update project, no longer masked array for gpi, lon, lat

.github/workflows/ci.yml

@@ -1,35 +1,44 @@
-name: tests
+name: Automated Tests
 
 on:
   push:
   pull_request:
   schedule:
-    - cron: '0 0 * * *' # daily
+    - cron: "0 0 * * *" # daily
 
 jobs:
   build:
+    name: Build py${{ matrix.python-version }} @ ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["ubuntu-latest", "windows-latest"] # currently windows is not tested
-        python-version: ['3.6', '3.7', '3.8']
-        ymlfile: ['environment.yml']
-    name: Py${{ matrix.python-version }}@${{ matrix.os }}|${{ matrix.ymlfile }}
-    runs-on: ${{ matrix.os }}
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: ["ubuntu-latest", "windows-latest"]
+        ymlfile: ["environment.yml"]
+
     steps:
       - uses: actions/checkout@v2
         with:
-          submodules: false
+          submodules: false # does not work with self-hosted testdata
+      - name: Checkout test data
+        shell: bash -l {0}
+        run : |
+          git submodule init
+          git submodule sync
+          git submodule update
       - uses: conda-incubator/setup-miniconda@v2.0.1
         with:
-          miniconda-version: "latest"
-          auto-update-conda: true
+          miniforge-variant: Mambaforge
+          miniforge-version: "latest"
+          channel-priority: flexible
           python-version: ${{ matrix.python-version }}
           environment-file: ${{ matrix.ymlfile }}
-          activate-environment: fibgrid_env
+          activate-environment: env
           auto-activate-base: false
-      - name: Print Infos
+      - name: Print infos
         shell: bash -l {0}
         run: |
+          git status
           conda info -a
           conda list
           pip list
@@ -39,15 +48,12 @@ jobs:
         shell: bash -l {0}
         run: |
           mkdir -p .artifacts
-          if [ ${{ matrix.ymlfile }} == "environment.yml" ]
-          then
-              filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
-              conda env export --no-builds | grep -v "prefix" > .artifacts/$filename
-          fi
+          filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
+          conda env export --no-builds | grep -v "prefix" > .artifacts/$filename
       - name: Install package and test
         shell: bash -l {0}
         run: |
-          pip install .
+          pip install -e .[testing]
           pytest --cache-clear
       - name: Upload Coverage
         shell: bash -l {0}
@@ -57,12 +63,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
           COVERALLS_PARALLEL: true
-      - name: Create wheel package
+      - name: Create wheel and dist package
         shell: bash -l {0}
         run: |
-          pip install wheel
+          git status
+          pip install setuptools_scm
           python setup.py sdist --dist-dir .artifacts/dist
-          python setup.py bdist_wheel --dist-dir .artifacts/dist
           ls .artifacts/dist
       - name: Upload Artifacts
         uses: actions/upload-artifact@v2

.gitignore

@@ -51,3 +51,4 @@ MANIFEST
 # Per-project virtualenvs
 .venv*/
 .conda*/
+.python-version

.readthedocs.yml

@@ -16,7 +16,12 @@ sphinx:
 formats:
   - pdf
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
+    - {path: ., method: pip}

CHANGELOG.rst

@@ -2,6 +2,11 @@
 Changelog
 =========
 
+Version 0.0.5
+=============
+
+- GPI, longitude, latitude of grid object no longer masked array
+
 Version 0.0.4
 =============
 

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2021 TU Wien, Department of Geodesy and Geoinformation
+Copyright (c) 2024 TU Wien
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -21,5 +21,5 @@ Creating Fibonacci grid and read pre-computed grids.
 Note
 ====
 
-This project has been set up using PyScaffold 4.0.1. For details and usage
+This project has been set up using PyScaffold 4.5. For details and usage
 information on PyScaffold see https://pyscaffold.org/.

docs/Makefile

@@ -11,7 +11,7 @@ AUTODOCDIR    = api
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1)
-$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/")
+$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/")
 endif
 
 .PHONY: help clean Makefile

docs/conf.py

@@ -9,14 +9,11 @@
 
 import os
 import sys
-import inspect
 import shutil
 
 # -- Path setup --------------------------------------------------------------
 
-__location__ = os.path.join(
-    os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
-)
+__location__ = os.path.dirname(__file__)
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -26,7 +23,7 @@
 # -- Run sphinx-apidoc -------------------------------------------------------
 # This hack is necessary since RTD does not issue `sphinx-apidoc` before running
 # `sphinx-build -b html . _build/html`. See Issue:
-# https://github.com/rtfd/readthedocs.org/issues/1139
+# https://github.com/readthedocs/readthedocs.org/issues/1139
 # DON'T FORGET: Check the box "Install your project inside a virtualenv using
 # setup.py install" in the RTD Advanced Settings.
 # Additionally it helps us to avoid running apidoc manually
@@ -46,11 +43,7 @@
 try:
     import sphinx
 
-    cmd_line_template = (
-        "sphinx-apidoc --implicit-namespaces -f -o {outputdir} {moduledir}"
-    )
-    cmd_line = cmd_line_template.format(
-        outputdir=output_dir, moduledir=module_dir)
+    cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}"
 
     args = cmd_line.split(" ")
     if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
@@ -79,13 +72,18 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "myst_nb",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = ".rst"
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
+}
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
@@ -95,16 +93,25 @@
 
 # General information about the project.
 project = "fibgrid"
-copyright = "2021, TU Wien"
+copyright = "2024, TU Wien"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# The short X.Y version.
-version = ""  # Is set by calling `setup.py docs`
-# The full version, including alpha/beta/rc tags.
-release = ""  # Is set by calling `setup.py docs`
+# version: The short X.Y version.
+# release: The full version, including alpha/beta/rc tags.
+# If you don’t need the separation provided between version and release,
+# just set them both to the same value.
+try:
+    from fibgrid import __version__ as version
+except ImportError:
+    version = ""
+
+if not version or version.lower() == "unknown":
+    version = os.getenv("READTHEDOCS_VERSION", "unknown")  # automatically set by RTD
+
+release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -143,6 +150,9 @@
 # If true, keep warnings as "system message" paragraphs in the built documents.
 # keep_warnings = False
 
+# If this is True, todo emits a warning for each TODO entries. The default is False.
+todo_emit_warnings = True
+
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -163,12 +173,7 @@
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-try:
-    from fibgrid import __version__ as version
-except ImportError:
-    pass
-else:
-    release = version
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 # html_short_title = None
@@ -272,12 +277,18 @@
 # -- External mapping --------------------------------------------------------
 python_version = ".".join(map(str, sys.version_info[0:2]))
 intersphinx_mapping = {
-    "sphinx": ("http://www.sphinx-doc.org/en/stable", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master", None),
     "python": ("https://docs.python.org/" + python_version, None),
     "matplotlib": ("https://matplotlib.org", None),
-    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
     "sklearn": ("https://scikit-learn.org/stable", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "setuptools": ("https://setuptools.pypa.io/en/stable/", None),
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
+
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+
+# -- MyST-NB config ----------------------------------------------------------
+nb_execution_mode = 'off'

docs/index.rst

@@ -43,18 +43,18 @@ Indices and tables
 * :ref:`modindex`
 * :ref:`search`
 
-.. _toctree: http://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html
-.. _reStructuredText: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
-.. _references: http://www.sphinx-doc.org/en/stable/markup/inline.html
-.. _Python domain syntax: http://sphinx-doc.org/domains.html#the-python-domain
-.. _Sphinx: http://www.sphinx-doc.org/
-.. _Python: http://docs.python.org/
-.. _Numpy: http://docs.scipy.org/doc/numpy
-.. _SciPy: http://docs.scipy.org/doc/scipy/reference/
+.. _toctree: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html
+.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
+.. _references: https://www.sphinx-doc.org/en/stable/markup/inline.html
+.. _Python domain syntax: https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html#the-python-domain
+.. _Sphinx: https://www.sphinx-doc.org/
+.. _Python: https://docs.python.org/
+.. _Numpy: https://numpy.org/doc/stable
+.. _SciPy: https://docs.scipy.org/doc/scipy/reference/
 .. _matplotlib: https://matplotlib.org/contents.html#
-.. _Pandas: http://pandas.pydata.org/pandas-docs/stable
-.. _Scikit-Learn: http://scikit-learn.org/stable
-.. _autodoc: http://www.sphinx-doc.org/en/stable/ext/autodoc.html
-.. _Google style: https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings
+.. _Pandas: https://pandas.pydata.org/pandas-docs/stable
+.. _Scikit-Learn: https://scikit-learn.org/stable
+.. _autodoc: https://www.sphinx-doc.org/en/master/ext/autodoc.html
+.. _Google style: https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings
 .. _NumPy style: https://numpydoc.readthedocs.io/en/latest/format.html
-.. _classical style: http://www.sphinx-doc.org/en/stable/domains.html#info-field-lists
+.. _classical style: https://www.sphinx-doc.org/en/master/domains.html#info-field-lists

docs/requirements.txt

@@ -2,4 +2,5 @@
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 sphinx>=3.2.1
+myst-nb
 # sphinx_rtd_theme

environment.yml

@@ -1,7 +1,4 @@
-name: fibgrid_env
-channels:
-  - defaults
-  - conda-forge
+name: env
 dependencies:
   - numpy
   - netCDF4
@@ -10,7 +7,3 @@ dependencies:
   - pip
   - pip:
     - pygeogrids
-    - pytest
-    - pytest-cov
-    - pytest-mpl
-    - flake8

pyproject.toml

@@ -1,8 +1,9 @@
 [build-system]
 # AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
-requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5", "wheel"]
+requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-# See configuration details in https://github.com/pypa/setuptools_scm
+# For smarter version schemes and other configuration options,
+# check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"