refactor: refactor dependencies for standard installation

setup.cfg → .flake8

@@ -1,52 +1,3 @@
-[metadata]
-name = pywatershed
-version = attr: pywatershed.version.__version__
-description = pywatershed is a hydrologic model
-long_description = pywatershed is a Python package for hydrologic modeling
-long_description_content_type = text/markdown
-author = USGS Enterprise Capacity Team
-author_email = modflow@usgs.gov
-maintainer = James McCreight
-maintainer_email = jmccreight@usgs.gov
-license = CC0
-license_files = LICENSE, LICENSE.md
-platform = Mac OS-X, Linux
-keywords = PRMS, hydrology
-classifiers =
-    Development Status :: 5 - Production/Stable
-    Intended Audience :: Science/Research
-    License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
-    Programming Language :: Python
-    Programming Language :: Python :: 3 :: Only
-    Topic :: Scientific/Engineering :: Hydrology
-url = https://github.com/EC-USGS/prmsNHMpy
-download_url = https://pypi.org/project/pywatershed
-project_urls =
-    Bug Tracker = https://github.com/EC-USGS/pywatershed/issues
-    Source Code = https://github.com/EC-USGS/pywatershed
-
-[options]
-include_package_data = True  # includes files listed in MANIFEST.in
-zip_safe = False
-packages = find:
-python_requires = >=3.7
-install_requires =
-    epiweeks		 
-    netCDF4
-    networkx
-    numpy
-    numba
-    pandas
-    pyyaml
-    xarray
-
-[options.package_data]
-pywatershed =
-    static/metadata/*.yaml
-
-[sdist]
-formats = zip
-
 [flake8]
 exclude =
     .git

.gitignore

@@ -1,5 +1,6 @@
 # python
 build/
+dist/
 *.egg-info/
 *.pkl
 
@@ -58,7 +59,7 @@ autotest/temp
 generated/
 
 # gis data
-examples/pynhm_gis
+examples/pywatershed_gis
 examples/pywatershed_gis
 examples/model_loop_custom_output
 

CITATION.cff

@@ -0,0 +1,20 @@
+cff-version: 1.2.0
+message: If you use this software, please cite the software itself.
+type: software
+title: pywatershed
+version: 3.3.7
+date-released: '2023-04-28'
+abstract: pywatershed is a Python package for hydrologic modeling.
+repository-artifact: https://pypi.org/project/pywatershed
+repository-code: https://github.com/modflowpy/flopy
+license: CC0-1.0
+authors:
+- family-names: McCreight
+  given-names: James
+  orcid: https://orcid.org/0000-0001-6018-425X
+- family-names: Langevin
+  given-names: Christian D.
+  orcid: https://orcid.org/0000-0001-5610-9759
+- family-names: Hughes
+  given-names: Joseph D.
+  orcid: https://orcid.org/0000-0003-1311-2354

MANIFEST.in

@@ -0,0 +1,15 @@
+prune .idea
+prune .git
+prune .github
+prune autotest
+prune autotest_exs
+prune bin
+prune ci
+prune doc
+prune evaluation
+prune examples
+prune prms_src
+prune reference
+prune resources
+prune test_data
+include pyproject.toml

README.md

@@ -3,6 +3,10 @@
 [![codecov-badge](https://codecov.io/gh/ec-usgs/pywatershed/branch/main/graph/badge.svg)](https://codecov.io/gh/ec-usgs/pywatershed)
 [![Documentation Status](https://readthedocs.org/projects/pywatershed/badge/?version=latest)](https://pywatershed.readthedocs.io/en/latest/?badge=latest)
 
+[![PyPI Version](https://img.shields.io/pypi/v/pywatershed.png)](https://pypi.python.org/pypi/pywatershed)
+[![PyPI Status](https://img.shields.io/pypi/status/pywatershed.png)](https://pypi.python.org/pypi/pywatershed)
+[![PyPI Versions](https://img.shields.io/pypi/pyversions/pywatershed.png)](https://pypi.python.org/pypi/pywatershed)
+
 [//]: # (<img src="https://raw.githubusercontent.com/ec-usgs/pywatershed/main/resources/images/prms_flow.png" alt="prms_flow" style="width:50;height:20">)
 
 Purpose

pyproject.toml

@@ -1,13 +1,101 @@
 [build-system]
-# Minimum requirements for the build system to execute
 requires = [
+    "setuptools >=61",
     "numpy",
-    "setuptools>=45",
-    "setuptools_scm[toml]>=6.2",
-    "wheel",
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "pywatershed"
+description = "pywatershed is a Python package for hydrologic modeling"
+authors = [
+    {name = "USGS Enterprise Capacity Team", email = "modflow@usgs.gov"},
+]
+maintainers = [
+    { name = "James L. McCreight", email = "jmccreight@usgs.gov" },
+    { name = "Joseph D. Hughes", email = "jdhughes@usgs.gov" },
+]
+keywords = ["hydrology", "PRMS"]
+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",
+    "Topic :: Scientific/Engineering :: Hydrology",
+]
+requires-python = ">=3.8,<3.11"
+dependencies = [
+    "numpy >=1.15.0",
+    "matplotlib >=1.4.0",
+    "epiweeks",
+    "netCDF4",
+    "networkx",
+    "numpy",
+    "numba",
+    "pandas",
+    "pint",
+    "xarray@git+https://github.com/pydata/xarray.git",
+    "xmltodict",
+    "pyyaml",
+]
+dynamic = ["version", "readme"]
+
+[project.optional-dependencies]
+lint = [
+    "cffconvert",
+    "black",
+    "click",
+    "isort",
+    "flake8",
+    "pylint",
+    "flynt",
+]
+test = [
+    "pywatershed[lint]",
+    "coverage",
+    "flaky",
+    "modflow-devtools",
+    "pytest",
+    "pytest-cov",
+    "pytest-env",
+    "pytest-order",
+    "pytest-xdist",
+]
+optional = [
+    "pydot",
+    "geos",
+    "cartopy",
+    "geopandas",
+    "hvplot",
+    "shapely <2.0.0",
+    "ipython",
+    "jupyter",
+    "jupyterlab",
+]
+
+[project.urls]
+Documentation = "https://pywatershed.readthedocs.io"
+"Bug Tracker" = "https://github.com/EC-USGS/pywatershed/issues"
+"Source Code" = "https://github.com/EC-USGS/pywatershed"
+
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.dynamic]
+version = { attr = "pywatershed.version.__version__" }
+readme = { file = ["README.md"], content-type = "text/markdown" }
+
+[tool.setuptools.packages.find]
+include = ["pywatershed", "pywatershed.*"]
+
+[tool.setuptools.package-data]
+"pywatershed.static.metadata" = ["*.yaml"]
+
 [tool.black]
 line-length = 79
 target_version = ["py39"]
@@ -20,6 +108,3 @@ verbose = true
 profile = "black"
 src_paths = ["pywatershed", "autotest", "test_data"]
 line_length = 79
-
-[tool.setuptools_scm]
-fallback_version = "999"

pywatershed/__init__.py

@@ -26,7 +26,7 @@
     Soltab,
 )
 from .utils.csv_utils import CsvFile
-from .version import __author__, __author_email__, __version__
+from .version import __version__
 
 __all__ = [
     "analysis",

pywatershed/analysis/model_graph.py

@@ -1,22 +1,8 @@
 import pathlib as pl
 import tempfile
-import warnings
 
 from ..base.model import Model
-
-try:
-    import pydot
-
-    has_pydot = True
-except ModuleNotFoundError:
-    has_pydot = False
-
-try:
-    from IPython.display import SVG, display
-
-    has_ipython = True
-except ModuleNotFoundError:
-    has_ipython = False
+from ..utils import import_optional_dependency
 
 
 class ModelGraph:
@@ -31,9 +17,7 @@ def __init__(
         node_spacing: float = 2.75,
         hide_variables: bool = True,
     ):
-        if not has_pydot:
-            warnings.warn("pydot not available")
-
+        self.pydot = import_optional_dependency("pydot")
         self.model = model
         self.show_params = show_params
         self.process_colors = process_colors
@@ -98,7 +82,7 @@ def build_graph(self):
         self.file_node = self._file_node(files)
 
         # build the graph
-        self.graph = pydot.Dot(
+        self.graph = self.pydot.Dot(
             graph_type="digraph",
             layout="neato",
             splines="polyline",
@@ -110,23 +94,23 @@ def build_graph(self):
             self.graph.add_node(self.process_nodes[process])
 
         for con in connections:
-            self.graph.add_edge(pydot.Edge(con[0], con[1], color=con[2]))
+            self.graph.add_edge(self.pydot.Edge(con[0], con[1], color=con[2]))
 
         return
 
     def SVG(self, verbose: bool = False):
         """Display an SVG in jupyter notebook (via tempfile)."""
 
-        if not has_ipython:
-            warnings.warn("IPython is not available")
+        ipdisplay = import_optional_dependency("IPython.display")
+
         tmp_file = pl.Path(tempfile.NamedTemporaryFile().name)
         if self.graph is None:
             self.build_graph()
         self.graph.write_svg(tmp_file)
         if verbose:
             print(f"Displaying SVG written to temp file: {tmp_file}")
 
-        display(SVG(tmp_file))
+        ipdisplay.display(ipdisplay.SVG(tmp_file))
         return
 
     def _process_node(self, process, show_params: bool = False):
@@ -193,7 +177,7 @@ def _process_node(self, process, show_params: bool = False):
         if self.process_colors:
             color_str = f'"{self.process_colors[cls]}"'
 
-        node = pydot.Node(
+        node = self.pydot.Node(
             cls,
             label=label,
             pos=f'"{self._current_pos},0!"',
@@ -220,7 +204,7 @@ def _file_node(self, files):
 
         label += f"</TABLE>>\n"
         label = label
-        node = pydot.Node(
+        node = self.pydot.Node(
             "Files",
             label=label,
             pos=f'"{self._current_pos},0!"',