build: update pyproject.toml to replace setup.cfg

.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/main.yml

@@ -39,7 +39,8 @@ jobs:
 
       - name: Install python packages
         run: |
-          .github/common/install-python.sh
+          pip install --upgrade pip
+          pip install ".[test]"
 
       - name: Download examples for pytest runs
         run: |

.github/workflows/pymake-gcc.yml

@@ -36,7 +36,8 @@ jobs:
 
       - name: Install python packages
         run: |
-          .github/common/install-python.sh
+          pip install --upgrade pip
+          pip install ".[test]"
 
       - name: Install GNU Fortran
         uses: modflowpy/install-gfortran-action@v1
@@ -85,7 +86,8 @@ jobs:
 
       - name: Install python packages
         run: |
-          .github/common/install-python.sh
+          pip install --upgrade pip
+          pip install ".[test]"
 
       - name: Setup symbolic link to gfortran on Linux
         run: |
@@ -140,7 +142,8 @@ jobs:
 
       - name: Install python packages
         run: |
-          .github/common/install-python.sh
+          pip install --upgrade pip
+          pip install ".[test]"
 
       - name: Install GNU Fortran
         uses: modflowpy/install-gfortran-action@v1
@@ -150,5 +153,6 @@ jobs:
           .github/common/download-examples.sh
 
       - name: Run pytest
+        working-directory: ./autotest
         run: |
           pytest -v --dist=loadfile -n=auto -m="base" --durations=0

.github/workflows/pymake-requests.yml

@@ -28,7 +28,8 @@ jobs:
 
       - name: Install python packages
         run: |
-          .github/common/install-python.sh
+          pip install --upgrade pip
+          pip install ".[test]"
 
       - name: Run pytest
         working-directory: ./autotest

README.md

@@ -2,19 +2,20 @@
 
 Python package for building MODFLOW-based programs from source files.
 
-### Version 1.2.8
+### Version 1.2.9.dev0
 
-![pymake continuous integration](https://github.com/modflowpy/pymake/workflows/pymake%20continuous%20integration/badge.svg)
+[![PyPI Version](https://img.shields.io/pypi/v/mfpymake.png)](https://pypi.python.org/pypi/mfpymake)
+[![Anaconda Version](https://anaconda.org/conda-forge/mfpymake/badges/version.svg)](https://anaconda.org/conda-forge/mfpymake)  
+[![pymake continuous integration](https://github.com/modflowpy/pymake/workflows/pymake%20continuous%20integration/badge.svg)](https://github.com/modflowpy/pymake/actions/workflows/main.yml)
 [![codecov](https://codecov.io/gh/modflowpy/pymake/branch/master/graph/badge.svg)](https://codecov.io/gh/modflowpy/pymake)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/fe4275a3cfb84acf9c84aba7b4ae2086)](https://www.codacy.com/gh/modflowpy/pymake/dashboard?utm_source=github.com&utm_medium=referral&utm_content=modflowpy/pymake&utm_campaign=Badge_Grade)
-[![Documentation Status](https://readthedocs.org/projects/mfpymake/badge/?version=latest)](https://mfpymake.readthedocs.io/en/latest/?badge=latest)
-[![PyPI Version](https://img.shields.io/pypi/v/mfpymake.png)](https://pypi.python.org/pypi/mfpymake)
+[![Documentation Status](https://readthedocs.org/projects/mfpymake/badge/?version=latest)](https://mfpymake.readthedocs.io/en/latest/?badge=latest)  
 
 This is a python package for compiling MODFLOW-based and other Fortran, C, and
 C++ programs. The package determines the build order using a directed acyclic
 graph and then compiles the source files using GNU compilers (`gcc`, `g++`,
-`gfortran`), Clang compilers (`clang`, `clang++`), Intel compilers (`ifort`,
-`icl`, `icc`, `mpiifort`), or the CRAY Fortran compiler (`ftn`).
+`gfortran`), Clang compilers (`clang`, `clang++`), or the Intel compilers (`ifort`,
+`icl`, `icc`, `mpiifort`).
 
 pymake can be run from the command line or it can be called from within python.
 By default, pymake sets the optimization level, Fortran flags, C/C++ flags, and
@@ -233,6 +234,12 @@ To install pymake using pip type:
 pip install mfpymake
 ```
 
+To install pymake using conda type:
+
+```
+conda install -c conda-forge mfpymake
+```
+
 To install pymake directly from the git repository type:
 
 ```

autotest/conftest.py

@@ -0,0 +1,101 @@
+import contextlib
+import os
+import re
+from importlib import metadata
+from pathlib import Path
+
+import pytest
+
+# import modflow-devtools fixtures
+
+pytest_plugins = ["modflow_devtools.fixtures"]
+
+
+# constants
+
+
+# misc utilities
+@contextlib.contextmanager
+def working_directory(path):
+    """Changes working directory and returns to previous on exit."""
+    prev_cwd = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(prev_cwd)
+
+
+def get_pymake_appdir():
+    appdir = Path.home() / ".pymake"
+    appdir.mkdir(parents=True, exist_ok=True)
+    return appdir
+
+
+def get_project_root_path() -> Path:
+    return Path(__file__).parent.parent
+
+
+# path fixtures
+
+
+# pytest configuration hooks
+
+
+@pytest.hookimpl(hookwrapper=True, tryfirst=True)
+def pytest_runtest_makereport(item, call):
+    # this is necessary so temp dir fixtures can
+    # inspect test results and check for failure
+    # (see https://doc.pytest.org/en/latest/example/simple.html#making-test-result-information-available-in-fixtures)
+
+    outcome = yield
+    rep = outcome.get_result()
+
+    # report attribute for each phase (setup, call, teardown)
+    # we're only interested in result of the function call
+    setattr(item, "rep_" + rep.when, rep)
+
+
+def pytest_report_header(config):
+    """Header for pytest to show versions of packages."""
+
+    required = []
+    extra = {}
+    for item in metadata.requires("flopy"):
+        pkg_name = re.findall(r"[a-z0-9_\-]+", item, re.IGNORECASE)[0]
+        if res := re.findall("extra == ['\"](.+)['\"]", item):
+            assert len(res) == 1, item
+            pkg_extra = res[0]
+            if pkg_extra not in extra:
+                extra[pkg_extra] = []
+            extra[pkg_extra].append(pkg_name)
+        else:
+            required.append(pkg_name)
+
+    processed = set()
+    lines = []
+    items = []
+    for name in required:
+        processed.add(name)
+        try:
+            version = metadata.version(name)
+            items.append(f"{name}-{version}")
+        except metadata.PackageNotFoundError:
+            items.append(f"{name} (not found)")
+    lines.append("required packages: " + ", ".join(items))
+    installed = []
+    not_found = []
+    for name in extra["optional"]:
+        if name in processed:
+            continue
+        processed.add(name)
+        try:
+            version = metadata.version(name)
+            installed.append(f"{name}-{version}")
+        except metadata.PackageNotFoundError:
+            not_found.append(name)
+    if installed:
+        lines.append("optional packages: " + ", ".join(installed))
+    if not_found:
+        lines.append("optional packages not found: " + ", ".join(not_found))
+    return "\n".join(lines)

pymake/config.py

@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
 __date__ = "July 5, 2023"
-__version__ = "1.2.8"
+__version__ = "1.2.9.dev0"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "[email protected]"
 __status__ = "Production"

pyproject.toml

@@ -1,14 +1,98 @@
 [build-system]
 # Minimum requirements for the build system to execute
 requires = [
-    "setuptools>=45",
+    "setuptools>=61",
     "wheel",
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "mfpymake"
+description = "pymake is a Python package to compile MODFLOW-based models."
+authors = [
+    { name = "mfpymake Team", email = "[email protected]" },
+]
+maintainers = [
+    { name = "Joseph D. Hughes", email = "[email protected]" },
+]
+keywords = ["MODFLOW", "groundwater", "hydrogeology"]
+license = { text = "CC0" }
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
+    "Programming Language :: Python :: 3 :: Only",
+    "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",
+    "requests",
+    "networkx >= 2.6.3",
+    "meson",
+    "ninja",
+    "pydotplus",
+]
+dynamic = ["version", "readme"]
+[project.optional-dependencies]
+lint = [
+    "black",
+    "cffconvert",
+    "flake8",
+    "isort",
+    "pylint",
+]
+test = [
+    "mfpymake[lint]",
+    "coverage",
+    "flaky",
+    "filelock",
+    "pytest",
+    "pytest-benchmark",
+    "pytest-cases",
+    "pytest-cov",
+    "pytest-dotenv",
+    "pytest-virtualenv",
+    "pytest-xdist",
+    "appdirs",
+    "matplotlib",
+    "modflow-devtools",
+    "flopy",
+]
+[project.scripts]
+mfpymake = "pymake.cmds.mfpymakecli:main"
+make-program = "pymake.cmds.build:main"
+make-code-json = "pymake.cmds.createjson:main"
+
+
+[project.urls]
+Documentation = "https://mfpymake.readthedocs.io"
+"Release Notes" = "https://github.com/modflowpy/flopy/blob/develop/docs/version_changes.md"
+"Bug Tracker" = "https://github.com/modflowpy/pymake/issues"
+"Source Code" = "https://github.com/modflowpy/pymake"
+
+
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.dynamic]
+version = { attr = "pymake.config.__version__" }
+readme = { file = ["README.md"], content-type = "text/markdown" }
+
+[tool.setuptools.packages.find]
+include = ["pymake", "pymake.*"]
+
+[tool.setuptools.package-data]
+"pymake.utils" = ["usgsprograms.txt"]
+
 [tool.black]
 line-length = 79
-target_version = ["py37"]
+target_version = ["py38"]
 
 [tool.flynt]
 line-length = 79
@@ -20,4 +104,4 @@ src_paths = ["pymake", "autotest", "examples"]
 line_length = 79
 
 [tool.setuptools_scm]
-fallback_version = "999"
+fallback_version = "999"