Merge pull request #40 from pysat/maint/pysat_dep

MAINT: pysat deprecations
pysat · Aug 13, 2024 · 53cfd3f · 53cfd3f
2 parents 59503ce + c9e70ab
commit 53cfd3f
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -12,26 +12,31 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     name: Documentation tests
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - 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: |
         mkdir pysatData
         python -c "import pysat; pysat.params['data_dirs'] = './pysatData'"
 
+    - name: Check documentation build
+      run: sphinx-build -E -b html docs dist/docs
+
+    - name: Check documentation links
+      run: sphinx-build -b linkcheck docs dist/docs
+
     - name: Load .zenodo.json to check for errors
       run: python -c "import json; json.loads(open('.zenodo.json').read())"
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -10,37 +10,35 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        numpy_ver: [latest]
+        python-version: ["3.11", "3.12"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        numpy_ver: ["latest"]
+        test_config: ["latest"]
         include:
-           - python-version: "3.8"
-             numpy_ver: "1.20"
+           - python-version: "3.10"
+             numpy_ver: "1.24"
              os: "ubuntu-latest"
+             test_config: "NEP29"
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install requirements for testing setup
-      run: |
-        pip install -r test_requirements.txt
-
     - name: Install NEP29 dependencies
-      if: ${{ matrix.numpy_ver != 'latest'}}
+      if: ${{ matrix.test_config == 'NEP29'}}
       run: |
-        pip install --no-binary :numpy: numpy==${{ matrix.numpy_ver }}
-        # Need to force a version of pandas compliant with NEP29
-        pip install "pandas<1.5"
+        pip install numpy==${{ matrix.numpy_ver }}
+        pip install --upgrade-strategy only-if-needed .[test]
 
-    - name: Install dependencies
+    - name: Install standard dependencies
+      if: ${{ matrix.test_config == 'latest'}}
       run: |
-        pip install -r requirements.txt
+        pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -54,9 +52,44 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Test with pytest
-      run: pytest --cov=pysatSeasons/
+      run: pytest
+
+    - name: Coveralls Parallel (Ubuntu)
+      if: startsWith(matrix.os, 'ubuntu')
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        COVERALLS_PARALLEL: true
+      run: |
+        curl -sL https://coveralls.io/coveralls-linux.tar.gz | tar -xz
+        ./coveralls report --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }}
 
-    - name: Publish results to coveralls
+    - name: Coveralls Parallel (Windows)
+      if: startsWith(matrix.os, 'windows')
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        COVERALLS_PARALLEL: true
+      run: |
+        curl -L https://github.com/coverallsapp/coverage-reporter/releases/latest/download/coveralls-windows.exe -o coveralls.exe
+        ./coveralls.exe report --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }}
+
+    - name: Coveralls Parallel (MacOS)
+      if: startsWith(matrix.os, 'macos')
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        COVERALLS_PARALLEL: true
+      run: |
+        coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    if: always()
+    runs-on: "ubuntu-latest"
+    steps:
+      - name: Coveralls Finish
+        env:
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+          COVERALLS_PARALLEL: true
+        run: |
+          curl -sL https://coveralls.io/coveralls-linux.tar.gz | tar -xz
+          ./coveralls done --build-number ${{ github.run_number }}
diff --git a/.github/workflows/pip_rc_install.yml b/.github/workflows/pip_rc_install.yml
@@ -4,22 +4,22 @@
 
 name: Test install of latest RC from pip
 
-on: [push]
+on: [workflow_dispatch]
 
 jobs:
   build:
     strategy:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10"]  # Keep this version at the highest supported Python version
+        python-version: ["3.12"]  # Keep this version at the highest supported Python version
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/pysat_rc.yml b/.github/workflows/pysat_rc.yml
@@ -11,24 +11,22 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install pysat RC
       run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysat
 
-    - name: Install standard dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install -r test_requirements.txt
+    - name: Install with standard dependencies
+      run:  pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -41,4 +39,17 @@ jobs:
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_PARALLEL: true
       run: coveralls --rcfile=setup.cfg --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
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,12 +2,14 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [0.X.X] - 202X-XX-XX
+## [0.2.1] - 202X-XX-XX
 - Maintenance
   - Update pytest syntax
   - Update Github Actions workflows
   - Add workflow for testing with pysat RC
   - Add workflow for testing the install of pysatSeasons RC from pip
+  - Dropped tests for deprecated pysat instruments
+  - Implement pyproject.toml
 
 ## [0.2.0] - 2022-08-12
 - New Features

diff --git a/demo/cosmic_and_ivm_demo.py b/demo/cosmic_and_ivm_demo.py
@@ -24,7 +24,7 @@
                      'the currently installed version. Please see the demo ',
                      'code in pysatSeasons v0.1.3 for COSMIC support when in ',
                      'pandas data format.'])
-    raise(ValueError, estr)
+    raise (ValueError, estr)
 
 
 def add_magnetic_coordinates(inst):

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,91 @@
+[build-system]
+requires = ["setuptools >= 38.6", "pip >= 10"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["pysatSeasons"]
+
+[project]
+name = "pysatSeasons"
+version = "0.2.0"
+description = "Seasonal analysis routines for pysat"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Russell Stoneback, et al.", email = "[email protected]"},
+]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Topic :: Scientific/Engineering :: Astronomy",
+  "Topic :: Scientific/Engineering :: Physics",
+  "Topic :: Scientific/Engineering :: Atmospheric Science",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Natural Language :: English",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.6",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Operating System :: POSIX :: Linux",
+  "Operating System :: MacOS :: MacOS X",
+  "Operating System :: Microsoft :: Windows"
+]
+keywords = [
+  "pysat",
+  "ionosphere",
+  "magnetosphere",
+  "solar wind",
+  "thermosphere",
+  "average",
+  "analysis",
+  "season",
+  "climatology"
+]
+dependencies = [
+  "matplotlib",
+  "numpy",
+  "pandas",
+  "pysat >= 3.0.4",
+  "xarray"
+]
+
+[project.optional-dependencies]
+pysatcdf = ["pysatCDF"]
+test = [
+  "coveralls",
+  "flake8",
+  "flake8-docstrings",
+  "hacking >= 1.0",
+  "pytest",
+  "pytest-cov",
+  "pytest-ordering"
+]
+doc = [
+  "extras_require",
+  "ipython",
+  "m2r2",
+  "numpydoc",
+  "sphinx",
+  "sphinx_rtd_theme >= 1.2.2, < 2.0.0"
+]
+
+[project.urls]
+Documentation = "https://pysatseasons.readthedocs.io/en/latest/"
+Source = "https://github.com/pysat/pysatSeasons"
+
+[tool.coverage.report]
+omit = ["*/instruments/templates/"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=pysatSeasons --cov-report xml"
+markers = [
+  "all_inst",
+  "download",
+  "no_download",
+  "load_options",
+  "new_tests",
+  "first",
+  "second"
+]
diff --git a/pysatSeasons/__init__.py b/pysatSeasons/__init__.py
@@ -18,7 +18,10 @@
 
 """
 
-import os
+try:
+    from importlib import metadata
+except ImportError:
+    import importlib_metadata as metadata
 
 # Import key modules and skip F401 testing in flake8
 from pysatSeasons._core import to_xarray_dataset  # noqa: F401
@@ -27,6 +30,4 @@
 from pysatSeasons import plot  # noqa: F401
 
 # set version
-here = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(here, 'version.txt')) as version_file:
-    __version__ = version_file.read().strip()
+__version__ = metadata.version('pysatSeasons')
diff --git a/pysatSeasons/_core.py b/pysatSeasons/_core.py
@@ -22,8 +22,8 @@ def to_xarray_dataset(data):
     Parameters
     ----------
     data : list-like
-        List-like (including ndarray, Series, DataFrames, Datasets or list-like of these object) to be converted
-        or combined into a single Dataset.
+        List-like (including ndarray, Series, DataFrames, Datasets or list-like
+        of these object) to be converted or combined into a single Dataset.
 
     Returns
     -------