Merge branch 'main' into ignore_leaf

.circleci/config.yml

@@ -8,7 +8,7 @@ commands:
       - run:
           name: Check-skip
           command: |
-            if [ ! -d "sktree" ]; then
+            if [ ! -d "treeple" ]; then
               echo "Build was not run due to skip, exiting job ${CIRCLE_JOB} for PR ${CIRCLE_PULL_REQUEST}."
               circleci-agent step halt;
             fi
@@ -55,13 +55,13 @@ commands:
             echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
             if [[ $(cat merge.txt) != "" ]]; then
               echo "Merging $(cat merge.txt)";
-              git remote add upstream https://github.com/neurodata/scikit-tree.git;
+              git remote add upstream https://github.com/neurodata/treeple.git;
               git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
               git fetch upstream main;
             fi
 
 jobs:
-  # Build scikit-tree from source
+  # Build treeple from source
   build_scikit_tree:
     docker:
       # CircleCI maintains a library of pre-built images
@@ -86,7 +86,7 @@ jobs:
             pip install .[build,doc]
 
       - run:
-          name: build scikit-tree
+          name: build treeple
           command: |
             spin build -j2
 
@@ -162,7 +162,7 @@ jobs:
           name: Install and configure dependencies
           command: |
             npm install --global [email protected]
-            git config --global user.email "circle@scikit-tree.com"
+            git config --global user.email "circle@treeple.com"
             git config --global user.name "Circle Ci"
 
       - add_ssh_keys:
@@ -184,7 +184,7 @@ jobs:
       - save_cache:
           key: website-cache
           paths:
-            - ~/sktree
+            - ~/treeple
 
 workflows:
   build-docs:

.flake8

@@ -25,7 +25,7 @@ exclude =
     build
     build-install 
     dist
-    sktree/_lib/
+    treeple/_lib/
     .asv
     env
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -23,7 +23,7 @@ Please be aware that we are a loose team of volunteers so patience is
 necessary; assistance handling other issues is very welcome. We value
 all user contributions, no matter how minor they are.
 
-See https://github.com/neurodata/scikit-tree/blob/main/CONTRIBUTING.md for more
+See https://github.com/neurodata/treeple/blob/main/CONTRIBUTING.md for more
 information on contributing.
 
 Thanks for contributing!

.github/label-globs.yml

@@ -1,15 +1,15 @@
 Cython:
-  - sktree/**/*.pyx.*
-  - sktree/**/*.pxd.*
-  - sktree/**/*.pxi.*
+  - treeple/**/*.pyx.*
+  - treeple/**/*.pxd.*
+  - treeple/**/*.pxi.*
 
 C/C++:
-  - sktree/**/*.c
-  - sktree/**/*.c.in
-  - sktree/**/*.c.old
-  - sktree/**/*.h
-  - sktree/**/*.h.in
-  - sktree/**/*.cpp
-  - sktree/**/*.cc
-  - sktree/**/*.cxx
-  - sktree/**/*.hpp
+  - treeple/**/*.c
+  - treeple/**/*.c.in
+  - treeple/**/*.c.old
+  - treeple/**/*.h
+  - treeple/**/*.h.in
+  - treeple/**/*.cpp
+  - treeple/**/*.cc
+  - treeple/**/*.cxx
+  - treeple/**/*.hpp

.github/workflows/build_wheels.yml

@@ -46,7 +46,7 @@ jobs:
       IS_32_BIT: ${{ matrix.os[2] == 'x86' }}
 
     steps:
-      - name: Checkout scikit-tree
+      - name: Checkout treeple
         uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
@@ -65,7 +65,7 @@ jobs:
         if: ${{ runner.os == 'Windows' && env.IS_32_BIT == 'false' }}
 
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].2
         # 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
@@ -120,7 +120,7 @@ jobs:
           pip install .[build]
 
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].2
         env:
           CIBW_BUILD: ${{ matrix.python[0] }}-macosx_arm64
           CIBW_ARCHS_MACOS: arm64
@@ -136,7 +136,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout scikit-tree
+      - name: Checkout treeple
         uses: actions/checkout@v4
 
       - name: Setup Python

.github/workflows/circle_artifacts.yml

@@ -9,7 +9,7 @@ permissions: read-all
 jobs:
   circleci_artifacts_redirector_job:
     runs-on: ubuntu-20.04
-    if: "github.repository == 'neurodata/scikit-tree' && github.event.context == 'ci/circleci: build_docs'"
+    if: "github.repository == 'neurodata/treeple' && github.event.context == 'ci/circleci: build_docs'"
     permissions:
       statuses: write
     name: Run CircleCI artifacts redirector

.github/workflows/main.yml

@@ -109,7 +109,7 @@ jobs:
           restore-keys: |
             ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-
 
-      - name: Setup build and install scikit-tree
+      - name: Setup build and install treeple
         run: |
           ./spin build -j 2 --forcesubmodule
           ./spin install
@@ -125,7 +125,7 @@ jobs:
 
       - name: Run unit tests and coverage
         run: |
-          pytest ./sktree
+          pytest ./treeple
 
       - name: debug
         run: |
@@ -137,7 +137,7 @@ jobs:
       - name: Save build
         uses: actions/upload-artifact@v4
         with:
-          name: sktree-build
+          name: treeple-build
           path: $PWD/build
 
   build_and_test_slow:
@@ -210,7 +210,7 @@ jobs:
           restore-keys: |
             ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-
 
-      - name: Setup build and install scikit-tree
+      - name: Setup build and install treeple
         run: |
           ./spin build -j4 --forcesubmodule
           ./spin install
@@ -245,7 +245,7 @@ jobs:
       - name: Save build
         uses: actions/upload-artifact@v4
         with:
-          name: sktree-build
+          name: treeple-build
           path: $PWD/build
 
   build-windows:
@@ -290,9 +290,9 @@ jobs:
           # Necessary because GitHub Actions checks out the repo to D:\ while OpenBLAS
           # got installed to C:\ higher up. The copying with `--win-cp-openblas` fails
           # when things are split over drives.
-          # cp C:\opt\64\bin\*.dll $pwd\build-install\Lib\site-packages\scikit-tree\.libs\
-          # python tools\openblas_support.py --write-init $PWD\build-install\Lib\site-packages\scikit-tree\
+          # cp C:\opt\64\bin\*.dll $pwd\build-install\Lib\site-packages\treeple\.libs\
+          # python tools\openblas_support.py --write-init $PWD\build-install\Lib\site-packages\treeple\
 
       - name: test
         run: |
-          pytest ./sktree
+          pytest ./treeple

.github/workflows/pr_checks.yml

@@ -9,7 +9,7 @@ on:
     branches:
       - main
     paths:
-      - "sktree/**"
+      - "treeple/**"
 
 jobs:
   changelog:
@@ -60,7 +60,7 @@ jobs:
             echo ""
             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 "in time for the next release of treeple."
             echo ""
             echo "Look at other entries in that file for inspiration and please"
             echo "reference this pull request using the ':pr:' directive and"

.github/workflows/pull_request_labeler.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: thomasjpfan/[email protected]
         continue-on-error: true
-        if: github.repository == 'neurodata/scikit-tree'
+        if: github.repository == 'neurodata/treeple'
         with:
           repo-token: "${{ secrets.GITHUB_TOKEN }}"
           configuration-path: ".github/label-globs.yml"

.gitignore

@@ -11,7 +11,7 @@ coverage
 .coverage.*
 
 commit.txt
-sktree/_lib/sklearn/
+treeple/_lib/sklearn/
 
 *.png
 _data

.gitmodules

@@ -1,4 +1,4 @@
-[submodule "sktree/_lib/sklearn"]
-	path = sktree/_lib/sklearn_fork
+[submodule "treeple/_lib/sklearn"]
+	path = treeple/_lib/sklearn_fork
 	url = https://github.com/neurodata/scikit-learn
 	branch = submodulev3

.pre-commit-config.yaml

@@ -20,18 +20,18 @@ repos:
       - id: cython-lint
       - id: double-quote-cython-strings
 
-  # Ruff sktree
+  # Ruff treeple
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.10
+    rev: v0.5.1
     hooks:
       - id: ruff
-        name: ruff sktree
+        name: ruff treeple
         args: ["--fix"]
-        files: ^sktree/
+        files: ^treeple/
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.10
+    rev: v0.5.1
     hooks:
       - id: ruff
         name: ruff tutorials and examples
@@ -47,7 +47,7 @@ repos:
       - id: codespell
         additional_dependencies:
           - tomli
-        files: ^sktree/|^doc/|^examples/|^tutorials/
+        files: ^treeple/|^doc/|^examples/|^tutorials/
         types_or: [python, bib, rst, inc]
 
   # yamllint
@@ -67,7 +67,7 @@ repos:
 
   # mypy
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.10.1
     hooks:
       - id: mypy
         # Avoid the conflict between mne/__init__.py and mne/__init__.pyi by ignoring the former
@@ -76,7 +76,7 @@ repos:
 
   # rstcheck
   - repo: https://github.com/rstcheck/rstcheck.git
-    rev: v6.2.0
+    rev: v6.2.4
     hooks:
       - id: rstcheck
         additional_dependencies:

.spin/cmds.py

@@ -20,8 +20,8 @@ def coverage(ctx, slowtest=True):
         pytest_args = (
             "-o",
             "python_functions=test_*",
-            "sktree",
-            "--cov=sktree",
+            "treeple",
+            "--cov=treeple",
             "--cov-report=xml",
             "--cov-config=pyproject.toml",
             "-k .",
@@ -30,8 +30,8 @@ def coverage(ctx, slowtest=True):
         pytest_args = (
             "-o",
             "python_functions=test_*",
-            "sktree",
-            "--cov=sktree",
+            "treeple",
+            "--cov=treeple",
             "--cov-report=xml",
             "--cov-config=pyproject.toml",
         )
@@ -46,9 +46,9 @@ def coverage(ctx, slowtest=True):
 @click.command()
 @click.option("--forcesubmodule", is_flag=False, help="Force submodule pull.")
 def setup_submodule(forcesubmodule=False):
-    """Build scikit-tree using submodules.
+    """Build treeple using submodules.
 
-    git submodule set-branch -b submodulev3 sktree/_lib/sklearn
+    git submodule set-branch -b submodulev3 treeple/_lib/sklearn
 
     git submodule update --recursive --remote
 
@@ -61,13 +61,13 @@ def setup_submodule(forcesubmodule=False):
     This will update the submodule, which then must be commited so that
     git knows the submodule needs to be at a certain commit hash.
     """
-    commit_fpath = "./sktree/_lib/commit.txt"
-    submodule = "./sktree/_lib/sklearn_fork"
+    commit_fpath = "./treeple/_lib/commit.txt"
+    submodule = "./treeple/_lib/sklearn_fork"
     commit = ""
     current_hash = ""
 
     # if the forked folder does not exist, we will need to force update the submodule
-    if not os.path.exists("./sktree/_lib/sklearn/") or forcesubmodule:
+    if not os.path.exists("./treeple/_lib/sklearn/") or forcesubmodule:
         # update git submodule
         util.run(["git", "submodule", "update", "--init", "--force"])
     else:
@@ -100,7 +100,7 @@ def setup_submodule(forcesubmodule=False):
             [
                 "mkdir",
                 "-p",
-                "./sktree/_lib/sklearn/",
+                "./treeple/_lib/sklearn/",
             ],
         )
         util.run(
@@ -117,17 +117,17 @@ def setup_submodule(forcesubmodule=False):
             [
                 "rm",
                 "-rf",
-                "sktree/_lib/sklearn",
+                "treeple/_lib/sklearn",
             ]
         )
 
-        if os.path.exists("sktree/_lib/sklearn_fork/sklearn") and (commit != current_hash):
+        if os.path.exists("treeple/_lib/sklearn_fork/sklearn") and (commit != current_hash):
             util.run(
                 [
                     "cp",
                     "-r",
-                    "sktree/_lib/sklearn_fork/sklearn",
-                    "sktree/_lib/sklearn",
+                    "treeple/_lib/sklearn_fork/sklearn",
+                    "treeple/_lib/sklearn",
                 ]
             )
 
@@ -155,7 +155,7 @@ def build(
     gcov=False,
     forcesubmodule=False,
 ):
-    """Build scikit-tree using submodules.
+    """Build treeple using submodules.
 
         git submodule update --recursive --remote
 
@@ -195,7 +195,7 @@ def asv(asv_args):
     """
     site_path = meson._get_site_packages()
     if site_path is None:
-        print("No built scikit-tree found; run `spin build` first.")
+        print("No built treeple found; run `spin build` first.")
         sys.exit(1)
 
     os.environ["ASV_ENV_DIR"] = "/Users/adam2392/miniforge3"