Merge pull request #40 from Billyzhang1229/fix/CI

Fix CI and update dependencies

.gitattributes

@@ -0,0 +1 @@
+*.ipynb linguist-vendored

.github/workflows/tests.yml

@@ -8,37 +8,37 @@ on:
 jobs:
   pre-commit:
     name: Lint
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-      - uses: pre-commit/[email protected].0
+      - uses: pre-commit/[email protected].1
 
   test:
     name: Python
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python: [ 3.7, 3.9, "3.10" ]
+        python: [ 3.9, "3.10", "3.11" ]
         os:  [ macos-latest, ubuntu-latest] # disable windows for now, windows-latest ]
     defaults:
       run:
         shell: bash
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.10.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Setup Python and cache deps
         uses: actions/setup-python@v4
@@ -60,17 +60,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.10.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Setup Python and cache deps
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
           cache: 'pip'
           cache-dependency-path: requirements/CI.txt
 

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
@@ -12,27 +12,27 @@ repos:
     hooks:
     -   id: copyright-year
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.1.0
+    rev: v3.12.0
     hooks:
       - id: reorder-python-imports
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.34.0
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py37-plus]
   - repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 24.3.0
     hooks:
       - id: black
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
     hooks:
       - id: flake8
-        additional_dependencies: ["flake8-bugbear==22.6.22", "flake8-builtins==1.5.3"]
+        additional_dependencies: ["flake8-bugbear==24.2.6", "flake8-builtins==2.2.0"]
   - repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.1
+    rev: 1.16.0
     hooks:
       - id: blacken-docs
         args: [--skip-errors]
-        additional_dependencies: [black==22.3.0]
+        additional_dependencies: [black==24.3.0]
         language_version: python3

requirements/CI.txt

@@ -1,10 +1,10 @@
 coverage==6.4.1
 coveralls==3.3.1
-numba==0.55.2
+numba==0.59.1
 pytest==7.1.2
 pytest-xdist==2.5.0
-tskit==0.5.0
-msprime==1.2.0
-sgkit==0.5.0
+tskit==0.5.6
+msprime==1.3.1
+sgkit==0.7.0
 dendropy==4.5.2
 importlib-metadata==4.13.0