Update linters and remove lint

.github/workflows/changelog.yml

@@ -0,0 +1,25 @@
+name: Check
+
+on:
+  pull_request:
+    types: [labeled, unlabeled, opened, reopened, synchronize]
+
+jobs:
+  check-changelog-entry:
+    name: changelog entry
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          # `towncrier check` runs `git diff --name-only origin/main...`, which
+          # needs a non-shallow clone.
+          fetch-depth: 0
+
+      - name: Check changelog
+        if: "!contains(github.event.pull_request.labels.*.name, 'Skip Changelog')"
+        run: |
+          if ! pipx run towncrier check --compare-with origin/${{ github.base_ref }}; then
+          echo "Please see https://landlab.readthedocs.io/en/master/development/contribution/index.html?highlight=towncrier#news-entries for guidance."
+            false
+          fi

.github/workflows/docs.yml

@@ -26,9 +26,9 @@ jobs:
         if:
           github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
           github.repository
-    
+
         runs-on: ubuntu-latest
-        
+
         defaults:
           run:
             shell: bash -l {0}
@@ -44,11 +44,10 @@ jobs:
 
           - name: Show conda installation info
             run: conda info
-    
+
           - name: Install dependencies
             run: |
-              conda install --file=requirements.txt
-              pip install -e ".[doc]"
+              pip install nox
 
           - name: Build documentation
-            run: make -C docs clean html            
+            run: nox -s build-docs

.github/workflows/flake8.yml → .github/workflows/lint.yml

@@ -1,10 +1,11 @@
-name: Flake8
+name: Lint
 
 on: [push, pull_request]
 
 jobs:
 
   lint:
+    name: Check for lint
     # We want to run on external PRs, but not on our own internal PRs as they'll be run
     # by the push to the branch. Without this if check, checks are duplicated since
     # internal PRs match both the push and pull_request events.
@@ -22,5 +23,5 @@ jobs:
 
       - name: Lint
         run: |
-          pip install flake8
-          flake8 sequence tests
+          pip install nox
+          nox -s lint

.github/workflows/notebooks.yml

@@ -11,9 +11,9 @@ jobs:
         if:
           github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
           github.repository
-    
+
         runs-on: ubuntu-latest
-        
+
         defaults:
           run:
             shell: bash -l {0}
@@ -29,10 +29,9 @@ jobs:
 
           - name: Show conda installation info
             run: conda info
-    
+
           - name: Install dependencies
-            run: |
-              pip install -e ".[notebook,dev]"
+            run: pip install nox
 
-          - name: Test notebooks
-            run: pytest --nbmake notebooks/*ipynb            
+          - name: Build documentation
+            run: nox -s test-notebooks

.github/workflows/prerelease.yml

@@ -28,19 +28,19 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: "3.9"
-      
+
       - name: Install twine
         run: |
           pip install --upgrade pip wheel setuptools
           pip install twine
           python --version
           pip --version
           twine --version
-        
+
       - name: Create source distribution
         run: |
           python setup.py sdist --dist-dir wheelhouse
-        
+
       - name: Upload source distribution
         run: |
           twine upload --skip-existing wheelhouse/*.tar.gz

.github/workflows/release.yml

@@ -28,19 +28,19 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: "3.9"
-      
+
       - name: Install twine
         run: |
           pip install --upgrade pip wheel setuptools
           pip install twine
           python --version
           pip --version
           twine --version
-        
+
       - name: Create source distribution
         run: |
           python setup.py sdist --dist-dir wheelhouse
-        
+
       - name: Upload source distribution
         run: |
           twine upload --skip-existing wheelhouse/*.tar.gz

.github/workflows/test.yml

@@ -35,26 +35,11 @@ jobs:
       - name: Show conda installation info
         run: conda info
 
-      - name: Build and install package
-        run: |
-          conda install rasterio richdem -c conda-forge
-          pip install .
-
-      - name: Install testing dependencies
-        run: pip install ".[dev]"
-
-      - name: Test package
-        run: |
-          python -c 'import sequence; print(sequence.__version__)'
-          pytest --cov=sequence --cov-report= --cov-report=xml -vvv
-
-      - name: Test command line
-        run: |
-          sequence --version
-          mkdir example
-          sequence --cd=example setup --set clock.stop=60000
-          sequence --cd=example --silent run
-          sequence --cd=data/marmara --silent run
+      - name: Install dependencies
+        run: pip install nox
+
+      - name: Build documentation
+        run: nox -s test
 
       - name: Coveralls
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'

.pre-commit-config.yaml

@@ -21,11 +21,13 @@ repos:
     require_serial: true
     types_or: [python, pyi, jupyter]
     additional_dependencies: [".[jupyter]"]
+
 - repo: https://gitlab.com/pycqa/flake8
   rev: 3.9.2
   hooks:
   - id: flake8
     # additional_dependencies: [flake8-bugbear]
+
 - repo: https://gitlab.com/iamlikeme/nbhooks
   rev: 1.0.0
   hooks:
@@ -35,9 +37,38 @@ repos:
     entry: nb-ensure-clean
     files: \.ipynb$
     language: python
-    language_version: python3
+    language_version: python3.8
+
 - repo: https://github.com/asottile/pyupgrade
   rev: v2.34.0
   hooks:
   -   id: pyupgrade
       args: [--py38-plus]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+    - id: isort
+      files: \.py$
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.3.0
+  hooks:
+    - id: check-builtin-literals
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-toml
+    - id: check-yaml
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: forbid-new-submodules
+    - id: trailing-whitespace
+
+# - repo: https://github.com/PyCQA/pydocstyle
+#   rev: 6.1.1
+#   hooks:
+#     - id: pydocstyle
+#       files: sequence/.*\.py$
+#       args:
+#         - --convention=numpy
+#         - --add-select=D417

CHANGES.rst

@@ -172,7 +172,7 @@ Other Changes and Additions
 
 
 0.1.2 (2020-03-04)
------------------- 
+------------------
 
 - Added sediment compaction
 
@@ -206,12 +206,11 @@ Other Changes and Additions
 
 
 0.1.1 (2018-08-24)
------------------- 
+------------------
 - Added versioneer for version management
 
 
 0.1.0 (2018-08-24)
------------------- 
+------------------
 
 - Initial release
-

LICENSE.rst

@@ -23,4 +23,3 @@ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 OTHER DEALINGS IN THE SOFTWARE.
-

MANIFEST.in

@@ -9,4 +9,3 @@ recursive-exclude docs *
 recursive-exclude news *
 recursive-exclude notebooks *
 recursive-exclude tests *
-