Merge pull request #30 from greglucas/mnt-cleanup

cleanup, linting, type annotations
SWxTREC · Jan 29, 2023 · 0bfed27 · 0bfed27
2 parents 606a11f + 9190a62
commit 0bfed27
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diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/download_mirror.py b/.github/workflows/download_mirror.py
@@ -1,7 +1,8 @@
-"""This is only for CI downloading/testing."""
-from pathlib import Path
+"""Only for CI downloading/testing."""
 import tarfile
 import urllib.request
+from pathlib import Path
+
 
 MSIS21_FILE = (
     "https://gist.github.com/greglucas/"

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -8,12 +8,22 @@ concurrency:
 
 on:
   push:
-    branches: [ '*' ]
+    branches: [ 'main' ]
   pull_request:
-    branches: [ main ]
 
 jobs:
-  build:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+            python-version: 3.11
+      - name: Install mypy
+        run: |
+          python -m pip install mypy numpy
+          mypy pymsis
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -60,11 +70,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install -v .[tests]
 
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --show-source --statistics
-
     - name: Test with pytest
       run: |
         # TODO: Get coverage for other modules without specifying pymsis.msis directly

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -91,7 +91,7 @@ jobs:
         run: |
           python .github/workflows/download_mirror.py
 
-      - uses: pypa/cibuildwheel@v2.11.2
+      - uses: pypa/cibuildwheel@v2.12.0
         with:
           only: ${{ matrix.only }}
 
@@ -103,7 +103,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         name: Install Python

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,17 @@
+ci:
+    autofix_prs: false
+repos:
+-   repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+    - id: black
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+    - id: isort
+      name: isort (python)
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.0.236'
+    hooks:
+    - id: ruff
+      args: [--fix]
diff --git a/README.md b/README.md
@@ -3,28 +3,26 @@
 ![image](https://swxtrec.github.io/pymsis/_static/pymsis-logo.png)
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5348502.svg)](https://doi.org/10.5281/zenodo.5348502)
-![PyPi](https://badge.fury.io/py/pymsis.svg)
-![Downloads](https://pepy.tech/badge/pymsis/month)
-![GitHubActions](https://github.com/SWxTREC/pymsis/actions/workflows/tests.yml/badge.svg)
+[![PyPi](https://badge.fury.io/py/pymsis.svg)](https://badge.fury.io/py/pymsis)
+[![Downloads](https://static.pepy.tech/badge/pymsis/month)](https://pepy.tech/project/pymsis)
+[![GitHubActions](https://github.com/SWxTREC/pymsis/actions/workflows/tests.yml/badge.svg)](https://github.com/SWxTREC/pymsis/actions?query=workflow%3Atests)
+[![codecov](https://codecov.io/gh/SWxTREC/pymsis/branch/main/graph/badge.svg?token=NSUGKPJ3F7)](https://codecov.io/gh/SWxTREC/pymsis)
 
-Pymsis is meant to be a minimal and fast Python wrapper of the NRLMSIS
-models. Documentation to get started quickly can be found on the [home
-page](https://swxtrec.github.io/pymsis/). It includes some
-[examples](https://swxtrec.github.io/pymsis/examples/index.html) that
-demonstrate how to access and plot the data.
+Pymsis is a minimal and fast Python wrapper of the NRLMSIS
+models (MSISE-00, MSIS2.0, MSIS2.1).
 
 ## Quickstart
 
-A few short lines of code to get started quickly with pymsis.
-Use Numpy to create a range of dates during the 2003 Halloween storm.
-Then run the model at the location (lon, lat) (0, 0) and 400 km altitude.
-The model will automatically download and access the F10.7 and ap data for you
-if you have an internet connection.
-The returned data structure has shape [ndates, nlons, nlats, nalts, 11],
-but note that for this example we only have one longitude, latitude, and altitude.
-The 11 is for each of the species MSIS calculates at each point of input.
-The first element is the Total Mass Density (kg/m3) and if we plot that over
-time, we can see how the mass density increased at 400 km altitude during this storm.
+[Web viewer](https://swx-trec.com/msis): An interactive website using pymsis through cloud-based serverless functions.
+[Project homepage](https://swxtrec.github.io/pymsis/): Location for all documentation.
+[API Reference](https://swxtrec.github.io/pymsis/reference/index.html): Details about the various options and configurations available in the functions.
+[Examples](https://swxtrec.github.io/pymsis/examples/index.html): Demo for how to access and plot the data.
+
+**A few short lines of code to get started quickly with pymsis.**
+
+1. Create a range of dates during the 2003 Halloween storm.
+2. Run the model at the desired location (lon, lat) (0, 0) and 400 km altitude.
+3. Plot the results to see how the mass density increased at 400 km altitude during this storm.
 
 ```python
 import numpy as np
@@ -38,15 +36,14 @@ data = msis.run(dates, 0, 0, 400, geomagnetic_activity=-1)
 import matplotlib.pyplot as plt
 # Total mass density over time
 plt.plot(dates, data[:, 0, 0, 0, 0])
-plt.tight_layout()
 plt.show()
 ```
 
-[Additional examples](https://swxtrec.github.io/pymsis/examples/index.html) that
-demonstrate how to access and plot the data.
-
-[API Documentation](https://swxtrec.github.io/pymsis/reference/index.html) with
-details about the various options and configurations available.
+> **note**
+>
+> * The model will automatically download and access the F10.7 and ap data for you if you have an internet connection.
+> * The returned data structure has shape [ndates, nlons, nlats, nalts, 11], but for this example we only have one point with many dates [ndates, 1, 1, 1, 11].
+> * The 11 is for each of the species MSIS calculates for each input point. The first element is the Total Mass Density (kg/m3).
 
 ## NRL Mass Spectrometer, Incoherent Scatter Radar Extended Model (MSIS)
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -1,21 +1,26 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""
+Configuration file for the Sphinx documentation builder.
+
+This file only contains a selection of the most common options. For a full
+list see the documentation:
+https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""
 
 # -- Path setup --------------------------------------------------------------
 
+import sys
+
 # 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
 # documentation root, use resolve() to make it absolute, like shown here.
 #
 from pathlib import Path
-import sys
+
 from sphinx_gallery.sorting import ExampleTitleSortKey
 
 import pymsis
 
+
 sys.path.insert(0, Path("../../pymsis").resolve())
 
 # -- Project information -----------------------------------------------------

diff --git a/docs/source/development/index.rst b/docs/source/development/index.rst
@@ -3,10 +3,33 @@
 Development
 ===========
 
-To contribute to pymsis, all you need to do is fork the GitHub repository,
+To contribute to pymsis, you can fork the GitHub repository,
 add your code, and make a pull request. If you are adding additional functionality,
 you should also include a test with your enhancement.
 
-Pymsis is purposefully minimal, with numpy as the only dependency.
+Pymsis is purposefully minimal, with Numpy as the only dependency.
 This makes it easy for other packages to leverage the interface to the Fortran
 code without imposing a specific data storage or plotting framework.
+
+A typical development workflow might look like the following:
+
+.. code:: bash
+    
+    # Install the development dependencies
+    pip install .[dev]
+
+    # Install the pre-commit hooks
+    pre-commit install
+
+    # Update the code on a feature branch
+    git checkout -b my-cool-feature
+
+    # Run the tests
+    pytest
+
+    # Commit the changes and push to your remote repository
+    git add my-file
+    git commit
+    git push -u origin my-cool-feature
+
+    # Go to GitHub and open a pull request!
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -3,8 +3,9 @@ Pymsis Documentation
 ====================
 
 This is a lightweight Python wrapper around the MSIS00 and MSIS2 Fortran source code.
-The `MSIS model <https://www.nrl.navy.mil/ssd/branches/7630/modeling-upper-atmosphere>`_ is
-developed by the Naval Research Laboratory.
+The `MSIS model <https://www.nrl.navy.mil/Our-Work/Areas-of-Research/Space-Science/>`_ is
+developed by the Naval Research Laboratory. For quick access to the model data without any code,
+there is a web viewer that uses pymsis: `<https://swx-trec.com/msis>`_.
 
 The :ref:`examples` are a good reference for quickly getting started with the Python code and demonstrate
 how to call the models and plot the results. The explicit interfaces are described in the :ref:`api`.

diff --git a/examples/plot_diurnal_variation.py b/examples/plot_diurnal_variation.py
@@ -6,8 +6,8 @@
 diurnal variation at a single location.
 
 """
-import matplotlib.pyplot as plt
 import matplotlib.dates as mdates
+import matplotlib.pyplot as plt
 import numpy as np
 
 from pymsis import msis

diff --git a/examples/plot_surface_animation.py b/examples/plot_surface_animation.py
@@ -7,10 +7,10 @@
 
 """
 import matplotlib
-from matplotlib.animation import FuncAnimation
 import matplotlib.dates as mdates
 import matplotlib.pyplot as plt
 import numpy as np
+from matplotlib.animation import FuncAnimation
 
 from pymsis import msis
 

diff --git a/pymsis/__init__.py b/pymsis/__init__.py
@@ -1,24 +1,4 @@
-import os
-from pathlib import Path
+"""Python interface to the MSIS codes."""
 
-__version__ = "0.6.0"
-
-# If we are on Windows, Python 3.8+ then we need to add a DLL search path
-# The libraries are located relative to this init file.
-if os.name == "nt":
-    pymsis_dir = None
-    pymsis_dir_libs = None
-    try:
-        # add folder to Windows DLL search paths
-        pymsis_dir = Path(__file__).resolve().parent
-        pymsis_dir_libs = pymsis_dir / ".libs"
-        # This was added in Python 3.8, so we can default to this
-        # once we only support 3.8+
-        os.add_dll_directory(pymsis_dir)
-        # Additionally, we need the .libs directory which has gfortran
-        os.add_dll_directory(pymsis_dir_libs)
 
-        os.environ["PATH"] = f"{pymsis_dir};{pymsis_dir_libs};" f"{os.environ['PATH']}"
-    except Exception:
-        pass
-    del pymsis_dir, pymsis_dir_libs
+__version__ = "0.6.0"