V042

.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/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/publish.yml

@@ -2,30 +2,30 @@ name: publish to pypi
 on:
   release:
     types: [published]
-    
+
 jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
       #----------------------------------------------
-      #       check-out repo and set-up python     
-      #----------------------------------------------    
+      #       check-out repo and set-up python
+      #----------------------------------------------
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
       #----------------------------------------------
-      #  -----  install & configure poetry  -----      
-      #----------------------------------------------          
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
         with:
-          version: 1.3.2
           virtualenvs-create: true
           virtualenvs-in-project: true
+          installer-parallel: true
+      #----------------------------------------------
+      #       load cached venv if cache exists
       #----------------------------------------------
-      #       load cached venv if cache exists      
-      #----------------------------------------------          
       - name: Load cached venv
         id: cached-poetry-dependencies
         uses: actions/cache@v3
@@ -34,14 +34,14 @@ jobs:
           key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
       - name: Install dependencies
       #----------------------------------------------
-      # install dependencies if cache does not exist 
-      #----------------------------------------------       
-        run: poetry install
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+        run: poetry install --without docs
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       #----------------------------------------------
-      #      config poetry and publish to pypi 
-      #----------------------------------------------         
+      #      config poetry and publish to pypi
+      #----------------------------------------------
       - name: Config
         run: poetry config pypi-token.pypi ${{ secrets.PYPI_TOKEN }}
-      - name: Publish 
+      - name: Publish
         run: poetry publish --build

.github/workflows/tests.yml

@@ -7,46 +7,46 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     if: "! contains(toJSON(github.event.commits.*.message), '[skip-tests]')"
     steps:
       #----------------------------------------------
-      #       check-out repo and set-up python     
+      #       check-out repo and set-up python
       #----------------------------------------------
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       #----------------------------------------------
-      #  -----  install & configure poetry  -----      
-      #----------------------------------------------          
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
         with:
-          version: 1.1.6
           virtualenvs-create: true
           virtualenvs-in-project: true
+          installer-parallel: true
+      #----------------------------------------------
+      #       load cached venv if cache exists
       #----------------------------------------------
-      #       load cached venv if cache exists      
-      #----------------------------------------------          
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
       #----------------------------------------------
-      # install dependencies if cache does not exist 
-      #----------------------------------------------          
+      # install dependencies if cache does not exist
+      #----------------------------------------------
       - name: Install dependencies
-        run: poetry install
+        run: poetry install --without docs
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       #----------------------------------------------
       #                 run tests
-      #----------------------------------------------          
+      #----------------------------------------------
       - name: Run tests
         run: |
           source .venv/bin/activate
-          poetry run pytest --cov tests/
+          poetry run pytest --cov tests/

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+exclude: '^.md'
+default_language_version:
+    python: python3.8
+
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+
+  # Using this mirror lets us use mypyc-compiled black, which is about 2x faster
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: "23.11.0"
+    hooks:
+      - id: black
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.6"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - pdf
+  # - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

Changelog.rst

@@ -9,12 +9,12 @@
 - Fitting functions (i.e., `drw_fit`) are now fully modular (allow user provided optimization function, prior function and etc.)
 - A new `addNoise` function to simulated random noise given measurement errors.
 - **Bug fixes:** #44
-- **API changes:** `n_iter` -> `n_opt` in fitting functions. 
+- **API changes:** `n_iter` -> `n_opt` in fitting functions.
 
 0.3.0 (2021-01-07)
 +++++++++++++++++++++
 
-- update parameter initialization in fit functions; removed `de` option #26, #27 
+- update parameter initialization in fit functions; removed `de` option #26, #27
 - add few utils functions #30, #25
 - add mcmc module #29
 - ts simulation now support linear error
@@ -48,4 +48,4 @@ First release!
 
 - Fully working CARMA kernels: `DRW_term`, `DHO_term` and `CARMA_term`
 - Functions to simulate CARMA time series given a kernel
-- Functions to fit arbitrary time series to CARMA models (still having instability issues with CARMA models higher than DHO/CARMA(2,1))
+- Functions to fit arbitrary time series to CARMA models (still having instability issues with CARMA models higher than DHO/CARMA(2,1))

README.md

@@ -1,5 +1,5 @@
 ![tests](https://github.com/ywx649999311/EzTao/workflows/tests/badge.svg)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ywx649999311/EzTao/v0.4.1?filepath=docs/notebooks)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ywx649999311/EzTao/v0.4.2?filepath=docs/notebooks)
 [![Documentation Status](https://readthedocs.org/projects/eztao/badge/?version=latest)](https://eztao.readthedocs.io/en/latest/)
 <a href="https://ascl.net/2201.001"><img src="https://img.shields.io/badge/ascl-2201.001-blue.svg?colorB=262255" alt="ascl:2201.001" /></a>
 # EzTao (易道)
@@ -15,12 +15,12 @@ pip install git+https://github.com/ywx649999311/EzTao.git
 ```
 ### Dependencies
 >```
->python = "^3.7"
+>python = ">=3.8,<3.12"
 >celerite = ">= 0.3.0"
->matplotlib = "^3.3.0"
 >scipy = "> 1.5.0"
 >numba = ">= 0.51.0"
->emcee = ">=3.0.0"
+>matplotlib = ">=3.3.3"
+>emcee = ">=0.3.0"
 >```
 
 ## Quick Examples
@@ -72,7 +72,7 @@ ax.plot(freq, best_psd(freq), label='Best-fit PSD')
 ```
 ![drw_psd](include/drw_psd.png)
 
-__Note:__ How well the input and best-fit PSD match is up to how good the best-fit parameters are, which is highly influenced by the quality of the input time series. 
+__Note:__ How well the input and best-fit PSD match is up to how good the best-fit parameters are, which is highly influenced by the quality of the input time series.
 
 For more examples, please check out the [online documentation](https://eztao.readthedocs.io/en/latest/) or run the tutorial notebooks at ->
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ywx649999311/EzTao/v0.4.0?filepath=docs/notebooks).
@@ -81,7 +81,7 @@ For more examples, please check out the [online documentation](https://eztao.rea
 `poetry` is used to solve dependencies and to build/publish this package. Below shows how setup the environment for development (assuming you already have `poetry` installed on your machine). _**Warning:**_ `poetry` is having issue installing `llvmlite = 0.34.0` (used for `eztao = ^0.4.0`) under Python 3.9. The issue disappears for Python 3.8.
 
 1. Clone this repository, and enter the repository folder.
-2. Create a python virtual environment and activate it (the virtual environment name must be '.venv'). 
+2. Create a python virtual environment and activate it (the virtual environment name must be '.venv').
     ```
     python -m venv .venv
     source .venv/bin/activate
@@ -91,7 +91,7 @@ For more examples, please check out the [online documentation](https://eztao.rea
    poetry install
    ```
 
-Now you should be ready to start adding new features. Be sure to checkout the normal practice regarding how to use `poetry` on its website. When you are ready to push, also make sure the poetry.lock file is checked-in if any dependency has changed. 
+Now you should be ready to start adding new features. Be sure to checkout the normal practice regarding how to use `poetry` on its website. When you are ready to push, also make sure the poetry.lock file is checked-in if any dependency has changed.
 
 ## Citation
 We are working on a paper to describe the full implementation of **EzTao**. In the meantime, if you find **EzTao** useful for your research, please consider acknowledging **EzTao** using the following:
@@ -112,4 +112,3 @@ archivePrefix = {ascl},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 ```
-

docs/conf.py

@@ -23,7 +23,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "EzTao"
-copyright = "2020, Weixiang Yu"
+copyright = "2020-2023, Weixiang Yu"
 author = "Weixiang Yu"
 
 # The full version, including alpha/beta/rc tags

docs/index.rst

@@ -1,8 +1,8 @@
 EzTao
 =====
-**EzTao** is a Python toolkit for conducting time-series analysis using continuous-time autoregressive moving average (CARMA) processes. It uses `celerite`_ (a fast gaussian processes regression library) to compute the likelihood of a set of proposed CARMA parameters given the input time series. Comparing to existing tools for performing CARMA analysis in Python which use *Kalman filter* to evaluate the likelihood function (e.g., `Kali`_), **EzTao** offers a more scalable solution (see the `celerite paper`_ for a comparison). 
+**EzTao** is a Python toolkit for conducting time-series analysis using continuous-time autoregressive moving average (CARMA) processes. It uses `celerite`_ (a fast gaussian processes regression library) to compute the likelihood of a set of proposed CARMA parameters given the input time series. Comparing to existing tools for performing CARMA analysis in Python which use *Kalman filter* to evaluate the likelihood function (e.g., `Kali`_), **EzTao** offers a more scalable solution (see the `celerite paper`_ for a comparison).
 
-**EzTao** consist of tools to both simulate CARMA processes and fit (maximum likelihood estimation or MLE) time series to CARMA models. The current version of **EzTao** is built on top of `celerite`_, future versions will take advantage of `celerite2`_ (still under active development) for a better integration with other probabilistic programing libraries such as `PyMC3`_. 
+**EzTao** consist of tools to both simulate CARMA processes and fit (maximum likelihood estimation or MLE) time series to CARMA models. The current version of **EzTao** is built on top of `celerite`_, future versions will take advantage of `celerite2`_ (still under active development) for a better integration with other probabilistic programing libraries such as `PyMC3`_.
 
 Installation
 ------------
@@ -49,4 +49,4 @@ Changelog
 .. _celerite paper: https://iopscience.iop.org/article/10.3847/1538-3881/aa9332
 .. _celerite2: https://github.com/exoplanet-dev/celerite2
 .. _PyMC3: https://docs.pymc.io/
-.. _pip: https://pip.pypa.io/en/stable/
+.. _pip: https://pip.pypa.io/en/stable/

docs/python/carma.rst

@@ -3,7 +3,7 @@ CARMA
 
 CARMA GP kernels
 ----------------
-.. note:: `term` is a `celerite` nomenclature, a `term` is just a GP kernel. For example, a ``DRW_term`` object defines a DRW kernel. 
+.. note:: `term` is a `celerite` nomenclature, a `term` is just a GP kernel. For example, a ``DRW_term`` object defines a DRW kernel.
 
 .. automodule:: eztao.carma.CARMATerm
     :members:
@@ -12,4 +12,4 @@ CARMA GP kernels
 CARMA utility functions
 -----------------------
 .. automodule:: eztao.carma.model_utils
-    :members:
+    :members:

docs/python/ts.rst

@@ -23,4 +23,4 @@ MCMC
 Time series utility functions
 -----------------------------
 .. automodule:: eztao.ts.utils
-    :members:
+    :members:

docs/python/viz.rst

@@ -2,4 +2,4 @@ Visualization Tools
 ===================
 
 .. automodule:: eztao.viz.mpl_viz
-    :members:
+    :members:

docs/requirements.txt

@@ -1,13 +1,13 @@
 # docs/requirements.txt
+jinja2<3.1
 sphinx==3.4.1
 sphinx_rtd_theme==0.5.0
 nbsphinx>=0.8.6
 sphinx-copybutton==0.3.1
 toml==0.10.2
 ipykernel
-numba==0.51.0
-celerite==0.4.0
-scipy==1.5.0
-emcee==3.0.0
-matplotlib==3.3.3
-jinja2<3.1
+numba>=0.51.0
+celerite>=0.4.0
+scipy>=1.5.0
+emcee>=3.0.0
+matplotlib>=3.3.3

environment.yml

@@ -3,11 +3,11 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - python=3.7
+  - python=3.8
   - matplotlib
   - numpy
   - emcee
   - pip:
     - corner
-    - eztao==0.4.1
+    - eztao==0.4.2
     - importlib-metadata