replicate pull request 44

.github/workflows/test.yml

@@ -0,0 +1,45 @@
+name: run-tests
+
+on:
+   pull_request:
+    branches:
+      - main
+   push:
+    branches:
+      - main
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies manually
+        run: |
+          pip install future matplotlib cartopy pandas requests seaborn jupyter-book scikit-learn ipywidgets
+          pip install pmagpy==4.2.106
+          pip install -e ./smpsite
+          pip install flake8 pytest pytest-cov
+      - 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=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest smpsite --cov --cov-report=html:coverage_re
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        # with:
+        #   directory: ./smpsite
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -3,4 +3,5 @@
 *.pyc
 *.csv
 *.png
-*.pdf
+*.pdf
+*egg-info*

Makefile

@@ -7,7 +7,7 @@ env :
 	conda env create -f environment.yml 
 	conda activate paleosampling
 	conda install ipykernel
-	python -m ipykernel install --user --name make-env --display-name "IPython - PaleoSampling"
+	python -m ipykernel install --user --name paleosampling --display-name "IPython - PaleoSampling"
 
 
 .PHONY : help

README.md

@@ -3,9 +3,12 @@
 For a detailed description of the project, take a look at [our preprint of a manuscript that is in revision at JGR](https://www.authorea.com/doi/full/10.22541/essoar.168881772.25833701).
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/PolarWandering/PaleoSampling/HEAD) 
-[![DOI](https://zenodo.org/badge/595793364.svg)](https://zenodo.org/badge/latestdoi/595793364) 
 [![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://polarwandering.github.io/PaleoSampling/) 
 [![Build Status](https://github.com/PolarWandering/PaleoSampling/actions/workflows/book.yml/badge.svg?branch=main)](https://github.com/PolarWandering/PaleoSampling/actions/workflows/book.yml?query=branch%3Amain)
+![Tests Passing](https://github.com/github/docs/actions/workflows/test.yml/badge.svg)
+[![codecov](https://codecov.io/gh/PolarWandering/PaleoSampling/graph/badge.svg?token=8BCZXZV5JP)](https://codecov.io/gh/PolarWandering/PaleoSampling)
+[![DOI](https://zenodo.org/badge/595793364.svg)](https://zenodo.org/badge/latestdoi/595793364) 
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![All Contributors](https://img.shields.io/github/all-contributors/PolarWandering/PaleoSampling?color=ee8449&style=flat-square)](#contributors)
 
 
@@ -43,7 +46,13 @@ install all the required dependencies. Beside some standard Python dependencies,
 `Pmagpy` using pip and the extra installation of the module `smpsite` (included in this repository). The package `smpsite` includes all the code used to make the simulations and compute the
 estimated poles.
 
-In order to install the environment, you can use conda or mamba (see [Managing Environments](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) for more information) with `conda env create -f environment.yml`. Alternatively, we included a `Makefile` that creates the conda environment and installs the associated iPython kernel so this environment can be accessible though Jupyter notebooks all at once. In order to use the Makefile, you need to open a terminal where the repository is located and enter
+In order to install the environment, you can use conda or mamba (see [Managing Environments](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) for more information) with `conda env create -f environment.yml`. Once the environment is created, you can create the associated iPython kernel with 
+```
+python -m ipykernel install --user --name paleostats --display-name "IPython - PaleoStats"
+```
+This will allow you to execute this environment directly from Jupyter notebooks. 
+
+Alternatively, we included a `Makefile` that creates the conda environment and installs the associated iPython kernel so this environment can be accessible though Jupyter notebooks all at once. In order to use the Makefile, you need to open a terminal where the repository is located and enter
 ```
 make env
 ```
@@ -56,7 +65,7 @@ or
 ```
 pip install -e smpsite
 ```
-if you are working in developer mode.
+if you are working in developer mode. 
 
 
 ### Makefile