From 5baa8a400dbe5162a77fa94658032765f1196542 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 21:54:46 +0100 Subject: [PATCH 01/11] Bump compat lower bounds --- Project.toml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Project.toml b/Project.toml index 1535110f..6de4f714 100644 --- a/Project.toml +++ b/Project.toml @@ -19,15 +19,15 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" [compat] AbstractFFTs = "0.5, 1" -DataAPI = "1.6" +DataAPI = "1.8" DataStructures = "0.18.3" -Distributions = "0.25" +Distributions = "0.25.57" LinearAlgebra = "1.6" MLJModelInterface = "1.6" Random = "1.6" -SpecialFunctions = "0.8, 0.9, 0.10, 1, 2" +SpecialFunctions = "1.8.4, 2" Statistics = "1.6" -StatsBase = "0.33, 0.34" +StatsBase = "0.33.3, 0.34" StatsFuns = "1" -Tables = "1" +Tables = "1.9" julia = "1.6" From 50c48f29d2cda30eeacd65db4b35f31c0b9eb976 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 21:55:00 +0100 Subject: [PATCH 02/11] Bump compat lower bounds for tests --- test/Project.toml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/test/Project.toml b/test/Project.toml index 630e595b..126d49ed 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -20,21 +20,21 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [compat] -Aqua = "0.8" -Distributions = "0.25" -DynamicHMC = "3" +Aqua = "0.8.1" +Distributions = "0.25.57" +DynamicHMC = "3.2" EvoTrees = "0.14.7, 0.15, 0.16" FFTW = "1.1" LogDensityProblems = "0.12, 1, 2" -LogExpFunctions = "0.3" -MLJBase = "0.19, 0.20, 0.21, 1" +LogExpFunctions = "0.3.26" +MLJBase = "0.20, 0.21, 1" MLJDecisionTreeInterface = "0.3, 0.4" MLJIteration = "0.5, 0.6" MLJLIBSVMInterface = "0.2" MLJModels = "0.16" MLJXGBoostInterface = "0.3" -OffsetArrays = "1" +OffsetArrays = "1.11" Statistics = "1.6" -StatsBase = "0.33, 0.34" -Tables = "1" +StatsBase = "0.33.3, 0.34" +Tables = "1.9" julia = "1.6" From a281ba036c2438bff855112d025c1031799e34ca Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 21:55:34 +0100 Subject: [PATCH 03/11] Test with downgraded dependencies --- .github/workflows/CI.yml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 1608d046..84feee19 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -8,7 +8,7 @@ on: jobs: test: - name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} + name: ${{ matrix.downgrade && 'Downgrade / ' || '' }}Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} runs-on: ${{ matrix.os }} strategy: fail-fast: false @@ -21,13 +21,21 @@ jobs: - ubuntu-latest arch: - x64 + downgrade: + - false include: - version: '1' os: macOS-latest arch: x64 + downgrade: false - version: '1' os: windows-latest arch: x64 + downgrade: false + - version: '1' + os: ubuntu-latest + arch: x64 + downgrade: true steps: - uses: actions/checkout@v4 - uses: julia-actions/setup-julia@v1 @@ -35,6 +43,11 @@ jobs: version: ${{ matrix.version }} arch: ${{ matrix.arch }} - uses: julia-actions/cache@v1 + - uses: cjdoris/julia-downgrade-compat-action@v1 + with: + skip: LinearAlgebra,Markdown,Printf,Random,Statistics + if: ${{ matrix.downgrade }} + name: Downgrade dependencies to oldest supported versions - uses: julia-actions/julia-buildpkg@v1 - uses: julia-actions/julia-runtest@v1 with: From 9bcce5f1da178187de419392201dfd6c0f5766a9 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 22:19:50 +0100 Subject: [PATCH 04/11] Bump XGBoost lower bound so tests pass with tolerance --- test/Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/Project.toml b/test/Project.toml index 126d49ed..b3b0fe8d 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -32,7 +32,7 @@ MLJDecisionTreeInterface = "0.3, 0.4" MLJIteration = "0.5, 0.6" MLJLIBSVMInterface = "0.2" MLJModels = "0.16" -MLJXGBoostInterface = "0.3" +MLJXGBoostInterface = "0.3.4" OffsetArrays = "1.11" Statistics = "1.6" StatsBase = "0.33.3, 0.34" From 918fc1b35aa0ba73d30a484c17edafc08e0638ec Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 22:20:07 +0100 Subject: [PATCH 05/11] Increment patch number --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 6de4f714..e63ba5fc 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "MCMCDiagnosticTools" uuid = "be115224-59cd-429b-ad48-344e309966f0" authors = ["David Widmann", "Seth Axen"] -version = "0.3.8" +version = "0.3.9" [deps] AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c" From 9c11cf8d285987a01bfd23611f6c39964f437fcd Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 22:21:23 +0100 Subject: [PATCH 06/11] Make tests and docs compats match --- docs/Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Project.toml b/docs/Project.toml index 4bb663da..1bb7e0b3 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -10,7 +10,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [compat] Documenter = "1" EvoTrees = "0.14.7, 0.15, 0.16" -MLJBase = "0.19, 0.20, 0.21, 1" +MLJBase = "0.20, 0.21, 1" MLJIteration = "0.5, 0.6" StatisticalMeasures = "0.1" Statistics = "1.6" From 2a1e5f1d8b6441f373ac359182195b49ffef5be4 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 23:36:32 +0100 Subject: [PATCH 07/11] Bump Tables to 1.11 EvoTrees recent versions use a method of `Tables.DataAPI.nrow` only defined in Tables v1.11. --- Project.toml | 2 +- test/Project.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index e63ba5fc..925435c3 100644 --- a/Project.toml +++ b/Project.toml @@ -29,5 +29,5 @@ SpecialFunctions = "1.8.4, 2" Statistics = "1.6" StatsBase = "0.33.3, 0.34" StatsFuns = "1" -Tables = "1.9" +Tables = "1.11" julia = "1.6" diff --git a/test/Project.toml b/test/Project.toml index b3b0fe8d..aa96ce45 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -36,5 +36,5 @@ MLJXGBoostInterface = "0.3.4" OffsetArrays = "1.11" Statistics = "1.6" StatsBase = "0.33.3, 0.34" -Tables = "1.9" +Tables = "1.11" julia = "1.6" From e402763e004f48a80eee48d57271f903519ea42d Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 13 Feb 2024 23:48:19 +0100 Subject: [PATCH 08/11] Replace `test/Project.toml` with an extras section in `Project.toml` --- Project.toml | 32 ++++++++++++++++++++++++++++++++ test/Project.toml | 40 ---------------------------------------- 2 files changed, 32 insertions(+), 40 deletions(-) delete mode 100644 test/Project.toml diff --git a/Project.toml b/Project.toml index 925435c3..1b7fa99f 100644 --- a/Project.toml +++ b/Project.toml @@ -18,12 +18,25 @@ StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" [compat] +Aqua = "0.8.1" AbstractFFTs = "0.5, 1" DataAPI = "1.8" DataStructures = "0.18.3" Distributions = "0.25.57" +DynamicHMC = "3.2" +EvoTrees = "0.14.7, 0.15, 0.16" +FFTW = "1.1" LinearAlgebra = "1.6" +LogDensityProblems = "0.12, 1, 2" +LogExpFunctions = "0.3.26" +MLJBase = "0.20, 0.21, 1" +MLJDecisionTreeInterface = "0.3, 0.4" +MLJIteration = "0.5, 0.6" +MLJLIBSVMInterface = "0.2" MLJModelInterface = "1.6" +MLJModels = "0.16" +MLJXGBoostInterface = "0.3.4" +OffsetArrays = "1.11" Random = "1.6" SpecialFunctions = "1.8.4, 2" Statistics = "1.6" @@ -31,3 +44,22 @@ StatsBase = "0.33.3, 0.34" StatsFuns = "1" Tables = "1.11" julia = "1.6" + +[extras] +Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" +DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" +EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5" +FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" +LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" +LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d" +MLJDecisionTreeInterface = "c6f25543-311c-4c74-83dc-3ea6d1015661" +MLJIteration = "614be32b-d00c-4edb-bd02-1eb411ab5e55" +MLJLIBSVMInterface = "61c7150f-6c77-4bb1-949c-13197eac2a52" +MLJModels = "d491faf4-2d78-11e9-2867-c94bc002c0b7" +MLJXGBoostInterface = "54119dfa-1dab-4055-a167-80440f4f7a91" +OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[targets] +test = ["Aqua", "DynamicHMC", "EvoTrees", "FFTW", "LogDensityProblems", "LogExpFunctions", "MLJBase", "MLJDecisionTreeInterface", "MLJIteration", "MLJLIBSVMInterface", "MLJModels", "MLJXGBoostInterface", "OffsetArrays", "Test"] diff --git a/test/Project.toml b/test/Project.toml deleted file mode 100644 index aa96ce45..00000000 --- a/test/Project.toml +++ /dev/null @@ -1,40 +0,0 @@ -[deps] -Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" -Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" -DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" -EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5" -FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" -LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d" -MLJDecisionTreeInterface = "c6f25543-311c-4c74-83dc-3ea6d1015661" -MLJIteration = "614be32b-d00c-4edb-bd02-1eb411ab5e55" -MLJLIBSVMInterface = "61c7150f-6c77-4bb1-949c-13197eac2a52" -MLJModels = "d491faf4-2d78-11e9-2867-c94bc002c0b7" -MLJXGBoostInterface = "54119dfa-1dab-4055-a167-80440f4f7a91" -OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[compat] -Aqua = "0.8.1" -Distributions = "0.25.57" -DynamicHMC = "3.2" -EvoTrees = "0.14.7, 0.15, 0.16" -FFTW = "1.1" -LogDensityProblems = "0.12, 1, 2" -LogExpFunctions = "0.3.26" -MLJBase = "0.20, 0.21, 1" -MLJDecisionTreeInterface = "0.3, 0.4" -MLJIteration = "0.5, 0.6" -MLJLIBSVMInterface = "0.2" -MLJModels = "0.16" -MLJXGBoostInterface = "0.3.4" -OffsetArrays = "1.11" -Statistics = "1.6" -StatsBase = "0.33.3, 0.34" -Tables = "1.11" -julia = "1.6" From 6c8a63300f6d242001b2f40ba71e59c14da05462 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Feb 2024 00:27:08 +0100 Subject: [PATCH 09/11] Add compat entry for Test --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index 1b7fa99f..960dfd4a 100644 --- a/Project.toml +++ b/Project.toml @@ -43,6 +43,7 @@ Statistics = "1.6" StatsBase = "0.33.3, 0.34" StatsFuns = "1" Tables = "1.11" +Test = "1.6" julia = "1.6" [extras] From 3f7c7606fbf3229dc79b431b9d5430f6214f9967 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Feb 2024 09:47:23 +0100 Subject: [PATCH 10/11] Skip downgrading Test --- .github/workflows/CI.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 84feee19..db0058b6 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -45,7 +45,7 @@ jobs: - uses: julia-actions/cache@v1 - uses: cjdoris/julia-downgrade-compat-action@v1 with: - skip: LinearAlgebra,Markdown,Printf,Random,Statistics + skip: LinearAlgebra,Markdown,Printf,Random,Statistics,Test if: ${{ matrix.downgrade }} name: Downgrade dependencies to oldest supported versions - uses: julia-actions/julia-buildpkg@v1 From eef39d22c43be625c68a3b74acf2e0317b2638d3 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Feb 2024 10:21:42 +0100 Subject: [PATCH 11/11] Bump EvoTrees lower-bound to 0.15 This avoids an error that only manifests on ~0.14.7 when using a single thread --- Project.toml | 2 +- docs/Project.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index 960dfd4a..31dd2a08 100644 --- a/Project.toml +++ b/Project.toml @@ -24,7 +24,7 @@ DataAPI = "1.8" DataStructures = "0.18.3" Distributions = "0.25.57" DynamicHMC = "3.2" -EvoTrees = "0.14.7, 0.15, 0.16" +EvoTrees = "0.15, 0.16" FFTW = "1.1" LinearAlgebra = "1.6" LogDensityProblems = "0.12, 1, 2" diff --git a/docs/Project.toml b/docs/Project.toml index 1bb7e0b3..bf6ae5f0 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -9,7 +9,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [compat] Documenter = "1" -EvoTrees = "0.14.7, 0.15, 0.16" +EvoTrees = "0.15, 0.16" MLJBase = "0.20, 0.21, 1" MLJIteration = "0.5, 0.6" StatisticalMeasures = "0.1"