Merge pull request #137 from pysat/maint/pyproject

MAINT: pyproject, pysat style updates

.github/workflows/docs.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]  # Keep this version at the highest supported Python version
 
     name: Documentation tests
     steps:
@@ -26,8 +26,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r test_requirements.txt
-        pip install -r requirements.txt
+        pip install .[doc]
 
     - name: Set up pysat
       run: |

.github/workflows/main.yml

@@ -12,13 +12,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10"]
-        numpy_ver: [latest]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.10", "3.11"]
+        numpy_ver: ["latest"]
+        test_config: ["latest"]
         include:
-          - python-version: "3.8"
-            numpy_ver: "1.20.3"
-            os: "ubuntu-latest"
+          - python-version: "3.9"
+            numpy_ver: "1.22"
+            os: ubuntu-latest
+            test_config: "NEP29"
+          - python-version: "3.6.8"
+            numpy_ver: "1.19.5"
+            os: "ubuntu-20.04"
+            test_config: "Ops"
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with numpy ${{ matrix.numpy_ver }}
     runs-on: ${{ matrix.os }}
@@ -29,15 +35,24 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install standard dependencies
+    - name: Install Operational dependencies
+      if: ${{ matrix.test_config == 'Ops'}}
       run: |
-        pip install -r test_requirements.txt
+        pip install --no-cache-dir numpy==${{ matrix.numpy_ver }}
+        pip install "cdflib<1.0"
         pip install -r requirements.txt
+        pip install -r test_requirements.txt
+        pip install .
 
     - name: Install NEP29 dependencies
-      if: ${{ matrix.numpy_ver != 'latest'}}
+      if: ${{ matrix.test_config == 'NEP29'}}
       run: |
         pip install numpy==${{ matrix.numpy_ver }}
+        pip install --upgrade-strategy only-if-needed .[test]
+
+    - name: Install standard dependencies
+      if: ${{ matrix.test_config == 'latest'}}
+      run: pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -51,9 +66,22 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Run unit and integration tests
-      run: pytest --cov=pysatModels/
+      run: pytest
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+        COVERALLS_PARALLEL: true
+      run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish

.github/workflows/pysat_rc.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]  # Keep this version at the highest supported Python version
         rc-package: ["pysat", "pysatNASA"]
 
     name: ${{ matrix.os }} with ${{ matrix.rc-package }} RC
@@ -30,19 +30,30 @@ jobs:
       run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ ${{ matrix.rc-package }}
 
     - name: Install standard dependencies
-      run: |
-        pip install -r test_requirements.txt
-        pip install -r requirements.txt
+      run: pip install .[test]
 
     - name: Set up pysat
       run: |
         mkdir pysatData
         python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
 
     - name: Run unit and integration tests
-      run: pytest --cov=pysatModels/
+      run: pytest
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+        COVERALLS_PARALLEL: true
+      run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish

.readthedocs.yml

@@ -0,0 +1,25 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

CHANGELOG.md

@@ -14,6 +14,8 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Updated tests to new pysat and pytest standards
   * Added a cap for pysatNASA
   * Removed backwards-support for pysat pre-3.0.4 functions
+  * Updated to use pyproject
+  * Added yaml for readthedocs
 * Documentation
   * Added badges and instructions for PyPi and Zenodo
 

README.md

@@ -30,7 +30,7 @@ the Space Physics community.  This module officially supports Python 3.6+.
 |   Common modules   | Community modules  |
 | ------------------ | ------------------ |
 | numpy              | pyForecastTools    |
-| pandas >= 1.4.0    | pysat >= 3.0.4     |
+| pandas             | pysat >= 3.0.4     |
 | requests           | pysatNASA <= 0.0.4 |
 | scipy              |                    |
 | xarray             |                    |

docs/conf.py

@@ -16,6 +16,7 @@
 import datetime as dt
 import json
 import os
+import pkg_resources
 import sys
 
 sys.path.insert(0, os.path.abspath('..'))
@@ -72,9 +73,7 @@
 #
 # The short X.Y version.
 module_dir = os.path.split(os.path.abspath(os.path.dirname(__file__)))[0]
-version_file = os.path.join(module_dir, project, 'version.txt')
-with open(version_file, 'r') as fin:
-    version = fin.read().strip()
+version = pkg_resources.get_distribution('pysatModels').version
 
 # The full version, including alpha/beta/rc tags.
 release = '{:s}-alpha'.format(version)
@@ -84,7 +83,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/installation.rst

@@ -20,15 +20,15 @@ Prerequisites
 pysatModels uses common Python modules, as well as modules developed by and for
 the Space Physics community.  This module officially supports Python 3.6+.
 
- ============== =================
+ ============== ==================
  Common modules Community modules
- ============== =================
-  numpy         pysat
-  pandas        pysatNASA
+ ============== ==================
+  numpy         pysat >= 3.0.4
+  pandas        pysatNASA <= 0.0.4
   requests      pyForecastTools
   scipy
   xarray
- ============== =================
+ ============== ==================
 
 
 .. _install-opt:

docs/overview.rst

@@ -11,7 +11,7 @@ output, and incorporating modelled data sets into general data analysis
 routines written to use data stored in
 `pysat.Instrument <https://pysat.readthedocs.io/en/latest/api.html#instrument>`_
 objects or
-`xarray.Datasets <https://xarray.pydata.org/en/stable/generated/xarray.Dataset.html>`_.
+`xarray.Datasets <https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html>`_.
 
 .. image:: images/pysatModels.png
     :width: 400px

pyproject.toml

@@ -0,0 +1,75 @@
+[build-system]
+requires = ["setuptools >= 38.6", "pip >= 10"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pysatModels"
+version = "0.1.0"
+description = "Supports model analysis and model-data comparisons"
+readme = "README.md"
+requires-python = ">=3.6"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Pysat Development Team", email = "[email protected]"},
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Intended Audience :: Science/Research",
+    "License :: Freely Distributable",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows"
+]
+dependencies = [
+  "numpy",
+  "packaging",
+  "pandas",
+  "pyForecastTools",
+  "pysat >= 3.0.4",
+  "pysatNASA <= 0.0.4",
+  "requests",
+  "scipy",
+  "xarray"
+]
+
+[project.optional-dependencies]
+test = [
+  "coveralls < 3.3",
+  "flake8",
+  "flake8-docstrings",
+  "hacking >= 1.0",
+  "pytest-cov",
+  "pytest-ordering"
+]
+doc = [
+  "extras_require",
+  "m2r2",
+  "numpydoc",
+  "sphinx",
+  "sphinx_rtd_theme >= 1.2.2, < 2.0.0"
+]
+
+[project.urls]
+Documentation = "https://pysatmodels.readthedocs.io/en/latest/"
+Source = "https://github.com/pysat/pysatModels"
+
+[tool.coverage.report]
+
+[tool.pytest.ini_options]
+addopts = "--cov=pysatModels"
+markers = [
+  "all_inst",
+  "download",
+  "no_download",
+  "load_options",
+  "new_tests",
+  "first",
+  "second"
+]

pysatModels/__init__.py

@@ -11,16 +11,18 @@
 """
 
 import logging
-import os
+
+try:
+    from importlib import metadata
+except ImportError:
+    import importlib_metadata as metadata
 
 # Import key modules and skip F401 testing in flake8
 from pysatModels import models  # noqa: F401
 from pysatModels import utils  # noqa: F401
 
 # Set the version
-local_dir = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(local_dir, 'version.txt')) as version_file:
-    __version__ = version_file.read().strip()
+__version__ = metadata.version('pysatModels')
 
 # Define a logger object to allow easier log handling
 logging.raiseExceptions = False
@@ -30,4 +32,4 @@
 logger.addHandler(handler)
 
 # Clean up variables
-del handler, local_dir, version_file
+del handler

pysatModels/models/pydineof_dineof.py

@@ -69,6 +69,8 @@
 
 _test_dates = {'': {tag: dt.datetime(2009, 1, 1) for tag in tags.keys()}}
 _test_download = {'': {'': False, 'test': True}}
+# TODO(#136): Remove when compliant with multi-day load tests
+_test_new_tests = {'': {'test': False}}
 
 # ----------------------------------------------------------------------------
 # Instrument methods

pysatModels/models/sami2py_sami2.py

@@ -49,6 +49,8 @@
 
 _test_dates = {'': {tag: dt.datetime(2019, 1, 1) for tag in tags.keys()}}
 _test_download = {'': {'': False, 'test': True}}
+# TODO(#136): Remove when compliant with multi-day load tests
+_test_new_tests = {'': {'test': False}}
 
 # ----------------------------------------------------------------------------
 # Instrument methods

pysatModels/models/ucar_tiegcm.py

@@ -53,7 +53,8 @@
 
 _test_dates = {'': {'': dt.datetime(2019, 1, 1),
                     'icon': dt.datetime(2020, 1, 10)}}
-_test_download = {'': {'': False, 'icon': True}}
+# TODO(#132): Turn on ICON download tests once pysatNASA 0.0.6 is released.
+_test_download = {'': {'': False, 'icon': False}}
 
 # ----------------------------------------------------------------------------
 # Instrument methods
@@ -243,7 +244,10 @@ def download(date_array, tag, inst_id, data_path=None, **kwargs):
 
     if tag == '':
         warnings.warn('Not implemented, currently no support for Globus.')
+    # TODO(#132): Ensure new download routine is used after pysatNASA release.
     elif tag == 'icon':
+        warnings.warn('Not implemented, requires pysatNASA 0.0.6.')
+    elif tag == 'future_icon':
         # Set up temporary directory for zip files
         temp_dir = tempfile.TemporaryDirectory()