pynumdiff 0.1.2__tar.gz → 0.2.1__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.
- pynumdiff-0.2.1/.coveragerc +19 -0
- pynumdiff-0.2.1/.editorconfig +11 -0
- pynumdiff-0.2.1/.github/workflows/release.yml +18 -0
- pynumdiff-0.2.1/.github/workflows/test.yml +25 -0
- pynumdiff-0.2.1/.gitignore +120 -0
- pynumdiff-0.2.1/.pylintrc +529 -0
- pynumdiff-0.2.1/.readthedocs.yaml +16 -0
- pynumdiff-0.2.1/CITATION.cff +33 -0
- pynumdiff-0.2.1/CONTRIBUTING.md +64 -0
- pynumdiff-0.2.1/LICENSE.txt +23 -0
- pynumdiff-0.2.1/PKG-INFO +186 -0
- pynumdiff-0.2.1/README.md +149 -0
- pynumdiff-0.2.1/docs/Makefile +20 -0
- pynumdiff-0.2.1/docs/source/LICENSE.rst +27 -0
- pynumdiff-0.2.1/docs/source/basis_fit.rst +5 -0
- pynumdiff-0.2.1/docs/source/code.rst +15 -0
- pynumdiff-0.2.1/docs/source/conf.py +52 -0
- pynumdiff-0.2.1/docs/source/contact.rst +8 -0
- pynumdiff-0.2.1/docs/source/contributing.rst +19 -0
- pynumdiff-0.2.1/docs/source/finite_difference.rst +10 -0
- pynumdiff-0.2.1/docs/source/index.rst +10 -0
- pynumdiff-0.2.1/docs/source/kalman_smooth.rst +14 -0
- pynumdiff-0.2.1/docs/source/linear_model.rst +5 -0
- pynumdiff-0.2.1/docs/source/optimize.rst +5 -0
- pynumdiff-0.2.1/docs/source/polynomial_fit.rst +5 -0
- pynumdiff-0.2.1/docs/source/smooth_finite_difference.rst +12 -0
- pynumdiff-0.2.1/docs/source/total_variation_regularization.rst +12 -0
- pynumdiff-0.2.1/docs/source/utils/evaluate.rst +5 -0
- pynumdiff-0.2.1/docs/source/utils/simulate.rst +5 -0
- pynumdiff-0.2.1/docs/source/utils/utility.rst +5 -0
- pynumdiff-0.2.1/docs/source/utils.rst +9 -0
- pynumdiff-0.2.1/logo.png +0 -0
- pynumdiff-0.2.1/notebooks/1_basic_tutorial.ipynb +822 -0
- pynumdiff-0.2.1/notebooks/2_optimizing_hyperparameters.ipynb +872 -0
- pynumdiff-0.2.1/notebooks/3_automatic_method_suggestion.ipynb +206 -0
- pynumdiff-0.2.1/notebooks/4_performance_analysis.ipynb +459 -0
- pynumdiff-0.2.1/notebooks/5_robust_outliers_demo.ipynb +205 -0
- pynumdiff-0.2.1/notebooks/6_multidimensionality_demo.ipynb +141 -0
- pynumdiff-0.2.1/notebooks/README.md +10 -0
- pynumdiff-0.2.1/pynumdiff/README.md +13 -0
- pynumdiff-0.2.1/pynumdiff/__init__.py +20 -0
- pynumdiff-0.2.1/pynumdiff/_version.py +34 -0
- pynumdiff-0.2.1/pynumdiff/basis_fit.py +123 -0
- pynumdiff-0.2.1/pynumdiff/finite_difference.py +127 -0
- pynumdiff-0.2.1/pynumdiff/kalman_smooth.py +351 -0
- pynumdiff-0.2.1/pynumdiff/linear_model.py +161 -0
- pynumdiff-0.2.1/pynumdiff/optimize.py +307 -0
- pynumdiff-0.2.1/pynumdiff/polynomial_fit.py +142 -0
- pynumdiff-0.2.1/pynumdiff/smooth_finite_difference.py +182 -0
- pynumdiff-0.2.1/pynumdiff/tests/conftest.py +23 -0
- pynumdiff-0.2.1/pynumdiff/tests/test_diff_methods.py +375 -0
- pynumdiff-0.2.1/pynumdiff/tests/test_optimize.py +44 -0
- pynumdiff-0.2.1/pynumdiff/tests/test_utils.py +125 -0
- pynumdiff-0.2.1/pynumdiff/total_variation_regularization.py +233 -0
- pynumdiff-0.2.1/pynumdiff/utils/__init__.py +0 -0
- pynumdiff-0.1.2/pynumdiff/total_variation_regularization/__chartrand_tvregdiff__.py → pynumdiff-0.2.1/pynumdiff/utils/_chartrand_tvregdiff.py +58 -134
- pynumdiff-0.2.1/pynumdiff/utils/evaluate.py +147 -0
- pynumdiff-0.2.1/pynumdiff/utils/old_pi_cruise_control.py +178 -0
- pynumdiff-0.2.1/pynumdiff/utils/simulate.py +335 -0
- pynumdiff-0.2.1/pynumdiff/utils/utility.py +209 -0
- pynumdiff-0.2.1/pynumdiff.egg-info/PKG-INFO +186 -0
- pynumdiff-0.2.1/pynumdiff.egg-info/SOURCES.txt +66 -0
- pynumdiff-0.2.1/pynumdiff.egg-info/requires.txt +20 -0
- pynumdiff-0.2.1/pyproject.toml +58 -0
- pynumdiff-0.1.2/PKG-INFO +0 -27
- pynumdiff-0.1.2/README.md +0 -219
- pynumdiff-0.1.2/pynumdiff/__init__.py +0 -12
- pynumdiff-0.1.2/pynumdiff/__version__.py +0 -57
- pynumdiff-0.1.2/pynumdiff/finite_difference/__init__.py +0 -5
- pynumdiff-0.1.2/pynumdiff/finite_difference/_finite_difference.py +0 -121
- pynumdiff-0.1.2/pynumdiff/kalman_smooth/__init__.py +0 -9
- pynumdiff-0.1.2/pynumdiff/kalman_smooth/_kalman_smooth.py +0 -646
- pynumdiff-0.1.2/pynumdiff/kalman_smooth/_kalman_smooth_old.py +0 -615
- pynumdiff-0.1.2/pynumdiff/linear_model/__init__.py +0 -49
- pynumdiff-0.1.2/pynumdiff/linear_model/_linear_model.py +0 -633
- pynumdiff-0.1.2/pynumdiff/optimize/__init__.py +0 -33
- pynumdiff-0.1.2/pynumdiff/optimize/__optimize__.py +0 -144
- pynumdiff-0.1.2/pynumdiff/optimize/finite_difference/__finite_difference__.py +0 -35
- pynumdiff-0.1.2/pynumdiff/optimize/finite_difference/__init__.py +0 -4
- pynumdiff-0.1.2/pynumdiff/optimize/kalman_smooth/__init__.py +0 -6
- pynumdiff-0.1.2/pynumdiff/optimize/kalman_smooth/__kalman_smooth__.py +0 -114
- pynumdiff-0.1.2/pynumdiff/optimize/linear_model/__init__.py +0 -8
- pynumdiff-0.1.2/pynumdiff/optimize/linear_model/__linear_model__.py +0 -184
- pynumdiff-0.1.2/pynumdiff/optimize/smooth_finite_difference/__init__.py +0 -9
- pynumdiff-0.1.2/pynumdiff/optimize/smooth_finite_difference/__smooth_finite_difference__.py +0 -183
- pynumdiff-0.1.2/pynumdiff/optimize/total_variation_regularization/__init__.py +0 -9
- pynumdiff-0.1.2/pynumdiff/optimize/total_variation_regularization/__total_variation_regularization__.py +0 -162
- pynumdiff-0.1.2/pynumdiff/smooth_finite_difference/__init__.py +0 -10
- pynumdiff-0.1.2/pynumdiff/smooth_finite_difference/_smooth_finite_difference.py +0 -350
- pynumdiff-0.1.2/pynumdiff/tests/test_finite_difference.py +0 -44
- pynumdiff-0.1.2/pynumdiff/tests/test_kalman_smooth.py +0 -58
- pynumdiff-0.1.2/pynumdiff/tests/test_linear_model.py +0 -101
- pynumdiff-0.1.2/pynumdiff/tests/test_optimize.py +0 -153
- pynumdiff-0.1.2/pynumdiff/tests/test_smooth_finite_difference.py +0 -82
- pynumdiff-0.1.2/pynumdiff/tests/test_total_variation_regularization.py +0 -117
- pynumdiff-0.1.2/pynumdiff/tests/test_utils.py +0 -20
- pynumdiff-0.1.2/pynumdiff/total_variation_regularization/__init__.py +0 -36
- pynumdiff-0.1.2/pynumdiff/total_variation_regularization/_total_variation_regularization.py +0 -393
- pynumdiff-0.1.2/pynumdiff/utils/__init__.py +0 -6
- pynumdiff-0.1.2/pynumdiff/utils/_pi_cruise_control.py +0 -65
- pynumdiff-0.1.2/pynumdiff/utils/evaluate.py +0 -213
- pynumdiff-0.1.2/pynumdiff/utils/old_pi_cruise_control.py +0 -228
- pynumdiff-0.1.2/pynumdiff/utils/simulate.py +0 -559
- pynumdiff-0.1.2/pynumdiff/utils/utility.py +0 -283
- pynumdiff-0.1.2/pynumdiff.egg-info/PKG-INFO +0 -27
- pynumdiff-0.1.2/pynumdiff.egg-info/SOURCES.txt +0 -47
- pynumdiff-0.1.2/pynumdiff.egg-info/requires.txt +0 -3
- pynumdiff-0.1.2/setup.py +0 -30
- {pynumdiff-0.1.2 → pynumdiff-0.2.1}/pynumdiff/tests/__init__.py +0 -0
- {pynumdiff-0.1.2 → pynumdiff-0.2.1}/pynumdiff.egg-info/dependency_links.txt +0 -0
- {pynumdiff-0.1.2 → pynumdiff-0.2.1}/pynumdiff.egg-info/top_level.txt +0 -0
- {pynumdiff-0.1.2 → pynumdiff-0.2.1}/setup.cfg +0 -0
|
@@ -0,0 +1,19 @@
|
|
|
1
|
+
[run]
|
|
2
|
+
omit =
|
|
3
|
+
pynumdiff/_version.py
|
|
4
|
+
pynumdiff/tests/*
|
|
5
|
+
pynumdiff/utils/old_pi_cruise_control.py
|
|
6
|
+
|
|
7
|
+
[report]
|
|
8
|
+
# uses regex to match lines; lines that head a block or function exclude that whole thing
|
|
9
|
+
exclude_lines =
|
|
10
|
+
pragma: no cover
|
|
11
|
+
if __name__ == .__main__.:
|
|
12
|
+
if diagflag:
|
|
13
|
+
if options is not None:
|
|
14
|
+
^def plot
|
|
15
|
+
^def plot_comparison
|
|
16
|
+
^def suggest_method
|
|
17
|
+
def _lorenz_xyz_odeint
|
|
18
|
+
^except ImportError:
|
|
19
|
+
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
on:
|
|
2
|
+
release:
|
|
3
|
+
types: [created]
|
|
4
|
+
jobs:
|
|
5
|
+
deploy-to-pypi:
|
|
6
|
+
runs-on: ubuntu-latest
|
|
7
|
+
env:
|
|
8
|
+
TWINE_USERNAME: __token__
|
|
9
|
+
TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
|
|
10
|
+
steps:
|
|
11
|
+
- uses: actions/checkout@v4
|
|
12
|
+
- uses: actions/setup-python@v5
|
|
13
|
+
with:
|
|
14
|
+
python-version: '3.x'
|
|
15
|
+
- run: |
|
|
16
|
+
pip install build wheel twine
|
|
17
|
+
python -m build
|
|
18
|
+
twine upload dist/*
|
|
@@ -0,0 +1,25 @@
|
|
|
1
|
+
on:
|
|
2
|
+
push:
|
|
3
|
+
branches:
|
|
4
|
+
- master
|
|
5
|
+
pull_request:
|
|
6
|
+
|
|
7
|
+
jobs:
|
|
8
|
+
run-tests:
|
|
9
|
+
runs-on: ubuntu-latest
|
|
10
|
+
steps:
|
|
11
|
+
- uses: actions/checkout@v4
|
|
12
|
+
with:
|
|
13
|
+
fetch-depth: 0 # important for Coveralls to read commit history
|
|
14
|
+
- uses: actions/setup-python@v5
|
|
15
|
+
with:
|
|
16
|
+
python-version: '3.13' # because cvxopt binaries for 3.14 don't yet exist, and building is terrible
|
|
17
|
+
- name: tests and coverage
|
|
18
|
+
run: | # some extra stuff here to make sure coverage works across multiprocessing
|
|
19
|
+
pip install -e .[advanced,dev] coveralls
|
|
20
|
+
coverage run --source=pynumdiff -m pytest -s
|
|
21
|
+
coverage xml
|
|
22
|
+
- uses: coverallsapp/github-action@v2
|
|
23
|
+
with:
|
|
24
|
+
format: cobertura
|
|
25
|
+
file: coverage.xml
|
|
@@ -0,0 +1,120 @@
|
|
|
1
|
+
# Byte-compiled / optimized / DLL files
|
|
2
|
+
__pycache__/
|
|
3
|
+
*.py[cod]
|
|
4
|
+
*$py.class
|
|
5
|
+
|
|
6
|
+
# C extensions
|
|
7
|
+
*.so
|
|
8
|
+
|
|
9
|
+
# Distribution / packaging
|
|
10
|
+
.Python
|
|
11
|
+
develop-eggs/
|
|
12
|
+
dist/
|
|
13
|
+
downloads/
|
|
14
|
+
eggs/
|
|
15
|
+
.eggs/
|
|
16
|
+
lib/
|
|
17
|
+
lib64/
|
|
18
|
+
parts/
|
|
19
|
+
sdist/
|
|
20
|
+
var/
|
|
21
|
+
wheels/
|
|
22
|
+
*.egg-info/
|
|
23
|
+
.installed.cfg
|
|
24
|
+
*.egg
|
|
25
|
+
MANIFEST
|
|
26
|
+
|
|
27
|
+
# PyInstaller
|
|
28
|
+
# Usually these files are written by a python script from a template
|
|
29
|
+
# before PyInstaller builds the exe, so as to inject date/other infos into it.
|
|
30
|
+
*.manifest
|
|
31
|
+
*.spec
|
|
32
|
+
|
|
33
|
+
# Installer logs
|
|
34
|
+
pip-log.txt
|
|
35
|
+
pip-delete-this-directory.txt
|
|
36
|
+
|
|
37
|
+
# Unit test / coverage reports
|
|
38
|
+
htmlcov/
|
|
39
|
+
.tox/
|
|
40
|
+
.coverage
|
|
41
|
+
.coverage.*
|
|
42
|
+
.cache
|
|
43
|
+
nosetests.xml
|
|
44
|
+
coverage.xml
|
|
45
|
+
*.cover
|
|
46
|
+
.hypothesis/
|
|
47
|
+
.pytest_cache/
|
|
48
|
+
|
|
49
|
+
# Translations
|
|
50
|
+
*.mo
|
|
51
|
+
*.pot
|
|
52
|
+
|
|
53
|
+
# Django stuff:
|
|
54
|
+
*.log
|
|
55
|
+
local_settings.py
|
|
56
|
+
db.sqlite3
|
|
57
|
+
|
|
58
|
+
# Flask stuff:
|
|
59
|
+
instance/
|
|
60
|
+
.webassets-cache
|
|
61
|
+
|
|
62
|
+
# Scrapy stuff:
|
|
63
|
+
.scrapy
|
|
64
|
+
|
|
65
|
+
# PyBuilder
|
|
66
|
+
target/
|
|
67
|
+
|
|
68
|
+
# Jupyter Notebook
|
|
69
|
+
.ipynb_checkpoints
|
|
70
|
+
|
|
71
|
+
# pyenv
|
|
72
|
+
.python-version
|
|
73
|
+
|
|
74
|
+
# celery beat schedule file
|
|
75
|
+
celerybeat-schedule
|
|
76
|
+
|
|
77
|
+
# SageMath parsed files
|
|
78
|
+
*.sage.py
|
|
79
|
+
|
|
80
|
+
# Environments
|
|
81
|
+
.env
|
|
82
|
+
.venv
|
|
83
|
+
env/
|
|
84
|
+
venv/
|
|
85
|
+
ENV/
|
|
86
|
+
env.bak/
|
|
87
|
+
venv.bak/
|
|
88
|
+
|
|
89
|
+
# Spyder project settings
|
|
90
|
+
.spyderproject
|
|
91
|
+
.spyproject
|
|
92
|
+
|
|
93
|
+
# Rope project settings
|
|
94
|
+
.ropeproject
|
|
95
|
+
|
|
96
|
+
# mkdocs documentation
|
|
97
|
+
/site
|
|
98
|
+
|
|
99
|
+
# mypy
|
|
100
|
+
.mypy_cache/
|
|
101
|
+
|
|
102
|
+
# add
|
|
103
|
+
*.[oa]
|
|
104
|
+
*~
|
|
105
|
+
.idea
|
|
106
|
+
.DS_Store
|
|
107
|
+
*.nc
|
|
108
|
+
*.csv
|
|
109
|
+
*.mat
|
|
110
|
+
.coverage
|
|
111
|
+
__pycache__
|
|
112
|
+
*.tar
|
|
113
|
+
*.tar.gz
|
|
114
|
+
*.zip
|
|
115
|
+
*.egg-info
|
|
116
|
+
dist
|
|
117
|
+
*.whl
|
|
118
|
+
.vscode
|
|
119
|
+
docs/build
|
|
120
|
+
pynumdiff/_version.py
|