An Introduction to Python Programming for Scientists and Engineers

This page provides links to the external web resources that we referred to in the textbook, and that we want to provide up-to-date references for.

The Anaconda Distribution

• Ref. 1: Anaconda Individual Edition: https://www.anaconda.com/products/individual
• Ref. 2: “Anaconda Navigator”: https://docs.continuum.io/anaconda/navigator/
• Ref. 3: “Getting Started with Navigator”: https://docs.continuum.io/anaconda/navigator/getting-started/

Programming Environments and Modules

• Ref. 4: “Command Line and Environment”: PYTHONPATH: https://docs.python.org/3/using/cmdline.html#envvar-PYTHONPATH
• Ref. 5: “Importing Jupyter Notebooks as Modules”: https://jupyter-notebook.readthedocs.io/en/stable/examples/Notebook/Importing%20Notebooks.html
• Ref. 6: pip Documentation: https://pip.pypa.io/en/stable/
• Ref. 7: PyCharm: https://www.jetbrains.com/pycharm/
• Ref. 8: “Python Packaging Authority”: https://www.pypa.io/en/latest/
• Ref. 9: “Python Package Index”: https://pypi.org/
• Ref. 10: “Python Packaging User Guide”: https://packaging.python.org/
• Ref. 11: “Spyder”: https://www.spyder-ide.org

Python Language Constructs

• Ref. 12: “Built-In Exceptions”: https://docs.python.org/3/library/exceptions.html
• Ref. 13: “Errors and Exceptions”: https://docs.python.org/3/tutorial/errors.html
• Ref. 14: “Functional Programming HOWTO”: https://docs.python.org/3/howto/functional.html
• Ref. 15: “Generators”: https://wiki.python.org/moin/Generators
• Ref. 16: “Operator precedence”: https://docs.python.org/3/reference/expressions.html#operator-precedence
• Ref. 17: “Python Programming/Operators”: https://en.wikibooks.org/wiki/Python_Programming/Operators
• Ref. 18: “string — Common String Operations”: https://docs.python.org/3/library/string.html
• Ref. 19: “Yield Expressions”: https://docs.python.org/3/reference/expressions.html?highlight=yield#yield-expressions

Plotting and Animation

• Ref. 20: “Cartopy Projection List”: https://scitools.org.uk/cartopy/docs/v0.13/crs/projections.html
• Ref. 21: Matplotlib “Animated Line Plot”: https://matplotlib.org/stable/gallery/animation/simple_anim.html
• Ref. 22: Matplotlib “Animation”: https://matplotlib.org/stable/api/animation_api.html
• Ref. 23: Matplotlib Colormaps: https://matplotlib.org/stable/tutorials/colors/colormaps.html
• Ref. 24: “matplotlib.colors”: https://matplotlib.org/stable/api/colors_api.html
• Ref. 25: Matplotlib Documentation: https://matplotlib.org/stable/contents.html
• Ref. 26: Matplotlib “Gallery”: https://matplotlib.org/stable/gallery/index.html
• Ref. 27: Matplotlib “Image Tutorial”: https://matplotlib.org/stable/tutorials/introductory/images.html
• Ref. 28: Matplotlib “Interpolations for imshow”: https://matplotlib.org/stable/gallery/images_contours_and_fields/interpolation_methods.html
• Ref. 29: Matplotlib “Legend Guide”: https://matplotlib.org/stable/tutorials/intermediate/legend_guide.html
• Ref. 30: Matplotlib “Linestyles”: https://matplotlib.org/stable/gallery/lines_bars_and_markers/linestyles.html
• Ref. 31: “matplotlib.markers”: https://matplotlib.org/stable/api/markers_api.html
• Ref. 32: “matplotlib.pyplot.axis”: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.axis.html
• Ref. 33: “matplotlib.pyplot.legend”: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
• Ref. 34: “matplotlib.pyplot.plot”: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.plot.html
• Ref. 35: Matplotlib “Text Rendering With LaTeX”: https://matplotlib.org/stable/tutorials/text/usetex.html
• Ref. 36: “Pygame Front Page”: https://www.pygame.org/docs/
• Ref. 37: “Pyplot Tutorial”: https://matplotlib.org/stable/tutorials/introductory/pyplot.html

Data and Image Analysis

• Ref. 38: “Masked Arrays”: https://numpy.org/doc/stable/reference/maskedarray.html
• Ref. 39: “NumPy Reference”: https://numpy.org/devdocs/reference/index.html
• Ref. 40: NumPy “Routines”: https://numpy.org/doc/stable/reference/routines.html
• Ref. 41: “numpy.floor”: https://numpy.org/doc/stable/reference/generated/numpy.floor.html
• Ref. 42: “numpy.genfromtxt”: https://numpy.org/doc/stable/reference/generated/numpy.genfromtxt.html
• Ref. 43: “numpy.ufunc.reduce”: https://numpy.org/doc/stable/reference/generated/numpy.ufunc.reduce.html
• Ref. 44: pandas “API Reference”: https://pandas.pydata.org/pandas-docs/stable/reference/index.html
• Ref. 45: pandas in 10 Minutes Guide: https://web.archive.org/web/20200726040111/https://pandas.pydata.org/docs/getting_started/10min.html. This link is to the Internet Archive Wayback Machine version. Unfortunately, the page is no longer available at its original location.
• Ref. 46: “pandas Documentation”: https://pandas.pydata.org/docs/
• Ref. 47: pandas “User Guide”: https://pandas.pydata.org/pandas-docs/stable/user_guide/index.html
• Ref. 48: “pandas.DataFrame.to_excel”: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_excel.html
• Ref. 49: “pandas.ExcelWriter”: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.ExcelWriter.html
• Ref. 50: “pandas.read_excel”: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_excel.html
• Ref. 51: “Pillow”: https://pillow.readthedocs.io/en/stable/
• Ref. 52: “scikit-image”: https://scikit-image.org/

File Input/Output and File Management

• Ref. 53: “csv — CSV File Reading and Writing”: https://docs.python.org/3/library/csv.html
• Ref. 54: “fnmatch — Unix Filename Pattern Matching”: https://docs.python.org/3/library/fnmatch.html
• Ref. 55: “glob — Unix Style Pathname Pattern Expansion:” https://docs.python.org/3/library/glob.html
• Ref. 56: “Importing data with genfromtxt”: https://numpy.org/doc/stable/user/basics.io.genfromtxt.html
• Ref. 57: “Input and Output”: https://scipy-cookbook.readthedocs.io/items/InputOutput.html
• Ref. 58: “netCDF4”: https://unidata.github.io/netcdf4-python/index.html
• Ref. 59: OpenPyXL “Tutorial”: https://openpyxl.readthedocs.io/en/stable/tutorial.html
• Ref. 60: “os.path — Common Pathname Manipulations”: https://docs.python.org/3/library/os.path.html
• Ref. 61: “pickle — Python Object Serialization”: https://docs.python.org/3/library/pickle.html

Documentation and Programming Style 

• Ref. 62: numpydoc Example: https://numpydoc.readthedocs.io/en/latest/example.html
• Ref. 63: numpydoc Style Guide: https://numpydoc.readthedocs.io/en/latest/format.html
• Ref. 64: “PEP 8 — Style Guide for Python Code”: https://www.python.org/dev/peps/pep-0008/
• Ref. 65: “reStructuredText Primer”: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
• Ref. 66: reStructuredText Quick Reference: https://docutils.sourceforge.io/docs/user/rst/quickref.html
• Ref. 67: “Sphinx: Python Documentation Generator”: https://www.sphinx-doc.org/en/master/
• Ref. 68: “sphinx.ext.autodoc”: https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html
• Ref. 69: Sphinx Directives: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html

Performance and Profiling

• Ref. 70: “line_profiler and kernprof”: https://github.com/pyutils/line_profiler
• Ref. 71: “line-profiler 3.3.0”: https://pypi.org/project/line-profiler/
• Ref. 72: “memory-profiler 0.58.0”: https://pypi.org/project/memory-profiler/
• Ref. 73: Memory-profiler API: https://github.com/pythonprofilers/memory_profiler#api
• Ref. 74: “Numba Documentation”: https://numba.readthedocs.io/en/stable/index.html
• Ref. 75: “The Python Profilers”: https://docs.python.org/3/library/profile.html
• Ref. 76: “timeit — Measure Execution Time of Small Code Snippets”: https://docs.python.org/3/library/timeit.html

Testing Programs

• Ref. 77: “pytest: Helps You Write Better Programs”: https://docs.pytest.org/en/stable/
• Ref. 78: tox: https://tox.readthedocs.io/en/latest/
• Ref. 79: “unittest — Unit Testing Framework”: https://docs.python.org/3/library/unittest.html

Managing Programs

• Ref. 80: Autotools: https://www.gnu.org/software/automake/manual/html_node/index.html
• Ref. 81: conda: https://docs.conda.io/en/latest/
• Ref. 82: “Cookiecutter: Better Project Templates”: https://cookiecutter.readthedocs.io/en/latest/
• Ref. 83: Git Documentation: https://git-scm.com/doc
• Ref. 84: Git GUI Clients: https://git-scm.com/downloads/guis
• Ref. 85: GitHub: https://github.com/
• Ref. 86: GitLab: https://about.gitlab.com/
• Ref. 87: Scientific Python Cookiecutter: https://nsls-ii.github.io/scientific-python-cookiecutter/

Talking With Other Languages

• Ref. 88: “Calling C/C++ Extensions with ctypes”: https://nesi.github.io/perf-training/python-scatter/ctypes
• Ref. 89: “ctypes — A Foreign Function Library for Python”: https://docs.python.org/3/library/ctypes.html
• Ref. 90: “Cython C-Extensions for Python”: https://cython.org/
• Ref. 91: “F2PY Users Guide and Reference Manual”: https://numpy.org/doc/stable/f2py/
• Ref. 92: “Using the GNU Compiler Collection (GCC)”: https://gcc.gnu.org/onlinedocs/gcc/

 Miscellaneous

• Ref. 93: “Concentration Gradients and Their Relation to Biased Random Walks”: https://www.mit.edu/~kardar/teaching/projects/chemotaxis(AndreaSchmidt)/gradients.htm
• Ref. 94: “Quicksort”: https://en.wikipedia.org/wiki/Quicksort
• Ref. 95: “Random Generator”: https://numpy.org/doc/stable/reference/random/generator.html
• Ref. 96: “Random sampling (numpy.random)”: https://numpy.org/doc/stable/reference/random/index.html
• Ref. 97: “Sorting”: https://wiki.python.org/moin/HowTo/Sorting