Merge pull request #129 from pysat/sty/pyproject

MAINT: pyproject.toml, docs

Author: jklenzing

.github/workflows/docs.yml

@@ -25,8 +25,7 @@ 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

@@ -11,12 +11,18 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11"]
         numpy_ver: ["latest"]
+        test_config: ["latest"]
         include:
-          - python-version: "3.8"
+          - python-version: "3.9"
             numpy_ver: "1.21"
-            os: "ubuntu-latest"
+            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 }}
@@ -31,14 +37,24 @@ jobs:
       if: ${{ matrix.os == 'macos-latest' }}
       run: brew reinstall gcc
 
+    - name: Install Operational dependencies
+      if: ${{ matrix.test_config == 'Ops'}}
+      run: |
+        pip install --no-cache-dir numpy==${{ matrix.numpy_ver }}
+        pip install -r requirements.txt
+        pip install -r test_requirements.txt
+        pip install .
+
     - name: Install NEP29 dependencies
-      if: ${{ matrix.numpy_ver != 'latest'}}
-      run: pip install numpy==${{ matrix.numpy_ver }}
+      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 -r requirements.txt
-        pip install -r test_requirements.txt
+        pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -52,9 +68,9 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Test with pytest
-      run: pytest -vs --cov=pysatNASA/
+      run: pytest
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+      run: coveralls --rcfile=pyproject.toml --service=github

CHANGELOG.md

@@ -49,6 +49,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Update meta label type for instruments
   * Updated GitHub Actions workflows for improved compliance with pip>=23.0
   * Added .readthedocs.yml to configure settings there.
+  * Use pyproject.toml to manage installation and metadata
 
 ## [0.0.4] - 2022-11-07
 * Update instrument tests with new test class

README.md

@@ -1,6 +1,6 @@
 <div align="left">
         <img height="0" width="0px">
-        <img width="20%" src="https://raw.githubusercontent.com/pysat/pysatNASA/main/docs/figures/logo.png" alt="pysatNASA" title="pysatNASA" </img>
+        <img width="20%" src="https://raw.githubusercontent.com/pysat/pysatNASA/main/docs/figures/pysatnasa_logo.png" alt="pysatNASA" title="pysatNASA" </img>
 </div>
 
 # pysatNASA: pysat support for NASA Space Science instruments
@@ -20,14 +20,14 @@ some examples on how to use the routines
 
 pysatNASA uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
-Python 3.8+.
+Python 3.6+.
 
 | Common modules   | Community modules | Optional Modules |
 | ---------------- | ----------------- |------------------|
 | beautifulsoup4   | cdflib            | pysatCDF         |
 | lxml             | pysat>=3.0.4      |                  |
 | netCDF4          |                   |                  |
-| numpy<1.24       |                   |                  |
+| numpy            |                   |                  |
 | pandas           |                   |                  |
 | requests         |                   |                  |
 | xarray           |                   |                  |
@@ -43,12 +43,12 @@ pip install pysatNASA
 git clone https://github.com/pysat/pysatNASA.git
 ```
 
-Change directories into the repository folder and run the setup.py file.  For
+Change directories into the repository folder and build the project.  For
 a local install use the "--user" flag after "install".
 
 ```
 cd pysatNASA/
-python setup.py install
+pip install .
 ```
 
 Note: pre-1.0.0 version

docs/conf.py

@@ -10,6 +10,7 @@
 
 import json
 import os
+import pkg_resources
 import sys
 sys.path.insert(0, os.path.abspath('..'))
 
@@ -63,9 +64,7 @@
 # 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.
-doc_dir = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(doc_dir, "..", project, "version.txt"), "r") as fin:
-    version = fin.read().strip()
+version = pkg_resources.get_distribution('pysatNASA').version
 release = '{:s}-alpha'.format(version)  # Include alpha/beta/rc tags.
 
 # The language for content autogenerated by Sphinx. Refer to documentation
@@ -97,7 +96,7 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-html_logo = os.path.join(os.path.abspath('.'), 'figures', 'logo.png')
+html_logo = os.path.join(os.path.abspath('.'), 'figures', 'pysatnasa_logo.png')
 html_theme_options = {'logo_only': True}
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/figures/logo.png renamed to docs/figures/pysatnasa_logo.png

@@ -40,24 +40,32 @@ Installation Options
 
 
 2. Install pysatNASA:
-   Change directories into the repository folder and run the setup.py file.
+   Change directories into the repository folder and build the project.
    There are a few ways you can do this:
 
    A. Install on the system (root privileges required)::
 
 
-        sudo python setup.py install
+        sudo pip install .
+
    B. Install at the user level::
 
 
-        python setup.py install --user
-   C. Install with the intent to develop locally::
+        pip install --user .
+
+   C. Install with the intent to change the code::
+
+
+        pip install --user -e .
 
+.. extras-require:: pysatcdf
+    :pyproject:
 
-        python setup.py develop --user
+.. extras-require:: test
+    :pyproject:
 
-.. extras-require:: all
-    :setup.cfg:
+.. extras-require:: doc
+    :pyproject:
 
 .. _post-install:
 

docs/installation.rst

@@ -5,7 +5,7 @@ This is a library of ``pysat`` instrument modules and methods designed to suppor
 NASA instruments and missions archived at the Community Data Analysis Web
 portal.
 
-.. image:: figures/logo.png
+.. image:: figures/pysatnasa_logo.png
     :width: 400px
     :align: center
     :alt: pysatNASA Logo, a blue planet with red orbiting python and the module name superimposed

docs/overview.rst

@@ -0,0 +1,88 @@
+[build-system]
+requires = ["setuptools", "pip >= 10"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pysatNASA"
+version = "0.0.5"
+description = "pysat support for NASA Instruments"
+readme = "README.md"
+requires-python = ">=3.6"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Jeff Klenzing, 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 :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Operating System :: POSIX :: Linux",
+  "Operating System :: MacOS :: MacOS X",
+  "Operating System :: Microsoft :: Windows"
+]
+keywords = [
+  "pysat",
+  "ionosphere",
+  "magnetosphere",
+  "solar wind",
+  "thermosphere"
+]
+dependencies = [
+  "beautifulsoup4",
+  "cdasws",
+  "cdflib >= 0.4.4",
+  "lxml",
+  "netCDF4",
+  "numpy",
+  "pandas",
+  "pysat >= 3.0.4",
+  "requests",
+  "xarray"
+]
+
+[project.optional-dependencies]
+pysatcdf = ["pysatCDF"]
+test = [
+  "coveralls < 3.3",
+  "flake8",
+  "flake8-docstrings",
+  "hacking >= 1.0",
+  "pytest",
+  "pytest-cov",
+  "pytest-ordering"
+]
+doc = [
+  "extras_require",
+  "ipython",
+  "m2r2",
+  "numpydoc",
+  "sphinx",
+  "sphinx_rtd_theme"
+]
+
+[project.urls]
+Documentation = "https://pysatnasa.readthedocs.io/en/latest/"
+Source = "https://github.com/pysat/pysatNASA"
+
+[tool.coverage.report]
+omit = ["*/instruments/templates/"]
+
+[tool.pytest.ini_options]
+addopts = "-vs --cov=pysatNASA"
+markers = [
+  "all_inst",
+  "download",
+  "no_download",
+  "load_options",
+  "first",
+  "second"
+]

pyproject.toml

@@ -6,13 +6,15 @@
 
 """
 
-import os
+import importlib
+import importlib_metadata
+
 from pysatNASA import constellations  # noqa F401
 from pysatNASA import instruments  # noqa F401
 
 # set version
-here = os.path.abspath(os.path.dirname(__file__))
-version_filename = os.path.join(here, 'version.txt')
-with open(version_filename, 'r') as version_file:
-    __version__ = version_file.read().strip()
-del here, version_filename, version_file
+try:
+    __version__ = importlib.metadata.version('pysatNASA')
+except AttributeError:
+    # Python 3.6 requires a different version
+    __version__ = importlib_metadata.version('pysatNASA')

pysatNASA/__init__.py

@@ -1,10 +1,10 @@
-netCDF4
-requests
 beautifulsoup4
-lxml
+cdasws
 cdflib>=0.4.4
+lxml
+netCDF4
 numpy
 pandas
 pysat>=3.0.4
-cdasws
+requests
 xarray

pysatNASA/version.txt

@@ -1,69 +1,12 @@
+# name and version must be maintained here as well for python 3.6 compatibility
+
 [metadata]
 name = pysatNASA
-version = file: pysatNASA/version.txt
-url = https://github.com/pysat/pysatNASA
-author = Jeff Klenzing
-author_email = [email protected]
-description = 'pysat support for NASA Instruments'
-keywords =
-  pysat
-  ionosphere
-classifiers =
-  Development Status :: 3 - Alpha
-  Topic :: Scientific/Engineering :: Physics
-  Topic :: Scientific/Engineering :: Atmospheric Science
-  Intended Audience :: Science/Research
-  License :: OSI Approved :: BSD License
-  Natural Language :: English
-  Programming Language :: Python :: 3.5
-  Programming Language :: Python :: 3.6
-  Programming Language :: Python :: 3.7
-  Operating System :: MacOS :: MacOS X
-  Operating System :: POSIX :: Linux
-license_file = LICENSE
-long_description = file: README.md
-long_description_content_type = text/markdown
-
-[options]
-python_requires = >= 3.5
-setup_requires =
-  setuptools >= 38.6
-  pip >= 10
-include_package_data = True
-zip_safe = False
-packages = find:
-install_requires =
-  cdasws
-  netCDF4
-  requests
-  beautifulsoup4
-  lxml
-  cdflib
-  numpy
-  pandas
-  xarray
-  pysat
-
-[options.extras_require]
-all =
-  pysatCDF
-
-[coverage:report]
-omit =
-  */instruments/templates/
+version = 0.0.5
 
 [flake8]
 max-line-length = 80
 ignore =
   D200
   D202
   W503
-
-[tool:pytest]
-markers =
-    all_inst: tests all instruments
-    download: tests for downloadable instruments
-    no_download: tests for instruments without download support
-    load_options: tests for instruments with additional options
-    first: first tests to run
-    second: second tests to run