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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,27 @@ | ||
| # Changelog | ||
| All notable changes to this project will be documented in this file. | ||
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||
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), | ||
| and this project, at least loosely, adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| This file contains the unreleased changes to the codebase. See CHANGELOG.md for | ||
| the released changes. | ||
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| ## Unreleased | ||
| ### Changed | ||
| - Third-order Roemer delay terms to ELL1 model | ||
| - Made the addition of a TZR TOA (`AbsPhase`) in the `TimingModel` explicit in `Residuals` class. | ||
| - Updated `CONTRIBUTING.rst` with the latest information. | ||
| - Made `TimingModel.params` and `TimingModel.ordered_params` identical. Deprecated `TimingModel.ordered_params`. | ||
| ### Added | ||
| - Third-order Roemer delay terms to ELL1 model | ||
| - Options to add a TZR TOA (`AbsPhase`) during the creation of a `TimingModel` using `ModelBuilder.__call__`, `get_model`, and `get_model_and_toas` | ||
| - `pint.print_info()` function for bug reporting | ||
| - Added an autocorrelation function to check for chain convergence in `event_optimize` | ||
| ### Fixed | ||
| - Deleting JUMP1 from flag tables will not prevent fitting | ||
| - Simulating TOAs from tim file when PLANET_SHAPIRO is true now works | ||
| - Docstrings for `get_toas()` and `get_model_and_toas()` | ||
| - Set `DelayComponent_list` and `NoiseComponent_list` to empty list if such components are absent | ||
| - Fix invalid access of `PLANET_SHAPIRO` in models without `Astrometry` | ||
| ### Removed |
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| Original file line number | Diff line number | Diff line change |
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@@ -20,11 +20,14 @@ Report bugs at https://github.com/nanograv/pint/issues. | |
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| If you are reporting a bug, please include: | ||
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| * Your operating system name and version. | ||
| * The output of ``pint.__version__`` and ``pint.__file__`` | ||
| * The output of ``pint.print_info()``. This command provides the version information of | ||
| the OS, Python, PINT, and the various dependencies along with other information about | ||
| your system. | ||
| * Any details about your local setup that might be helpful in troubleshooting, | ||
| such as the command used to install PINT and whether you are using a virtualenv. | ||
| * Detailed steps to reproduce the bug, as simply as possible. | ||
| such as the command used to install PINT and whether you are using a virtualenv, | ||
| conda environment, etc. | ||
| * Detailed steps to reproduce the bug, as simply as possible. A self-contained | ||
| code snippet that triggers the issue will be most helpful. | ||
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| Submit Feedback | ||
| ~~~~~~~~~~~~~~~ | ||
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@@ -74,22 +77,37 @@ to write good documentation, you come to understand the code very well. | |
| Get Started! | ||
| ------------ | ||
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| Ready to contribute? Here's how to set up PINT for local development. | ||
| Ready to contribute? Here's how to set up `PINT` for local development. | ||
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| 1. Fork_ the ``pint`` repo on GitHub. | ||
| 1. Fork_ the `PINT` repo on GitHub. | ||
| 2. Clone your fork locally:: | ||
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| $ git clone [email protected]:your_name_here/pint.git | ||
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| 3. Install your local copy into a virtualenv. Assuming you have | ||
| virtualenvwrapper installed, this is how you set up your fork for local | ||
| 3. Install your local copy into a `conda`_ environment. Assuming you have | ||
| `conda` installed, this is how you set up your fork for local | ||
| development:: | ||
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| $ mkvirtualenv pint | ||
| $ conda create -n pint-devel python=3.10 | ||
| $ conda activate pint-devel | ||
| $ cd PINT/ | ||
| $ conda install -c conda-forge --file requirements_dev.txt | ||
| $ conda install -c conda-forge --file requirements.txt | ||
| $ pip install -e . | ||
| $ pre-commit install | ||
| The last command installs pre-commit hooks which will squawk at you while trying | ||
| to commit changes that don't adhere to our `Coding Style`_. | ||
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| Alternatively, this can also be done using `virtualenv`. Assuming you have | ||
| `virtualenvwrapper` installed, this is how you set up your fork for local | ||
| development:: | ||
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| $ mkvirtualenv pint-devel | ||
| $ cd PINT/ | ||
| $ pip install -r requirements_dev.txt | ||
| $ pip install -r requirements.txt | ||
| $ pip install -e . | ||
| $ pre-commit install | ||
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| 4. Create a branch for local development:: | ||
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@@ -107,13 +125,13 @@ Ready to contribute? Here's how to set up PINT for local development. | |
| 6. Commit your changes and push your branch to GitHub:: | ||
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| $ git add . | ||
| $ git commit -m "Your detailed description of your changes." | ||
| $ git commit -m "Detailed description of your changes." | ||
| $ git push origin name-of-your-bugfix-or-feature | ||
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| 7. Submit a pull request through the GitHub website. | ||
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| 8. Check that our automatic testing "Travis CI" passes your code. If | ||
| problems crop up, fix them, commit the changes, and push a new version, | ||
| 8. Check that our automatic testing in "GitHub Actions" passes for your code. | ||
| If problems crop up, fix them, commit the changes, and push a new version, | ||
| which will automatically update the pull request:: | ||
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| $ git add pint/file-i-just-fixed.py | ||
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@@ -125,21 +143,28 @@ Ready to contribute? Here's how to set up PINT for local development. | |
| functional changes. If accepted, it will be merged into the master branch. | ||
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| .. _Fork: https://help.github.com/en/articles/fork-a-repo | ||
| .. _`conda`: https://docs.conda.io/ | ||
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| Pull Request Guidelines | ||
| ----------------------- | ||
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| Before you submit a pull request, check that it meets these guidelines: | ||
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| 1. Try to write clear :ref:`pythonic` code, follow our :ref:`CodingStyle`, and think | ||
| 1. Try to write clear `Pythonic`_ code, follow our `Coding Style`_, and think | ||
| about how others might use your new code. | ||
| 2. The pull request should include tests that cover both the expected | ||
| behavior and sensible error reporting when given bad input. | ||
| 3. If the pull request adds or changes functionality, the docs should | ||
| be updated. Put your new functionality into a function with a | ||
| docstring. Check the HTML documentation produced by ``make docs`` | ||
| to make sure your new documentation appears and looks reasonable. | ||
| 4. The pull request should work for Python 2.7 and 3.6+. Check | ||
| https://travis-ci.org/nanograv/pint/pull_requests | ||
| and make sure that the tests pass for all supported Python versions. | ||
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| If the new functionality needs a more detailed explanation than can be | ||
| put in a docstring, add it to ``docs/explanation.rst``. Make sure that | ||
| the docstring contains a brief description as well. | ||
| 4. The pull request should work for and 3.8+. Make sure that all the | ||
| CI tests for the pull request pass. | ||
| 5. Update ``CHANGELOG-unreleased.md`` with an appropriate entry. Please note | ||
| that ``CHANGELOG.md`` should not be updated for pull requests. | ||
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| .. _`Pythonic`: https://peps.python.org/pep-0008/ | ||
| .. _`Coding Style`: https://nanograv-pint.readthedocs.io/en/latest/coding-style.html | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -36,16 +36,17 @@ PINT | |
| PINT is not TEMPO3 | ||
| ------------------ | ||
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| PINT is a project to develop a new pulsar timing solution based on | ||
| PINT is a project to develop a pulsar timing solution based on | ||
| python and modern libraries. It is still in active development, | ||
| but it can already produce residuals from most "normal" | ||
| but it is in production use by the NANOGrav collaboration and | ||
| it has been demonstrated produce residuals from most "normal" | ||
| timing models that agree with Tempo and Tempo2 to within ~10 | ||
| nanoseconds. It can be used within python scripts or notebooks, | ||
| and there are several command line tools that come with it. | ||
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| The primary reasons we are developing PINT are: | ||
| The primary reasons PINT was developed are: | ||
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| * To have a robust system to check high-precision timing results that is | ||
| * To have a robust system to produce high-precision timing results that is | ||
| completely independent of TEMPO and Tempo2 | ||
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| * To make a system that is easy to extend and modify due to a good design | ||
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@@ -57,7 +58,13 @@ IMPORTANT Notes! | |
| PINT has a naming conflict with the `pint <https://pypi.org/project/Pint/>`_ units package available from PyPI (i.e. using pip) and conda. | ||
| Do **NOT** ``pip install pint`` or ``conda install pint``! See below! | ||
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| PINT requires `longdouble` arithmetic within `numpy`, which is currently not supported natively on M1 Macs (e.g., with the `ARM64 conda build <https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/>`_). So it may be better to install the standard `osx-64` build and rely on Rosetta. | ||
| PINT requires ``longdouble`` (80- or 128-bit floating point) arithmetic within ``numpy``, which is currently not supported natively on M1/M2 Macs. | ||
| However, you can use an x86 version of ``conda`` even on an M1/M2 Mac (which will run under Rosetta emulation): | ||
| see `instructions for using Apple Intel packages on Apple | ||
| silicon <https://conda-forge.org/docs/user/tipsandtricks.html#installing-apple-intel-packages-on-apple-silicon>`_. | ||
| It's possible to have `parallel versions of conda for x86 and | ||
| ARM <https://towardsdatascience.com/python-conda-environments-for-both-arm64-and-x86-64-on-m1-apple-silicon-147b943ffa55>`_. | ||
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| Installing | ||
| ---------- | ||
|
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@@ -96,19 +103,17 @@ it, ensuring that all dependencies needed to run PINT are available:: | |
| $ cd PINT | ||
| $ pip install . | ||
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| Complete installation instructions are available here_. | ||
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| .. _here: https://nanograv-pint.readthedocs.io/en/latest/installation.html | ||
| Complete installation instructions are available on `readthedocs <https://nanograv-pint.readthedocs.io/en/latest/installation.html>`_. | ||
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| Using | ||
| ----- | ||
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| See the online documentation_. Specifically: | ||
| See the online documentation_. Specifically: | ||
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| * `tutorials <https://nanograv-pint.readthedocs.io/en/latest/tutorials.html>`_ | ||
| * `Tutorials <https://nanograv-pint.readthedocs.io/en/latest/tutorials.html>`_ | ||
| * `API reference <https://nanograv-pint.readthedocs.io/en/latest/reference.html>`_ | ||
| * `How to's for common tasks <https://github.com/nanograv/PINT/wiki/How-To>`_ | ||
| * `How-Tos for common tasks <https://github.com/nanograv/PINT/wiki/How-To>`_ | ||
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| Are you a NANOGrav member? Then join the #pint channel in the NANOGrav slack. | ||
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@@ -119,10 +124,13 @@ email [email protected] or one of the people below: | |
| * Paul Ray ([email protected]) | ||
| * David Kaplan ([email protected]) | ||
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| Want to do something new? Submit a github `issue <https://github.com/nanograv/PINT/issues>`_. | ||
| Want to do something new? Submit a github `issue <https://github.com/nanograv/PINT/issues>`_. | ||
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| .. _documentation: http://nanograv-pint.readthedocs.io/en/latest/ | ||
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| And for more details, please read and cite(!) the PINT paper_. | ||
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| .. _paper: https://ui.adsabs.harvard.edu/abs/2021ApJ...911...45L/abstract | ||
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| Articles that cite the PINT paper can be found in an ADS `Library <https://ui.adsabs.harvard.edu/search/q=citations(bibcode%3A2021ApJ...911...45L)&sort=date%20desc%2C%20bibcode%20desc&p_=0>`_. | ||
| A list of software packages that use PINT can be found `here <https://nanograv-pint.readthedocs.io/en/latest/dependent-packages.html>`_. | ||
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