jaxspec 0.2.1.dev2__tar.gz → 0.2.2__tar.gz

jaxspec-0.2.2/.dockerignore

@@ -0,0 +1,14 @@
+*.ipynb
+*.npz
+*.arf
+*.rmf
+*.lock
+
+data
+data_to_test
+didier_test
+docs
+.cache
+.github
+.ipynb_checkpoints
+.venv

jaxspec-0.2.2/.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

jaxspec-0.2.2/.github/workflows/documentation-links.yml

@@ -0,0 +1,22 @@
+# .github/workflows/documentation-links.yml
+
+name: readthedocs/actions
+on:
+  pull_request_target:
+    types:
+      - opened
+    # Execute this action only on PRs that touch
+    # documentation files.
+    # paths:
+    #   - "docs/**"
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "jaxspec"

jaxspec-0.2.2/.github/workflows/publish.yml

@@ -0,0 +1,21 @@
+name: Python package
+on:
+  push:
+    tags:
+      - "v*.*.*"
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish package
+        run: uv publish --token ${{ secrets.PYPI_TOKEN }}

jaxspec-0.2.2/.github/workflows/test-and-coverage.yml

@@ -0,0 +1,49 @@
+name: Unit tests
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'README.md'
+  pull_request:
+    paths-ignore:
+      - 'README.md'
+
+permissions:
+  contents: read
+
+jobs:
+  tests:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - uses: dorny/paths-filter@v3
+      id: filter
+      with:
+        filters: |
+          src:
+            - 'src/**'
+          pyproject:
+            - 'pyproject.toml'
+
+    - name: Build docker images
+      if: steps.filter.outputs.src == 'true' || steps.filter.outputs.pyproject == 'true'
+      run: docker build . -t xspec-tests
+
+    - name: Test with pytest
+      if: steps.filter.outputs.src == 'true' || steps.filter.outputs.pyproject == 'true'
+      run: docker run -t -v ./:/shared xspec-tests uv run pytest --cov jaxspec --cov-report xml:/shared/coverage.xml
+
+    - name: "Upload coverage to Codecov"
+      if: steps.filter.outputs.src == 'true'
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: true
+        verbose: true

jaxspec-0.2.2/.gitignore

@@ -0,0 +1,200 @@
+
+# Created by https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks
+# Edit at https://www.toptal.com/developers/gitignore?templates=python,jupyternotebooks
+
+### JupyterNotebooks ###
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+main.py
+doc_notebooks/
+
+.ipynb_checkpoints
+tests/data/
+*.ipynb
+poetry.lock
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+### Python ###
+# 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 gallery 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
+
+# IPython
+
+# 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__/
+
+# 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 files
+.idea/
+
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+# End of https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks

jaxspec-0.2.2/.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+fail_fast: true
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+     # - id: check-added-large-files
+     #   args: ["--maxkb=5000"]
+      - id: check-toml
+      - id: check-json
+      - id: check-symlinks
+      - id: debug-statements
+      - id: detect-private-key
+      - id: check-yaml
+        args:
+          - --unsafe
+      - id: trailing-whitespace
+        exclude: \.(fits|pha|arf|rmf)$  # Exclude .fits, .pha, .arf, .rmf files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.6
+    hooks:
+      - id: ruff
+        args: ["--fix", "--output-format=full"]
+        exclude: ^docs/|\.(fits|pha|arf|rmf)$  # Exclude docs and .fits, .pha, .arf, .rmf files
+      - id: ruff-format
+        exclude: \.(fits|pha|arf|rmf)$  # Exclude .fits, .pha, .arf, .rmf files
+
+#  - repo: local
+#    hooks:
+#      - id: tests
+#        name: tests
+#        language: system
+#        types: [python]
+#        pass_filenames: false
+#        entry: poetry run pytest

jaxspec-0.2.2/.readthedocs.yaml

@@ -0,0 +1,42 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  # These packages are needed to build docs with image optimization
+  jobs:
+    post_create_environment:
+      # Install uv
+      - pip install uv
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      - uv pip install -r pyproject.toml
+      # Using insiders versions of mkdocs-material & mkdocstrings
+      - uv pip uninstall mkdocs-material # mkdocstrings mkdocstrings-python
+      - uv pip install git+https://$GH_TOKEN@github.com/squidfunk/mkdocs-material-insiders.git@9.5.36-insiders-4.53.13
+      - uv pip install mkdocstrings mkdocstrings-python
+      - uv pip install mkdocs-autorefs
+      - uv pip install mkdocs-jupyter # This is bugged, I enforced it manually, let's see if it works
+
+  apt_packages:
+    - libcairo2-dev
+    - libfreetype6-dev
+    - libffi-dev
+    - libjpeg-dev
+    - libpng-dev
+    - libz-dev
+    - pngquant
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats:
+  - pdf

jaxspec-0.2.2/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# 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
+sdupourque@irap.omp.eu.
+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.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## 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.

jaxspec-0.2.2/Dockerfile

@@ -0,0 +1,19 @@
+# syntax=docker/dockerfile:1
+FROM renecoty/heasoft:v6.34
+
+WORKDIR /jaxspec
+
+USER root
+# Project initialization:
+RUN apt-get update && \
+    apt-get install -y git
+
+RUN pip install uv
+
+ADD src /jaxspec/src
+ADD tests /jaxspec/tests
+ADD pyproject.toml /jaxspec/pyproject.toml
+ADD README.md /jaxspec/README.md
+
+RUN uv sync --no-group docs --no-group dev --python 3.12
+ENV PATH="/app/.venv/bin:$PATH"

{jaxspec-0.2.1.dev2 → jaxspec-0.2.2}/PKG-INFO

@@ -1,42 +1,37 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: jaxspec
-Version: 0.2.1.dev2
+Version: 0.2.2
 Summary: jaxspec is a bayesian spectral fitting library for X-ray astronomy.
-License: MIT
-Author: sdupourque
-Author-email: sdupourque@irap.omp.eu
-Requires-Python: >=3.10,<3.13
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: arviz (>=0.17.1,<0.21.0)
-Requires-Dist: astropy (>=6.0.0,<7.0.0)
-Requires-Dist: catppuccin (>=2.3.4,<3.0.0)
-Requires-Dist: chainconsumer (>=1.1.2,<2.0.0)
-Requires-Dist: cmasher (>=1.6.3,<2.0.0)
-Requires-Dist: flax (>=0.10.1,<0.11.0)
-Requires-Dist: interpax (>=0.3.3,<0.4.0)
-Requires-Dist: jax (>=0.5.0,<0.6.0)
-Requires-Dist: jaxns (>=2.6.7,<3.0.0)
-Requires-Dist: jaxopt (>=0.8.1,<0.9.0)
-Requires-Dist: matplotlib (>=3.8.0,<4.0.0)
-Requires-Dist: mendeleev (>=0.15,<0.20)
-Requires-Dist: networkx (>=3.1,<4.0)
-Requires-Dist: numpy (<2.0.0)
-Requires-Dist: numpyro (>=0.16.1,<0.17.0)
-Requires-Dist: optimistix (>=0.0.7,<0.0.11)
-Requires-Dist: pandas (>=2.2.0,<3.0.0)
-Requires-Dist: pooch (>=1.8.2,<2.0.0)
-Requires-Dist: scipy (<1.15)
-Requires-Dist: seaborn (>=0.13.1,<0.14.0)
-Requires-Dist: simpleeval (>=0.9.13,<1.1.0)
-Requires-Dist: sparse (>=0.15.4,<0.16.0)
-Requires-Dist: tinygp (>=0.3.0,<0.4.0)
-Requires-Dist: watermark (>=2.4.3,<3.0.0)
-Project-URL: Documentation, https://jaxspec.readthedocs.io/en/latest/
 Project-URL: Homepage, https://github.com/renecotyfanboy/jaxspec
+Project-URL: Documentation, https://jaxspec.readthedocs.io/en/latest/
+Author-email: sdupourque <sdupourque@irap.omp.eu>
+License-Expression: MIT
+License-File: LICENSE.md
+Requires-Python: <3.13,>=3.10
+Requires-Dist: arviz<0.21.0,>=0.17.1
+Requires-Dist: astropy<7,>=6.0.0
+Requires-Dist: catppuccin<3,>=2.3.4
+Requires-Dist: chainconsumer<2,>=1.1.2
+Requires-Dist: cmasher<2,>=1.6.3
+Requires-Dist: flax<0.11,>=0.10.3
+Requires-Dist: interpax<0.4,>=0.3.5
+Requires-Dist: jax<0.6,>=0.5.0
+Requires-Dist: jaxns<3,>=2.6.7
+Requires-Dist: jaxopt<0.9,>=0.8.3
+Requires-Dist: matplotlib<4,>=3.8.0
+Requires-Dist: mendeleev<0.20,>=0.15
+Requires-Dist: networkx~=3.1
+Requires-Dist: numpy<2.0.0
+Requires-Dist: numpyro<0.18,>=0.17.0
+Requires-Dist: optimistix<0.0.11,>=0.0.10
+Requires-Dist: pandas<3,>=2.2.0
+Requires-Dist: pooch<2,>=1.8.2
+Requires-Dist: scipy<1.15
+Requires-Dist: seaborn<0.14,>=0.13.1
+Requires-Dist: simpleeval<1.1.0,>=0.9.13
+Requires-Dist: sparse<0.16,>=0.15.4
+Requires-Dist: tinygp<0.4,>=0.3.0
+Requires-Dist: watermark<3,>=2.4.3
 Description-Content-Type: text/markdown
 
 <p align="center">
@@ -97,4 +92,3 @@ If you use `jaxspec` in your research, please consider citing the following arti
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 ```
-

jaxspec-0.2.2/docs/contribute/index.md

@@ -0,0 +1,51 @@
+## Install `jaxspec` repository locally
+
+Adding content to the `jaxspec`'s source code requires you to clone the repository locally. This is done by running the
+following command in your terminal:
+
+``` bash
+git clone https://github.com/renecotyfanboy/jaxspec
+cd jaxspec
+```
+
+## Set up a clean environment
+
+`jaxspec` uses [Poetry](https://python-poetry.org/) to manage its dependencies. We recommand to start from a fresh
+Python environment, and install Poetry. If you use conda, you can create a new environment with
+
+``` bash
+conda create -n jaxspec python=3.10
+conda activate jaxspec
+```
+
+To install Poetry, run the following in the (`jaxspec`) environment:
+
+``` bash
+pip install poetry
+```
+
+Then, to install `jaxspec`'s dependencies, run the following command in the directory where you cloned the repository:
+
+``` bash
+poetry install
+```
+
+# Code quality
+
+We use [ruff](https://docs.astral.sh/ruff/) to enforce code quality standards, which proposes both a linter and a
+formatter. They are set up with the pre-commit hooks (see below).
+
+## Pre-commit hooks
+
+We use [pre-commit](https://pre-commit.com/) to run the linter and formatter automatically before each commit.
+All the hooks are defined in `.pre-commit-config.yaml` and can be run manually with
+
+``` bash
+poetry run pre-commit run --all-files
+```
+
+If you want to install the pre-commit hooks so they run automatically, use
+
+``` bash
+poetry run pre-commit install
+```