From cd51f6bd891dbd4edaa7fd30d0d787bbff6e0ed0 Mon Sep 17 00:00:00 2001 From: Michael Zingale Date: Wed, 10 Dec 2025 13:45:58 -0500 Subject: [PATCH 1/2] some work on JB 2 --- content/10-testing/pytest | 11 ---- content/_toc.yml | 97 -------------------------------- content/myst.yml | 115 ++++++++++++++++++++++++++++++++++++++ 3 files changed, 115 insertions(+), 108 deletions(-) delete mode 100644 content/10-testing/pytest delete mode 100644 content/_toc.yml create mode 100644 content/myst.yml diff --git a/content/10-testing/pytest b/content/10-testing/pytest deleted file mode 100644 index fb7db8c3..00000000 --- a/content/10-testing/pytest +++ /dev/null @@ -1,11 +0,0 @@ -pip3 install -U pytest --user - -note: it might install it in ~/.local/bin/ but you might have a -different version of pytest elsewhere in your path. - -the older version was `py.test` now, it is `pytest` - -to make sure that you get the version consistent with your install, you can do: - -python3 -m pytest - diff --git a/content/_toc.yml b/content/_toc.yml deleted file mode 100644 index 6a8039a8..00000000 --- a/content/_toc.yml +++ /dev/null @@ -1,97 +0,0 @@ -format: jb-book -root: Introduction -parts: - - caption: Getting Started - chapters: - - file: 01-python/installing - - file: 01-python/using - - file: 01-python/w1-jupyter.ipynb - - - caption: Python Basics - chapters: - - file: 01-python/basics - sections: - - file: 01-python/w1-python-datatypes.ipynb - - file: 01-python/w2-python-advanced-datatypes.ipynb - - file: 01-python/w2-python-control-flow.ipynb - - file: 01-python/w2-python-exercises.ipynb - - file: 01-python/functions-classes - sections: - - file: 01-python/w3-python-functions.ipynb - - file: 01-python/w3-python-exercises.ipynb - - file: 01-python/w4-python-classes.ipynb - - file: 01-python/w4-python-modules.ipynb - - file: 01-python/w4-python-exercises.ipynb - - file: 01-python/misc - sections: - - file: 01-python/w3-python-exceptions.ipynb - - file: 01-python/python-io.ipynb - - file: 01-python/w5-python-more-examples.ipynb - - - caption: Arrays - chapters: - - file: 02-numpy/numpy - sections: - - file: 02-numpy/numpy-basics.ipynb - - file: 02-numpy/numpy-advanced.ipynb - - file: 02-numpy/numpy-exercises.ipynb - - - caption: Scientific Python - chapters: - - file: 04-matplotlib/matplotlib - sections: - - file: 04-matplotlib/matplotlib-basics.ipynb - - file: 04-matplotlib/matplotlib-exercises.ipynb - - file: 05-scipy/scipy - sections: - - file: 05-scipy/scipy-basics.ipynb - - file: 05-scipy/scipy-exercises.ipynb - - file: 05-scipy/scipy-basics-2.ipynb - - file: 05-scipy/scipy-exercises-2.ipynb - - file: 06-sympy/sympy - sections: - - file: 06-sympy/sympy-examples.ipynb - - file: 06-sympy/sympy-exercises.ipynb - - - caption: Machine Learning - chapters: - - file: 11-machine-learning/neural-net-basics - sections: - - file: 11-machine-learning/gradient-descent - - file: 11-machine-learning/neural-net-derivation - - file: 11-machine-learning/neural-net-hidden - sections: - - file: 11-machine-learning/neural-net-improvements - - file: 11-machine-learning/machine-learning-libraries - sections: - - file: 11-machine-learning/keras-mnist - - file: 11-machine-learning/keras-clustering - - - caption: Python packaging and applications - chapters: - - file: 09-packages/python-modules - - file: 09-packages/python-arguments - - file: 09-packages/python-more-modules - - file: 09-packages/python-packages - - file: 09-packages/python-tools - - - caption: Git and Github - chapters: - - file: git/version-control - - file: git/git - - file: git/github - - file: git/pull-requests - - - caption: Unit tests - chapters: - - file: 10-testing/testing - - file: 10-testing/pytest - sections: - - file: 10-testing/more-pytest - - file: 10-testing/real-world-example - - - caption: Extensions - chapters: - - file: 12-extensions/extensions-overview - - file: 12-extensions/extensions-example - diff --git a/content/myst.yml b/content/myst.yml new file mode 100644 index 00000000..33556fa8 --- /dev/null +++ b/content/myst.yml @@ -0,0 +1,115 @@ +version: 1 +project: + title: 'PHY 546: Python for Scientific Computing' + authors: + - name: Michael Zingale + url: https://zingale.github.io + github: zingale + bluesky: michaelzingale.bsky.social + + copyright: '2025' + github: sbu-python-class/python-science + thebe: + binder: + repo: sbu-python-class/python-science + provider: github + url: https://mybinder.org + ref: main + exports: + - format: pdf + template: plain_latex_book + output: exports/book.pdf + toc: + - file: Introduction.md + - title: Getting Started + children: + - file: 01-python/installing.md + - file: 01-python/using.md + - file: 01-python/w1-jupyter.ipynb + - title: Python Basics + children: + - file: 01-python/basics.md + children: + - file: 01-python/w1-python-datatypes.ipynb + - file: 01-python/w2-python-advanced-datatypes.ipynb + - file: 01-python/w2-python-control-flow.ipynb + - file: 01-python/w2-python-exercises.ipynb + - file: 01-python/functions-classes.md + children: + - file: 01-python/w3-python-functions.ipynb + - file: 01-python/w3-python-exercises.ipynb + - file: 01-python/w4-python-classes.ipynb + - file: 01-python/w4-python-modules.ipynb + - file: 01-python/w4-python-exercises.ipynb + - file: 01-python/misc.md + children: + - file: 01-python/w3-python-exceptions.ipynb + - file: 01-python/python-io.ipynb + - file: 01-python/w5-python-more-examples.ipynb + - title: Arrays + children: + - file: 02-numpy/numpy.md + children: + - file: 02-numpy/numpy-basics.ipynb + - file: 02-numpy/numpy-advanced.ipynb + - file: 02-numpy/numpy-exercises.ipynb + - title: Scientific Python + children: + - file: 04-matplotlib/matplotlib.md + children: + - file: 04-matplotlib/matplotlib-basics.ipynb + - file: 04-matplotlib/matplotlib-exercises.ipynb + - file: 05-scipy/scipy.md + children: + - file: 05-scipy/scipy-basics.ipynb + - file: 05-scipy/scipy-exercises.ipynb + - file: 05-scipy/scipy-basics-2.ipynb + - file: 05-scipy/scipy-exercises-2.ipynb + - file: 06-sympy/sympy.md + children: + - file: 06-sympy/sympy-examples.ipynb + - file: 06-sympy/sympy-exercises.ipynb + - title: Machine Learning + children: + - file: 11-machine-learning/neural-net-basics.md + children: + - file: 11-machine-learning/gradient-descent.ipynb + - file: 11-machine-learning/neural-net-derivation.md + - file: 11-machine-learning/neural-net-hidden.md + children: + - file: 11-machine-learning/neural-net-improvements.md + - file: 11-machine-learning/machine-learning-libraries.md + children: + - file: 11-machine-learning/keras-mnist.ipynb + - file: 11-machine-learning/keras-clustering.ipynb + - title: Python packaging and applications + children: + - file: 09-packages/python-modules.md + - file: 09-packages/python-arguments.md + - file: 09-packages/python-more-modules.md + - file: 09-packages/python-packages.md + - file: 09-packages/python-tools.md + - title: Git and Github + children: + - file: git/version-control.md + - file: git/git.md + - file: git/github.md + - file: git/pull-requests.md + - title: Unit tests + children: + - file: 10-testing/testing.md + - file: 10-testing/pytest.md + children: + - file: 10-testing/more-pytest.md + - file: 10-testing/real-world-example.md + - title: Extensions + children: + - file: 12-extensions/extensions-overview.md + - file: 12-extensions/extensions-example.md +site: + options: + folders: true + template: book-theme + +html: + announcement: "" From 7b754c5e3d30dbb38765a323227d9c5fbf044201 Mon Sep 17 00:00:00 2001 From: Michael Zingale Date: Wed, 10 Dec 2025 14:19:26 -0500 Subject: [PATCH 2/2] more progress --- content/myst.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/content/myst.yml b/content/myst.yml index 33556fa8..c8676a22 100644 --- a/content/myst.yml +++ b/content/myst.yml @@ -109,7 +109,8 @@ project: site: options: folders: true + #logo: farnsworth.png # use this to change the logo at the top + hide_myst_branding: true template: book-theme -html: - announcement: "" +