Merge branch 'landlab:master' into riverTemperatureDynamics_dev

.github/dependabot.yml

@@ -12,7 +12,7 @@ updates:
     labels: ["skip news", "dependencies"]
 
   - package-ecosystem: "pip"
-    directory: "."
+    directory: "/requirements"
     schedule:
       interval: "daily"
     target-branch: "dependencies"

.github/workflows/changelog.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # `towncrier check` runs `git diff --name-only origin/main...`, which
           # needs a non-shallow clone.

.github/workflows/docs.yml

@@ -19,7 +19,7 @@ jobs:
             shell: bash -l {0}
 
         steps:
-          - uses: actions/checkout@v3
+          - uses: actions/checkout@v4
           - name: Set up Python 3.11
             uses: actions/setup-python@v4
             with:

.github/workflows/lint.yml

@@ -15,7 +15,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:

.github/workflows/prerelease.yml

@@ -71,7 +71,7 @@ jobs:
             os: "windows-latest"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Use Python 3.10
         uses: actions/setup-python@v4
@@ -80,7 +80,7 @@ jobs:
 
       - name: Set up QEMU  # Needed to build aarch64 wheels
         if: runner.os == 'Linux'
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
         with:
           platforms: all
 
@@ -90,7 +90,7 @@ jobs:
           python -m cibuildwheel --only ${{ matrix.cibw-only }} --print-build-identifiers
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.15.0
+        uses: pypa/cibuildwheel@v2.16.2
         with:
           only: ${{ matrix.cibw-only }}
 
@@ -103,7 +103,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build sdist
         run: pipx run build --sdist

.github/workflows/rebase_dependencies.yml

@@ -8,7 +8,7 @@ jobs:
     name: Rebase `dependencies` with `master`
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
           ref: dependencies

.github/workflows/release.yml

@@ -72,7 +72,7 @@ jobs:
             os: "windows-latest"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Use Python 3.10
         uses: actions/setup-python@v4
@@ -81,7 +81,7 @@ jobs:
 
       - name: Set up QEMU  # Needed to build aarch64 wheels
         if: runner.os == 'Linux'
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
         with:
           platforms: all
 
@@ -91,7 +91,7 @@ jobs:
           python -m cibuildwheel --only ${{ matrix.cibw-only }} --print-build-identifiers
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.15.0
+        uses: pypa/cibuildwheel@v2.16.2
         with:
           only: ${{ matrix.cibw-only }}
 
@@ -104,7 +104,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build sdist
         run: pipx run build --sdist

.github/workflows/test-notebooks.yml

@@ -25,7 +25,7 @@ jobs:
         markers: ["slow", "not slow"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: mamba-org/setup-micromamba@v1
         with:

.github/workflows/test.yml

@@ -35,7 +35,7 @@ jobs:
         pytest-marker: ["slow", "not slow"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: mamba-org/setup-micromamba@v1
         with:

.pre-commit-config.yaml

@@ -61,7 +61,11 @@ repos:
   rev: 5.12.0
   hooks:
   - id: isort
-    files: \.py$
+    name: isort (python)
+    types: [python]
+  - id: isort
+    name: isort (cython)
+    types: [cython]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0

.readthedocs.yaml

@@ -12,7 +12,6 @@ sphinx:
 
 python:
   install:
-    - requirements: docs/requirements.in
+    - requirements: docs/requirements.txt
     - method: pip
       path: .
-  system_packages: false

MANIFEST.in

@@ -13,6 +13,7 @@ recursive-include docs *.txt
 recursive-include landlab *.pyx *.pxd *.hpp
 recursive-include landlab README.md
 recursive-include landlab/data *
+recursive-include requirements *.md *.txt
 recursive-include tests *py
 recursive-include tests *.asc
 recursive-include tests *.dbf

README.rst

@@ -20,7 +20,7 @@
     :target: https://coveralls.io/r/landlab/landlab
 
 .. image:: https://mybinder.org/badge_logo.svg
- :target: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/welcome.ipynb
+ :target: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/welcome.ipynb
 
 =======
 Landlab
@@ -107,11 +107,11 @@ Run on Binder
 To launch an instance of
 Binder and `explore the notebooks click here`_.
 
-.. _explore the notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/welcome.ipynb
+.. _explore the notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/welcome.ipynb
 
 To launch a Binder instance that goes straight to the `teaching notebooks click here`_.
 
-.. _teaching notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/teaching/welcome_teaching.ipynb
+.. _teaching notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/teaching/welcome_teaching.ipynb
 
 Run on EarthscapeHub
 ````````````````````