Merge branch 'master' of https://github.com/mbakker7/ttim

.coveragerc

@@ -0,0 +1,6 @@
+[run]
+omit =
+    */ttim/circinhom.py
+    */ttim/besselnumba_total.py
+    */ttim/aquifernew.py
+    */ttim/kuhlman_invlap.py

.github/workflows/ci.yml

@@ -0,0 +1,50 @@
+name: ttim
+
+on:
+  # Trigger the workflow on push or pull request on master
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.ci.txt ]; then pip install -r requirements.ci.txt; fi
+          pip install flake8 pytest
+          pip install codecov
+          pip install pytest-cov
+          pip install coveralls
+          pip install -e .
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics
+
+      - name: Run tests
+        run: |
+          py.test ./tests
+
+      - name: Publish to coveralls.io
+        run: coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

README.md

@@ -1,5 +1,6 @@
-[![Linux+/+macOS](https://travis-ci.org/mbakker7/ttim.svg?branch=master)](https://travis-ci.org/mbakker7/ttim)
+[![ttim](https://github.com/mbakker7/ttim/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/mbakker7/ttim/actions/workflows/ci.yml)
 [![Coverage Status](https://coveralls.io/repos/github/mbakker7/ttim/badge.svg?branch=master)](https://coveralls.io/github/mbakker7/ttim?branch=master)
+![PyPI](https://img.shields.io/pypi/v/ttim?color=green)
 
 # TTim, A Multi-Layer, Transient, Analytic Element Model
 
@@ -16,7 +17,7 @@ TTim is coded in Python and uses numba to speed up evaluation of the line elemen
 
 ## Latest version
 New in version 0.5:
-* FORTRAN extension has been ported to Python and numba (many thanks to Davíd Brakenhoff)
+* FORTRAN extension has been ported to Python and numba (many thanks to Davíd Brakenhoff)
 * Python invlap routine (again with numba) ported from routine by Kris Kuhlman
 * New invlap routine requires fewer terms in inverse Laplace transform (M=10 is usually enough)
 * Calibrate now works on ranges of parameters.
@@ -39,7 +40,7 @@ To update TTim type:
 
     pip install ttim --upgrade
 
-To uninstall TTi type:
+To uninstall TTim type:
 
     pip uninstall ttim
 
@@ -52,6 +53,6 @@ To uninstall TTi type:
 
 Some of the papers that you may want to cite when using TTim are:
 
-* M. Bakker. 2013. Semi-analytic modeling of transient multi-layer flow with TTim. Hydrogeology Journal, 21: 935Ð943.
+* M. Bakker. 2013. Semi-analytic modeling of transient multi-layer flow with TTim. Hydrogeology Journal, 21: 935�943.
 * M .Bakker. 2013. Analytic modeling of transient multi-layer flow. In: Advances in Hydrogeology, edited by P Mishra and K Kuhlman, Springer, Heidelberg, 95-114.
 

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+addopts=--durations=0 -v --cov ttim --cov-config=.coveragerc --ignore=test_bessel.py
+markers =
+    notebooks: run notebooks

requirements.ci.txt

@@ -0,0 +1,7 @@
+numpy>=1.17
+scipy>=1.5
+numba>=0.5
+matplotlib>=3.1,<3.5.0
+lmfit>=1.0
+pandas>=1.1
+jupyter>=1.0.0

setup.py

@@ -1,28 +1,30 @@
+from os import path
+
 from setuptools import setup
+
 version = {}
 with open("ttim/version.py") as fp:
     exec(fp.read(), version)
 
 l_d = ""
-try:
-    import pypandoc
-
-    l_d = pypandoc.convert("README.md", "rst")
-except:
-    pass
+this_directory = path.abspath(path.dirname(__file__))
+with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
+    l_d = f.read()
 
 
 setup(
     name="ttim",
     version=version["__version__"],
     description="Transient multi-layer AEM Model",
     long_description=l_d,
+    long_description_content_type='text/markdown',
     author="Mark Bakker",
     author_email="markbak@gmail.com",
     url="https://github.com/mbakker7/ttim",
     license="MIT",
     packages=["ttim"],
     python_requires='>=3.7',
-    install_requires=["numpy>=1.17", "scipy>=1.5", "numba>=0.5", "matplotlib>=3.1", "lmfit>=1.0", "pandas>=1.1"],
+    install_requires=["numpy>=1.17", "scipy>=1.5", "numba>=0.5",
+                      "matplotlib>=3.1", "lmfit>=1.0", "pandas>=1.1"],
     classifiers=['Topic :: Scientific/Engineering :: Hydrology'],
 )

tests/test_notebooks.py

@@ -1,6 +1,9 @@
 import os
+import shutil
+import subprocess
+import tempfile
+
 import pytest
-import shutil, tempfile
 
 nbdir = os.path.join('notebooks')
 
@@ -24,6 +27,7 @@ def get_jupyter_kernel():
 
     return kernel    
 
+@pytest.mark.notebooks
 @pytest.mark.parametrize("fn", get_notebooks())
 def test_notebook(fn):
 

ttim/aquifernew.py

@@ -1,3 +1,4 @@
+# flake8: noqa
 import numpy as np
 import matplotlib.pyplot as plt
 import inspect # Used for storing the input

ttim/circinhom.py

@@ -1,3 +1,4 @@
+# flake8: noqa
 import numpy as np
 from scipy.special import kv, iv # Needed for K1 in Well class, and in CircInhom
 from .aquifer import AquiferData