Merge branch 'main' into Feature/ras_1d

.github/workflows/continuous-integration.yml

@@ -26,6 +26,7 @@ jobs:
         os: ["ubuntu-latest"]
 
     runs-on: ${{ matrix.os }}
+    environment: ci-env
 
     steps:
     - uses: actions/checkout@v4
@@ -45,6 +46,15 @@ jobs:
         ruff check
         ruff format --check
 
-    - name: Test with pytest
+    - name: Run tests with coverage
       run: |
-        pytest
+        pytest --cov=src --cov-report term-missing
+
+    - name: Run coverage
+      run: |
+        coverage xml
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/[email protected]
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yml

@@ -0,0 +1,27 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: mambaforge-latest
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+conda:
+   environment: docs/environment.yml

README.md

@@ -2,11 +2,16 @@
 [![CI](https://github.com/fema-ffrd/rashdf/actions/workflows/continuous-integration.yml/badge.svg?branch=main)](https://github.com/fema-ffrd/rashdf/actions/workflows/continuous-integration.yml)
 [![Release](https://github.com/fema-ffrd/rashdf/actions/workflows/release.yml/badge.svg)](https://github.com/fema-ffrd/rashdf/actions/workflows/release.yml)
 [![PyPI version](https://badge.fury.io/py/rashdf.svg)](https://badge.fury.io/py/rashdf)
+[![codecov](https://codecov.io/gh/fema-ffrd/rashdf/graph/badge.svg?token=CTIIONEHV1)](https://codecov.io/gh/fema-ffrd/rashdf)
+[![Documentation Status](https://readthedocs.org/projects/rashdf/badge/?version=latest)](https://rashdf.readthedocs.io/en/latest/?badge=latest)
 
 Read data from [HEC-RAS](https://www.hec.usace.army.mil/software/hec-ras/) [HDF](https://github.com/HDFGroup/hdf5) files.
 
 *Pronunciation: `raz·aitch·dee·eff`*
 
+## Documentation
+[rashdf on ReadTheDocs](http://rashdf.readthedocs.io/)
+
 ## Install
 ```bash
 $ pip install rashdf
@@ -97,9 +102,6 @@ Example: write structures GeoJSON to `stdout`:
 $ rashdf structures Potomac.p01.hdf
 ```
 
-## Documentation
-Coming soon.
-
 ## Developer Setup
 Create a virtual environment in the project directory:
 ```

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/environment.yml

@@ -0,0 +1,9 @@
+name: rashdf-docs
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - pip
+  - pip:
+      - -e ../[docs]

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/RasGeomHdf.rst

@@ -0,0 +1,18 @@
+RasGeomHdf
+==========
+.. currentmodule:: rashdf
+.. autoclass:: RasGeomHdf
+   :show-inheritance:
+   :members: projection,
+             mesh_area_names,
+             mesh_areas,
+             mesh_cell_polygons,
+             mesh_cell_points,
+             mesh_cell_faces,
+             bc_lines,
+             breaklines,
+             refinement_regions,
+             structures,
+             get_geom_attrs,
+             get_geom_structures_attrs,
+             get_geom_2d_flow_area_attrs

docs/source/RasHdf.rst

@@ -0,0 +1,7 @@
+RasHdf
+======
+.. currentmodule:: rashdf
+.. autoclass:: RasHdf
+   :show-inheritance:
+   :special-members: __init__,
+                     open_uri

docs/source/RasPlanHdf.rst

@@ -0,0 +1,11 @@
+RasPlanHdf
+==========
+.. currentmodule:: rashdf
+.. autoclass:: RasPlanHdf
+   :show-inheritance:
+   :members: get_plan_info_attrs,
+             get_plan_param_attrs,
+             get_meteorology_precip_attrs,
+             get_results_unsteady_attrs,
+             get_results_unsteady_summary_attrs,
+             get_results_volume_accounting_attrs

docs/source/conf.py

@@ -0,0 +1,39 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import sys
+
+sys.path.insert(0, "src")
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "rashdf"
+copyright = "2024, fema-ffrd"
+author = "fema-ffrd"
+release = "0.2.1"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx_rtd_theme",
+    "numpydoc",
+]
+
+numpydoc_show_class_members = False
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# html_theme = "alabaster"
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,102 @@
+.. rashdf documentation master file, created by
+   sphinx-quickstart on Mon Jun  3 15:55:12 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+rashdf Documentation
+====================
+:code:`rashdf` is a library for reading data from `HEC-RAS <https://www.hec.usace.army.mil/software/hec-ras/>`_
+HDF5 files. It is a wrapper around the :code:`h5py` library, and provides an interface with 
+convenience functions for reading key HEC-RAS geometry data, output data,
+and metadata.
+
+Installation
+============
+With :code:`pip`::
+
+   pip install rashdf
+
+
+Quickstart
+==========
+Reading geometry from a HEC-RAS geometry HDF file::
+
+   >>> from rashdf import RasGeomHdf
+   >>> with RasGeomHdf('Muncie.g05.hdf') as geom_hdf:
+   ...     projection = geom_hdf.projection()
+   ...     mesh_area_names = geom_hdf.mesh_area_names()
+   ...     mesh_areas = geom_hdf.mesh_areas()
+   ...     mesh_cell_points = geom_hdf.mesh_cell_points()
+   >>> projection
+   <Projected CRS: EPSG:2965>
+   Name: NAD83 / Indiana East (ftUS)
+   Axis Info [cartesian]:
+   - E[east]: Easting (US survey foot)
+   - N[north]: Northing (US survey foot)
+   Area of Use:
+   - undefined
+   Coordinate Operation:
+   - name: unnamed
+   - method: Transverse Mercator
+   Datum: North American Datum 1983
+   - Ellipsoid: GRS 1980
+   - Prime Meridian: Greenwich
+   >>> mesh_area_names
+   ['2D Interior Area', 'Perimeter_NW']
+   >>> mesh_areas
+             mesh_name                                           geometry
+   0  2D Interior Area  POLYGON ((409537.180 1802597.310, 409426.140 1...
+   1      Perimeter_NW  POLYGON ((403914.470 1804971.220, 403008.310 1...
+   >>> mesh_cell_points
+                mesh_name  cell_id                        geometry
+   0     2D Interior Area        0  POINT (406000.000 1805000.000)
+   1     2D Interior Area        1  POINT (406050.000 1805000.000)
+   2     2D Interior Area        2  POINT (406100.000 1805000.000)
+   3     2D Interior Area        3  POINT (406150.000 1805000.000)
+   4     2D Interior Area        4  POINT (406200.000 1805000.000)
+   ...                ...      ...                             ...
+   5785      Perimeter_NW      514  POINT (403731.575 1804124.860)
+   5786      Perimeter_NW      515  POINT (403650.619 1804121.731)
+   5787      Perimeter_NW      516  POINT (403585.667 1804141.139)
+   5788      Perimeter_NW      517  POINT (403534.818 1804186.902)
+   5789      Perimeter_NW      518  POINT (403632.837 1804235.708)
+
+Reading plan data from a HEC-RAS plan HDF file hosted on AWS S3
+(note, this requires installation of the optional :code:`fsspec`
+and :code:`s3fs` libraries as well as configuration of S3
+credentials)::
+
+   >>> from rashdf import RasPlanHdf
+   >>> with RasPlanHdf.open_uri('s3://bucket/ElkMiddle.p01.hdf') as plan_hdf:
+   ...     plan_info = plan_hdf.get_plan_info_attrs()
+   >>> plan_info
+   {'Base Output Interval': '1HOUR', 'Computation Time Step Base': '1MIN',
+   'Flow Filename': 'ElkMiddle.u01', 'Flow Title': 'Jan_1996',
+   'Geometry Filename': 'ElkMiddle.g01', 'Geometry Title': 'ElkMiddle',
+   'Plan Filename': 'ElkMiddle.p01', 'Plan Name': 'Jan_1996',
+   'Plan ShortID': 'Jan_1996', 'Plan Title': 'Jan_1996',
+   'Project Filename': 'g:\\Jan1996_Kanawha_CloudPrep\\Elk Middle\\ElkMiddle.prj',
+   'Project Title': 'ElkMiddle',
+   'Simulation End Time': datetime.datetime(1996, 2, 7, 12, 0),
+   'Simulation Start Time': datetime.datetime(1996, 1, 14, 12, 0),
+   'Time Window': [datetime.datetime(1996, 1, 14, 12, 0),
+   datetime.datetime(1996, 2, 7, 12, 0)]}
+
+
+API
+===
+.. toctree::
+   :maxdepth: 1
+
+   RasGeomHdf
+   RasPlanHdf
+   RasHdf
+
+:code:`rashdf` provides two primary classes for reading data from
+HEC-RAS geometry and plan HDF files: :code:`RasGeomHdf` and :code:`RasPlanHdf`.
+Both of these classes inherit from the :code:`RasHdf` base class, which
+inherits from the :code:`h5py.File` class.
+
+Note that :code:`RasPlanHdf` inherits from :code:`RasGeomHdf`, so all of the
+methods available in :code:`RasGeomHdf` are also available in :code:`RasPlanHdf`.

pyproject.toml

@@ -12,11 +12,12 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
-version = "0.2.1"
+version = "0.2.2"
 dependencies = ["h5py", "geopandas", "pyarrow"]
 
 [project.optional-dependencies]
-dev = ["pre-commit", "ruff", "pytest"]
+dev = ["pre-commit", "ruff", "pytest", "pytest-cov"]
+docs = ["sphinx", "numpydoc", "sphinx_rtd_theme"]
 
 [project.urls]
 repository = "https://github.com/fema-ffrd/rashdf"
@@ -28,10 +29,12 @@ rashdf = "cli:main"
 pythonpath = "src"
 testpaths = "tests"
 
-# TODO: linting for docstrings.
-# https://github.com/fema-ffrd/rashdf/issues/15
-# [tool.ruff.lint]
-# select = ["D"]
+[tool.ruff.lint]
+select = ["D"]
 
-# [tool.ruff.lint.pydocstyle]
-# convention = "numpy"
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["D"]
+"docs/**" = ["D"]