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V0.6 #212

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merged 40 commits into from
May 11, 2023
Merged

V0.6 #212

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4bf4d97
wip
Mar 21, 2023
6ccb2c7
format
Mar 21, 2023
e8062da
added decoupled
Mar 29, 2023
c6b1d74
4majortom
Mar 29, 2023
74a3366
Docs pytree (#211)
thomaspinder Apr 8, 2023
4b9f5f9
Cleanup (#205)
thomaspinder Apr 9, 2023
fb2b2f2
Update README (#220)
thomaspinder Apr 10, 2023
46b7253
Refactor decoupled sampling for v0.6
thomaspinder Apr 10, 2023
ca2fa7c
Strip out header text
thomaspinder Apr 10, 2023
0ec837c
Fix missing jit import
thomaspinder Apr 10, 2023
6ec004e
Add minimal pytree checks for linops. (Better testing needed in futur…
daniel-dodd Apr 11, 2023
caeeb4d
Add pytree tests for gps (tests still need improving). (#223)
daniel-dodd Apr 11, 2023
a2b16b8
Add minimal pytree tests for variational (tests need improving). (#224)
daniel-dodd Apr 11, 2023
df2d22b
Add tests for kernels and likelihoods (#225)
frazane Apr 11, 2023
f458367
Add save/load fns
thomaspinder Apr 11, 2023
6e3b4b2
Drop test
thomaspinder Apr 11, 2023
c6a8c79
Format
thomaspinder Apr 11, 2023
e977d13
Format
thomaspinder Apr 11, 2023
9cc68d8
Add acknowledgement
thomaspinder Apr 12, 2023
4853ebf
Merge pull request #228 from JaxGaussianProcesses/save_load
daniel-dodd Apr 12, 2023
68e204a
Spatial modelling example with decoupled sampling (#234)
frazane Apr 26, 2023
75f9ddd
Introduce beartype & fix types (#230)
st-- Apr 27, 2023
21a12df
`pre-commit` setup & code changes (#241)
st-- Apr 27, 2023
2aba697
Poisson likelihood (#231)
frazane Apr 29, 2023
5381567
wip (#243)
henrymoss Apr 30, 2023
c07935a
Arccosine kernel (#245)
henrymoss Apr 30, 2023
731e088
Add static field to base, update tests to run on 3.11, fix 3.11 compa…
daniel-dodd Apr 30, 2023
17d3f96
Revamp docs (#233)
thomaspinder May 11, 2023
38de408
Update mplstyle ref
thomaspinder May 11, 2023
a2f3d1e
Update workflows
thomaspinder May 11, 2023
79e711f
Fix workflow
thomaspinder May 11, 2023
1cf3c4f
Remove deprecated kernel logo
thomaspinder May 11, 2023
a07012b
Install LaTeX
thomaspinder May 11, 2023
76b7c8e
Install LaTeX
thomaspinder May 11, 2023
1172bd9
Install LaTeX
thomaspinder May 11, 2023
1da81d3
Update data paths
thomaspinder May 11, 2023
6d3fffb
Add generating process figure
thomaspinder May 11, 2023
84da0c2
Update poissong figs
thomaspinder May 11, 2023
ca2ac13
Cleaup spatial cells
thomaspinder May 11, 2023
6fa6d4f
Drop sharp bits
thomaspinder May 11, 2023
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153 changes: 0 additions & 153 deletions .circleci/config.yml

This file was deleted.

12 changes: 0 additions & 12 deletions .coveragerc

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1 change: 0 additions & 1 deletion .gitattributes

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4 changes: 2 additions & 2 deletions .github/CODE_OF_CONDUCT.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,6 @@ This code of conduct applies to all communication: this includes IRC, the mailin
- Unwelcome sexual attention.
- Advocating for, or encouraging, any of the above behaviour.
- Repeated harassment of others. In general, if someone asks you to stop, then stop.
- When we disagree, we try to understand why. Disagreements, both social and technical, happen all the time and GPJax is no exception. It is important that we resolve disagreements and differing views constructively. Remember that we're different. The strength of GPJax comes from its varied community, people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn't mean that they're wrong. Don't forget that it is human to err and blaming each other doesn't get us anywhere, rather offer to help resolving issues and to help learn from mistakes.
- When we disagree, we try to understand why. Disagreements, both social and technical, happen all the time and GPJax is no exception. It is important that we resolve disagreements and differing views constructively. Remember that we're different. The strength of GPJax comes from its varied community, people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn't mean that they're wrong. Don't forget that it is human to err and blaming each other doesn't get us anywhere, rather offer to help resolving issues and to help learn from mistakes.

Text adapted from the [Speak Up! project](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html) and [Django](https://www.djangoproject.com/conduct/)
Text adapted from the [Speak Up! project](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html) and [Django](https://www.djangoproject.com/conduct/)
18 changes: 18 additions & 0 deletions .github/codecov.yml
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@@ -0,0 +1,18 @@
# codecov used to be able to find this anywhere, now we have to manually
# tell it where to look
comment: false

codecov:
notify:
require_ci_to_pass: no

coverage:
status:
patch:
default:
target: 50%
if_no_uploads: error
if_not_found: success
if_ci_failed: failure
project:
default: false
21 changes: 21 additions & 0 deletions .github/dependabot.yml
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@@ -0,0 +1,21 @@
version: 2
updates:
- package-ecosystem: github-actions
directory: "/"
schedule:
interval: weekly
- package-ecosystem: pip
directory: "/.github/workflows"
schedule:
interval: weekly
- package-ecosystem: pip
directory: "/docs"
schedule:
interval: weekly
- package-ecosystem: pip
directory: "/"
schedule:
interval: weekly
versioning-strategy: lockfile-only
allow:
- dependency-type: "all"
66 changes: 66 additions & 0 deletions .github/labels.yml
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@@ -0,0 +1,66 @@
---
# Labels names are important as they are used by Release Drafter to decide
# regarding where to record them in changelog or if to skip them.
#
# The repository labels will be automatically configured using this file and
# the GitHub Action https://github.com/marketplace/actions/github-labeler.
- name: breaking
description: Breaking Changes
color: bfd4f2
- name: bug
description: Something isn't working
color: d73a4a
- name: build
description: Build System and Dependencies
color: bfdadc
- name: ci
description: Continuous Integration
color: 4a97d6
- name: dependencies
description: Pull requests that update a dependency file
color: 0366d6
- name: documentation
description: Improvements or additions to documentation
color: 0075ca
- name: duplicate
description: This issue or pull request already exists
color: cfd3d7
- name: enhancement
description: New feature or request
color: a2eeef
- name: github_actions
description: Pull requests that update Github_actions code
color: "000000"
- name: good first issue
description: Good for newcomers
color: 7057ff
- name: help wanted
description: Extra attention is needed
color: 008672
- name: invalid
description: This doesn't seem right
color: e4e669
- name: performance
description: Performance
color: "016175"
- name: python
description: Pull requests that update Python code
color: 2b67c6
- name: question
description: Further information is requested
color: d876e3
- name: refactoring
description: Refactoring
color: ef67c4
- name: removal
description: Removals and Deprecations
color: 9ae7ea
- name: style
description: Style
color: c120e5
- name: testing
description: Testing
color: b1fc6f
- name: wontfix
description: This will not be worked on
color: ffffff
38 changes: 12 additions & 26 deletions .github/pull_request_template.md
Original file line number Diff line number Diff line change
@@ -1,33 +1,19 @@
<!--- Please provide a general summary of your changes in the title above -->
## Type of changes

## Pull request type
- [ ] Bug fix
- [ ] New feature
- [ ] Documentation / docstrings
- [ ] Tests
- [ ] Other

<!-- Please try to limit your pull request to one type, submit multiple pull requests if needed. -->
## Checklist

Please check the type of change your PR introduces:
- [ ] I've formatted the new code by running `poetry run pre-commit run --all-files --show-diff-on-failure` before committing.
- [ ] I've added tests for new code.
- [ ] I've added docstrings for the new code.

- [ ] Bugfix
- [ ] Feature
- [ ] Code style update (formatting, renaming)
- [ ] Refactoring (no functional changes, no api changes)
- [ ] Build related changes
- [ ] Documentation content changes
- [ ] Other (please describe):
## Description

## What is the current behavior?

<!-- Please describe the current behavior that you are modifying, or link to a relevant issue. -->
Please describe your changes here. If this fixes a bug, please link to the issue, if possible.

Issue Number: N/A

## What is the new behavior?

<!-- Please describe the behavior or changes that are being added by this PR. -->

-
-
-

## Other information

<!-- Any other information that is important to this PR such as screenshots of how the component looks before and after the change. -->
28 changes: 28 additions & 0 deletions .github/release-drafter.yml
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@@ -0,0 +1,28 @@
categories:
- title: ":boom: Breaking Changes"
label: "breaking"
- title: ":rocket: Features"
label: "enhancement"
- title: ":fire: Removals and Deprecations"
label: "removal"
- title: ":beetle: Fixes"
label: "bug"
- title: ":racehorse: Performance"
label: "performance"
- title: ":rotating_light: Testing"
label: "testing"
- title: ":construction_worker: Continuous Integration"
label: "ci"
- title: ":books: Documentation"
label: "documentation"
- title: ":hammer: Refactoring"
label: "refactoring"
- title: ":lipstick: Style"
label: "style"
- title: ":package: Dependencies"
labels:
- "dependencies"
- "build"
template: |
## Changes
$CHANGES
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