyt/mfethuls/tree/master/docs"
+Repository = "https://github.com/lucaAyt/mfethuls"
+Issues = "https://github.com/lucaAyt/mfethuls/issues"
+Changelog = "https://github.com/lucaAyt/mfethuls/releases"
+
+[project.scripts]
+mfethuls = "mfethuls.main:main"
+mfethuls-app = "mfethuls.app.launch:main"
+mfethuls-tutorial = "mfethuls.tutorials:main"

mfethuls-0.3.1/setup.cfg

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

mfethuls-0.3.1/src/mfethuls/__init__.py

@@ -0,0 +1,26 @@
+from .comparison import ComparisonSet, load_experiments, load_samples
+from .settings import use_test_env
+from .experiments import Registry
+
+
+def plot_experiments(*args, **kwargs):
+	from .plotting.comparison import plot_experiments as _plot_experiments
+
+	return _plot_experiments(*args, **kwargs)
+
+
+def set_plot_backend(backend):
+	"""Default plotting backend: "matplotlib" (publication, vector SVG) or "plotly" (interactive)."""
+	from .plotting.backend import set_default_backend
+
+	set_default_backend(backend)
+
+__all__ = [
+	"ComparisonSet",
+	"Registry",
+	"load_experiments",
+	"load_samples",
+	"plot_experiments",
+	"set_plot_backend",
+	"use_test_env",
+]

mfethuls-0.3.1/src/mfethuls/_files.py

@@ -0,0 +1,22 @@
+"""Small file helpers shared by the manifest and the saved settings."""
+
+from __future__ import annotations
+
+import os
+import time
+
+
+def replace_with_retry(source: str, target: str, attempts: int = 10) -> None:
+    """``os.replace``, retried briefly: on Windows it fails while another process has the target open.
+
+    Virus scanners, indexers and sync clients (OneDrive) open freshly written files for
+    a moment; waiting a little and trying again is enough.
+    """
+    for attempt in range(attempts):
+        try:
+            os.replace(source, target)
+            return
+        except PermissionError:
+            if attempt == attempts - 1:
+                raise
+            time.sleep(0.05 * (attempt + 1))

mfethuls-0.3.1/src/mfethuls/app/__init__.py

@@ -0,0 +1,6 @@
+"""The mfethuls Streamlit app: ``mfethuls-app`` starts it on this computer.
+
+- :mod:`mfethuls.app.page`: the page, drawn by ``run(backend)``
+- :mod:`mfethuls.app.backend`: where its data comes from (:class:`LocalBackend`)
+- :mod:`mfethuls.app.register`: the "Register new data" dialog
+"""