Merge branch 'master' into mdpiper/update-examples

Author: mdpiper

.github/workflows/format.yml

@@ -35,12 +35,8 @@ jobs:
           conda info
           conda list
 
-      - name: Install requirements
-        run: |
-          conda install --file=requirements.txt --file=requirements-testing.txt
-
       - name: Build and install package
-        run: pip install -e .
+        run: pip install -e .[testing]
 
       - name: Test
         run: |

.github/workflows/lint.yml

@@ -1,54 +1,7 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
+*.egg-info/
 *.py[cod]
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
+.coverage
+.ipynb_checkpoints/
+__pycache__/
 build/
-develop-eggs/
 dist/
-downloads/
-eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.cache
-nosetests.xml
-coverage.xml
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/

.github/workflows/test.yml

@@ -0,0 +1,65 @@
+repos:
+- repo: https://github.com/psf/black
+  rev: 23.12.1
+  hooks:
+  - id: black
+    name: black
+    description: "Black: The uncompromising Python code formatter"
+    entry: black
+    language: python
+    language_version: python3
+    minimum_pre_commit_version: 2.9.2
+    require_serial: true
+    types_or: [python, pyi]
+
+- repo: https://github.com/pycqa/flake8
+  rev: 7.0.0
+  hooks:
+  - id: flake8
+    additional_dependencies:
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-simplify
+    args: [--max-line-length=88]
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.15.0
+  hooks:
+  - id: pyupgrade
+    args: [--py310-plus]
+
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  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: mixed-line-ending
+    - id: trailing-whitespace
+    - id: name-tests-test
+    - id: file-contents-sorter
+      files: |
+        (?x)^(
+          .*requirements(-\w+)?.(in|txt)|
+          requirements/.*\.txt|
+          .gitignore
+        )
+
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.8.0
+  hooks:
+  - id: mypy
+    language_version: python3.12
+    files: heat/.*\.py$
+    additional_dependencies:
+      - types-PyYAML

.gitignore

@@ -31,7 +31,7 @@ Changelog for bmi-example-python
 - Match bmipy (#12)
 - Use GitHub Actions for continuous integration (#15)
 - Dimensionalize flattened values passed into set_value (#17)
-- Update CI (#18) 
+- Update CI (#18)
 - Switch from versioneer to zest.releaser
 - Remove obsolete docs directory
 
@@ -46,4 +46,3 @@ Changelog for bmi-example-python
 ------------------
 
 - Initial release
-

.pre-commit-config.yaml

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT 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.
-

CHANGES.rst

@@ -38,7 +38,7 @@ def initialize(self, filename=None):
         if filename is None:
             self._model = Heat()
         elif isinstance(filename, str):
-            with open(filename, "r") as file_obj:
+            with open(filename) as file_obj:
                 self._model = Heat.from_file_like(file_obj.read())
         else:
             self._model = Heat.from_file_like(filename)

LICENSE

@@ -53,7 +53,8 @@ def solve_2d(temp, spacing, out=None, alpha=1.0, time_step=1.0):
     return np.add(temp, out, out=out)
 
 
-class Heat(object):
+class Heat:
+
     """Solve the Heat equation on a grid.
 
     Examples

heat/bmi_heat.py

@@ -0,0 +1,103 @@
+from __future__ import annotations
+
+import os
+import pathlib
+import shutil
+
+import nox
+
+PROJECT = "heat"
+ROOT = pathlib.Path(__file__).parent
+
+
+@nox.session
+def test(session: nox.Session) -> None:
+    """Run the tests."""
+    session.install(".[testing]")
+
+    args = ["--cov", PROJECT, "-vvv"] + session.posargs
+
+    if "CI" in os.environ:
+        args.append(f"--cov-report=xml:{ROOT.absolute()!s}/coverage.xml")
+    session.run("pytest", *args)
+
+    if "CI" not in os.environ:
+        session.run("coverage", "report", "--ignore-errors", "--show-missing")
+
+
+@nox.session
+def lint(session: nox.Session) -> None:
+    """Look for lint."""
+    session.install("pre-commit")
+    session.run("pre-commit", "run", "--all-files")
+
+
+@nox.session
+def build(session: nox.Session) -> None:
+    session.install("pip")
+    session.install("build")
+    session.run("python", "--version")
+    session.run("pip", "--version")
+    session.run("python", "-m", "build", "--outdir", "./build/wheelhouse")
+
+
+@nox.session(name="publish-testpypi")
+def publish_testpypi(session):
+    """Publish wheelhouse/* to TestPyPI."""
+    session.run("twine", "check", "build/wheelhouse/*")
+    session.run(
+        "twine",
+        "upload",
+        "--skip-existing",
+        "--repository-url",
+        "https://test.pypi.org/legacy/",
+        "build/wheelhouse/*.tar.gz",
+    )
+
+
+@nox.session(name="publish-pypi")
+def publish_pypi(session):
+    """Publish wheelhouse/* to PyPI."""
+    session.run("twine", "check", "build/wheelhouse/*")
+    session.run(
+        "twine",
+        "upload",
+        "--skip-existing",
+        "build/wheelhouse/*.tar.gz",
+    )
+
+
+@nox.session(python=False)
+def clean(session):
+    """Remove all .venv's, build files and caches in the directory."""
+    folders = (
+        (ROOT,) if not session.posargs else (pathlib.Path(f) for f in session.posargs)
+    )
+    for folder in folders:
+        if not str(folder.resolve()).startswith(str(ROOT.resolve())):
+            session.log(f"skipping {folder}: folder is outside of repository")
+            continue
+
+        with session.chdir(folder):
+            session.log(f"cleaning {folder}")
+
+            shutil.rmtree("build", ignore_errors=True)
+            shutil.rmtree("dist", ignore_errors=True)
+            shutil.rmtree(f"src/{PROJECT}.egg-info", ignore_errors=True)
+            shutil.rmtree(".pytest_cache", ignore_errors=True)
+            shutil.rmtree(".venv", ignore_errors=True)
+
+            for pattern in ["*.py[co]", "__pycache__"]:
+                _clean_rglob(pattern)
+
+
+def _clean_rglob(pattern):
+    nox_dir = pathlib.Path(".nox")
+
+    for p in pathlib.Path(".").rglob(pattern):
+        if nox_dir in p.parents:
+            continue
+        if p.is_dir():
+            p.rmdir()
+        else:
+            p.unlink()

heat/heat.py

@@ -1,7 +1,7 @@
+black
+bmi-tester
 coveralls
+isort
 pytest
 pytest-cov
-black
-isort
 ruff
-bmi-tester

noxfile.py

@@ -1,4 +1,4 @@
+bmipy
 numpy
-scipy
 pyyaml
-bmipy
+scipy