Update compatibility bounds, fixed tolerances and issues in quadratic regularization (#194)

* update compat bounds

* update buildkite julia ver

* rollback

* fix approx tol

* action update

* action all update

* various bounds

* atol

* remove

* Apply suggestions from code review

* More updates

* Use conda installation on buildkite

* Remove Manifest.toml files

* Update .gitignore

* Update examples/nmf/Project.toml

* Run CI on macOS

* Use `sources` in Project.toml

* atol on gpu test

* Remove `strict` kwarg from `makedocs`

* Add julia cache to docs CI

* fix f32

* Update test/gpu/simple_gpu.jl

Co-authored-by: David Widmann <[email protected]>

* Fix (?) convergence criterion

* Fix (?) sign error

* A few more changes

* More fixes

* Revert a few changes

* Don't use `mul!`

* Update simple_gpu.jl

* Update regularization parameter in the test

* Update src/quadratic_newton.jl

* Try to revert GPU tests

* Fix format action

* Fix and improve tests

* formatting

* typo

* Fix format

* Set permissions for GH actions

---------

Co-authored-by: syz <[email protected]>
Co-authored-by: David Widmann <[email protected]>

Author: 3 people

.buildkite/pipeline.yml

@@ -14,3 +14,4 @@ steps:
 
 env:
   GROUP: GPU
+  PYTHON: ""

.github/workflows/CI.yml

@@ -12,59 +12,53 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+  actions: write
+  contents: read
+
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ matrix.version == 'nightly' }}
+    continue-on-error: ${{ matrix.version == 'pre' }}
     strategy:
       matrix:
         version:
-          - '1.6'
+          - 'min'
+          - 'lts'
           - '1'
-          - 'nightly'
+          - 'pre'
         os:
           - ubuntu-latest
+          - macOS-latest
           - windows-latest
-        arch:
-          - x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Install python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
-          architecture: ${{ matrix.arch }}
+          python-version: '3.13'
       - run: python -m pip install pot
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
         with:
           coverage: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }}
         env:
           PYTHON: python
           GROUP: OptimalTransport
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.version == '1' && matrix.os == 'ubuntu-latest'
-      - uses: codecov/codecov-action@v2
+      - uses: codecov/codecov-action@v5
         if: matrix.version == '1' && matrix.os == 'ubuntu-latest'
         with:
-          file: lcov.info
-      - uses: coverallsapp/github-action@master
+          files: lcov.info
+      - uses: coverallsapp/github-action@v2
         if: matrix.version == '1' && matrix.os == 'ubuntu-latest'
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: lcov.info
+          file: lcov.info

.github/workflows/CompatHelper.yml

@@ -7,7 +7,7 @@ jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2 # to determine subdirectories of examples
+      - uses: actions/checkout@v4 # to determine subdirectories of examples
       - name: "Add the General registry via Git"
         run: |
           import Pkg

.github/workflows/DocsPreviewCleanup.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

.github/workflows/Documentation.yml

@@ -13,20 +13,32 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 
+permissions:
+  actions: write
+  contents: read
+
 jobs:
   build:
+    # These permissions are needed to:
+    # - Deploy the documentation: https://documenter.juliadocs.org/stable/man/hosting/#Permissions
+    # - Delete old caches: https://github.com/julia-actions/cache#usage
+    permissions:
+      actions: write
+      contents: write
+      pull-requests: read
+      statuses: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Install python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
-          architecture: ${{ matrix.arch }}
+          python-version: '3.13'
       - run: python -m pip install pot
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
+      - uses: julia-actions/cache@v2
       - name: Install dependencies
         run: |
           using Pkg: Pkg

.github/workflows/Format.yml

@@ -7,8 +7,8 @@ jobs:
   format:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: 1
       - name: Format code
@@ -21,4 +21,4 @@ jobs:
       - uses: reviewdog/action-suggester@v1
         with:
           tool_name: JuliaFormatter
-          fail_on_error: true
+          fail_level: error

.gitignore

@@ -26,9 +26,7 @@ docs/src/examples/
 # It records a fixed state of all packages used by the project. As such, it should not be
 # committed for packages, but should be committed for applications that require a static
 # environment.
-/Manifest.toml
-/test/Manifest.toml
-/test/gpu/Manifest.toml
+Manifest.toml
 
 # Files generated by Jupyter Notebooks
 *.ipynb_checkpoints
@@ -38,3 +36,6 @@ docs/src/examples/
 *~undo-tree~*
 \#*\#
 .\#*
+
+# VS Code settings
+.vscode/*

Project.toml

@@ -1,7 +1,7 @@
 name = "OptimalTransport"
 uuid = "7e02d93a-ae51-4f58-b602-d97af76e3b33"
 authors = ["zsteve <[email protected]>"]
-version = "0.3.20"
+version = "0.3.21"
 
 [deps]
 ExactOptimalTransport = "24df6009-d856-477c-ac5c-91f668376b31"
@@ -12,12 +12,14 @@ NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 
 [compat]
-ExactOptimalTransport = "0.1, 0.2"
-IterativeSolvers = "0.8.4, 0.9"
-LogExpFunctions = "0.2, 0.3"
-NNlib = "0.6, 0.7, 0.8"
+Distances = "0.10"
+ExactOptimalTransport = "0.2"
+IterativeSolvers = "0.9"
+LogExpFunctions = "0.3"
+NNlib = "0.9"
+PythonOT = "0.1"
 Reexport = "1"
-julia = "1"
+julia = "1.10"
 
 [extras]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"