From 38d904d6ca1779832f83a40059a239821e0d976e Mon Sep 17 00:00:00 2001 From: Neven Caplar Date: Mon, 21 Aug 2023 14:41:42 -0700 Subject: [PATCH 1/8] docstrings, optional argument in quasisep kernels --- src/tinygp/kernels/quasisep.py | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/src/tinygp/kernels/quasisep.py b/src/tinygp/kernels/quasisep.py index a6f5d75b..7a9bff62 100644 --- a/src/tinygp/kernels/quasisep.py +++ b/src/tinygp/kernels/quasisep.py @@ -379,7 +379,10 @@ class SHO(Quasisep): Args: omega: The parameter :math:`\omega`. quality: The parameter :math:`Q`. - sigma: The parameter :math:`\sigma`. + sigma (optional): The parameter :math:`\sigma`. Defaults to a value of + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ omega: JAXArray @@ -453,7 +456,10 @@ class Exp(Quasisep): Args: scale: The parameter :math:`\ell`. - sigma: The parameter :math:`\sigma`. + sigma (optional): The parameter :math:`\sigma`. Defaults to a value of + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray @@ -487,7 +493,10 @@ class Matern32(Quasisep): Args: scale: The parameter :math:`\ell`. - sigma: The parameter :math:`\sigma`. + sigma (optional): The parameter :math:`\sigma`. Defaults to a value of + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray sigma: JAXArray = field(default_factory=lambda: jnp.ones(())) @@ -529,7 +538,10 @@ class Matern52(Quasisep): Args: scale: The parameter :math:`\ell`. - sigma: The parameter :math:`\sigma`. + sigma (optional): The parameter :math:`\sigma`. Defaults to a value of + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray @@ -591,7 +603,10 @@ class Cosine(Quasisep): Args: scale: The parameter :math:`\ell`. - sigma: The parameter :math:`\sigma`. + sigma (optional): The parameter :math:`\sigma`. Defaults to a value of + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray sigma: JAXArray = field(default_factory=lambda: jnp.ones(())) From 42d693edc71107901a9e1732b48db01f868dc65c Mon Sep 17 00:00:00 2001 From: Neven Caplar Date: Mon, 21 Aug 2023 14:51:36 -0700 Subject: [PATCH 2/8] Added news doc --- news/176.doc | 1 + 1 file changed, 1 insertion(+) create mode 100644 news/176.doc diff --git a/news/176.doc b/news/176.doc new file mode 100644 index 00000000..8bb7843e --- /dev/null +++ b/news/176.doc @@ -0,0 +1 @@ +Clarified in documentation that sigma argument is optional in quasisep kernesls \ No newline at end of file From cd0c8137f5bcc5a11450ffe3ce3fa782035ee45f Mon Sep 17 00:00:00 2001 From: Neven Caplar Date: Tue, 22 Aug 2023 10:35:02 -0700 Subject: [PATCH 3/8] indent, typo and whitespaces fix --- src/tinygp/kernels/quasisep.py | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/src/tinygp/kernels/quasisep.py b/src/tinygp/kernels/quasisep.py index 7a9bff62..c5c1b0ee 100644 --- a/src/tinygp/kernels/quasisep.py +++ b/src/tinygp/kernels/quasisep.py @@ -379,10 +379,10 @@ class SHO(Quasisep): Args: omega: The parameter :math:`\omega`. quality: The parameter :math:`Q`. - sigma (optional): The parameter :math:`\sigma`. Defaults to a value of - 1. Specifying the explicit value here provides a slight performance - boost compared to independently multiplying the kernel with a - prefactor. + sigma (optional): The parameter :math:`\sigma`. Defaults to a value of + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ omega: JAXArray @@ -457,9 +457,9 @@ class Exp(Quasisep): Args: scale: The parameter :math:`\ell`. sigma (optional): The parameter :math:`\sigma`. Defaults to a value of - 1. Specifying the explicit value here provides a slight performance - boost compared to independently multiplying the kernel with a - prefactor. + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray @@ -494,9 +494,9 @@ class Matern32(Quasisep): Args: scale: The parameter :math:`\ell`. sigma (optional): The parameter :math:`\sigma`. Defaults to a value of - 1. Specifying the explicit value here provides a slight performance - boost compared to independently multiplying the kernel with a - prefactor. + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray sigma: JAXArray = field(default_factory=lambda: jnp.ones(())) @@ -539,9 +539,9 @@ class Matern52(Quasisep): Args: scale: The parameter :math:`\ell`. sigma (optional): The parameter :math:`\sigma`. Defaults to a value of - 1. Specifying the explicit value here provides a slight performance - boost compared to independently multiplying the kernel with a - prefactor. + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray @@ -604,9 +604,9 @@ class Cosine(Quasisep): Args: scale: The parameter :math:`\ell`. sigma (optional): The parameter :math:`\sigma`. Defaults to a value of - 1. Specifying the explicit value here provides a slight performance - boost compared to independently multiplying the kernel with a - prefactor. + 1. Specifying the explicit value here provides a slight performance + boost compared to independently multiplying the kernel with a + prefactor. """ scale: JAXArray sigma: JAXArray = field(default_factory=lambda: jnp.ones(())) From 561473fcee6c6b790d660121c13e825f2b2b9fcd Mon Sep 17 00:00:00 2001 From: Neven Caplar Date: Tue, 22 Aug 2023 10:36:47 -0700 Subject: [PATCH 4/8] typo fix --- news/176.doc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/news/176.doc b/news/176.doc index 8bb7843e..4e11fec6 100644 --- a/news/176.doc +++ b/news/176.doc @@ -1 +1 @@ -Clarified in documentation that sigma argument is optional in quasisep kernesls \ No newline at end of file +Clarified in documentation that sigma argument is optional in quasisep kernels \ No newline at end of file From 41dee255729337d86716a2edf3e66adbaea295c0 Mon Sep 17 00:00:00 2001 From: Neven Caplar Date: Tue, 22 Aug 2023 10:44:09 -0700 Subject: [PATCH 5/8] zenodo add --- .zenodo.json | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 .zenodo.json diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 00000000..5bec5b29 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,46 @@ +{ + "creators": [ + { + "orcid": "0000-0002-9328-5652", + "affiliation": "Center for Computational Astrophysics, Flatiron Institute, New York, NY, USA", + "name": "Foreman-Mackey, Daniel" + }, + { + "orcid": "0000-0003-0048-1118", + "affiliation": "Indian Institute of Technology Gandhinagar: Gandhinagar, Gujarat, IN", + "name": "Yadav, Sachin" + }, + { + "orcid": "0009-0000-1930-8150", + "affiliation": "Massachusetts Institute of Technology, Probabilistic Computing Project, Cambridge, MA, USA", + "name": "Becker, McCoy Reynolds" + }, + { + "orcid": "0000-0002-0440-9597", + "name": "Killestein, Thomas", + "affiliation": "Department of Physics, University of Warwick, Coventry, UK" + }, + { + "affiliation": "School of Public Health, Imperial College London, UK", + "name": "Rashid, Theo" + }, + { + "orcid": "0000-0003-1354-0578", + "affiliation": "Helmholtz-Zentrum Dresden-Rossendorf e.V.", + "name": "Schmerler, Steve" + }, + { + "orcid": "0000-0003-1001-0707", + "affiliation": "Department of Physics and Astronomy, Aarhus University, DK", + "name": "Tronsgaard, René" + }, + { + "orcid": "0000-0003-3287-5250", + "affiliation": "Department of Astronomy and the DiRAC Institute, University of Washington, Seattle, WA, USA", + "name": "Caplar, Neven" + } + ], + "license": "MIT", + "title": "dfm/tinygp: The tiniest of Gaussian Process libraries", + "description": "tinygp is an extremely lightweight library for building Gaussian Process (GP) models in Python, built on top of JAX. It has a nice interface, and it's pretty fast. Thanks to JAX, tinygp supports things like GPU acceleration and automatic differentiation.\n\nCheck out the docs for more info: https://tinygp.readthedocs.io" +} From 77e9f74d4a86aa3f66c9c81cd44fe78c3d59e30b Mon Sep 17 00:00:00 2001 From: Neven Caplar Date: Tue, 22 Aug 2023 10:46:47 -0700 Subject: [PATCH 6/8] news, period at the end --- news/176.doc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/news/176.doc b/news/176.doc index 4e11fec6..70f62c2f 100644 --- a/news/176.doc +++ b/news/176.doc @@ -1 +1 @@ -Clarified in documentation that sigma argument is optional in quasisep kernels \ No newline at end of file +Clarified in documentation that sigma argument is optional in quasisep kernels. \ No newline at end of file From ba8ed1627f1184c917d1bc836cbc5687ee17f9fa Mon Sep 17 00:00:00 2001 From: Dan Foreman-Mackey Date: Tue, 22 Aug 2023 21:18:02 -0400 Subject: [PATCH 7/8] Fixing end of file lint --- news/176.doc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/news/176.doc b/news/176.doc index 70f62c2f..1ea7a7ab 100644 --- a/news/176.doc +++ b/news/176.doc @@ -1 +1 @@ -Clarified in documentation that sigma argument is optional in quasisep kernels. \ No newline at end of file +Clarified in documentation that sigma argument is optional in quasisep kernels. From 80a97f0eab53f95a45ea48a34ce55f9c69b5c485 Mon Sep 17 00:00:00 2001 From: Dan Foreman-Mackey Date: Tue, 22 Aug 2023 21:19:34 -0400 Subject: [PATCH 8/8] Fixing indentation issue --- src/tinygp/kernels/quasisep.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tinygp/kernels/quasisep.py b/src/tinygp/kernels/quasisep.py index d8915f5e..433efb6f 100644 --- a/src/tinygp/kernels/quasisep.py +++ b/src/tinygp/kernels/quasisep.py @@ -390,7 +390,7 @@ class SHO(Quasisep): Args: omega: The parameter :math:`\omega`. quality: The parameter :math:`Q`. - sigma (optional): The parameter :math:`\sigma`. Defaults to a value of + sigma (optional): The parameter :math:`\sigma`. Defaults to a value of 1. Specifying the explicit value here provides a slight performance boost compared to independently multiplying the kernel with a prefactor.