Merge main

Signed-off-by: Adam Li <[email protected]>
neurodata · Sep 11, 2023 · 7cfc220 · 7cfc220
2 parents 14c62b2 + 8770f55
commit 7cfc220
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,13 +1,6 @@
 # See: https://circleci.com/blog/deploying-documentation-to-github-pages-with-continuous-integration/
 version: 2.1
 
-# Aliases to reuse
-_defaults: &defaults
-  docker:
-    # CircleCI maintains a library of pre-built images
-    # documented at https://circleci.com/docs/2.0/circleci-images/
-    - image: cimg/python:3.9
-
 # document commands used by downstream jobs
 commands:
   check-skip:
@@ -70,7 +63,10 @@ commands:
 jobs:
   # Build scikit-tree from source
   build_scikit_tree:
-    <<: *defaults
+    docker:
+      # CircleCI maintains a library of pre-built images
+      # documented at https://circleci.com/doc/2.0/circleci-images/
+      - image: cimg/python:3.9
     steps:
       - checkout
       - check-skip
@@ -110,7 +106,10 @@ jobs:
             - .
 
   build_docs:
-    <<: *defaults
+    docker:
+      # CircleCI maintains a library of pre-built images
+      # documented at https://circleci.com/doc/2.0/circleci-images/
+      - image: cimg/python:3.9
     steps:
       - attach_workspace:
           at: ~/
@@ -131,15 +130,15 @@ jobs:
             python ./spin docs
 
       - store_artifacts:
-          path: docs/_build/html
+          path: doc/_build/html
           destination: dev
 
       - store_artifacts:
-          path: docs/_build/html_stable/
+          path: doc/_build/html_stable/
           destination: stable
 
       - persist_to_workspace:
-          root: docs/_build
+          root: doc/_build
           paths:
             - html
             - html_stable
@@ -151,7 +150,7 @@ jobs:
       - checkout
 
       - attach_workspace:
-          at: docs/_build
+          at: doc/_build
 
       - restore_cache:
           keys:
@@ -174,10 +173,10 @@ jobs:
           command: |
             if [ "${CIRCLE_BRANCH}" == "main" ]; then
               echo "Deploying dev docs for ${CIRCLE_BRANCH}.";
-              gh-pages --dotfiles --message "docs updates [skip ci] (${CIRCLE_BUILD_NUM})" --dist docs/_build/html --dest ./dev
+              gh-pages --dotfiles --message "docs updates [skip ci] (${CIRCLE_BUILD_NUM})" --dist doc/_build/html --dest ./dev
             else
               echo "Deploying stable docs for ${CIRCLE_BRANCH}.";
-              gh-pages --dotfiles --message "docs updates [skip ci] (${CIRCLE_BUILD_NUM})" --dist docs/_build/html --dest ./stable
+              gh-pages --dotfiles --message "docs updates [skip ci] (${CIRCLE_BUILD_NUM})" --dist doc/_build/html --dest ./stable
             fi;
 
       - save_cache:
@@ -186,16 +185,13 @@ jobs:
             - ~/sktree
 
 workflows:
-  default:
+  build-docs:
     jobs:
-      - build_scikit_tree:
-          name: build_scikit_tree
+      - build_scikit_tree
       - build_docs:
-          name: build_docs
           requires:
             - build_scikit_tree
       - docs-deploy:
-          name: docs-deploy
           requires:
             - build_docs
           filters:

diff --git a/.codespellignore b/.codespellignore
@@ -1,3 +1,4 @@
 raison
 nd
-parth
+parth
+ot
diff --git a/.flake8 b/.flake8
@@ -18,14 +18,16 @@ exclude =
     .pytest_cache
     .circleci
     paper
-    docs/_build
-    docs/generated
-    docs/auto_examples
+    doc/_build
+    doc/generated
+    doc/auto_examples
     validation
     build
     build-install 
     dist
     sktree/_lib/
+    .asv
+    env
 
 per-file-ignores =
     # __init__.py files are allowed to have unused imports

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -41,7 +41,7 @@ jobs:
 
     steps:
       - name: Checkout scikit-tree
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - uses: actions/[email protected]
         with:
@@ -60,7 +60,7 @@ jobs:
         if: ${{ runner.os == 'Windows' && env.IS_32_BIT == 'false' }}
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.14.0
+        uses: pypa/cibuildwheel@v2.15.0
         # Build all wheels here, apart from macosx_arm64, linux_aarch64
         # cibuildwheel is currently unable to pass configuration flags to
         # CIBW_BUILD_FRONTEND https://github.com/pypa/cibuildwheel/issues/1227
@@ -94,7 +94,7 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/[email protected]
@@ -109,7 +109,7 @@ jobs:
           python spin setup-submodule
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.14.0
+        uses: pypa/cibuildwheel@v2.15.0
         env:
           CIBW_BUILD: ${{ matrix.python[0] }}-macosx_arm64
           CIBW_ARCHS_MACOS: arm64
@@ -126,7 +126,7 @@ jobs:
 
     steps:
       - name: Checkout scikit-tree
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4

diff --git a/.github/workflows/circle_artifacts.yml b/.github/workflows/circle_artifacts.yml
@@ -1,25 +1,27 @@
 name: CircleCI artifacts redirector
 on: [status]
 
-permissions: read-all
-
+# Restrict the permissions granted to the use of secrets.GITHUB_TOKEN in this
+# github actions workflow:
+# https://docs.github.com/en/actions/security-guides/automatic-token-authentication
+permissions:
+  statuses: write
+
 jobs:
   circleci_artifacts_redirector_job:
-    runs-on: ubuntu-latest
-    if: "${{ github.event.context == 'ci/circleci: build_docs' }}"
-    permissions:
-      statuses: write
+    runs-on: ubuntu-20.04
+    if: "github.repository == 'neurodata/scikit-tree' && github.event.context == 'ci/circleci: build_docs'"
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step
-        id: step1
         uses: larsoner/circleci-artifacts-redirector-action@master
         with:
-          api-token: ${{ secrets.CIRCLECI_TOKEN }}
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+          api-token: ${{ secrets.CIRCLE_TOKEN }}
           artifact-path: 0/dev/index.html
           circleci-jobs: build_docs
           job-title: Check the rendered docs here!
+
       - name: Check the URL
         if: github.event.status != 'pending'
         run: |

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -32,7 +32,7 @@ jobs:
       matrix:
         os: [ubuntu-22.04, macos-latest]
         python-version: [3.9, "3.10", "3.11"]
-        poetry-version: [1.3.0]
+        poetry-version: [1.5.0]
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -42,7 +42,7 @@ jobs:
       FORCE_SUBMODULE: True
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/[email protected]
@@ -84,7 +84,7 @@ jobs:
 
       - name: Setup compiler cache
         uses: actions/cache@v3
-        id: cache-ccache
+        id: cache-ccachev1
         # Reference: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key
         # NOTE: The caching strategy is modeled in a way that it will always have a unique cache key for each workflow run
         # (even if the same workflow is run multiple times). The restore keys are not unique and for a partial match, they will
@@ -150,7 +150,7 @@ jobs:
     if: startsWith(github.ref, 'refs/tags/')
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/[email protected]
         with:
@@ -193,7 +193,7 @@ jobs:
     #   runs-on: windows-2019
     #   steps:
     #     - name: Checkout
-    #       uses: actions/checkout@v3
+    #       uses: actions/checkout@v4
     #       with:
     #         submodules: recursive
 

diff --git a/.github/workflows/pr_checks.yml b/.github/workflows/pr_checks.yml
@@ -22,7 +22,7 @@ jobs:
         run: |
           echo "PR_NUMBER=${{ github.event.pull_request.number }}" >> $GITHUB_ENV
           echo "TAGGED_MILESTONE=${{ github.event.pull_request.milestone.title }}" >> $GITHUB_ENV
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: "0"
       - name: Check that CHANGELOG has been updated
@@ -37,14 +37,14 @@ jobs:
           then
             exit 0
           fi
-          all_changelogs=$(cat ./docs/whats_new/v*.rst)
+          all_changelogs=$(cat ./doc/whats_new/v*.rst)
           if [[ "$all_changelogs" =~ :pr:\`$PR_NUMBER\` ]]
           then
             echo "Changelog has been updated."
             # If the pull request is milestoned check the correspondent changelog
-            if exist -f ./docs/whats_new/v${TAGGED_MILESTONE:0:4}.rst
+            if exist -f ./doc/whats_new/v${TAGGED_MILESTONE:0:4}.rst
             then
-              expected_changelog=$(cat ./docs/whats_new/v${TAGGED_MILESTONE:0:4}.rst)
+              expected_changelog=$(cat ./doc/whats_new/v${TAGGED_MILESTONE:0:4}.rst)
               if [[ "$expected_changelog" =~ :pr:\`$PR_NUMBER\` ]]
               then
                 echo "Changelog and milestone correspond."
@@ -58,8 +58,8 @@ jobs:
           else
             echo "A Changelog entry is missing."
             echo ""
-            echo "Please add an entry to the changelog at 'docs/whats_new/v*.rst'"
-            echo "to docsument your change assuming that the PR will be merged"
+            echo "Please add an entry to the changelog at 'doc/whats_new/v*.rst'"
+            echo "to document your change assuming that the PR will be merged"
             echo "in time for the next release of scikit-tree."
             echo ""
             echo "Look at other entries in that file for inspiration and please"

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
@@ -31,7 +31,7 @@ jobs:
         poetry-version: [1.3.0]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Python 3.10
         uses: actions/[email protected]
         with:

diff --git a/.gitignore b/.gitignore
@@ -14,20 +14,26 @@ sktree/_lib/sklearn/
 *.png
 
 # Sphinx documentation
-docs/_build/
-docs/generated/
-docs/auto_examples/
-docs/auto_tutorials/
-docs/modules/generated/
-docs/sphinxext/cachedir
+doc/_build/
+doc/generated/
+doc/auto_examples/
+doc/auto_tutorials/
+doc/modules/generated/
+doc/sphinxext/cachedir
 pip-log.txt
 .coverage
 tags
-docs/coverages
-docs/samples
+doc/coverages
+doc/samples
 cover
 examples/*.jpg
 
+env/
+html/
+results/
+scikit-learn/
+benchmarks/cache/
+
 # Pycharm
 .idea/
 

diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,4 @@
 [submodule "sktree/_lib/sklearn"]
 	path = sktree/_lib/sklearn_fork
 	url = https://github.com/neurodata/scikit-learn
-	branch = v1.3
+	branch = submodulev3