From 3b8ef66ada674802a0955a3ef5ae366258d78c4a Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 12:28:54 +0100 Subject: [PATCH 01/13] Fix lower bounds --- Project.toml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Project.toml b/Project.toml index fc6cf524..b87ba47a 100644 --- a/Project.toml +++ b/Project.toml @@ -36,27 +36,27 @@ PathfinderDynamicHMCExt = "DynamicHMC" PathfinderTuringExt = ["Accessors", "DynamicPPL", "MCMCChains", "Turing"] [compat] -Accessors = "0.1" +Accessors = "0.1.1" Distributions = "0.25" DynamicPPL = "0.21, 0.22, 0.23, 0.24" -Folds = "0.2" -ForwardDiff = "0.10" +Folds = "0.2.2" +ForwardDiff = "0.10.13" IrrationalConstants = "0.1.1, 0.2" LinearAlgebra = "1.6" -LogDensityProblems = "2" +LogDensityProblems = "2.1.0" MCMCChains = "5, 6" Optim = "1.4" -Optimization = "3" -OptimizationOptimJL = "0.1, 0.2" +Optimization = "3.5" +OptimizationOptimJL = "0.1.1, 0.2" PDMats = "0.11.26" PSIS = "0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9" ProgressLogging = "0.1.4" Random = "1.6" Requires = "1" -SciMLBase = "1.8.1, 2" +SciMLBase = "1.61.2, 2" Statistics = "1.6" StatsBase = "0.33, 0.34" -Transducers = "0.4.5" +Transducers = "0.4.55" Turing = "0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30" UnPack = "1" julia = "1.6" From 374508a3dabfbb5be8a6ebae3c6a2a513024ba31 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 12:29:14 +0100 Subject: [PATCH 02/13] Increment patch number --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index b87ba47a..400b26bb 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Pathfinder" uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" authors = ["Seth Axen and contributors"] -version = "0.8.2" +version = "0.8.3" [deps] Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" From 688b718879e3dfd4c937a9b9cef0f7169d9d5098 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 13:42:19 +0100 Subject: [PATCH 03/13] Refine lower bounds using integrations --- Project.toml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/Project.toml b/Project.toml index 400b26bb..d1e1a6bc 100644 --- a/Project.toml +++ b/Project.toml @@ -37,15 +37,16 @@ PathfinderTuringExt = ["Accessors", "DynamicPPL", "MCMCChains", "Turing"] [compat] Accessors = "0.1.1" -Distributions = "0.25" -DynamicPPL = "0.21, 0.22, 0.23, 0.24" +Distributions = "0.25.57" +DynamicHMC = "3.4.0" +DynamicPPL = "0.21.5, 0.22, 0.23, 0.24" Folds = "0.2.2" ForwardDiff = "0.10.13" IrrationalConstants = "0.1.1, 0.2" LinearAlgebra = "1.6" LogDensityProblems = "2.1.0" -MCMCChains = "5, 6" -Optim = "1.4" +MCMCChains = "5.1.0, 6" +Optim = "1.6.2" Optimization = "3.5" OptimizationOptimJL = "0.1.1, 0.2" PDMats = "0.11.26" @@ -55,9 +56,9 @@ Random = "1.6" Requires = "1" SciMLBase = "1.61.2, 2" Statistics = "1.6" -StatsBase = "0.33, 0.34" -Transducers = "0.4.55" -Turing = "0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30" +StatsBase = "0.33.1, 0.34" +Transducers = "0.4.66" +Turing = "0.24.2, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30" UnPack = "1" julia = "1.6" From 892b9c115449c47af7fdd7f579a7f5a565905844 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 13:42:44 +0100 Subject: [PATCH 04/13] Update lower bounds for integration tests --- test/integration/AdvancedHMC/Project.toml | 16 ++++++++-------- test/integration/DynamicHMC/Project.toml | 14 +++++++------- test/integration/Turing/Project.toml | 4 ++-- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/test/integration/AdvancedHMC/Project.toml b/test/integration/AdvancedHMC/Project.toml index 61a60925..0f3ffef4 100644 --- a/test/integration/AdvancedHMC/Project.toml +++ b/test/integration/AdvancedHMC/Project.toml @@ -17,15 +17,15 @@ TransformedLogDensities = "f9bc47f6-f3f8-4f3b-ab21-f8bc73906f26" [compat] AdvancedHMC = "0.4, 0.5, 0.6" -Distributions = "0.25" -ForwardDiff = "0.10" -LogDensityProblems = "1, 2" -LogDensityProblemsAD = "1" +Distributions = "0.25.57" +ForwardDiff = "0.10.13" +LogDensityProblems = "2.1.0" +LogDensityProblemsAD = "1.0.1, 2" MCMCDiagnosticTools = "0.3" -Optim = "1.4" -Pathfinder = "0.7, 0.8" +Optim = "1.6.2" +Pathfinder = "0.8" Statistics = "1" -StatsFuns = "0.9, 1" +StatsFuns = "1" TransformVariables = "0.6, 0.7, 0.8" -TransformedLogDensities = "1" +TransformedLogDensities = "1.0.2" julia = "1.6" diff --git a/test/integration/DynamicHMC/Project.toml b/test/integration/DynamicHMC/Project.toml index d270e4b1..4f332c77 100644 --- a/test/integration/DynamicHMC/Project.toml +++ b/test/integration/DynamicHMC/Project.toml @@ -14,14 +14,14 @@ TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff" TransformedLogDensities = "f9bc47f6-f3f8-4f3b-ab21-f8bc73906f26" [compat] -DynamicHMC = "3" -LogDensityProblems = "1, 2" -LogDensityProblemsAD = "1" +DynamicHMC = "3.4.0" +LogDensityProblems = "2.1.0" +LogDensityProblemsAD = "1.0.1" MCMCDiagnosticTools = "0.3" -Optim = "1.4" -Pathfinder = "0.7, 0.8" +Optim = "1.6.2" +Pathfinder = "0.8" Statistics = "1" -StatsFuns = "0.9, 1" +StatsFuns = "1" TransformVariables = "0.6, 0.7, 0.8" -TransformedLogDensities = "1" +TransformedLogDensities = "1.0.2" julia = "1.6" diff --git a/test/integration/Turing/Project.toml b/test/integration/Turing/Project.toml index b448a485..dbd99810 100644 --- a/test/integration/Turing/Project.toml +++ b/test/integration/Turing/Project.toml @@ -5,6 +5,6 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] -Pathfinder = "0.5, 0.6, 0.7, 0.8" -Turing = "0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30" +Pathfinder = "0.8" +Turing = "0.24.2, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30" julia = "1.6" From 463847cad4574ed1c0ff5421894facede6a2cfb0 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 13:52:26 +0100 Subject: [PATCH 05/13] Add downgrade step to CI --- .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 66bcb77c..9d77dab4 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -14,7 +14,7 @@ concurrency: cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }} jobs: test: - name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ matrix.num_threads }} threads - ${{ github.event_name }} + name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ matrix.num_threads }} threads - ${{ matrix.downgrade && 'downgrade- ' || '' }}${{ github.event_name }} runs-on: ${{ matrix.os }} strategy: fail-fast: false @@ -29,6 +29,14 @@ jobs: num_threads: - 1 - 2 + downgrade: + - false + include: + - version: '1' + os: ubuntu-latest + arch: x64 + num_threads: 2 + downgrade: true steps: - uses: actions/checkout@v2 - uses: julia-actions/setup-julia@v1 @@ -36,6 +44,11 @@ jobs: version: ${{ matrix.version }} arch: ${{ matrix.arch }} - uses: julia-actions/cache@v1 + - uses: cjdoris/julia-downgrade-compat-action@v1 + with: + skip: LinearAlgebra,Random,Statistics + if: ${{ matrix.downgrade }} + name: Downgrade dependencies to oldest supported versions - uses: julia-actions/julia-buildpkg@v1 - name: Fix Transducers to last-compatible version run: julia --project -e 'using Pkg; Pkg.pin(name="Transducers", version=v"0.4.75")' From b29c8e888a6b100703fafde81bfdc48a9cff5ec1 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 13:52:36 +0100 Subject: [PATCH 06/13] Remove pinning of Transducers compat --- .github/workflows/CI.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 9d77dab4..d536c5c4 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -50,8 +50,6 @@ jobs: if: ${{ matrix.downgrade }} name: Downgrade dependencies to oldest supported versions - uses: julia-actions/julia-buildpkg@v1 - - name: Fix Transducers to last-compatible version - run: julia --project -e 'using Pkg; Pkg.pin(name="Transducers", version=v"0.4.75")' - uses: julia-actions/julia-runtest@v1 env: JULIA_NUM_THREADS: ${{ matrix.num_threads }} From 1f41722774b3c08b506a2304be99c528159a49d8 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 14:05:49 +0100 Subject: [PATCH 07/13] Rename run --- .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 d536c5c4..4fe5f72f 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -14,7 +14,7 @@ concurrency: cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }} jobs: test: - name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ matrix.num_threads }} threads - ${{ matrix.downgrade && 'downgrade- ' || '' }}${{ github.event_name }} + name: ${{ matrix.downgrade && '/ Downgrade / ' || '' }}Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ matrix.num_threads }} threads - ${{ github.event_name }} runs-on: ${{ matrix.os }} strategy: fail-fast: false From 1dc06f5ba7a724943e4858ba0345fa32e270a3d2 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 14:06:18 +0100 Subject: [PATCH 08/13] Remove nightly tests from integration tests --- .github/workflows/IntegrationTests.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/IntegrationTests.yml b/.github/workflows/IntegrationTests.yml index a617b994..fd2d1aec 100644 --- a/.github/workflows/IntegrationTests.yml +++ b/.github/workflows/IntegrationTests.yml @@ -16,11 +16,6 @@ jobs: - DynamicHMC - AdvancedHMC - Turing - include: - - package: DynamicHMC - version: 'nightly' - - package: Turing - version: 'nightly' steps: - uses: actions/checkout@v2 - uses: julia-actions/setup-julia@v1 From e26b7ab88400910bfd3b4e18f551d09af1465841 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 14:08:36 +0100 Subject: [PATCH 09/13] Add downgrade integration tests --- .github/workflows/IntegrationTests.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/IntegrationTests.yml b/.github/workflows/IntegrationTests.yml index fd2d1aec..9f129512 100644 --- a/.github/workflows/IntegrationTests.yml +++ b/.github/workflows/IntegrationTests.yml @@ -6,7 +6,7 @@ on: pull_request: jobs: test: - name: ${{ matrix.package }} - Julia ${{ matrix.version }} + name: ${{ matrix.downgrade && '/ Downgrade / ' || '' }}${{ matrix.package }} - Julia ${{ matrix.version }} runs-on: ubuntu-latest strategy: fail-fast: false @@ -16,12 +16,20 @@ jobs: - DynamicHMC - AdvancedHMC - Turing + downgrade: + - true + - false steps: - uses: actions/checkout@v2 - uses: julia-actions/setup-julia@v1 with: version: ${{ matrix.version }} arch: x64 + - uses: cjdoris/julia-downgrade-compat-action@v1 + with: + skip: LinearAlgebra,Random,Statistics + if: ${{ matrix.downgrade }} + name: Downgrade dependencies to oldest supported versions - uses: julia-actions/julia-buildpkg@v1 - run: | julia --code-coverage=user -e ' From 755c5cb689961c8f651418250408f21d3f8ca272 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 16:25:39 +0100 Subject: [PATCH 10/13] Work around compilation issues on Requires v1.0.3 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index d1e1a6bc..f8d4d000 100644 --- a/Project.toml +++ b/Project.toml @@ -53,7 +53,7 @@ PDMats = "0.11.26" PSIS = "0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9" ProgressLogging = "0.1.4" Random = "1.6" -Requires = "1" +Requires = "1.1" SciMLBase = "1.61.2, 2" Statistics = "1.6" StatsBase = "0.33.1, 0.34" From 91cbdfee8501e0f3a7f08f3cd45633eb84b4cb1a Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 16:30:04 +0100 Subject: [PATCH 11/13] Remove redundant slash from job name --- .github/workflows/CI.yml | 2 +- .github/workflows/IntegrationTests.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 4fe5f72f..f1b05a22 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -14,7 +14,7 @@ concurrency: cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }} jobs: test: - name: ${{ matrix.downgrade && '/ Downgrade / ' || '' }}Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ matrix.num_threads }} threads - ${{ github.event_name }} + name: ${{ matrix.downgrade && 'Downgrade / ' || '' }}Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ matrix.num_threads }} threads - ${{ github.event_name }} runs-on: ${{ matrix.os }} strategy: fail-fast: false diff --git a/.github/workflows/IntegrationTests.yml b/.github/workflows/IntegrationTests.yml index 9f129512..5a0c7868 100644 --- a/.github/workflows/IntegrationTests.yml +++ b/.github/workflows/IntegrationTests.yml @@ -6,7 +6,7 @@ on: pull_request: jobs: test: - name: ${{ matrix.downgrade && '/ Downgrade / ' || '' }}${{ matrix.package }} - Julia ${{ matrix.version }} + name: ${{ matrix.downgrade && 'Downgrade / ' || '' }}${{ matrix.package }} - Julia ${{ matrix.version }} runs-on: ubuntu-latest strategy: fail-fast: false From fab61b9413069d64414b2ed423c12c9b6968e390 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 16:33:30 +0100 Subject: [PATCH 12/13] Make docs compat consistent with package --- docs/Project.toml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/Project.toml b/docs/Project.toml index 0314a3cb..32cadbd8 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -17,13 +17,13 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] AdvancedHMC = "0.4, 0.5, 0.6" Documenter = "1" -DynamicHMC = "3" -ForwardDiff = "0.10" -LogDensityProblems = "1, 2" -LogDensityProblemsAD = "1, 2" +DynamicHMC = "3.4.0" +ForwardDiff = "0.10.13" +LogDensityProblems = "2.1.0" +LogDensityProblemsAD = "1.0.1" Pathfinder = "0.8" -StatsFuns = "0.9, 1" +StatsFuns = "1" StatsPlots = "0.14, 0.15" TransformVariables = "0.6, 0.7, 0.8" -TransformedLogDensities = "1" -Turing = "0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30" +TransformedLogDensities = "1.0.2" +Turing = "0.24.2, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30" From bc57d5c616eb5b7669c4de13232d63560bdb273f Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Mon, 12 Feb 2024 16:55:27 +0100 Subject: [PATCH 13/13] Fix compats for lower bound docs build --- Project.toml | 2 +- docs/Project.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Project.toml b/Project.toml index f8d4d000..5dfada2f 100644 --- a/Project.toml +++ b/Project.toml @@ -45,7 +45,7 @@ ForwardDiff = "0.10.13" IrrationalConstants = "0.1.1, 0.2" LinearAlgebra = "1.6" LogDensityProblems = "2.1.0" -MCMCChains = "5.1.0, 6" +MCMCChains = "5.3.0, 6" Optim = "1.6.2" Optimization = "3.5" OptimizationOptimJL = "0.1.1, 0.2" diff --git a/docs/Project.toml b/docs/Project.toml index 32cadbd8..0b63c9c2 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -20,10 +20,10 @@ Documenter = "1" DynamicHMC = "3.4.0" ForwardDiff = "0.10.13" LogDensityProblems = "2.1.0" -LogDensityProblemsAD = "1.0.1" +LogDensityProblemsAD = "1.4" Pathfinder = "0.8" StatsFuns = "1" -StatsPlots = "0.14, 0.15" +StatsPlots = "0.14.21, 0.15" TransformVariables = "0.6, 0.7, 0.8" TransformedLogDensities = "1.0.2" Turing = "0.24.2, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30"