Jupytext on GitHub
``` -```{nb-code} ipython3 +```{code-cell} ipython3 %%latex $\frac{\pi}{2}$ ``` -```{nb-code} ipython3 +```{code-cell} ipython3 %load_ext rpy2.ipython ``` -```{nb-code} ipython3 +```{code-cell} ipython3 %%R library(ggplot2) ggplot(data=data.frame(x=c('A', 'B'), y=c(5, 2)), aes(x,weight=y)) + geom_bar() ``` -```{nb-code} ipython3 +```{code-cell} ipython3 %matplotlib inline import pandas as pd pd.Series({'A':5, 'B':2}).plot(figsize=(3,2), kind='bar') diff --git a/tests/notebooks/mirror/ipynb_to_myst/Notebook with many hash signs.mystnb b/tests/notebooks/mirror/ipynb_to_myst/Notebook with many hash signs.mystnb index a83d13a42..3055620cd 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/Notebook with many hash signs.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/Notebook with many hash signs.mystnb @@ -12,7 +12,7 @@ This is a notebook that contains many hash signs. Hopefully its python representation is not recognized as a Sphinx Gallery script... ################################################################## -```{nb-code} ipython3 +```{code-cell} ipython3 some = 1 code = 2 some+code diff --git a/tests/notebooks/mirror/ipynb_to_myst/Notebook with metadata and long cells.mystnb b/tests/notebooks/mirror/ipynb_to_myst/Notebook with metadata and long cells.mystnb index a836a3250..2221f240d 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/Notebook with metadata and long cells.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/Notebook with metadata and long cells.mystnb @@ -27,7 +27,7 @@ with a code block inside it After that cell we'll have a code cell -```{nb-code} ipython3 +```{code-cell} ipython3 2 + 2 @@ -36,7 +36,7 @@ After that cell we'll have a code cell Followed by a raw cell -```{nb-raw} +```{raw-cell} This is the content of the raw cell @@ -48,7 +48,7 @@ of the raw cell This is a markdown cell with cell metadata `{"key": "value"}` -```{nb-code} ipython3 +```{code-cell} ipython3 --- .class: null tags: [parameters] @@ -56,7 +56,7 @@ tags: [parameters] """This is a code cell with metadata `{"tags":["parameters"], ".class":null}`""" ``` -```{nb-raw} +```{raw-cell} :key: value This is a raw cell with cell metadata `{"key": "value"}` diff --git a/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_R_magic.mystnb b/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_R_magic.mystnb index f58a11c0c..21b50fefe 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_R_magic.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_R_magic.mystnb @@ -11,23 +11,23 @@ nbformat_minor: 2 This notebook shows the use of R cells to generate plots -```{nb-code} ipython2 +```{code-cell} ipython2 %load_ext rpy2.ipython ``` -```{nb-code} ipython2 +```{code-cell} ipython2 %%R suppressMessages(require(tidyverse)) ``` -```{nb-code} ipython2 +```{code-cell} ipython2 %%R ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point() ``` The default plot dimensions are not good for us, so we use the -w and -h parameters in %%R magic to set the plot size -```{nb-code} ipython2 +```{code-cell} ipython2 %%R -w 400 -h 240 ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point() ``` diff --git a/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_more_R_magic_111.mystnb b/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_more_R_magic_111.mystnb index 3d62e7b4f..e2ef4883c 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_more_R_magic_111.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/Notebook_with_more_R_magic_111.mystnb @@ -7,7 +7,7 @@ nbformat: 4 nbformat_minor: 2 --- -```{nb-code} ipython3 +```{code-cell} ipython3 %load_ext rpy2.ipython import pandas as pd @@ -21,7 +21,7 @@ df = pd.DataFrame( ) ``` -```{nb-code} ipython3 +```{code-cell} ipython3 %%R -i df library("ggplot2") ggplot(data = df) + geom_point(aes(x = X, y = Y, color = Letter, size = Z)) diff --git a/tests/notebooks/mirror/ipynb_to_myst/R notebook with invalid cell keys.mystnb b/tests/notebooks/mirror/ipynb_to_myst/R notebook with invalid cell keys.mystnb index ffc1c578c..73a5eb305 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/R notebook with invalid cell keys.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/R notebook with invalid cell keys.mystnb @@ -9,7 +9,7 @@ nbformat_minor: 2 This notebook was created with IRKernel 0.8.12, and is not completely valid, as the code cell below contains an unexpected 'source' entry. This did cause https://github.com/mwouts/jupytext/issues/234. Note that the problem is solved when one upgrades to IRKernel 1.0.0. -```{nb-code} r +```{code-cell} r library("ggplot2") ggplot(mtcars, aes(mpg)) + stat_ecdf() ``` diff --git a/tests/notebooks/mirror/ipynb_to_myst/Reference Guide for Calysto Scheme.mystnb b/tests/notebooks/mirror/ipynb_to_myst/Reference Guide for Calysto Scheme.mystnb index f7af16537..a29544249 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/Reference Guide for Calysto Scheme.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/Reference Guide for Calysto Scheme.mystnb @@ -86,15 +86,15 @@ Calysto Scheme may not implement all of those. Some useful and suggestive ones: * \Sigma - Σ * \_i - subscript i, such as vectorᵢ -```{nb-code} scheme +```{code-cell} scheme (define α 67) ``` -```{nb-code} scheme +```{code-cell} scheme α ``` -```{nb-code} scheme +```{code-cell} scheme (define i 2) (define vectorᵢ (vector-ref (vector 0 6 3 2) i)) vectorᵢ @@ -102,33 +102,33 @@ vectorᵢ ### Rich media -```{nb-code} scheme +```{code-cell} scheme (import "calysto.display") ``` -```{nb-code} scheme +```{code-cell} scheme (calysto.display.HTML "This is bold, italics, underlined.") ``` -```{nb-code} scheme +```{code-cell} scheme (import "calysto.graphics") ``` -```{nb-code} scheme +```{code-cell} scheme (define canvas (calysto.graphics.Canvas)) ``` -```{nb-code} scheme +```{code-cell} scheme (define ball (calysto.graphics.Circle '(150 150) 100)) ``` -```{nb-code} scheme +```{code-cell} scheme (ball.draw canvas) ``` ### Shell commands -```{nb-code} scheme +```{code-cell} scheme ! ls /tmp ``` @@ -159,11 +159,11 @@ You can import and use any Python library in Calysto Scheme. In addition, if you wish, you can execute expressions and statements in a Python environment: -```{nb-code} scheme +```{code-cell} scheme (python-eval "1 + 2") ``` -```{nb-code} scheme +```{code-cell} scheme (python-exec " def mypyfunc(a, b): @@ -173,17 +173,17 @@ def mypyfunc(a, b): This is a shared environment with Scheme: -```{nb-code} scheme +```{code-cell} scheme (mypyfunc 4 5) ``` You can use `func` to turn a Scheme procedure into a Python function, and `define!` to put it into the shared enviornment with Python: -```{nb-code} scheme +```{code-cell} scheme (define! mypyfunc2 (func (lambda (n) n))) ``` -```{nb-code} scheme +```{code-cell} scheme (python-eval "mypyfunc2(34)") ``` @@ -211,7 +211,7 @@ You can use `func` to turn a Scheme procedure into a Python function, and `defin Calysto Scheme acts as if it has a call stack, for easier debugging. For example: -```{nb-code} scheme +```{code-cell} scheme (define fact (lambda (n) (if (= n 1) @@ -219,7 +219,7 @@ Calysto Scheme acts as if it has a call stack, for easier debugging. For example (* n (fact (- n 1)))))) ``` -```{nb-code} scheme +```{code-cell} scheme (fact 5) ``` @@ -237,15 +237,15 @@ That will allow infinite recursive loops without keeping track of the "stack". ## SCHEMEPATH SCHEMEPATH is a list of search directories used with (load NAME). This is a reference, so you should append to it rather than attempting to redefine it. -```{nb-code} scheme +```{code-cell} scheme SCHEMEPATH ``` -```{nb-code} scheme +```{code-cell} scheme (set-cdr! (cdr SCHEMEPATH) (list "/var/modules")) ``` -```{nb-code} scheme +```{code-cell} scheme SCHEMEPATH ``` @@ -253,7 +253,7 @@ SCHEMEPATH Note that you can use the word `lambda` or \lambda and then press [TAB] -```{nb-code} scheme +```{code-cell} scheme (define factorial (λ (n) (cond @@ -261,25 +261,25 @@ Note that you can use the word `lambda` or \lambda and then press [TAB] (else (* n (factorial (- n 1))))))) ``` -```{nb-code} scheme +```{code-cell} scheme (factorial 5) ``` ## define-syntax (define-syntax NAME RULES): a method for creating macros -```{nb-code} scheme +```{code-cell} scheme (define-syntax time [(time ?exp) (let ((start (current-time))) ?exp (- (current-time) start))]) ``` -```{nb-code} scheme +```{code-cell} scheme (time (car '(1 2 3 4))) ``` -```{nb-code} scheme +```{code-cell} scheme ;;--------------------------------------------------------------------- ;; collect is like list comprehension in Python @@ -298,19 +298,19 @@ Note that you can use the word `lambda` or \lambda and then press [TAB] (filter-map f pred? (cdr values)))))) ``` -```{nb-code} scheme +```{code-cell} scheme (collect (* n n) for n in (range 10)) ``` -```{nb-code} scheme +```{code-cell} scheme (collect (* n n) for n in (range 5 20 3)) ``` -```{nb-code} scheme +```{code-cell} scheme (collect (* n n) for n in (range 10) if (> n 5)) ``` -```{nb-code} scheme +```{code-cell} scheme ;;--------------------------------------------------------------------- ;; for loops @@ -350,7 +350,7 @@ Note that you can use the word `lambda` or \lambda and then press [TAB] (for-iterate2 (+ i 1) (cdr values) f))))) ``` -```{nb-code} scheme +```{code-cell} scheme (define matrix2d '((10 20) (30 40) @@ -364,7 +364,7 @@ Note that you can use the word `lambda` or \lambda and then press [TAB] ((190 200 210) (220 230 240)))) ``` -```{nb-code} scheme +```{code-cell} scheme (begin (define hello 0) (for 5 times do (set! hello (+ hello 1))) @@ -372,23 +372,23 @@ Note that you can use the word `lambda` or \lambda and then press [TAB] ) ``` -```{nb-code} scheme +```{code-cell} scheme (for sym in '(a b c d) do (define x 1) (set! x sym) (print x)) ``` -```{nb-code} scheme +```{code-cell} scheme (for n in (range 10 20 2) do (print n)) ``` -```{nb-code} scheme +```{code-cell} scheme (for n at (i j) in matrix2d do (print (list n 'coords: i j))) ``` -```{nb-code} scheme +```{code-cell} scheme (for n at (i j k) in matrix3d do (print (list n 'coords: i j k))) ``` -```{nb-code} scheme +```{code-cell} scheme (define-syntax scons [(scons ?x ?y) (cons ?x (lambda () ?y))]) @@ -431,33 +431,33 @@ Note that you can use the word `lambda` or \lambda and then press [TAB] (define ! (lambda (n) (nth n facts))) ``` -```{nb-code} scheme +```{code-cell} scheme (! 5) ``` -```{nb-code} scheme +```{code-cell} scheme (nth 10 facts) ``` -```{nb-code} scheme +```{code-cell} scheme (nth 20 fibs) ``` -```{nb-code} scheme +```{code-cell} scheme (first 30 fibs) ``` ## for-each (for-each PROCEDURE LIST): apply PROCEDURE to each item in LIST; like `map` but don't return results -```{nb-code} scheme +```{code-cell} scheme (for-each (lambda (n) (print n)) '(3 4 5)) ``` ## format (format STRING ITEM ...): format the string with ITEMS as arguments -```{nb-code} scheme +```{code-cell} scheme (format "This uses formatting ~a ~s ~%" 'apple 'apple) ``` @@ -467,7 +467,7 @@ Turns a lambda into a Python function. (func (lambda ...)) -```{nb-code} scheme +```{code-cell} scheme (func (lambda (n) n)) ``` diff --git a/tests/notebooks/mirror/ipynb_to_myst/The flavors of raw cells.mystnb b/tests/notebooks/mirror/ipynb_to_myst/The flavors of raw cells.mystnb index ae7a8876d..40b7bd95a 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/The flavors of raw cells.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/The flavors of raw cells.mystnb @@ -7,36 +7,36 @@ nbformat: 4 nbformat_minor: 2 --- -```{nb-raw} +```{raw-cell} :raw_mimetype: text/latex $1+1$ ``` -```{nb-raw} +```{raw-cell} :raw_mimetype: text/restructuredtext :math:`1+1` ``` -```{nb-raw} +```{raw-cell} :raw_mimetype: text/html Bold text ``` -```{nb-raw} +```{raw-cell} :raw_mimetype: text/markdown **Bold text** ``` -```{nb-raw} +```{raw-cell} :raw_mimetype: text/x-python 1 + 1 ``` -```{nb-raw} +```{raw-cell} Not formatted ``` diff --git a/tests/notebooks/mirror/ipynb_to_myst/World population.mystnb b/tests/notebooks/mirror/ipynb_to_myst/World population.mystnb index cf606a1b7..1031875de 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/World population.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/World population.mystnb @@ -15,7 +15,7 @@ In the below we retrieve population data from the [World Bank](http://www.worldbank.org/) using the [wbdata](https://github.com/OliverSherouse/wbdata) python package -```{nb-code} ipython3 +```{code-cell} ipython3 import pandas as pd import wbdata as wb @@ -26,7 +26,7 @@ pd.options.display.max_columns = 20 Corresponding indicator is found using search method - or, directly, the World Bank site. -```{nb-code} ipython3 +```{code-cell} ipython3 wb.search_indicators('Population, total') # SP.POP.TOTL # wb.search_indicators('area') # => https://data.worldbank.org/indicator is easier to use @@ -34,7 +34,7 @@ wb.search_indicators('Population, total') # SP.POP.TOTL Now we download the population data -```{nb-code} ipython3 +```{code-cell} ipython3 indicators = {'SP.POP.TOTL': 'Population, total', 'AG.SRF.TOTL.K2': 'Surface area (sq. km)', 'AG.LND.TOTL.K2': 'Land area (sq. km)', @@ -45,20 +45,20 @@ data World is one of the countries -```{nb-code} ipython3 +```{code-cell} ipython3 data.loc['World'] ``` Can we classify over continents? -```{nb-code} ipython3 +```{code-cell} ipython3 data.loc[(slice(None), '2017-01-01'), :]['Population, total'].dropna( ).sort_values().tail(60).index.get_level_values('country') ``` Extract zones manually (in order of increasing population) -```{nb-code} ipython3 +```{code-cell} ipython3 zones = ['North America', 'Middle East & North Africa', 'Latin America & Caribbean', 'Europe & Central Asia', 'Sub-Saharan Africa', 'South Asia', @@ -67,7 +67,7 @@ zones = ['North America', 'Middle East & North Africa', And extract population information (and check total is right) -```{nb-code} ipython3 +```{code-cell} ipython3 population = data.loc[zones]['Population, total'].swaplevel().unstack() population = population[zones] assert all(data.loc['World']['Population, total'] == population.sum(axis=1)) @@ -75,11 +75,11 @@ assert all(data.loc['World']['Population, total'] == population.sum(axis=1)) ## Stacked area plot with matplotlib -```{nb-code} ipython3 +```{code-cell} ipython3 import matplotlib.pyplot as plt ``` -```{nb-code} ipython3 +```{code-cell} ipython3 plt.clf() plt.figure(figsize=(10, 5), dpi=100) plt.stackplot(population.index, population.values.T / 1e9) @@ -97,14 +97,14 @@ selected legends) are [on their way](https://github.com/plotly/plotly.js/pull/2960) at Plotly. For now we just do a stacked bar plot. -```{nb-code} ipython3 +```{code-cell} ipython3 import plotly.offline as offline import plotly.graph_objs as go offline.init_notebook_mode() ``` -```{nb-code} ipython3 +```{code-cell} ipython3 bars = [go.Bar(x=population.index, y=population[zone], name=zone) for zone in zones] fig = go.Figure(data=bars, diff --git a/tests/notebooks/mirror/ipynb_to_myst/cat_variable.mystnb b/tests/notebooks/mirror/ipynb_to_myst/cat_variable.mystnb index 5f3f73a75..c8c496684 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/cat_variable.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/cat_variable.mystnb @@ -7,6 +7,6 @@ nbformat: 4 nbformat_minor: 2 --- -```{nb-code} ipython3 +```{code-cell} ipython3 cat = 42 ``` diff --git a/tests/notebooks/mirror/ipynb_to_myst/convert_to_py_then_test_with_update83.mystnb b/tests/notebooks/mirror/ipynb_to_myst/convert_to_py_then_test_with_update83.mystnb index 0fd8a165a..90ecd5dd0 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/convert_to_py_then_test_with_update83.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/convert_to_py_then_test_with_update83.mystnb @@ -7,7 +7,7 @@ nbformat: 4 nbformat_minor: 2 --- -```{nb-code} ipython3 +```{code-cell} ipython3 %%time print('asdf') @@ -15,6 +15,6 @@ print('asdf') Thanks for jupytext! -```{nb-code} ipython3 +```{code-cell} ipython3 ``` diff --git a/tests/notebooks/mirror/ipynb_to_myst/csharp.mystnb b/tests/notebooks/mirror/ipynb_to_myst/csharp.mystnb index 51c96049e..b18b07049 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/csharp.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/csharp.mystnb @@ -9,13 +9,13 @@ nbformat_minor: 1 We start with... -```{nb-code} csharp +```{code-cell} csharp Console.WriteLine("Hello World!"); ``` Then we do a plot with Plotly, following the [Plotting with XPlot](https://github.com/dotnet/interactive/blob/master/NotebookExamples/csharp/Docs/Plotting%20with%20Xplot.ipynb) example from `dotnet/interactive`: -```{nb-code} csharp +```{code-cell} csharp using XPlot.Plotly; var bar = new Graph.Bar @@ -32,10 +32,10 @@ display(chart); We also test the math outputs as in the [Math and Latex](https://github.com/dotnet/interactive/blob/master/NotebookExamples/csharp/Docs/Math%20and%20LaTeX.ipynb) example: -```{nb-code} csharp +```{code-cell} csharp (LaTeXString)@"\begin{align} e^{i \pi} = -1\end{align}" ``` -```{nb-code} csharp +```{code-cell} csharp (MathString)@"e^{i \pi} = -1" ``` diff --git a/tests/notebooks/mirror/ipynb_to_myst/demo_gdl_fbp.mystnb b/tests/notebooks/mirror/ipynb_to_myst/demo_gdl_fbp.mystnb index 90f4ff13a..a1d7e9a81 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/demo_gdl_fbp.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/demo_gdl_fbp.mystnb @@ -15,7 +15,7 @@ Demonstration of GDL [(gnudatalanguage)](https://github.com/gnudatalanguage/gdl) This notebook creates a Shepp-Logan phantom, projects it and then performs an FBP reconstruction. -```{nb-code} +```{code-cell} ;; L.A. Shepp and B.F. Logan, “The Fourier reconstruction of a head section,” ;; IEEE Trans. Nucl. Sci. 21(3), 21–43 (1974). function shepplogan, size = size @@ -61,12 +61,12 @@ function shepplogan, size = size end ``` -```{nb-code} +```{code-cell} ;; Enable inline plotting !inline=1 ``` -```{nb-code} +```{code-cell} phantom = shepplogan() window, 0, xsize=256, ysize=256 tvscl, phantom > 0.95 @@ -74,7 +74,7 @@ tvscl, phantom > 0.95 Now we define simple forward and backprojection functions: -```{nb-code} +```{code-cell} function proj, image, angle sino_size_x = max(size(image,/dim)) @@ -93,7 +93,7 @@ function proj, image, angle end ``` -```{nb-code} +```{code-cell} function back, sino, angle image_size = n_elements(sino[*,0]) @@ -112,7 +112,7 @@ end This allows us to create a sinogram: -```{nb-code} +```{code-cell} angles = findgen(360) sino = proj(phantom, angles) window, 0, xsize=256, ysize=360 @@ -121,7 +121,7 @@ tvscl, sino On this we can apply a simple FBP reconstruction: -```{nb-code} +```{code-cell} ;; G.L. Zeng, “Revisit of the Ramp Filter,” ;; IEEE Trans. Nucl. Sci. 62(1), 131–136 (2015). function fbp, sino, angles @@ -155,7 +155,7 @@ function fbp, sino, angles end ``` -```{nb-code} +```{code-cell} reconstruction = fbp(sino, angles) window, 0, xsize=512, ysize=256 diff --git a/tests/notebooks/mirror/ipynb_to_myst/evcxr_jupyter_tour.mystnb b/tests/notebooks/mirror/ipynb_to_myst/evcxr_jupyter_tour.mystnb index 73db0bf07..127ca11c9 100644 --- a/tests/notebooks/mirror/ipynb_to_myst/evcxr_jupyter_tour.mystnb +++ b/tests/notebooks/mirror/ipynb_to_myst/evcxr_jupyter_tour.mystnb @@ -13,7 +13,7 @@ For those not already familiar with Jupyter notebook, it lets you write code int ## Printing to outputs and evaluating expressions Lets print something to stdout and stderr then return a final expression to see how that's presented. Note that stdout and stderr are separate streams, so may not appear in the same order is their respective print statements. -```{nb-code} +```{code-cell} println!("Hello world"); eprintln!("Hello error"); format!("Hello {}", "world") @@ -22,40 +22,40 @@ format!("Hello {}", "world") ## Assigning and making use of variables We define a variable `message`, then in the subsequent cell, modify the string and finally print it out. We could also do all this in the one cell if we wanted. -```{nb-code} +```{code-cell} let mut message = "Hello ".to_owned(); ``` -```{nb-code} +```{code-cell} message.push_str("world!"); ``` -```{nb-code} +```{code-cell} message ``` ## Defining and redefining functions Next we'll define a function -```{nb-code} +```{code-cell} pub fn fib(x: i32) -> i32 { if x <= 2 {0} else {fib(x - 2) + fib(x - 1)} } ``` -```{nb-code} +```{code-cell} (1..13).map(fib).collect::