ufs2arco 0.0.2__tar.gz

ufs2arco-0.0.2/.github/workflows/ci.yaml

@@ -0,0 +1,95 @@
+# This uses actios:
+#  checkout: https://github.com/actions/checkout
+#  cache: https://github.com/actions/cache
+#  codecov-action: https://github.com/codecov/codecov-action
+
+name: CI
+on:
+  push:
+    branches:
+      - "*"
+  pull_request:
+    branches:
+      - "*"
+  workflow_dispatch:
+    logLevel:
+      options:
+        - info
+        - warning
+        - debug
+
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build (${{ matrix.python-version }} | ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: "latest"
+          environment-file: environment.yaml
+          create-args: python=${{ matrix.python-version }}
+          init-shell: bash
+      - name: Install ufs2arco
+        shell: bash -l {0}
+        run: |
+          python -V
+          python -c "import setuptools; print(setuptools.__version__)"
+          python -m pip install -e . --no-deps
+      - name: Run Unit Tests
+        shell: bash -l {0}
+        run: |
+          python -V
+          coverage run --rcfile=coverage.toml -m pytest --verbose
+      - name: Get coverage report
+        shell: bash -l {0}
+        run: |
+          coverage report -m ; coverage xml
+
+  windows-build:
+    name: Build (${{ matrix.python-version }} | ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["windows-latest"]
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: "latest"
+          environment-file: environment.yaml
+          create-args: python=${{ matrix.python-version }}
+          init-shell: powershell
+      - name: Install ufs2arco
+        shell: pwsh
+        run: |
+          python -V
+          python -c "import setuptools; print(setuptools.__version__)"
+          python -m pip install -e . --no-deps
+      - name: Run Unit Tests
+        shell: pwsh
+        run: |
+          python -V
+          coverage run --rcfile=coverage.toml -m pytest --verbose
+      - name: Get coverage report
+        shell: pwsh
+        run: |
+          coverage report -m ; coverage xml

ufs2arco-0.0.2/.github/workflows/publish.yaml

@@ -0,0 +1,29 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ufs2arco
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

ufs2arco-0.0.2/.gitignore

@@ -0,0 +1,164 @@
+# Additions
+.DS_Store
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

ufs2arco-0.0.2/.readthedocs.yaml

@@ -0,0 +1,31 @@
+# .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-22.9"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+conda:
+    environment: environment.yaml
+
+# 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
+# python:
+#    install:
+#    - requirements: docs/requirements.txt

ufs2arco-0.0.2/LICENSE

@@ -0,0 +1,174 @@
+Copyright (c) 2023 ufs2arco Contributors
+
+This file is part of ufs2arco, which is made available under version 3
+of the Gnu Lesser General Public License, which is provided below.
+
+The intent of this license is to ensure free and unrestricted access to
+the ufs2arco software, and to pass on those rights to modified versions
+of this software.
+
+                    GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

ufs2arco-0.0.2/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.1
+Name: ufs2arco
+Version: 0.0.2
+Summary: Tools for converting Unified Forecast System (UFS) output to Analysis Ready, Cloud Optimized (ARCO) format
+Author-email: Timothy Smith <tim.smith@noaa.gov>, Lauryn Eldridge <leldridge@wvhtf.org>, Ken Witt <kwitt@wvhtf.org>
+Project-URL: source, https://github.com/NOAA-PSL/ufs2arco
+Project-URL: documentation, https://ufs2arco.readthedocs.io/en/latest/
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: xarray
+Requires-Dist: netCDF4
+Requires-Dist: h5netcdf
+Requires-Dist: bottleneck
+Requires-Dist: dask[complete]
+Requires-Dist: zarr
+Requires-Dist: cftime
+Requires-Dist: fsspec
+Requires-Dist: s3fs
+Requires-Dist: gcsfs
+Requires-Dist: pytest
+Requires-Dist: coverage
+Provides-Extra: documentation
+Requires-Dist: jupyter; extra == "documentation"
+Requires-Dist: nbsphinx; extra == "documentation"
+Requires-Dist: sphinx-book-theme; extra == "documentation"
+
+# ufs2arco
+Tools for converting Unified Forecast System (UFS) output to Analysis Ready, Cloud Optimized (ARCO) format
+
+## Installation
+
+
+### Installation from pip
+
+```bash
+pip install ufs2arco
+```
+
+### Installation from GitHub
+
+To obtain the latest development version, clone
+[the repository](https://github.com/NOAA-PSL/ufs2arco>)
+and install it as follows
+
+```bash
+git clone https://github.com/NOAA-PSL/ufs2arco.git
+cd ufs2arco
+pip install -e .
+```

ufs2arco-0.0.2/README.md

@@ -0,0 +1,23 @@
+# ufs2arco
+Tools for converting Unified Forecast System (UFS) output to Analysis Ready, Cloud Optimized (ARCO) format
+
+## Installation
+
+
+### Installation from pip
+
+```bash
+pip install ufs2arco
+```
+
+### Installation from GitHub
+
+To obtain the latest development version, clone
+[the repository](https://github.com/NOAA-PSL/ufs2arco>)
+and install it as follows
+
+```bash
+git clone https://github.com/NOAA-PSL/ufs2arco.git
+cd ufs2arco
+pip install -e .
+```

ufs2arco-0.0.2/coverage.toml

@@ -0,0 +1,5 @@
+[tool.coverage.run]
+omit = [
+    "tests/*.py",
+    "**/__init__.py",
+]

ufs2arco-0.0.2/docs/.gitignore

@@ -0,0 +1 @@
+generated/

ufs2arco-0.0.2/docs/Makefile

@@ -0,0 +1,23 @@
+# 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     = .
+BUILDDIR      = _build
+
+fresh: clean
+	rm -f generated/*.rst
+
+# 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)

ufs2arco-0.0.2/docs/_templates/autosummary/class.rst

@@ -0,0 +1,26 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: Methods
+   .. autosummary::
+      :toctree:
+   {% for item in methods %}
+      {{ name }}.{{ item }}
+   {% endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+   .. autosummary::
+   {% for item in attributes %}
+      {{ name }}.{{ item }}
+   {% endfor %}
+   {% endif %}
+   {% endblock %}

ufs2arco-0.0.2/docs/api.rst

@@ -0,0 +1,10 @@
+API Reference
+#############
+
+
+.. autosummary::
+   :toctree: generated/
+
+   ufs2arco.FV3Dataset
+   ufs2arco.MOM6Dataset
+   ufs2arco.CICE6Dataset

ufs2arco-0.0.2/docs/conf.py

@@ -0,0 +1,50 @@
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+import datetime
+sys.path.insert(0, os.path.abspath("../"))
+
+project = 'ufs2arco'
+copyright = f"2023-{datetime.datetime.now().year}, ufs2arco developers"
+author = 'ufs2arco developers'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+        "sphinx.ext.autodoc",
+        "sphinx.ext.autosummary",
+        "sphinx.ext.napoleon",
+        "nbsphinx",
+        ]
+
+numpydoc_show_class_members = False
+napolean_google_docstring = True
+napolean_numpy_docstring = False
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+napoleon_custom_sections = [("Returns", "params_style"),
+                            ("Sets Attributes", "params_style"),
+                            ("Assumptions", "notes_style"),
+                            ]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_book_theme'
+html_static_path = ['_static']
+
+html_theme_options = {
+    "repository_url": "https://github.com/NOAA-PSL/ufs2arco",
+    "use_repository_button": True,
+}