Skip to content

Commit 4fc5b0d

Browse files
paldaypalday
committed
Merge branch 'main' of github.com:JuliaStats/MixedModels.jl into glmm_dispersion_deviance
2 parents 3fbaaf8 + 12fe4b7 commit 4fc5b0d

22 files changed

+359
-147
lines changed

‎.JuliaFormatter.toml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1 +1,2 @@
11
style = "blue"
2+
join_lines_based_on_source = true

‎.github/pull_request_template.md‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,8 @@
1+
Thanks for contributing!
2+
3+
Did behavior change? Did you add need features? If so, please update NEWS.md
4+
- [ ] add entry in NEWS.md
5+
- [ ] after opening this PR, add a reference and run `docs/NEWS-update.jl` to update the cross-references.
6+
7+
Should we release your changes right away? If so, bump the version:
8+
- [ ] I've bumped the version appropriately

‎.github/workflows/Format.yml‎

Lines changed: 0 additions & 33 deletions
This file was deleted.

‎.github/workflows/ci.yml‎

Lines changed: 37 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
1+
name: current release
2+
on:
3+
push:
4+
branches:
5+
- main
6+
paths-ignore:
7+
- 'LICENSE.md'
8+
- 'README.md'
9+
pull_request:
10+
branches:
11+
- main
12+
paths-ignore:
13+
- 'LICENSE.md'
14+
- 'README.md'
15+
jobs:
16+
ci:
17+
runs-on: ${{ matrix.os }}
18+
strategy:
19+
matrix:
20+
julia-version: [1]
21+
julia-arch: [x64]
22+
os: [ubuntu-18.04]
23+
steps:
24+
- name: Cancel Previous Runs
25+
uses: styfle/[email protected]
26+
with:
27+
all_but_latest: true
28+
access_token: ${{ github.token }}
29+
- uses: actions/checkout@v2
30+
- uses: julia-actions/setup-julia@v1
31+
with:
32+
version: ${{ matrix.julia-version }}
33+
- uses: julia-actions/[email protected]
34+
- uses: julia-actions/[email protected]
35+
env:
36+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
37+
- uses: julia-actions/[email protected]

‎.github/workflows/documenter.yml‎

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -3,15 +3,26 @@ on:
33
push:
44
branches: [main]
55
tags: [v*]
6+
paths-ignore:
7+
- 'LICENSE.md'
8+
- 'README.md'
69
pull_request:
710
branches:
811
- main
912
- v3.x
13+
paths-ignore:
14+
- 'LICENSE.md'
15+
- 'README.md'
1016
jobs:
1117
Documenter:
1218
name: Documentation
1319
runs-on: ubuntu-20.04
1420
steps:
21+
- name: Cancel Previous Runs
22+
uses: styfle/[email protected]
23+
with:
24+
all_but_latest: true
25+
access_token: ${{ github.token }}
1526
- uses: actions/checkout@v2
1627
- uses: julia-actions/setup-julia@v1
1728
with:

‎.github/workflows/Tier1.yml‎ renamed to ‎.github/workflows/lts.yml‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,14 @@
1-
name: Tier 1
1+
name: LTS
22
on:
33
push:
44
branches:
55
- main
6-
- v3.x
76
paths-ignore:
87
- 'LICENSE.md'
98
- 'README.md'
109
pull_request:
1110
branches:
1211
- main
13-
- v3.x
1412
paths-ignore:
1513
- 'LICENSE.md'
1614
- 'README.md'
@@ -23,6 +21,11 @@ jobs:
2321
julia-arch: [x64]
2422
os: [ubuntu-18.04, macos-10.15, windows-2019]
2523
steps:
24+
- name: Cancel Previous Runs
25+
uses: styfle/[email protected]
26+
with:
27+
all_but_latest: true
28+
access_token: ${{ github.token }}
2629
- uses: actions/checkout@v2
2730
- uses: julia-actions/setup-julia@v1
2831
with:

‎.github/workflows/Future.yml‎ renamed to ‎.github/workflows/nightly.yml‎

Lines changed: 13 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,31 @@
1-
name: Future
1+
name: nightly
22
on:
3+
push:
4+
branches:
5+
- main
6+
paths-ignore:
7+
- 'LICENSE.md'
8+
- 'README.md'
39
pull_request:
410
branches:
511
- main
612
paths-ignore:
713
- 'LICENSE.md'
814
- 'README.md'
9-
workflow_dispatch:
1015
jobs:
1116
ci:
1217
runs-on: ${{ matrix.os }}
1318
strategy:
14-
fail-fast: false
1519
matrix:
1620
julia-version: [nightly]
1721
julia-arch: [x64]
1822
os: [ubuntu-18.04]
1923
steps:
24+
- name: Cancel Previous Runs
25+
uses: styfle/[email protected]
26+
with:
27+
all_but_latest: true
28+
access_token: ${{ github.token }}
2029
- uses: actions/checkout@v2
2130
- uses: julia-actions/setup-julia@v1
2231
with:
@@ -25,4 +34,4 @@ jobs:
2534
- uses: julia-actions/[email protected]
2635
env:
2736
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
28-
# OPENBLAS_CORETYPE: haswell
37+
- uses: julia-actions/[email protected]

‎.github/workflows/style.yml‎

Lines changed: 35 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
name: Style-Enforcer
2+
on:
3+
push:
4+
branches:
5+
- 'main'
6+
tags: '*'
7+
pull_request:
8+
types: [opened, synchronize, reopened, ready_for_review]
9+
# note: keep in sync with `format/run.jl`
10+
paths-ignore:
11+
- 'README.md'
12+
- '.gitignore'
13+
jobs:
14+
format-check:
15+
name: Style Enforcement (Julia ${{ matrix.julia-version }} - ${{ github.event_name }})
16+
# Run on push's or non-draft PRs
17+
if: (github.event_name == 'push') || (github.event.pull_request.draft == false)
18+
runs-on: ubuntu-latest
19+
strategy:
20+
matrix:
21+
julia-version: [1.6]
22+
steps:
23+
- uses: julia-actions/setup-julia@latest
24+
with:
25+
version: ${{ matrix.julia-version }}
26+
- uses: actions/checkout@v1
27+
- name: Instantiate `format` environment and format
28+
run: |
29+
julia --project=format -e 'using Pkg; Pkg.instantiate()'
30+
julia --project=format 'format/run.jl'
31+
- uses: reviewdog/action-suggester@v1
32+
if: github.event_name == 'pull_request'
33+
with:
34+
tool_name: JuliaFormatter
35+
fail_on_error: true

‎NEWS.md‎

Lines changed: 23 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,21 @@
1+
MixedModels v4.6.3 Release Notes
2+
========================
3+
* Add precompile statements to speed up first `LinearMixedModel` and Bernoulli `GeneralizedLinearModel` fit [#608]
4+
5+
MixedModels v4.6.2 Release Notes
6+
========================
7+
* Efficiency improvements in `predict`, both in memory and computation [#604]
8+
* Changed the explanation of `predict`'s keyword argument `new_re_levels` in a way that is clearer about the behavior when there are multiple grouping variables. [#603]
9+
* Fix the default behavior of `new_re_levels=:missing` to match the docstring. Previously, the default was `:population`, in disagreement with the docstring. [#603]
10+
11+
MixedModels v4.6.1 Release Notes
12+
========================
13+
* Loosen type restriction on `shortestcovint(::MixedModelBootstrap)` to `shortestcovint(::MixedModelFitCollection)`. [#598]
14+
15+
MixedModels v4.6.0 Release Notes
16+
========================
17+
* Experimental support for initializing `GeneralizedLinearMixedModel` fits from a linear mixed model instead of a marginal (non-mixed) generalized linear model. [#588]
18+
119
MixedModels v4.5.0 Release Notes
220
========================
321
* Allow constructing a `GeneralizedLinearMixedModel` with constant response, but don't update the ``L`` matrix nor initialize its deviance. This allows for the model to still be used for simulation where the response will be changed before fitting. [#578]
@@ -317,3 +335,8 @@ Package dependencies
317335
[#573]: https://github.com/JuliaStats/MixedModels.jl/issues/573
318336
[#577]: https://github.com/JuliaStats/MixedModels.jl/issues/577
319337
[#578]: https://github.com/JuliaStats/MixedModels.jl/issues/578
338+
[#588]: https://github.com/JuliaStats/MixedModels.jl/issues/588
339+
[#598]: https://github.com/JuliaStats/MixedModels.jl/issues/598
340+
[#603]: https://github.com/JuliaStats/MixedModels.jl/issues/603
341+
[#604]: https://github.com/JuliaStats/MixedModels.jl/issues/604
342+
[#608]: https://github.com/JuliaStats/MixedModels.jl/issues/608

‎Project.toml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
name = "MixedModels"
22
uuid = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
33
author = ["Phillip Alday <[email protected]>", "Douglas Bates <[email protected]>", "Jose Bayoan Santiago Calderon <[email protected]>"]
4-
version = "4.5.0"
4+
version = "4.6.3"
55

66
[deps]
77
Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"
@@ -37,7 +37,7 @@ PooledArrays = "0.5, 1"
3737
ProgressMeter = "1.7"
3838
StaticArrays = "0.11, 0.12, 1"
3939
StatsBase = "0.31, 0.32, 0.33"
40-
StatsFuns = "0.8, 0.9"
40+
StatsFuns = "0.8, 0.9, 1"
4141
StatsModels = "0.6.23"
4242
StructTypes = "1"
4343
Tables = "1"

0 commit comments

Comments
 (0)