Merge pull request #65 from MODFLOW-USGS/v0.1.5

Release 0.1.5

.flake8

@@ -0,0 +1,29 @@
+[flake8]
+exclude =
+    .git
+    __pycache__
+    build
+    dist
+    examples
+    autotest
+ignore =
+    # https://flake8.pycqa.org/en/latest/user/error-codes.html
+    F401,
+    # https://pycodestyle.readthedocs.io/en/latest/intro.html#error-codes
+    # Indentation
+    E121, E122, E126, E127, E128,
+    # Whitespace
+    E203, E221, E222, E226, E231, E241,
+    # Import
+    E402,
+    # Line length
+    E501, E502,
+    # Statement
+    E722, E741,
+    # Whitespace warning
+    W291, W292, W293,
+    # Blank line warning
+    W391,
+    # Line break warning
+    W503, W504
+statistics = True

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
         with:
           python-version: 3.8
           cache: 'pip'
-          cache-dependency-path: setup.cfg
+          cache-dependency-path: pyproject.toml
 
       - name: Install Python packages
         run: |
@@ -132,7 +132,7 @@ jobs:
           python-version: ${{ matrix.python }}
           cache: 'pip'
           cache-dependency-path: |
-            modflow-devtools/setup.cfg
+            modflow-devtools/pyproject.toml
             modflow6-examples/etc/requirements*.txt
 
       - name: Install Python packages

.github/workflows/release.yml

@@ -30,7 +30,7 @@ jobs:
         with:
           python-version: 3.8
           cache: 'pip'
-          cache-dependency-path: setup.cfg
+          cache-dependency-path: pyproject.toml
 
       - name: Install Python dependencies
         run: |
@@ -214,7 +214,7 @@ jobs:
         with:
           python-version: 3.8
           cache: 'pip'
-          cache-dependency-path: setup.cfg
+          cache-dependency-path: pyproject.toml
 
       - name: Install Python dependencies
         run: |

HISTORY.md

@@ -1,3 +1,9 @@
+### Version 0.1.5
+
+#### Refactoring
+
+* [refactor(metadata)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/2edeacfd8cb10081c22d1ab0799aba1fa7522c0d): Use pyproject.toml, retire setup.cfg (#63). Committed by w-bonelli on 2023-01-19.
+
 ### Version 0.1.4
 
 #### Bug fixes

MANIFEST.in

@@ -1,4 +1,5 @@
 global-exclude .DS_Store *.pyc *.pyo *.pyd *.swp *.bak *~ .* *.sh *.yml *.md *.toml
 exclude autotest/*
 include pyproject.toml
-include version.txt
+include version.txt
+include README.md

README.md

@@ -1,6 +1,6 @@
 # MODFLOW developer tools
 
-### Version 0.1.4 — release candidate
+### Version 0.1.5 — release candidate
 [![GitHub tag](https://img.shields.io/github/tag/MODFLOW-USGS/modflow-devtools.svg)](https://github.com/MODFLOW-USGS/modflow-devtools/tags/latest)
 [![PyPI Version](https://img.shields.io/pypi/v/modflow-devtools.png)](https://pypi.python.org/pypi/modflow-devtools)
 [![PyPI Versions](https://img.shields.io/pypi/pyversions/modflow-devtools.png)](https://pypi.python.org/pypi/modflow-devtools)

docs/conf.py

@@ -8,7 +8,7 @@
 
 project = "modflow-devtools"
 author = "MODFLOW Team"
-release = "0.1.4"
+release = "0.1.5"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/md/zip.md

@@ -1,3 +1,34 @@
 # `MFZipFile`
 
-Python's [`ZipFile`](https://docs.python.org/3/library/zipfile.html) doesn't [preserve file permissions at extraction time](https://bugs.python.org/issue15795). The `MFZipFile` subclass modifies `ZipFile.extract()` to do so, as per the recommendation [here](https://stackoverflow.com/questions/39296101/python-zipfile-removes-execute-permissions-from-binaries), and maintains identical behavior otherwise.
+Python's [`ZipFile`](https://docs.python.org/3/library/zipfile.html) doesn't [preserve file permissions at extraction time](https://bugs.python.org/issue15795). The `MFZipFile` subclass:
+
+- modifies `ZipFile.extract()` to preserve permissions per the [recommendation here](https://stackoverflow.com/questions/39296101/python-zipfile-removes-execute-permissions-from-binaries)
+- adds a static `ZipFile.compressall()` method to create a zip file from files and directories
+- maintains an otherwise identical API
+
+## `compressall`
+
+The `compressall` method is a static method that creates a zip file from lists of files and/or directories. It is a convenience method that wraps `ZipFile.write()`, `ZipFile.close()`, etc.
+
+```python
+from zipfile import ZipFile
+from modflow_devtools.zip import MFZipFile
+
+def test_compressall(function_tmpdir):
+    zip_file = function_tmpdir / "output.zip"
+
+    input_dir = function_tmpdir / "input"
+    input_dir.mkdir()
+
+    with open(input_dir / "data.txt", "w") as f:
+        f.write("hello world")
+
+    MFZipFile.compressall(str(zip_file), dir_pths=str(input_dir))
+    assert zip_file.exists()
+
+    output_dir = function_tmpdir / "output"
+    output_dir.mkdir()
+
+    ZipFile(zip_file).extractall(path=str(output_dir))
+    assert (output_dir / "data.txt").is_file()
+```

modflow_devtools/__init__.py

@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
-__date__ = "Jan 18, 2023"
-__version__ = "0.1.4"
+__date__ = "Jan 19, 2023"
+__version__ = "0.1.5"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "[email protected]"
 __status__ = "Production"

modflow_devtools/test/test_zip.py

@@ -0,0 +1,92 @@
+import os
+import shutil
+import sys
+import zipfile
+from os import environ
+from pathlib import Path
+from pprint import pprint
+from zipfile import ZipFile
+
+import pytest
+from modflow_devtools.markers import excludes_platform
+from modflow_devtools.misc import get_suffixes, set_dir
+from modflow_devtools.zip import MFZipFile
+
+_bin_path = Path(environ.get("BIN_PATH")).expanduser().absolute()
+_ext, _ = get_suffixes(sys.platform)
+
+
+@pytest.fixture(scope="module")
+def empty_archive(module_tmpdir) -> Path:
+    # https://stackoverflow.com/a/25195628/6514033
+    data = b"PK\x05\x06\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00"
+    path = module_tmpdir / "empty.zip"
+
+    with open(path, "wb") as zip:
+        zip.write(data)
+
+    return path
+
+
+@pytest.fixture(scope="module")
+def nonempty_archive(module_tmpdir) -> Path:
+    if not _bin_path.is_dir():
+        pytest.skip(f"BIN_PATH ({_bin_path}) is not a directory")
+
+    zip_path = module_tmpdir / "nonempty.zip"
+    txt_path = module_tmpdir / "hw.txt"
+    exe_path = _bin_path / f"mf6{_ext}"
+
+    # create a zip file with a text file and an executable
+    shutil.copy(exe_path, module_tmpdir)
+    with open(txt_path, "w") as f:
+        f.write("hello world")
+
+    with set_dir(module_tmpdir):
+        zip = MFZipFile(zip_path.name, "w")
+        zip.write(txt_path.name, compress_type=zipfile.ZIP_DEFLATED)
+        zip.write(exe_path.name, compress_type=zipfile.ZIP_DEFLATED)
+        zip.close()
+
+    return zip_path
+
+
+def test_compressall(function_tmpdir):
+    zip_file = function_tmpdir / "output.zip"
+    input_dir = function_tmpdir / "input"
+    input_dir.mkdir()
+
+    with open(input_dir / "data.txt", "w") as f:
+        f.write("hello world")
+
+    MFZipFile.compressall(str(zip_file), dir_pths=str(input_dir))
+
+    pprint(list(function_tmpdir.iterdir()))
+    assert zip_file.exists()
+
+    output_dir = function_tmpdir / "output"
+    output_dir.mkdir()
+
+    ZipFile(zip_file).extractall(path=str(output_dir))
+
+    pprint(list(output_dir.iterdir()))
+    assert (output_dir / "data.txt").is_file()
+
+
+def test_extractall_empty(empty_archive, function_tmpdir):
+    zf = MFZipFile(empty_archive, "r")
+    zf.extractall(str(function_tmpdir))
+
+    assert not any(function_tmpdir.iterdir())
+
+
+@pytest.mark.parametrize("mf", [True, False])
+@excludes_platform("Windows")
+def test_preserves_execute_permission(function_tmpdir, nonempty_archive, mf):
+    zip = MFZipFile(nonempty_archive) if mf else ZipFile(nonempty_archive)
+    zip.extractall(path=str(function_tmpdir))
+
+    exe_path = function_tmpdir / f"mf6{_ext}"
+
+    assert exe_path.is_file()
+    assert os.access(exe_path, os.X_OK) == mf

pyproject.toml

@@ -1,11 +1,80 @@
 [build-system]
 # Minimum requirements for the build system to execute
 requires = [
-    "setuptools>=45",
-    "wheel",
+    "setuptools>=61",
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "modflow-devtools"
+description = "Python tools for MODFLOW development"
+authors = [
+    {name = "Joseph D. Hughes", email = "[email protected]"},
+]
+maintainers = [
+    {name = "Joseph D. Hughes", email = "[email protected]"},
+]
+keywords = [
+    "MODFLOW",
+    "development",
+    "utilities",
+    "groundwater",
+    "hydrogeology"
+]
+readme = "README.md"
+license = {text = "CC0"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Hydrology"
+]
+requires-python = ">=3.8"
+dependencies = [
+    "numpy",
+    "pytest"
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+lint = [
+    "black",
+    "cffconvert",
+    "flake8",
+    "isort",
+    "pylint"
+]
+test = [
+    "modflow-devtools[lint]",
+    "coverage",
+    "flaky",
+    "filelock",
+    "meson!=0.63.0",
+    "ninja",
+    "pytest-cases",
+    "pytest-cov",
+    "pytest-dotenv",
+    "pytest-xdist",
+    "PyYaml"
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "myst-parser"
+]
+
+[project.urls]
+"Documentation" = "https://modflow-devtools.readthedocs.io/en/latest/"
+"Bug Tracker" = "https://github.com/MODFLOW-USGS/modflow-devtools/issues"
+"Source Code" = "https://github.com/MODFLOW-USGS/modflow-devtools"
+
+
 [tool.black]
 line-length = 79
 target_version = ["py37"]
@@ -19,6 +88,13 @@ profile = "black"
 src_paths = ["src/modflow_devtools"]
 line_length = 79
 
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.dynamic]
+version = {file = "version.txt"}
+
 [tool.setuptools_scm]
 fallback_version = "999"