Merge pull request #3 from gboeing/update

update to v0.3.0

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,39 @@
+---
+name: Bug report
+about: Report a bug in Pynamical's code
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Read these instructions carefully**
+
+Please don't use the issue tracker to ask "how-to" or usage questions. If asked here, they will be closed automatically. Instead, ask "how-to" and usage questions on [StackOverflow](https://stackoverflow.com/).
+
+Bug reports are for reporting a bug you have found in Pynamical's codebase. Your issue will be closed automatically if you don't provide the requested information that we need in order to help you. Before you proceed, review the contributing guidelines in this repo's CONTRIBUTING.md file. If you installed Pynamical via conda and are experiencing installation problems, please open an issue at its [feedstock](https://github.com/conda-forge/pynamical-feedstock/issues). If you've found a problem in Pynamical itself, first search the open/closed issues and StackOverflow to see if the problem has already been noted. If it hasn't, fill in the bug reporting template below. We need this information to assist you:
+
+**Problem description**
+  - What did you do?
+  - What did you expect to happen?
+  - And what actually happened instead?
+
+**Environment information**
+  - What operating system are you using?
+  - What Python version are you using?
+  - What Pynamical version are you using?
+  - Provide a complete list of your environment's packages and their versions (for example, run `conda list` or `pip list` then paste the output between the two "details" tags below)
+
+<details>
+# paste the output of your Python packages/versions here between these two "details" tags
+
+</details>
+
+**Provide a complete minimal reproducible example**
+
+Your example code snippet here must be *minimal* so it doesn't contain extraneous code unrelated to your specific problem and it must be *complete* so we can independently run it from top to bottom by copying/pasting it into a Python interpreter. That means all imports and all variables must be defined. If you're unsure how to create a good reproducible example, read [this guide](https://stackoverflow.com/help/minimal-reproducible-example). Do not post a screenshot of your code or error message: provide it as text.
+
+```python
+# your code goes here
+
+```

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,30 @@
+---
+name: Feature proposal
+about: Propose an enhancement before opening a pull request to add it
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Read these instructions carefully**
+
+Please don't use the issue tracker to ask "how-to" or usage questions. If asked here, they will be closed automatically. Instead, ask "how-to" and usage questions on [StackOverflow](https://stackoverflow.com/).
+
+Feature requests are for proposing an enhancement to Pynamical before opening a pull request to add your proposed functionality to the codebase. Your issue will be closed automatically if you don't provide the requested information that we need below. Before you proceed, review the contributing guidelines in this repo's CONTRIBUTING.md file.
+
+**Is your feature proposal related to a problem?**
+
+A clear and concise description of what the problem is.
+
+**Describe the solution you'd like to propose**
+
+A clear and concise description of what you want to change in Pynamical and how you plan to implement it.
+
+**Describe alternatives you've considered**
+
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+
+Provide a complete minimal working example of code to demonstrate your use case. Add any additional code snippets, context, or screenshots about the feature proposal to demonstrate its importance and feasibility.

.github/pull_request_template.md

@@ -0,0 +1,9 @@
+**Read these instructions carefully**
+
+Before you proceed, review the contributing guidelines in this repo's CONTRIBUTING.md file, especially the sections on project coding standards and tests.
+
+In this pull request, please include:
+
+  - a reference to related issue(s)
+  - a description of the changes proposed in the pull request
+  - an example code snippet illustrating usage of the new functionality

.github/workflows/tests.yml

@@ -0,0 +1,69 @@
+name: tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+
+  build:
+
+    name: Python ${{ matrix.python-version }} ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.6', '3.7', '3.8', '3.9']
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Cache conda
+        uses: actions/cache@v2
+        env:
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('tests/environment-dev.yml') }}
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          use-only-tar-bz2: true  # required for caching
+          show-channel-urls: true
+          channel-priority: strict
+          activate-environment: pynamical-dev
+          environment-file: tests/environment-dev.yml
+
+      - name: Install pynamical
+        run: |
+          python setup.py install
+          conda list
+          conda info --all
+
+      - name: Lint code
+        run: |
+          isort . --check-only
+          black . --line-length 100 --check --diff
+          flake8 .
+          pydocstyle .
+
+      - name: Test docs
+        run: make -C ./docs html
+
+      - name: Test code
+        run: |
+          coverage run --source ./pynamical --module pytest --verbose
+          coverage xml -i
+          coverage report -m
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v1

CONTRIBUTING.md

@@ -1,21 +1,32 @@
-Thanks for using pynamical and for considering contributing to it!
+# Pynamical contributing guidelines
+
+Thanks for using Pynamical and for considering contributing to it by opening an issue or pull request.
+
+#### If you have a "how-to" or usage question rather than a bug report or new feature proposal:
+
+  - please ask your question on [StackOverflow](https://stackoverflow.com/search?q=pynamical)
+
+#### If you're having an installation problem:
+
+  - make sure you've followed the installation instructions in the [documentation](https://pynamical.readthedocs.io/)
+  - if you installed Pynamical via conda-forge, please open an issue at its [feedstock](https://github.com/conda-forge/pynamical-feedstock/issues)
 
 #### If you've found a bug:
 
   - read the error message and [documentation](https://pynamical.readthedocs.io/)
-  - search through the [open issues](https://github.com/gboeing/pynamical/issues?q=is%3Aopen+is%3Aissue) and [closed issues](https://github.com/gboeing/pynamical/issues?q=is%3Aissue+is%3Aclosed) first
-  - if the problem is with a dependency of this project, open an issue on the dependency's repo
-  - if the problem is with pynamical and you can fix it simply, please submit a PR
-  - if the problem persists, please open an issue in the [issue tracker](https://github.com/gboeing/pynamical/issues) filling out all sections of the template, including a minimal working example to reproduce the problem
+  - search through the [open issues](https://github.com/gboeing/pynamical/issues?q=is%3Aopen+is%3Aissue) and [closed issues](https://github.com/gboeing/pynamical/issues?q=is%3Aissue+is%3Aclosed) to see if it has already been reported
+  - if the problem is with a dependency of this project, open an issue in the dependency's repo
+  - if the problem is with Pynamical and you can fix it simply, please open a pull request
+  - if the problem persists, please open an issue in the [issue tracker](https://github.com/gboeing/pynamical/issues) filling out all sections of the template, including a minimal working example so others can independently and completely reproduce the problem
 
 #### If you have a feature proposal or want to contribute:
 
   - post your proposal on the [issue tracker](https://github.com/gboeing/pynamical/issues) so we can review it together (some proposals may not be a good fit for the project)
-  - fork the repo, make your change (adhering to pynamical's existing coding, commenting, and docstring styles), [test it](https://github.com/gboeing/pynamical/tree/master/tests), and submit a PR
+  - fork the repo, make your change, [test it](./tests), and submit a PR
   - respond to code review
-
-#### If this is a general/usage question (rather than a bug report or proposed PR):
-
-  - please ask your question on [StackOverflow](https://stackoverflow.com/search?q=pynamical)
+  - adhere to the following project standards
+    - `black` code style with max line length of 100
+    - `isort` sorted imports
+    - `numpy` style docstrings
 
 Every piece of software is a work in progress. This project is the result of many hours of work contributed freely by myself and the many people that build the projects it depends on. Thank you for contributing!

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2020 Geoff Boeing https://geoffboeing.com/
+Copyright (c) 2015-2021 Geoff Boeing https://geoffboeing.com/
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -8,27 +8,22 @@
 
 **Python package for modeling, simulating, visualizing, and animating discrete nonlinear dynamical systems and chaos**
 
-pynamical uses pandas, numpy, and numba for fast simulation, and matplotlib for visualizations and animations to explore system behavior. Compatible with Python 2 and 3.
+Pynamical uses pandas, numpy, and numba for fast simulation, and matplotlib for visualizations and animations to explore system behavior.
 
 Pynamical comes packaged with the logistic map, the Singer map, and the cubic map predefined. The models may be run with a range of parameter values over a set of time steps, and the resulting numerical output is returned as a pandas DataFrame. Pynamical can then visualize this output in various ways, including with bifurcation diagrams, two-dimensional phase diagrams, three-dimensional phase diagrams, and cobweb plots.
 
-You can read/cite the journal article about pynamical: Boeing, G. 2016. "[Visual Analysis of Nonlinear Dynamical Systems: Chaos, Fractals, Self-Similarity and the Limits of Prediction](https://geoffboeing.com/publications/nonlinear-chaos-fractals-prediction/)." *Systems*, 4 (4), 37. doi:10.3390/systems4040037.
+**Citation info**: Boeing, G. 2016. "[Visual Analysis of Nonlinear Dynamical Systems: Chaos, Fractals, Self-Similarity and the Limits of Prediction](https://geoffboeing.com/publications/nonlinear-chaos-fractals-prediction/)." *Systems*, 4 (4), 37. doi:10.3390/systems4040037.
 
 ## Install:
 
 You can install pynamical with [conda](https://anaconda.org/conda-forge/pynamical):
 
 ```
-conda install -c conda-forge pynamical
+conda config --prepend channels conda-forge
+conda create -n pynamical --strict-channel-priority jupyterlab pynamical
 ```
 
-Alternatively, you can run pynamical + Jupyter directly from this
-[docker container](https://hub.docker.com/r/gboeing/pynamical), 
-or you can install it with pip:
-
-```
-pip install pynamical
-```
+Alternatively, you can run pynamical + Jupyter directly from its [Docker container](https://hub.docker.com/r/gboeing/pynamical), or you can install it with pip.
 
 ## Documentation:
 

codecov.yml

@@ -0,0 +1,6 @@
+coverage:
+  status:
+    project:
+      default:
+        target: auto  # compare against coverage from the base commit
+        threshold: 0.1%  # allow coverage to drop by X% and still pass