nanodent 0.0.3__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nanodent-0.0.3/.github/dependabot.yml +6 -0
- nanodent-0.0.3/.github/workflows/ci.yml +69 -0
- nanodent-0.0.3/.github/workflows/release.yml +159 -0
- nanodent-0.0.3/.gitignore +145 -0
- nanodent-0.0.3/.pre-commit-config.yaml +38 -0
- nanodent-0.0.3/.readthedocs.yml +18 -0
- nanodent-0.0.3/CITATION.cff +14 -0
- nanodent-0.0.3/COPYING.md +6 -0
- nanodent-0.0.3/LICENSE.md +8 -0
- nanodent-0.0.3/PKG-INFO +153 -0
- nanodent-0.0.3/README.md +120 -0
- nanodent-0.0.3/codecov.yml +10 -0
- nanodent-0.0.3/doc/Makefile +20 -0
- nanodent-0.0.3/doc/api.rst +9 -0
- nanodent-0.0.3/doc/conf.py +43 -0
- nanodent-0.0.3/doc/index.rst +16 -0
- nanodent-0.0.3/doc/intro.rst +2 -0
- nanodent-0.0.3/doc/make.bat +35 -0
- nanodent-0.0.3/notebooks/demo.ipynb +448 -0
- nanodent-0.0.3/pyproject.toml +82 -0
- nanodent-0.0.3/src/nanodent/__init__.py +137 -0
- nanodent-0.0.3/src/nanodent/analysis/__init__.py +46 -0
- nanodent-0.0.3/src/nanodent/analysis/filters.py +64 -0
- nanodent-0.0.3/src/nanodent/analysis/force_peaks.py +159 -0
- nanodent-0.0.3/src/nanodent/analysis/oliver_pharr.py +970 -0
- nanodent-0.0.3/src/nanodent/analysis/onset.py +271 -0
- nanodent-0.0.3/src/nanodent/analysis/quality.py +476 -0
- nanodent-0.0.3/src/nanodent/analysis/unloading.py +105 -0
- nanodent-0.0.3/src/nanodent/io.py +546 -0
- nanodent-0.0.3/src/nanodent/models.py +544 -0
- nanodent-0.0.3/src/nanodent/plotting.py +876 -0
- nanodent-0.0.3/src/nanodent/study.py +1300 -0
- nanodent-0.0.3/tests/__init__.py +0 -0
- nanodent-0.0.3/tests/conftest.py +17 -0
- nanodent-0.0.3/tests/data/experiment_a.hld +2813 -0
- nanodent-0.0.3/tests/data/experiment_b.hld +2816 -0
- nanodent-0.0.3/tests/data/experiment_c.hld +2617 -0
- nanodent-0.0.3/tests/data/experiment_d.hld +2811 -0
- nanodent-0.0.3/tests/test_analysis.py +1004 -0
- nanodent-0.0.3/tests/test_io.py +360 -0
- nanodent-0.0.3/tests/test_plotting.py +480 -0
- nanodent-0.0.3/tests/test_study.py +1472 -0
- nanodent-0.0.3/uv.toml +5 -0
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strategy:
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description: "Choose whether to build only, publish to TestPyPI, or publish to PyPI"
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required: true
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build:
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f"tag {expected_ref}, but GitHub provided {ref!r}."
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)
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print(f"Publishing from {ref}, matching project version {version}.")
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*$py.class
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# Distribution / packaging
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.Python
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build/
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MANIFEST
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# PyInstaller
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.coverage
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# Image files
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*.png
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# Model files
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*.pkl
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repos:
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2
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+
- repo: https://github.com/kynan/nbstripout
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3
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rev: 0.9.1
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|
4
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hooks:
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5
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- id: nbstripout
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6
|
+
files: ".ipynb"
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7
|
+
|
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8
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+
- repo: https://github.com/astral-sh/ruff-pre-commit
|
|
9
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rev: v0.15.7
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10
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hooks:
|
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# Run the linter
|
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12
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- id: ruff-check
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13
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+
args: [ --fix, --show-fixes ]
|
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types_or: [ python, pyi, pyproject ]
|
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# Run the formatter
|
|
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- id: ruff-format
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types_or: [ python, pyi ]
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# Add some general purpose useful hooks
|
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- repo: https://github.com/pre-commit/pre-commit-hooks
|
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rev: v6.0.0
|
|
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hooks:
|
|
23
|
+
# Make sure that contained YAML files are well-formed
|
|
24
|
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- id: check-yaml
|
|
25
|
+
# Trim trailing whitespace of all sorts
|
|
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|
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- id: trailing-whitespace
|
|
27
|
+
# Apply a file size limit of 500kB
|
|
28
|
+
- id: check-added-large-files
|
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29
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# Simple parser validation of e.g. pyproject.toml
|
|
30
|
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- id: check-toml
|
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|
+
# Unify file endings
|
|
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|
+
- id: end-of-file-fixer
|
|
33
|
+
|
|
34
|
+
# GitHub Actions Workflow linter
|
|
35
|
+
- repo: https://github.com/rhysd/actionlint
|
|
36
|
+
rev: v1.7.11
|
|
37
|
+
hooks:
|
|
38
|
+
- id: actionlint
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
cff-version: 1.2.0
|
|
2
|
+
message: If you want to cite this software, you can do so using the metadata from this file.
|
|
3
|
+
title: nanodent
|
|
4
|
+
abstract: Analyze data from nanoindentation experiments.
|
|
5
|
+
authors:
|
|
6
|
+
- family-names: Isensee
|
|
7
|
+
given-names: Thomas
|
|
8
|
+
orcid: "https://orcid.org/0000-0002-7242-4529"
|
|
9
|
+
version: 0.0.1
|
|
10
|
+
keywords:
|
|
11
|
+
- nanoindentation
|
|
12
|
+
date-released: "2026-03-21"
|
|
13
|
+
license: MIT
|
|
14
|
+
repository-code: https://github.com/thomasisensee/nanodent
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
Copyright 2026, The copyright holders according to COPYING.md
|
|
2
|
+
|
|
3
|
+
|
|
4
|
+
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:
|
|
5
|
+
|
|
6
|
+
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
|
|
7
|
+
|
|
8
|
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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.
|
nanodent-0.0.3/PKG-INFO
ADDED
|
@@ -0,0 +1,153 @@
|
|
|
1
|
+
Metadata-Version: 2.4
|
|
2
|
+
Name: nanodent
|
|
3
|
+
Version: 0.0.3
|
|
4
|
+
Summary: Analysis package for nanoindentation experimental data.
|
|
5
|
+
Project-URL: repository, https://github.com/thomasisensee/nanodent
|
|
6
|
+
Author-email: Thomas Isensee <thomas.isensee@iwr.uni-heidelberg.de>
|
|
7
|
+
License-Expression: MIT
|
|
8
|
+
License-File: LICENSE.md
|
|
9
|
+
Classifier: Intended Audience :: Science/Research
|
|
10
|
+
Classifier: Operating System :: OS Independent
|
|
11
|
+
Classifier: Programming Language :: Python :: 3
|
|
12
|
+
Requires-Python: >=3.10
|
|
13
|
+
Requires-Dist: matplotlib
|
|
14
|
+
Requires-Dist: numpy
|
|
15
|
+
Requires-Dist: scipy
|
|
16
|
+
Provides-Extra: dev
|
|
17
|
+
Requires-Dist: mypy; extra == 'dev'
|
|
18
|
+
Requires-Dist: pytest; extra == 'dev'
|
|
19
|
+
Requires-Dist: pytest-cov; extra == 'dev'
|
|
20
|
+
Requires-Dist: ruff; extra == 'dev'
|
|
21
|
+
Provides-Extra: docs
|
|
22
|
+
Requires-Dist: myst-parser; extra == 'docs'
|
|
23
|
+
Requires-Dist: sphinx; extra == 'docs'
|
|
24
|
+
Requires-Dist: sphinx-rtd-theme; extra == 'docs'
|
|
25
|
+
Provides-Extra: lint
|
|
26
|
+
Requires-Dist: mypy; extra == 'lint'
|
|
27
|
+
Requires-Dist: ruff; extra == 'lint'
|
|
28
|
+
Provides-Extra: tests
|
|
29
|
+
Requires-Dist: nbval; extra == 'tests'
|
|
30
|
+
Requires-Dist: pytest; extra == 'tests'
|
|
31
|
+
Requires-Dist: pytest-cov; extra == 'tests'
|
|
32
|
+
Description-Content-Type: text/markdown
|
|
33
|
+
|
|
34
|
+
# nanodent
|
|
35
|
+
|
|
36
|
+
[](https://opensource.org/licenses/MIT)
|
|
37
|
+
[](https://github.com/thomasisensee/nanodent/actions/workflows/ci.yml)
|
|
38
|
+
[](https://codecov.io/github/thomasisensee/nanodent)
|
|
39
|
+
|
|
40
|
+
|
|
41
|
+
## Installation
|
|
42
|
+
|
|
43
|
+
The Python package `nanodent` can be installed from PyPI:
|
|
44
|
+
|
|
45
|
+
```
|
|
46
|
+
python -m pip install nanodent
|
|
47
|
+
```
|
|
48
|
+
|
|
49
|
+
## Development installation
|
|
50
|
+
|
|
51
|
+
If you want to contribute to the development of `nanodent`, we recommend the
|
|
52
|
+
following editable installation from this repository:
|
|
53
|
+
|
|
54
|
+
```
|
|
55
|
+
git clone https://github.com/thomasisensee/nanodent
|
|
56
|
+
cd nanodent
|
|
57
|
+
python -m pip install --editable .[dev,docs,lint,tests]
|
|
58
|
+
```
|
|
59
|
+
|
|
60
|
+
Having done so, the test suite can be run using `pytest`:
|
|
61
|
+
|
|
62
|
+
```
|
|
63
|
+
python -m pytest
|
|
64
|
+
```
|
|
65
|
+
|
|
66
|
+
## Quick Start
|
|
67
|
+
|
|
68
|
+
`nanodent` loads `.hld` as the canonical source.
|
|
69
|
+
|
|
70
|
+
```python
|
|
71
|
+
from datetime import datetime, timedelta
|
|
72
|
+
|
|
73
|
+
import matplotlib.pyplot as plt
|
|
74
|
+
|
|
75
|
+
from nanodent import (
|
|
76
|
+
load_folder,
|
|
77
|
+
plot_experiments,
|
|
78
|
+
plot_group_timeline,
|
|
79
|
+
save_experiment_plots,
|
|
80
|
+
)
|
|
81
|
+
|
|
82
|
+
study = load_folder("path/to/experiment-folder")
|
|
83
|
+
filtered_study = study.classify_quality()
|
|
84
|
+
filtered_study = filtered_study.analyze_oliver_pharr()
|
|
85
|
+
hardness_rows = filtered_study.scalar_series("hardness")
|
|
86
|
+
pop_in_rows = filtered_study.detect_force_peaks().scalar_series("pop_in_load")
|
|
87
|
+
manual_groups = filtered_study.group_by_datetime_ranges(
|
|
88
|
+
[
|
|
89
|
+
(
|
|
90
|
+
datetime(2026, 3, 4, 13, 0, 0),
|
|
91
|
+
datetime(2026, 3, 4, 15, 0, 0),
|
|
92
|
+
),
|
|
93
|
+
]
|
|
94
|
+
)
|
|
95
|
+
|
|
96
|
+
timeline_fig, timeline_ax = plot_group_timeline(
|
|
97
|
+
filtered_study,
|
|
98
|
+
max_gap=timedelta(minutes=30),
|
|
99
|
+
)
|
|
100
|
+
|
|
101
|
+
fig, ax = plt.subplots()
|
|
102
|
+
plot_experiments(
|
|
103
|
+
ax,
|
|
104
|
+
filtered_study,
|
|
105
|
+
fit_kwargs={"color": "gray", "linestyle": "solid", "linewidth": 2},
|
|
106
|
+
zero_onset=False,
|
|
107
|
+
cmap="rainbow",
|
|
108
|
+
)
|
|
109
|
+
|
|
110
|
+
ax.set_xlabel("Displacement h / nm")
|
|
111
|
+
ax.set_ylabel("Force P / μN")
|
|
112
|
+
|
|
113
|
+
saved = save_experiment_plots(
|
|
114
|
+
filtered_study, "plots/", zero_onset=False
|
|
115
|
+
)
|
|
116
|
+
|
|
117
|
+
filtered_study.save_session("analysis-session.pkl")
|
|
118
|
+
resumed_study = load_folder("path/to/experiment-folder").load_session(
|
|
119
|
+
"analysis-session.pkl"
|
|
120
|
+
)
|
|
121
|
+
```
|
|
122
|
+
|
|
123
|
+
`Study.classify_quality()` keeps all experiments loaded but marks
|
|
124
|
+
heuristically bad runs as `enabled=False` with a short `disabled_reason`,
|
|
125
|
+
currently including `gradual_onset`, `flat_force`, and local-jump outliers
|
|
126
|
+
such as `outlier_disp` or `outlier_force`.
|
|
127
|
+
Grouping and plotting ignore disabled experiments by default; group summaries
|
|
128
|
+
include them by default so quality decisions stay visible. Pass
|
|
129
|
+
`include_disabled=True` when you want disabled runs included in plots or
|
|
130
|
+
grouping output. `plot_experiments(...)` and `save_experiment_plots(...)`
|
|
131
|
+
always visualize the test force-displacement curve.
|
|
132
|
+
|
|
133
|
+
The public API also exposes:
|
|
134
|
+
|
|
135
|
+
- `load_experiment(path) -> Experiment`
|
|
136
|
+
- `load_folder(path) -> Study`
|
|
137
|
+
- `Study.analyze_oliver_pharr(...) -> Study`
|
|
138
|
+
- `Study.scalar_series(...) -> list[dict[str, Any]]`
|
|
139
|
+
- `Study.save_session(path) -> Path`
|
|
140
|
+
- `Study.load_session(path) -> Study`
|
|
141
|
+
- `Study.group_by_datetime_ranges(...) -> list[ExperimentGroup]`
|
|
142
|
+
- `Study.group_by_time_gap(...) -> list[ExperimentGroup]`
|
|
143
|
+
- `plot_group_timeline(...) -> tuple[Figure, Axes]`
|
|
144
|
+
- `plot_experiments(...) -> Axes`
|
|
145
|
+
- `save_experiment_plots(...) -> list[Path]`
|
|
146
|
+
|
|
147
|
+
|
|
148
|
+
## Demo notebook using methods provided by py4dgeo
|
|
149
|
+
Use the [demo notebook](https://github.com/thomasisensee/nanodent/blob/main/notebooks/demo.ipynb) to test the functionality of `nanodent` and see how it can be used to analyze and visualize nanoindentation experiments.
|
|
150
|
+
|
|
151
|
+
## Acknowledgments
|
|
152
|
+
|
|
153
|
+
This repository was set up using the [SSC Cookiecutter for Python Packages](https://github.com/ssciwr/cookiecutter-python-package).
|