LogPSplinePSD 0.0.3__tar.gz

logpsplinepsd-0.0.3/.github/workflows/ci.yml

@@ -0,0 +1,39 @@
+name: Tests and Coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4.2.2
+        with:
+          fetch-depth: 0
+          ref: main       # Replace with your branch
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[dev]
+          pre-commit install
+
+      - name: pre-commit
+        run: pre-commit run --all-files --verbose --show-diff-on-failure
+        continue-on-error: true  # Allow failure for this step
+
+      - name: pytest
+        run: pytest --cov='log_psplines' --cov-report term-missing --cov-report=xml
+
+      - name: Coveralls
+        uses: coverallsapp/github-action@v2

logpsplinepsd-0.0.3/.github/workflows/docs.yml

@@ -0,0 +1,38 @@
+name: build-docs
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+  workflow_dispatch:
+
+# This job installs dependencies, builds the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4.2.2
+        with:
+          fetch-depth: 0
+          ref: main       # Replace with your branch
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip' # Enable caching for pip dependencies
+
+      - run: python -m pip install -e .[dev]
+      - run: |
+          cp *.rst docs/
+          jupyter-book build docs/
+
+      # Push the book's HTML to github-pages
+      - name: GitHub Pages action
+        uses: peaceiris/actions-gh-pages@v3.9.3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html

logpsplinepsd-0.0.3/.github/workflows/pypi.yml

@@ -0,0 +1,48 @@
+name: Release
+
+on:
+  push:
+    branches:
+      - main
+
+
+jobs:
+
+  release:
+    runs-on: ubuntu-latest
+    concurrency: release
+    permissions:
+      id-token: write
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4.2.2
+        with:
+          fetch-depth: 0
+          ref: main       # Replace with your branch
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip' # Enable caching for pip dependencies
+
+
+      - name: Semantic Version Release
+        id: release
+        # Adjust tag with desired version if applicable.
+        uses: python-semantic-release/python-semantic-release@v9.12.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          git_committer_name: "github-actions"
+          git_committer_email: "actions@users.noreply.github.com"
+
+
+      - name: build dist for pypi
+        if: steps.release.outputs.released == 'true'
+        run: |
+          python -m pip install --upgrade build
+          python -m build --sdist --wheel --outdir dist/
+
+      - name: pypi-publish
+        if: steps.release.outputs.released == 'true'
+        uses: pypa/gh-action-pypi-publish@v1.12.3

logpsplinepsd-0.0.3/.gitignore

@@ -0,0 +1,288 @@
+### venv template
+# Virtualenv
+# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
+.Python
+[Bb]in
+[Ii]nclude
+[Ll]ib
+[Ll]ib64
+[Ll]ocal
+[Ss]cripts
+pyvenv.cfg
+*.hdf5
+*.pdf
+*.png
+*.DS_Store
+plots/
+*.npy
+*output/
+*.txt
+.venv
+pip-selfcheck.json
+*.idea
+### PythonVanilla template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+
+### VirtualEnv template
+# Virtualenv
+# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
+.Python
+[Bb]in
+[Ii]nclude
+[Ll]ib
+[Ll]ib64
+[Ll]ocal
+[Ss]cripts
+pyvenv.cfg
+.venv
+pip-selfcheck.json
+
+### JupyterNotebooks template
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+/src/log_psplines/_version.py
+/docs/studies/lvk/lvkdata_cache.pkl
+/docs/studies/lvk/strain_cache.hdf5
+
+
+*.gwf
+
+*.h5

logpsplinepsd-0.0.3/.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: check-yaml
+        args: [ --unsafe ]
+  - repo: https://github.com/PyCQA/isort
+    rev: 6.0.1
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
+  - repo: https://github.com/psf/black
+    rev: "25.1.0"
+    hooks:
+      - id: black-jupyter

logpsplinepsd-0.0.3/CHANGELOG.rst

@@ -0,0 +1,217 @@
+.. _changelog:
+
+=========
+CHANGELOG
+=========
+
+
+.. _changelog-v0.0.3:
+
+v0.0.3 (2025-07-16)
+===================
+
+Unknown
+-------
+
+* Merge branch 'main' of github.com:nz-gravity/LogPSplinePSD (`4c72cc2`_)
+
+.. _4c72cc2: https://github.com/nz-gravity/LogPSplinePSD/commit/4c72cc2028d58dceeb717915f6bf2d9fb194a9c2
+
+
+.. _changelog-v0.0.2:
+
+v0.0.2 (2025-07-16)
+===================
+
+Bug Fixes
+---------
+
+* fix: fix pypi name bug (`b4b06db`_)
+
+* fix: pypi readme fix and updating demo (`7ecc602`_)
+
+Chores
+------
+
+* chore(release): 0.0.2 (`1d35bb9`_)
+
+Unknown
+-------
+
+* Merge branch 'main' of github.com:nz-gravity/LogPSplinePSD (`5121194`_)
+
+.. _b4b06db: https://github.com/nz-gravity/LogPSplinePSD/commit/b4b06db36c36e72793d659e317ce26af52108865
+.. _7ecc602: https://github.com/nz-gravity/LogPSplinePSD/commit/7ecc602bc7c066bcd9b86be4340575d10057c01c
+.. _1d35bb9: https://github.com/nz-gravity/LogPSplinePSD/commit/1d35bb982f74f1ae9be5021a983f4267b0627cfc
+.. _5121194: https://github.com/nz-gravity/LogPSplinePSD/commit/5121194a38c18dfbf31e7bcc9c3751409d4cb9b7
+
+
+.. _changelog-v0.0.1:
+
+v0.0.1 (2025-07-16)
+===================
+
+Bug Fixes
+---------
+
+* fix: add gwpy for dev options (`964e40e`_)
+
+* fix: add arviz (`7a0925c`_)
+
+* fix: add diagostics and ar dataset for tstig (`a43ee40`_)
+
+* fix: add demo to docs (`235c3ec`_)
+
+* fix: init weights with mse istead of lnl (`9df1e5d`_)
+
+Chores
+------
+
+* chore(release): 0.0.1 (`027591f`_)
+
+Unknown
+-------
+
+* Update pypi.yml (`88c8f9b`_)
+
+* edit readme (`60af98d`_)
+
+* add: add option for mh and nuts (`3a08b99`_)
+
+* refactoring to use a common parent class (`1fb79e8`_)
+
+* change to just vanilla metropolis-hastings (get rid of covar matrix adaptation) (`b0cd698`_)
+
+* Merge pull request #3 from nz-gravity/adding_adaptive_mcmc
+
+Adding adaptive MCMC (`fd9a95b`_)
+
+* init (`c41038c`_)
+
+* fix tests (`328e854`_)
+
+* Update docs.yml (`5877ec0`_)
+
+* Update README.rst (`20d3f39`_)
+
+* add line locator (`dc6469c`_)
+
+* add fix (`7f32bbb`_)
+
+* refactor (`a061028`_)
+
+* add docs (`6b3905f`_)
+
+* add examples (`cf42e6f`_)
+
+* add psd approx (`18d0075`_)
+
+* Merge branch 'main' of github.com:avivajpeyi/LogPSplinePSD (`a2035bb`_)
+
+* Create LICENSE (`8fff25b`_)
+
+* fix readme (`939cbdb`_)
+
+* add workflows (`73fd427`_)
+
+* Merge branch 'main' of github.com:avivajpeyi/LogPSplinePSD (`194fae8`_)
+
+* Merge pull request #1 from avivajpeyi/pre-commit-ci-update-config
+
+[pre-commit.ci] pre-commit autoupdate (`7231c3b`_)
+
+* [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+for more information, see https://pre-commit.ci (`6641a63`_)
+
+* [pre-commit.ci] pre-commit autoupdate
+
+updates:
+- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v5.0.0)
+- https://github.com/pre-commit/mirrors-isort → https://github.com/PyCQA/isort
+- [github.com/PyCQA/isort: v5.10.1 → 6.0.1](https://github.com/PyCQA/isort/compare/v5.10.1...6.0.1)
+- https://github.com/ambv/black → https://github.com/psf/black
+- [github.com/psf/black: 23.10.0 → 25.1.0](https://github.com/psf/black/compare/23.10.0...25.1.0)
+- [github.com/psf/black: 23.10.0 → 25.1.0](https://github.com/psf/black/compare/23.10.0...25.1.0) (`98ae77a`_)
+
+* add welch psd (`d7121d6`_)
+
+* add LVK plots (`f818caa`_)
+
+* add LVK example and parametric model (`0666415`_)
+
+* hackig on alternative model (`4197563`_)
+
+* add LVK example (`922f870`_)
+
+* add LVK example (`4944aa1`_)
+
+* add lvk noise (`d93f36b`_)
+
+* add tests (`c9e3c79`_)
+
+* more hacking (`fda820d`_)
+
+* add ci (`3539ffb`_)
+
+* add whitepsace (`3274b74`_)
+
+* hacking with Benjamin (`23210a3`_)
+
+* init project packaging (`5685aac`_)
+
+* improve knot allocation (`8e4ad33`_)
+
+* optimise starting weights (`1942d60`_)
+
+* generate data for testing (`0d619ce`_)
+
+* start hacking (`cd4026f`_)
+
+.. _964e40e: https://github.com/nz-gravity/LogPSplinePSD/commit/964e40e8191ad20bdf3028bb268196312983058d
+.. _7a0925c: https://github.com/nz-gravity/LogPSplinePSD/commit/7a0925cf8158fe5122ce68b9a41b9534af638099
+.. _a43ee40: https://github.com/nz-gravity/LogPSplinePSD/commit/a43ee406b85b00fe480c36f9fbe1b45ce70a0683
+.. _235c3ec: https://github.com/nz-gravity/LogPSplinePSD/commit/235c3ec5191c5c71952a820697d4416fc9b319e5
+.. _9df1e5d: https://github.com/nz-gravity/LogPSplinePSD/commit/9df1e5d7527d08602a4402cb038e88c8aa474128
+.. _027591f: https://github.com/nz-gravity/LogPSplinePSD/commit/027591fd3b4ecd334d784f25395d7bd5353c9ab2
+.. _88c8f9b: https://github.com/nz-gravity/LogPSplinePSD/commit/88c8f9bc873be650cbcac1a2a3440db803b0afe5
+.. _60af98d: https://github.com/nz-gravity/LogPSplinePSD/commit/60af98d50e3370107a7373018d72041a7f67e11d
+.. _3a08b99: https://github.com/nz-gravity/LogPSplinePSD/commit/3a08b992d695f4bd9c9c8130989ee3de51341fed
+.. _1fb79e8: https://github.com/nz-gravity/LogPSplinePSD/commit/1fb79e8689f87f89a4363d264bb1e33fbaf9217c
+.. _b0cd698: https://github.com/nz-gravity/LogPSplinePSD/commit/b0cd6985070d56f217c4f63c6bc4f8da66c565ec
+.. _fd9a95b: https://github.com/nz-gravity/LogPSplinePSD/commit/fd9a95bc154a1b7d009b3c4cb680a3cee9abfa5d
+.. _c41038c: https://github.com/nz-gravity/LogPSplinePSD/commit/c41038cdc5ae858db11022f599862bf3becf4a69
+.. _328e854: https://github.com/nz-gravity/LogPSplinePSD/commit/328e854df63dec4eacc4ec2738021c6c183489fb
+.. _5877ec0: https://github.com/nz-gravity/LogPSplinePSD/commit/5877ec0c672fe51ad7013ebcdc931e30df990356
+.. _20d3f39: https://github.com/nz-gravity/LogPSplinePSD/commit/20d3f393a5446bb1cd32f1661edd7993fff8ba97
+.. _dc6469c: https://github.com/nz-gravity/LogPSplinePSD/commit/dc6469cff708fb172d5e90f2871ee57fb8e6c43a
+.. _7f32bbb: https://github.com/nz-gravity/LogPSplinePSD/commit/7f32bbba2ddd96a0db3667ad1312b8acf7855a3d
+.. _a061028: https://github.com/nz-gravity/LogPSplinePSD/commit/a06102836f95960b1699a073adbf441ea195b75c
+.. _6b3905f: https://github.com/nz-gravity/LogPSplinePSD/commit/6b3905f03298d737dc1b940f7b4756dcbe122998
+.. _cf42e6f: https://github.com/nz-gravity/LogPSplinePSD/commit/cf42e6f83eece3202eb747f09b1af55887082abb
+.. _18d0075: https://github.com/nz-gravity/LogPSplinePSD/commit/18d007562a3e31dbed39a8c3b199252f951d03f7
+.. _a2035bb: https://github.com/nz-gravity/LogPSplinePSD/commit/a2035bb40da74aa11dfd740af7b98af0a9d33ba5
+.. _8fff25b: https://github.com/nz-gravity/LogPSplinePSD/commit/8fff25b4ae70f2627ca45c37ed57af842dd13353
+.. _939cbdb: https://github.com/nz-gravity/LogPSplinePSD/commit/939cbdb650fbfdf460666ebb6f7e465f799e6e6e
+.. _73fd427: https://github.com/nz-gravity/LogPSplinePSD/commit/73fd4276b6f44d68cfbb7fb16797be891f7e114a
+.. _194fae8: https://github.com/nz-gravity/LogPSplinePSD/commit/194fae8d527bd7998dda38adaf0b96002c070414
+.. _7231c3b: https://github.com/nz-gravity/LogPSplinePSD/commit/7231c3b1de002ee47b10286c4f799ae3551d4c40
+.. _6641a63: https://github.com/nz-gravity/LogPSplinePSD/commit/6641a63c97f0c5392207fd56977ee37cf9811ac6
+.. _98ae77a: https://github.com/nz-gravity/LogPSplinePSD/commit/98ae77ad38feaca0d65566f26d42e3adafe9f772
+.. _d7121d6: https://github.com/nz-gravity/LogPSplinePSD/commit/d7121d6c1cd87a65355b4a6f6260578b90223339
+.. _f818caa: https://github.com/nz-gravity/LogPSplinePSD/commit/f818caaa86467d5f26fb116a2c29c7a360ff41cf
+.. _0666415: https://github.com/nz-gravity/LogPSplinePSD/commit/0666415347785d67b2865efe521648a7a89ee000
+.. _4197563: https://github.com/nz-gravity/LogPSplinePSD/commit/4197563ebdd5da00a781dc22556eeb925f1cceaf
+.. _922f870: https://github.com/nz-gravity/LogPSplinePSD/commit/922f87003a657d1578a98c3d3d803055f7969fe2
+.. _4944aa1: https://github.com/nz-gravity/LogPSplinePSD/commit/4944aa1501d382d8ee4f6e06780c672e588b843d
+.. _d93f36b: https://github.com/nz-gravity/LogPSplinePSD/commit/d93f36bcba5a70f2d90b40c3934de265f72cb65f
+.. _c9e3c79: https://github.com/nz-gravity/LogPSplinePSD/commit/c9e3c790dff28a51bf9dc97b56bd63ccbcddd43b
+.. _fda820d: https://github.com/nz-gravity/LogPSplinePSD/commit/fda820dd58f3072c86876d2a2ae218869f656f6e
+.. _3539ffb: https://github.com/nz-gravity/LogPSplinePSD/commit/3539ffb0b1d87445201633488da63743454e0c7f
+.. _3274b74: https://github.com/nz-gravity/LogPSplinePSD/commit/3274b74c1f0c59ea43825bdca177f99f8c8fe097
+.. _23210a3: https://github.com/nz-gravity/LogPSplinePSD/commit/23210a35eb751832563a69101817ba906b82edba
+.. _5685aac: https://github.com/nz-gravity/LogPSplinePSD/commit/5685aac389781eaeeadda6a1c31f2820b61cbed1
+.. _8e4ad33: https://github.com/nz-gravity/LogPSplinePSD/commit/8e4ad33d4e99f20a2a76d40dd8539838ed5462ea
+.. _1942d60: https://github.com/nz-gravity/LogPSplinePSD/commit/1942d6079393eb78ddcc07a7a4265805bcfcb010
+.. _0d619ce: https://github.com/nz-gravity/LogPSplinePSD/commit/0d619ceba76869e3ec3b2d015987a77a1671cf19
+.. _cd4026f: https://github.com/nz-gravity/LogPSplinePSD/commit/cd4026f9c50b1384a4cfba70cf8e67f938a254ac

logpsplinepsd-0.0.3/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, nz-gravity
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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