flowMC 0.3.4__tar.gz → 0.4.0__tar.gz

flowmc-0.4.0/.gitattributes

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+docs/** linguist-vendored
+example/** linguist-vendored

flowmc-0.4.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

flowmc-0.4.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

flowmc-0.4.0/.github/workflows/pre-commit.yml

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+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install .
+    - uses: pre-commit/action@v3.0.1

flowmc-0.4.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

flowmc-0.4.0/.github/workflows/run_tests.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Run Tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run tests and coverage
+        run: |
+          uv run coverage run --source=src -m pytest test
+          uv run coveralls --service=github-actions
+        env:
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+
+      - name: Run build
+        run: uv build

flowmc-0.4.0/.github/workflows/workflowsjoss.yml

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+name: Update-Joss
+
+on: 
+  push:
+    branches:
+      - main
+      - 40-joss-paper
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf

flowmc-0.4.0/.gitignore

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+*.pyc
+flowMC/nfmodel/__pycache__/maf.cpython-37.pyc
+log_dir/
+*.pkl
+flowMC/nfmodel/realNVP_white.py
+example/kepler/kepler_white.py
+example/kepler/kepler_analyse.py
+dist
+*egg-info*
+docs/build/*
+*_autosummary
+README.md
+*settings.json
+*build*
+test_docs/test_quickstart.ipynb

flowmc-0.4.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/ambv/black
+    rev: 25.1.0
+    hooks:
+    - id: black
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.9.10'
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+  - repo: https://github.com/RobertCraigie/pyright-python
+    rev: v1.1.396
+    hooks:
+    - id: pyright
+      additional_dependencies: [beartype, einops, jax, jaxtyping, pytest, typing_extensions, equinox, optax, tqdm]
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.1
+    hooks:
+    - id: nbqa-black
+      additional_dependencies: [ipython==8.12, black]
+    - id: nbqa-ruff-format
+      additional_dependencies: [ipython==8.12, ruff]

flowmc-0.4.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+kazewong.physics@gmail.com.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

flowmc-0.4.0/CONTRIBUTING.md

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+
+### Expectations
+
+flowMC is developed and maintained in my spare time and, while I try to be
+responsive, I don't always get to every issue immediately. If it has been more
+than a week or two, feel free to ping me (@kazewong) to try to get my attention. This is
+subject to changes as the community grows.
+
+### Did you find a bug?
+
+**Ensure the bug was not already reported** by searching on GitHub under
+[Issues](https://github.com/kazewong/flowMC/issues). If you're unable to find an
+open issue addressing the problem, [open a new
+one](https://github.com/kazewong/flowMC/issues/new). Be sure to include a **title
+and clear description**, as much relevant information as possible, and the
+simplest possible **code sample** demonstrating the expected behavior that is
+not occurring. Also label the issue with the bug label.
+
+### Did you write a patch that fixes a bug?
+
+Open a new GitHub pull request with the patch. Ensure the PR description clearly
+describes the problem and solution. Include the relevant issue number if
+applicable.
+
+### Do you intend to add a new feature or change an existing feature?
+
+Please follow the following principle when you are thinking about adding a new
+feature or changing an existing feature:
+
+1. The new feature should be able to take advantage of `jax.jit` whenever possible.
+2. Light weight and modular implementation is preferred.
+3. The core package only does sampling. If you have a concrete example that
+   involves a complete analysis such as plotting and models, see the next
+   contribution guide.
+
+Suggestions for new features are welcome on [flowMC support
+group](https://groups.google.com/u/1/g/flowmc). Note that features related to the
+core algorithm are unlikely to be accepted since that may include a lot of
+breaking changes.
+
+### Do you intend to introduce an example or tutorial?
+
+Open a new GitHub pull request with the example or tutorial. The example should
+be self-contained and keep import from other packages to minimal. Leave the
+case-specific analysis detail out. For more extensive tutorial, we encourage the
+community to link the minimal example hosted on the flowMC documentation to
+documentation from other packages.
+
+### Do you have question about the code?
+
+Do not open an issue. Instead, find whether there are already existing threads
+on the [flowMC support group](https://groups.google.com/u/1/g/flowmc). If not,
+please open a new conversation there.

{flowmc-0.3.4/src/flowMC.egg-info → flowmc-0.4.0}/PKG-INFO

@@ -1,33 +1,70 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: flowMC
-Version: 0.3.4
+Version: 0.4.0
 Summary: Normalizing flow exhanced sampler in jax
-Home-page: https://github.com/kazewong/flowMC
-Author: Kaze Wong, Marylou Gabrié, Dan Foreman-Mackey
-Author-email: kazewong.physics@gmail.com
-License: MIT
-Keywords: sampling,inference,machine learning,normalizing,autodiff,jax
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
+Project-URL: Documentation, https://github.com/kazewong/flowMC
+Author: Marylou Gabrié, Dan Foreman-Mackey
+Author-email: Kaze Wong <kazewong.physics@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2022 Kaze Wong & contributor
+        
+        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.
 License-File: LICENSE
-Requires-Dist: jax>=0.4.12
-Requires-Dist: jaxlib>=0.4.12
-Requires-Dist: equinox>=0.10.6
-Requires-Dist: optax>=0.1.5
-Requires-Dist: evosax>=0.1.4
-Requires-Dist: tqdm
-Requires-Dist: corner
+Keywords: autodiff,inference,jax,machine learning,normalizing,sampling
+Requires-Python: >=3.11
+Requires-Dist: chex>=0.1.87
+Requires-Dist: coveralls>=4.0.1
+Requires-Dist: equinox>=0.11.9
+Requires-Dist: jax[cuda12]==0.5.0
+Requires-Dist: jaxtyping>=0.2.36
+Requires-Dist: optax>=0.2.4
+Requires-Dist: pre-commit==4.0.1
+Requires-Dist: pyright==1.1.389
+Requires-Dist: pytest==8.3.3
+Requires-Dist: ruff==0.8.0
+Requires-Dist: scikit-learn>=1.6.0
+Requires-Dist: tqdm>=4.67.1
+Provides-Extra: docs
+Requires-Dist: mkdocs-gen-files==0.5.0; extra == 'docs'
+Requires-Dist: mkdocs-jupyter==0.25.1; extra == 'docs'
+Requires-Dist: mkdocs-literate-nav==0.6.1; extra == 'docs'
+Requires-Dist: mkdocs-material==9.5.47; extra == 'docs'
+Requires-Dist: mkdocs==1.6.1; extra == 'docs'
+Requires-Dist: mkdocstrings[python]==0.27.0; extra == 'docs'
+Requires-Dist: pymdown-extensions==10.12; extra == 'docs'
+Provides-Extra: visualize
+Requires-Dist: arviz>=0.21.0; extra == 'visualize'
+Requires-Dist: corner>=2.2.3; extra == 'visualize'
+Description-Content-Type: text/markdown
 
 # flowMC
 
 **Normalizing-flow enhanced sampling package for probabilistic inference**
 
 <a href="https://flowmc.readthedocs.io/en/main/">
-<img src="https://badgen.net/badge/Read/the doc/blue" alt="doc"/>
+<img src="https://readthedocs.org/projects/flowmc/badge/?version=main&style=flat-square" alt="doc"/>
 </a>
-<a href="https://github.com/kazewong/FlowMC/blob/Packaging/LICENSE">
-<img src="https://badgen.net/badge/License/MIT/blue" alt="doc"/>
+<a href="https://github.com/kazewong/flowMC/blob/Packaging/LICENSE">
+<img src="https://img.shields.io/badge/License-MIT-blue?style=flat-square" alt="doc"/>
 </a>
+<a href='https://coveralls.io/github/kazewong/flowMC?branch=main'><img src='https://img.shields.io/coverallsCoverage/github/kazewong/flowMC?style=flat-square' alt='Coverage Status' /></a>
 
 ![flowMC_logo](./docs/logo_0810.png)
 

{flowmc-0.3.4 → flowmc-0.4.0}/README.md

@@ -3,11 +3,12 @@
 **Normalizing-flow enhanced sampling package for probabilistic inference**
 
 <a href="https://flowmc.readthedocs.io/en/main/">
-<img src="https://badgen.net/badge/Read/the doc/blue" alt="doc"/>
+<img src="https://readthedocs.org/projects/flowmc/badge/?version=main&style=flat-square" alt="doc"/>
 </a>
-<a href="https://github.com/kazewong/FlowMC/blob/Packaging/LICENSE">
-<img src="https://badgen.net/badge/License/MIT/blue" alt="doc"/>
+<a href="https://github.com/kazewong/flowMC/blob/Packaging/LICENSE">
+<img src="https://img.shields.io/badge/License-MIT-blue?style=flat-square" alt="doc"/>
 </a>
+<a href='https://coveralls.io/github/kazewong/flowMC?branch=main'><img src='https://img.shields.io/coverallsCoverage/github/kazewong/flowMC?style=flat-square' alt='Coverage Status' /></a>
 
 ![flowMC_logo](./docs/logo_0810.png)
 

flowmc-0.4.0/docs/FAQ.md

@@ -0,0 +1,37 @@
+FAQ
+===
+
+**My local sampler is not accepting**
+
+This usually means you are setting the step size of the local samplerto be too big.
+Try reducing the step size in your local sampler.
+
+Alternative, this could also mean your sampler is proposing in region where the likelihood is ill-defined (i.e. NaN either in likelihood or its derivative if you are using a gradient-based local sampler).
+It is worth making sure your likelihood is well-defined within your range of prior.
+
+**In order for my local sampler to accept, I have to choose a very small step size, which makes my chain very correlated.**
+
+This usually indicate some of your parameters are much better measured than others.
+Since taking a small step in those directions will already change your likelihood value by a lot, the exploration power of the local sampler in other parameters are limited by those which are well measured.
+Currently, we support different step size for different parameters, which you can tune to see whether that improves the situation or not.
+If you know the scale of each parameter ahead of time, reparameterizing them to maintain roughly equal scale across parameters also helps.
+
+**My global sample's loss is exploding/not decreasing**
+
+This usually means your learning rate used for training the normalizing flow is too large.
+Try reducing the learning rate by a factor of ten.
+
+Another reason for a flat loss is your local sampler is not accepting at all.
+This is a bit rarer since this means your data used to train the normalizing flow is just your prior, which the normalizing flow should still be able to learn.
+
+**The sampler is stuck a bit until it starts sampling**
+
+If you use the option ``Jit`` in constructing the local sampler, the code will compile your code to speed up the execution.
+The sampler is not really stuck, but it is compiling the code. Depending on how you code up your likelihood function, the compilation can take a while.
+If you don't want to wait, you can set ``Jit=False``, which would increase the sampling time.
+
+**The compilation is slow**
+
+If you have a likelihood with many lines, Jax will take a long time to compile the code.
+Jax is known to be slow in compilation, especially if your computational graph uses some sort of loop that call a function many times.
+While we cannot fundamentally get rid of the problem, [using a jax.lax.scan](https://docs.kidger.site/equinox/tricks/#low-overhead-training-loops) is usually how we deal with it.

flowmc-0.4.0/docs/communityExamples.md

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+# Community examples
+
+The core design philosophy of flowMC is to stay lean and simple, so we decided to leave most of the use case-specific optimization to the users. Hence, we keep most of the flowMC internals away from most of the users,
+so the only interfaces with flowMC are really defining your likelihood and tuning the sampler parameters exposed on the top level.
+That said, it would be useful to have references to see how to use/tune flowMC for different use cases, therefore in this page we host a number of community examples that are contributed by the users.
+If you find flowMC useful, please consider contributing your example to this page. This will help other users (and perhaps your future students) to get started quickly.
+
+## Examples
+
+- [jim - A JAX-based gravitational-wave inference toolkit](https://github.com/kazewong/jim)
+- [Bayeux - Stitching together models and samplers](https://github.com/jax-ml/bayeux)
+  - [Colab example](https://colab.research.google.com/drive/1-PhneVVik5GUq6w2HlKOsqvus13ZLaBH?usp=sharing)
+- [Markovian Flow Matching: Accelerating MCMC with Continuous Normalizing Flows](https://arxiv.org/pdf/2405.14392)