D95eq 1.2.0__tar.gz

d95eq-1.2.0/.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

d95eq-1.2.0/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) Mathieu Daëron
+
+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.

d95eq-1.2.0/PKG-INFO

@@ -0,0 +1,41 @@
+Metadata-Version: 2.4
+Name: D95eq
+Version: 1.2.0
+Summary: Test for clumped isotope equilibrium and estimate carbonate formation temperatures from dual clumped isotope measurements
+Author-email: Mathieu Daëron <mathieu@daeron.fr>, Timothy Pollard <timothy.pollard@unimelb.edu.au>
+Requires-Python: >=3.14
+Description-Content-Type: text/markdown
+License-Expression: MIT
+License-File: LICENSE
+Requires-Dist: correldata>=2.0.0
+Requires-Dist: lmfit>=1.3.4
+Requires-Dist: matplotlib>=3.10.8
+Requires-Dist: ogls>=1.0.1
+Requires-Dist: tqdm>=4.67.1
+Requires-Dist: typer>=0.21.1
+Requires-Dist: typing-extensions>=4.15.0
+Project-URL: Documentation, https://mdaeron.github.io/D95eq
+Project-URL: Home, https://github.com/mdaeron/D95eq
+
+# D95eq
+
+(because 47 + 48 = 95)
+
+
+
+Test for clumped isotope equilibrium and estimate carbonate formation temperatures from dual clumped isotope measurements
+
+Formation temperatures are estimated either by direct intersection with the equilibrium curve or by projection on the equilibrium curve following an aribitrary kinetic fractionation slope.
+
+Returns p-values and (statistically correlated) temperature estimates with full error propagation accounting for:
+
++ Arbitrarily correlated analytical errors in Δ<sub>47</sub> and Δ<sub>48</sub> measurements
+
++ Arbitrarily correlated calibration errors on equilibrium Δ<sub>47</sub> and Δ<sub>48</sub> laws
+
++ Uncertainty in the kinetic fractionation slope
+
+  
+
+<img align="center" src="examples/example_plot.png">
+

d95eq-1.2.0/build-metadata.py

@@ -0,0 +1,34 @@
+import tomllib
+import pathlib
+import datetime
+
+srcpath = next(pathlib.Path("src").glob("*/__init__.py")).parent
+
+with open('pyproject.toml', 'rb') as fid:
+	toml = tomllib.load(fid)
+
+export = []
+with open(srcpath / '_metadata.py', 'w') as fid:
+
+	align = 16
+	for field, content in (
+		('version',     toml['project']['version']),
+		('description', toml['project']['description']),
+		('author',      None),
+		('authors',     ' & '.join([', '.join(_['name'] for _ in toml['project']['authors'][:-1]), toml['project']['authors'][-1]['name']])),
+		('contact',     toml['project']['authors'][0]['email']),
+		('license',     toml['project']['license']),
+		('copyright',   toml['project']['authors'][0]['name']),
+		('date',        datetime.date.today().isoformat()),
+	):
+		if content is None:
+			continue
+		name = f'__{field}__'
+		fid.write(f'{name:<{align}s}= "{content}"\n')
+		export.append(f'"{name}"')
+	fid.write(f'{"__all__":<{align}s}= [{', '.join(export)}]\n')
+
+
+
+with open(srcpath / '_metadata.py', 'r') as fid:
+	print(fid.read())

d95eq-1.2.0/build_doc.py

@@ -0,0 +1,6 @@
+import pdoc
+
+pdoc.render.configure(search = False)
+
+with open('../docs/index.html', 'w') as fid:
+	fid.write(pdoc.pdoc('D95eq'))

d95eq-1.2.0/calib_coefs/D47_calib_coefs.csv

@@ -0,0 +1,4 @@
+degree,     coef,    SE_coef,  correl_coef,             ,             
+     0, 0.174378, 0.00491111,  1.000000000, -0.937970050,  0.886577100
+     1, -18.1422,    5.63233, -0.937970050,  1.000000000, -0.989942490
+     2,  42657.2,    1277.13,  0.886577100, -0.989942490,  1.000000000

d95eq-1.2.0/calib_coefs/D48_calib_coefs.csv

@@ -0,0 +1,6 @@
+degree,         coef,     SE_coef,  correl_coef,             ,             ,             ,             
+     0,     0.121352,  0.00271974,  1.000000000, -0.664408766,  0.664408766, -0.664408766,  0.664408766
+     1,       6.2299,    0.229338, -0.664408766,  1.000000000, -1.000000000,  1.000000000, -1.000000000
+     2,     -13483.2,     496.352,  0.664408766, -1.000000000,  1.000000000, -1.000000000,  1.000000000
+     3,  9.33758e+06,      343740, -0.664408766,  1.000000000, -1.000000000,  1.000000000, -1.000000000
+     4, -7.70485e+08, 2.83635e+07,  0.664408766, -1.000000000,  1.000000000, -1.000000000,  1.000000000

d95eq-1.2.0/calib_coefs/calib_coefs.py

@@ -0,0 +1,20 @@
+import numpy as _np
+import correldata
+from D95eq import Engine
+from D95eq import _compute_D48_calib_coefficients
+
+
+coefs = Engine.D47_calib_coefs
+data = correldata.CorrelData({
+	'degree' : _np.array([k for k,v in enumerate(coefs)]),
+	'coef': correldata.uarray(coefs),
+})
+data.to_csv('D47_calib_coefs.csv', correl_format = 'z.9f')
+
+
+coefs = _compute_D48_calib_coefficients()
+data = correldata.CorrelData({
+	'degree' : _np.array([k for k,v in enumerate(coefs)]),
+	'coef': correldata.uarray(coefs),
+})
+data.to_csv('D48_calib_coefs.csv', correl_format = 'z.9f')

d95eq-1.2.0/changelog.md

@@ -0,0 +1,7 @@
+# Changelog
+
+## v1.2.0
+
+2026-05-30
+
+* First public release

d95eq-1.2.0/docpages/cli.md

@@ -0,0 +1,7 @@
+# 2. Command-line interface
+
+`D95eq` also provides a command-line interface (CLI).
+
+## 2.1 Simple examples
+
+(work in progress)

d95eq-1.2.0/docpages/install.md

@@ -0,0 +1,15 @@
+# 1. Installation
+
+## 1.1 Recommended method
+
+The recommended way is to use via `uv` ([https://docs.astral.sh/uv]()).
+
+If you only want to run the command-line interface (CLI): after installing `uv`, this should be as simple as `uvx D95eq` or `uv tool install D95eq`.
+
+If you want to import `D95eq` in some Python code, once you are within a `uv` project (`uv init`), you can install the module with `uv add D95eq`.
+
+After installation, open a new shell window and try `D95eq --help`.
+
+## 1.2 Other methods
+
+You can of course install globally via `pip` (`pip install D95eq`), or only install the CLI using `pipx` (`pipx install D95eq`).