From ea39c57448ea8d8851d5c91af284d15526be0778 Mon Sep 17 00:00:00 2001 From: Phillip Alday <me@phillipalday.com> Date: Sat, 2 Mar 2024 10:32:45 -0600 Subject: [PATCH 1/4] add precompile workfload for PCA --- src/MixedModels.jl | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/MixedModels.jl b/src/MixedModels.jl index 9052d5b1f..18d5e5fba 100644 --- a/src/MixedModels.jl +++ b/src/MixedModels.jl @@ -198,15 +198,19 @@ using PrecompileTools sleepstudy = MixedModels.dataset(:sleepstudy) contra = MixedModels.dataset(:contra) progress = false + io = IOBuffer() @compile_workload begin # all calls in this block will be precompiled, regardless of whether # they belong to your package or not (on Julia 1.8 and higher) # these are relatively small models and so shouldn't increase precompile times all that much # while still massively boosting load and TTFX times - fit(MixedModel, - @formula(reaction ~ 1 + days + (1 + days | subj)), - sleepstudy; progress) + m = fit(MixedModel, + @formula(reaction ~ 1 + days + (1 + days | subj)), + sleepstudy; progress) + show(io, m) + show(io, m.PCA.subj) + show(io, m.rePCA) fit(MixedModel, @formula(use ~ 1 + age + abs2(age) + urban + livch + (1 | urban & dist)), contra, From d18ad35ed8ddecd3dd26e8acd694148c59136761 Mon Sep 17 00:00:00 2001 From: Phillip Alday <me@phillipalday.com> Date: Sat, 2 Mar 2024 14:05:45 -0600 Subject: [PATCH 2/4] ignore version specific manifests --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 119a53c1a..7cf172276 100644 --- a/.gitignore +++ b/.gitignore @@ -4,8 +4,8 @@ docs/src/assets/*.svg test/scratch.jl tune.json Manifest.toml +Manifest-v*.toml settings.json docs/jmd LocalPreferences.toml benchmark.md - From 4b6648564f051517dc0f407210dd88ce7ee2bc00 Mon Sep 17 00:00:00 2001 From: Phillip Alday <palday@users.noreply.github.com> Date: Wed, 6 Mar 2024 00:35:07 +0000 Subject: [PATCH 3/4] Update src/MixedModels.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- src/MixedModels.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/MixedModels.jl b/src/MixedModels.jl index cca120f83..664b5db0a 100644 --- a/src/MixedModels.jl +++ b/src/MixedModels.jl @@ -218,8 +218,8 @@ include("profile/profile.jl") # these are relatively small models and so shouldn't increase precompile times all that much # while still massively boosting load and TTFX times m = fit(MixedModel, - @formula(reaction ~ 1 + days + (1 + days | subj)), - sleepstudy; progress) + @formula(reaction ~ 1 + days + (1 + days | subj)), + sleepstudy; progress) show(io, m) show(io, m.PCA.subj) show(io, m.rePCA) From d203396c8026ecd880f0b104d9db89bb6ef449ff Mon Sep 17 00:00:00 2001 From: Phillip Alday <phillip.alday@beacon.bio> Date: Tue, 3 Sep 2024 11:38:20 -0500 Subject: [PATCH 4/4] patch bump, NEWS --- NEWS.md | 5 +++++ Project.toml | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 1a53f74ee..4e2304383 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +MixedModels v4.25.4 Release Notes +============================== +- Added additional precompilation for rePCA. [#749] + MixedModels v4.25.3 Release Notes ============================== - Fix a bug in the handling of rank deficiency in the `simulate[!]` code. This has important correctness implications for bootstrapping models with rank-deficient fixed effects (as can happen in the case of partial crossing of the fixed effects / missing cells). [#778] @@ -545,6 +549,7 @@ Package dependencies [#740]: https://github.com/JuliaStats/MixedModels.jl/issues/740 [#744]: https://github.com/JuliaStats/MixedModels.jl/issues/744 [#748]: https://github.com/JuliaStats/MixedModels.jl/issues/748 +[#749]: https://github.com/JuliaStats/MixedModels.jl/issues/749 [#755]: https://github.com/JuliaStats/MixedModels.jl/issues/755 [#756]: https://github.com/JuliaStats/MixedModels.jl/issues/756 [#767]: https://github.com/JuliaStats/MixedModels.jl/issues/767 diff --git a/Project.toml b/Project.toml index 122ab02b0..bc051ae95 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "MixedModels" uuid = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316" author = ["Phillip Alday <me@phillipalday.com>", "Douglas Bates <dmbates@gmail.com>", "Jose Bayoan Santiago Calderon <jbs3hp@virginia.edu>"] -version = "4.25.3" +version = "4.25.4" [deps] Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"