rnamelt 0.1.0__tar.gz

rnamelt-0.1.0/.gitignore

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+__pycache__

rnamelt-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 tspich
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rnamelt-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: rnamelt
+Version: 0.1.0
+Summary: Two-state thermodynamic analysis (ΔH, ΔS, ΔG, Tm) of RNA melting curves
+Project-URL: Homepage, https://github.com/tspich/RNAmelt
+Project-URL: Issues, https://github.com/tspich/RNAmelt/issues
+Author: tspich, RaumZeit
+License: MIT
+License-File: LICENSE
+Keywords: melting curve,rna,thermodynamics
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=1.5
+Requires-Dist: scipy>=1.10
+Provides-Extra: plots
+Requires-Dist: matplotlib>=3.5; extra == 'plots'
+Description-Content-Type: text/markdown
+
+# rnamelt
+
+[![PyPI](https://img.shields.io/pypi/v/rnamelt.svg)](https://pypi.org/project/rnamelt/)
+[![Python versions](https://img.shields.io/pypi/pyversions/rnamelt.svg)](https://pypi.org/project/rnamelt/)
+[![License: MIT](https://img.shields.io/pypi/l/rnamelt.svg)](https://github.com/tspich/RNAmelt/blob/main/LICENSE)
+
+Two-state thermodynamic analysis (ΔH, ΔS, ΔG, Tm) of UV-absorbance and
+fluorescence RNA / DNA melting curves. One small, dependency-light Python
+package that works as a library, a CLI, and a browser app.
+
+- **Library** — `from rnamelt import MeltAnalysis`, typed result objects,
+  optional `matplotlib` plotting.
+- **CLI** — `rnamelt FILE.csv [...]` for batch / scripted runs.
+- **Browser** — the same Python pipeline runs client-side via Pyodide.
+  Live demo: <https://tspich.github.io/RNAmelt/>.
+
+## Install
+
+```bash
+pip install rnamelt                 # base — numpy, pandas, scipy
+pip install 'rnamelt[plots]'        # adds matplotlib for .plot() helpers
+```
+
+Requires Python ≥ 3.10.
+
+## Quickstart
+
+```python
+from rnamelt import MeltAnalysis
+
+m = MeltAnalysis.from_csv("melt.csv", struct_type="heterodimer")
+r = m.single("sample_1", oligo=0.5)     # oligo in µM
+print(r.Tm_fit, r.fit.dH, r.fit.dG)
+```
+
+```bash
+rnamelt melt.csv --column sample_1 --oligo 0.5 --struct-type heterodimer
+```
+
+## CSV input format
+
+```
+temperature, sample_1, sample_2, ...
+20.0,        0.412,    0.388, ...
+20.5,        0.415,    0.391, ...
+```
+
+- Column 0: temperature in °C (any header name).
+- Columns 1+: absorbance or fluorescence (any header name).
+- Rows entirely NaN, or with a missing temperature, are dropped.
+
+## CLI
+
+Same orchestrator as the library. JSON on stdout; pass `--csv-out` for a
+results CSV in the same format the browser produces.
+
+```bash
+# van't Hoff + full fit on every signal column
+rnamelt melt.csv --csv-out batch.csv
+
+# single column
+rnamelt melt.csv --column sample_1 --struct-type heterodimer \
+    --oligo 5.0 --T-low 20 --T-high 90 --csv-out single.csv
+
+# shared-ΔH joint fit across columns
+rnamelt melt.csv --column __multi__ --struct-type heterodimer \
+    --oligo-multi sample_1=0.5 --oligo-multi sample_2=5.0
+
+# concentration-series van't Hoff (1/Tm vs ln(C_T/f))
+rnamelt melt.csv --column __concentration__ --struct-type heterodimer \
+    --oligo-multi sample_1=0.5 --oligo-multi sample_2=5.0 --oligo-multi sample_3=50 \
+    --csv-out conc.csv
+```
+
+`rnamelt --help` lists every flag, including three solver-tuning groups
+(`scipy.optimize.least_squares` overrides, van't Hoff linearisation,
+full-fit initial guesses). Exit codes: `0` success, `1` analysis error,
+`2` bad input.
+
+## Python API
+
+The recommended surface is `MeltAnalysis`. It holds the DataFrame and
+every configuration knob (struct type, salt, transition window, baseline
+offsets, solver / vH / fit-init overrides) and exposes the three modes as
+methods returning typed result objects from `rnamelt.results`.
+
+```python
+from rnamelt import MeltAnalysis, FitFailed
+
+m = MeltAnalysis.from_csv(
+    "melt.csv",
+    struct_type="heterodimer",   # "heterodimer" | "homodimer" | "monomer"
+    salt=150.0,                  # NaCl (mM) — metadata only
+    T_low=None, T_high=None,     # transition window (°C); None = full range
+    bl_lower_offset=10.0,        # folded baseline span above T_low (°C)
+    bl_upper_offset=10.0,        # unfolded baseline span below T_high (°C)
+)
+m.signal_columns                 # ['sample_1', 'sample_2', ...]
+```
+
+### Three modes
+
+```python
+# Single column — returns SingleResult; numpy arrays live on the object
+r = m.single("sample_1", oligo=0.5)
+r.Tm_raw, r.vh.dH, r.fit.Tm, r.fit.dG
+
+try:
+    r.fit.require()              # raises FitFailed if not r.fit.ok
+except FitFailed as e:
+    print(e)
+
+# Shared-ΔH joint fit across columns
+multi = m.multi({"sample_1": 0.5, "sample_2": 5.0, "sample_3": 50.0})
+multi.dH, multi.dS
+for c in multi.columns:
+    print(c.name, c.Tm_fit, c.oligoC)
+
+# Concentration-series van't Hoff — three regressions (raw / vH / full fit)
+conc = m.concentration({"sample_1": 0.5, "sample_2": 5.0, "sample_3": 50.0})
+for s in (conc.series_raw, conc.series_vh, conc.series_fit):
+    if s.ok:
+        print(s.dH, s.dG_37, s.r_squared)
+
+# Every column at once
+batch = m.single_all(oligo=0.5)  # dict[str, SingleResult]
+
+# Export forms (same shape the browser download produces)
+r.to_dict(); r.to_dataframe(); r.to_csv("out.csv")
+```
+
+### From raw arrays — no CSV
+
+`signals` accepts a 1D array, a `{name: array}` mapping, or a 2D array
+(one column per signal, with optional `names=`):
+
+```python
+import numpy as np
+from rnamelt import MeltAnalysis
+
+T = np.linspace(20, 90, 71)
+
+m = MeltAnalysis.from_arrays(T, signal_F4)                        # 1D
+m = MeltAnalysis.from_arrays(T, {"F4": sigF4, "F5": sigF5})       # mapping
+m = MeltAnalysis.from_arrays(T, arr2d, names=["A", "B", "C"])     # 2D
+```
+
+### Plotting (optional)
+
+`pip install 'rnamelt[plots]'`. Each result class has a `.plot()` method
+that lazy-imports `rnamelt.plots`, so matplotlib never enters the
+browser/Pyodide bundle.
+
+```python
+fig, axes = m.single("F4").plot(figsize=(15, 5))      # raw / vH / full fit
+fig, ax   = m.multi(oligo_multi).plot()
+fig, axes = m.concentration(oligo_multi).plot()
+
+# Convenience shortcut on the analyzer
+fig, axes, result = m.plot("F4")
+```
+
+### Functional helpers (back-compat)
+
+Thin wrappers around the same orchestrator that take a cleaned
+`pandas.DataFrame` and return the legacy dict directly:
+
+```python
+import pandas as pd
+from rnamelt import (
+    analyze_single, analyze_multi, analyze_concentration, analyze_csv,
+)
+from rnamelt.cleaning import clean
+
+df = clean(pd.read_csv("melt.csv"))
+analyze_single(df, "sample_1", struct_type="heterodimer", oligo=0.5)
+analyze_multi(df, {"sample_1": 0.5, "sample_2": 5.0})
+analyze_concentration(df, {"sample_1": 0.5, "sample_2": 5.0})
+
+# read_csv + clean + dispatch in one call
+analyze_csv("melt.csv", mode="single", column="sample_1", oligo=0.5)
+```
+
+## Analysis modes
+
+All three modes go through `rnamelt.analysis_melting.run(df, params)`;
+the `column` param selects the mode.
+
+| `column` value         | Mode                                | What it does |
+|------------------------|-------------------------------------|--------------|
+| any signal-column name | **Single column**                   | Tm by baseline intersection, van't Hoff linearisation, and a full two-state nonlinear fit. Returns ΔH / ΔS / ΔG / Tm from each method. |
+| `__multi__`            | **Shared-ΔH joint fit**             | Fit every column with common ΔH, ΔS but independent baselines. Each column carries its own concentration. |
+| `__concentration__`    | **Concentration-series van't Hoff** | Three Tm values per column (raw / vH / full-fit) → `1/Tm = (R/ΔH)·ln(C_T/f) + ΔS/ΔH` regression for each. `f = 1` (homodimer) or `f = 4` (heterodimer). |
+
+## Two-state model
+
+Observed signal is a linear combination of folded and unfolded baselines,
+weighted by the fraction unfolded θ(T):
+
+```
+A(T) = (m_F·T + b_F)·(1 − θ) + (m_U·T + b_U)·θ
+K(T) = exp(−ΔG / RT),    ΔG = ΔH − T·ΔS
+θ    = K / (1 + K)                       (monomer)
+θ    = (√(1 + 8·c₀·K) − 1) / (4·c₀·K)    (dimer)
+```
+
+Units: ΔH in kcal/mol, ΔS in kcal/(mol·K), T in K
+(`T_K = T_C − T0`, `T0 = −273.15`).
+
+## Browser app
+
+The same Python package runs client-side via [Pyodide](https://pyodide.org/);
+no server, no upload, no install. Drop a CSV onto
+<https://tspich.github.io/RNAmelt/> to try it. The source for the page is
+`index.html` in the [repository](https://github.com/tspich/RNAmelt).
+
+## Development
+
+```bash
+git clone https://github.com/tspich/RNAmelt
+cd RNAmelt
+pip install -e '.[plots]'
+
+pytest tests/                 # or: python -m unittest discover tests
+python -m build               # sdist + wheel into dist/
+```
+
+Module layering is strict: `functions` → `methods` → `analysis_melting` →
+`api` → `__main__` / browser. `functions` stays stateless. `plots` is
+lazy-imported so the browser bundle never pulls matplotlib.
+
+## License
+
+[MIT](LICENSE).
+
+## Links
+
+- Source: <https://github.com/tspich/RNAmelt>
+- Issues: <https://github.com/tspich/RNAmelt/issues>
+- Live demo: <https://tspich.github.io/RNAmelt/>

rnamelt-0.1.0/README.md

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+# rnamelt
+
+[![PyPI](https://img.shields.io/pypi/v/rnamelt.svg)](https://pypi.org/project/rnamelt/)
+[![Python versions](https://img.shields.io/pypi/pyversions/rnamelt.svg)](https://pypi.org/project/rnamelt/)
+[![License: MIT](https://img.shields.io/pypi/l/rnamelt.svg)](https://github.com/tspich/RNAmelt/blob/main/LICENSE)
+
+Two-state thermodynamic analysis (ΔH, ΔS, ΔG, Tm) of UV-absorbance and
+fluorescence RNA / DNA melting curves. One small, dependency-light Python
+package that works as a library, a CLI, and a browser app.
+
+- **Library** — `from rnamelt import MeltAnalysis`, typed result objects,
+  optional `matplotlib` plotting.
+- **CLI** — `rnamelt FILE.csv [...]` for batch / scripted runs.
+- **Browser** — the same Python pipeline runs client-side via Pyodide.
+  Live demo: <https://tspich.github.io/RNAmelt/>.
+
+## Install
+
+```bash
+pip install rnamelt                 # base — numpy, pandas, scipy
+pip install 'rnamelt[plots]'        # adds matplotlib for .plot() helpers
+```
+
+Requires Python ≥ 3.10.
+
+## Quickstart
+
+```python
+from rnamelt import MeltAnalysis
+
+m = MeltAnalysis.from_csv("melt.csv", struct_type="heterodimer")
+r = m.single("sample_1", oligo=0.5)     # oligo in µM
+print(r.Tm_fit, r.fit.dH, r.fit.dG)
+```
+
+```bash
+rnamelt melt.csv --column sample_1 --oligo 0.5 --struct-type heterodimer
+```
+
+## CSV input format
+
+```
+temperature, sample_1, sample_2, ...
+20.0,        0.412,    0.388, ...
+20.5,        0.415,    0.391, ...
+```
+
+- Column 0: temperature in °C (any header name).
+- Columns 1+: absorbance or fluorescence (any header name).
+- Rows entirely NaN, or with a missing temperature, are dropped.
+
+## CLI
+
+Same orchestrator as the library. JSON on stdout; pass `--csv-out` for a
+results CSV in the same format the browser produces.
+
+```bash
+# van't Hoff + full fit on every signal column
+rnamelt melt.csv --csv-out batch.csv
+
+# single column
+rnamelt melt.csv --column sample_1 --struct-type heterodimer \
+    --oligo 5.0 --T-low 20 --T-high 90 --csv-out single.csv
+
+# shared-ΔH joint fit across columns
+rnamelt melt.csv --column __multi__ --struct-type heterodimer \
+    --oligo-multi sample_1=0.5 --oligo-multi sample_2=5.0
+
+# concentration-series van't Hoff (1/Tm vs ln(C_T/f))
+rnamelt melt.csv --column __concentration__ --struct-type heterodimer \
+    --oligo-multi sample_1=0.5 --oligo-multi sample_2=5.0 --oligo-multi sample_3=50 \
+    --csv-out conc.csv
+```
+
+`rnamelt --help` lists every flag, including three solver-tuning groups
+(`scipy.optimize.least_squares` overrides, van't Hoff linearisation,
+full-fit initial guesses). Exit codes: `0` success, `1` analysis error,
+`2` bad input.
+
+## Python API
+
+The recommended surface is `MeltAnalysis`. It holds the DataFrame and
+every configuration knob (struct type, salt, transition window, baseline
+offsets, solver / vH / fit-init overrides) and exposes the three modes as
+methods returning typed result objects from `rnamelt.results`.
+
+```python
+from rnamelt import MeltAnalysis, FitFailed
+
+m = MeltAnalysis.from_csv(
+    "melt.csv",
+    struct_type="heterodimer",   # "heterodimer" | "homodimer" | "monomer"
+    salt=150.0,                  # NaCl (mM) — metadata only
+    T_low=None, T_high=None,     # transition window (°C); None = full range
+    bl_lower_offset=10.0,        # folded baseline span above T_low (°C)
+    bl_upper_offset=10.0,        # unfolded baseline span below T_high (°C)
+)
+m.signal_columns                 # ['sample_1', 'sample_2', ...]
+```
+
+### Three modes
+
+```python
+# Single column — returns SingleResult; numpy arrays live on the object
+r = m.single("sample_1", oligo=0.5)
+r.Tm_raw, r.vh.dH, r.fit.Tm, r.fit.dG
+
+try:
+    r.fit.require()              # raises FitFailed if not r.fit.ok
+except FitFailed as e:
+    print(e)
+
+# Shared-ΔH joint fit across columns
+multi = m.multi({"sample_1": 0.5, "sample_2": 5.0, "sample_3": 50.0})
+multi.dH, multi.dS
+for c in multi.columns:
+    print(c.name, c.Tm_fit, c.oligoC)
+
+# Concentration-series van't Hoff — three regressions (raw / vH / full fit)
+conc = m.concentration({"sample_1": 0.5, "sample_2": 5.0, "sample_3": 50.0})
+for s in (conc.series_raw, conc.series_vh, conc.series_fit):
+    if s.ok:
+        print(s.dH, s.dG_37, s.r_squared)
+
+# Every column at once
+batch = m.single_all(oligo=0.5)  # dict[str, SingleResult]
+
+# Export forms (same shape the browser download produces)
+r.to_dict(); r.to_dataframe(); r.to_csv("out.csv")
+```
+
+### From raw arrays — no CSV
+
+`signals` accepts a 1D array, a `{name: array}` mapping, or a 2D array
+(one column per signal, with optional `names=`):
+
+```python
+import numpy as np
+from rnamelt import MeltAnalysis
+
+T = np.linspace(20, 90, 71)
+
+m = MeltAnalysis.from_arrays(T, signal_F4)                        # 1D
+m = MeltAnalysis.from_arrays(T, {"F4": sigF4, "F5": sigF5})       # mapping
+m = MeltAnalysis.from_arrays(T, arr2d, names=["A", "B", "C"])     # 2D
+```
+
+### Plotting (optional)
+
+`pip install 'rnamelt[plots]'`. Each result class has a `.plot()` method
+that lazy-imports `rnamelt.plots`, so matplotlib never enters the
+browser/Pyodide bundle.
+
+```python
+fig, axes = m.single("F4").plot(figsize=(15, 5))      # raw / vH / full fit
+fig, ax   = m.multi(oligo_multi).plot()
+fig, axes = m.concentration(oligo_multi).plot()
+
+# Convenience shortcut on the analyzer
+fig, axes, result = m.plot("F4")
+```
+
+### Functional helpers (back-compat)
+
+Thin wrappers around the same orchestrator that take a cleaned
+`pandas.DataFrame` and return the legacy dict directly:
+
+```python
+import pandas as pd
+from rnamelt import (
+    analyze_single, analyze_multi, analyze_concentration, analyze_csv,
+)
+from rnamelt.cleaning import clean
+
+df = clean(pd.read_csv("melt.csv"))
+analyze_single(df, "sample_1", struct_type="heterodimer", oligo=0.5)
+analyze_multi(df, {"sample_1": 0.5, "sample_2": 5.0})
+analyze_concentration(df, {"sample_1": 0.5, "sample_2": 5.0})
+
+# read_csv + clean + dispatch in one call
+analyze_csv("melt.csv", mode="single", column="sample_1", oligo=0.5)
+```
+
+## Analysis modes
+
+All three modes go through `rnamelt.analysis_melting.run(df, params)`;
+the `column` param selects the mode.
+
+| `column` value         | Mode                                | What it does |
+|------------------------|-------------------------------------|--------------|
+| any signal-column name | **Single column**                   | Tm by baseline intersection, van't Hoff linearisation, and a full two-state nonlinear fit. Returns ΔH / ΔS / ΔG / Tm from each method. |
+| `__multi__`            | **Shared-ΔH joint fit**             | Fit every column with common ΔH, ΔS but independent baselines. Each column carries its own concentration. |
+| `__concentration__`    | **Concentration-series van't Hoff** | Three Tm values per column (raw / vH / full-fit) → `1/Tm = (R/ΔH)·ln(C_T/f) + ΔS/ΔH` regression for each. `f = 1` (homodimer) or `f = 4` (heterodimer). |
+
+## Two-state model
+
+Observed signal is a linear combination of folded and unfolded baselines,
+weighted by the fraction unfolded θ(T):
+
+```
+A(T) = (m_F·T + b_F)·(1 − θ) + (m_U·T + b_U)·θ
+K(T) = exp(−ΔG / RT),    ΔG = ΔH − T·ΔS
+θ    = K / (1 + K)                       (monomer)
+θ    = (√(1 + 8·c₀·K) − 1) / (4·c₀·K)    (dimer)
+```
+
+Units: ΔH in kcal/mol, ΔS in kcal/(mol·K), T in K
+(`T_K = T_C − T0`, `T0 = −273.15`).
+
+## Browser app
+
+The same Python package runs client-side via [Pyodide](https://pyodide.org/);
+no server, no upload, no install. Drop a CSV onto
+<https://tspich.github.io/RNAmelt/> to try it. The source for the page is
+`index.html` in the [repository](https://github.com/tspich/RNAmelt).
+
+## Development
+
+```bash
+git clone https://github.com/tspich/RNAmelt
+cd RNAmelt
+pip install -e '.[plots]'
+
+pytest tests/                 # or: python -m unittest discover tests
+python -m build               # sdist + wheel into dist/
+```
+
+Module layering is strict: `functions` → `methods` → `analysis_melting` →
+`api` → `__main__` / browser. `functions` stays stateless. `plots` is
+lazy-imported so the browser bundle never pulls matplotlib.
+
+## License
+
+[MIT](LICENSE).
+
+## Links
+
+- Source: <https://github.com/tspich/RNAmelt>
+- Issues: <https://github.com/tspich/RNAmelt/issues>
+- Live demo: <https://tspich.github.io/RNAmelt/>

rnamelt-0.1.0/pyproject.toml

@@ -0,0 +1,41 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "rnamelt"
+version = "0.1.0"
+description = "Two-state thermodynamic analysis (ΔH, ΔS, ΔG, Tm) of RNA melting curves"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "MIT" }
+authors = [
+    { name = "tspich" },
+    { name = "RaumZeit" },
+]
+keywords = ["rna", "melting curve", "thermodynamics"]
+dependencies = [
+    "numpy>=1.23",
+    "pandas>=1.5",
+    "scipy>=1.10",
+]
+
+[project.optional-dependencies]
+plots = ["matplotlib>=3.5"]
+
+[project.scripts]
+rnamelt = "rnamelt.__main__:main"
+
+[project.urls]
+Homepage = "https://github.com/tspich/RNAmelt"
+Issues = "https://github.com/tspich/RNAmelt/issues"
+
+[tool.hatch.build.targets.wheel]
+packages = ["rnamelt"]
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "rnamelt",
+    "README.md",
+    "pyproject.toml",
+]

rnamelt-0.1.0/rnamelt/__init__.py

@@ -0,0 +1,54 @@
+"""rnamelt — RNA / DNA melting-curve thermodynamic analysis.
+
+Public API:
+    MeltAnalysis                                          — class façade
+    analyze_single, analyze_multi, analyze_concentration  — DataFrame in
+    analyze_csv                                           — path in
+"""
+
+from rnamelt.api import (
+    MeltAnalysis,
+    analyze_concentration,
+    analyze_csv,
+    analyze_multi,
+    analyze_single,
+)
+from rnamelt.methods import FIT_INIT_DEFAULTS, SOLVER_DEFAULTS, VH_DEFAULTS
+from rnamelt.results import (
+    BatchResult,
+    ConcentrationCurve,
+    ConcentrationResult,
+    ConcentrationSeries,
+    FitFailed,
+    FullFit,
+    MultiColumnResult,
+    MultiResult,
+    SingleResult,
+    VanHoffFit,
+)
+
+ANALYSES = [
+    "rnamelt.analysis_melting",
+]
+
+__all__ = [
+    "MeltAnalysis",
+    "analyze_single",
+    "analyze_multi",
+    "analyze_concentration",
+    "analyze_csv",
+    "SingleResult",
+    "MultiResult",
+    "MultiColumnResult",
+    "ConcentrationResult",
+    "ConcentrationCurve",
+    "ConcentrationSeries",
+    "BatchResult",
+    "VanHoffFit",
+    "FullFit",
+    "FitFailed",
+    "SOLVER_DEFAULTS",
+    "VH_DEFAULTS",
+    "FIT_INIT_DEFAULTS",
+    "ANALYSES",
+]