diff --git a/.gitignore b/.gitignore index ad000a25..b88fd663 100644 --- a/.gitignore +++ b/.gitignore @@ -9,6 +9,7 @@ MANIFEST .DS_Store .cache +.pytest_cache .coverage htmlcov diff --git a/.travis.yml b/.travis.yml index 2b142f57..a1d91939 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,6 +37,7 @@ env: matrix: - REPO_TYPE=conda - REPO_TYPE=venv + - REPO_TYPE=stencila - REPO_TYPE=julia - REPO_TYPE=r - REPO_TYPE=dockerfile diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index dee6249a..76ba863a 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -65,9 +65,9 @@ RUN apt-get update && \ EXPOSE 8888 -{% if env -%} -# Almost all environment variables -{% for item in env -%} +{% if build_env -%} +# Environment variables required for build +{% for item in build_env -%} ENV {{item[0]}} {{item[1]}} {% endfor -%} {% endif -%} @@ -94,6 +94,14 @@ USER root COPY src/ ${HOME} RUN chown -R ${NB_USER}:${NB_USER} ${HOME} +{% if env -%} +# The rest of the environment +{% for item in env -%} +ENV {{item[0]}} {{item[1]}} +{% endfor -%} +{% endif -%} + + # Run assemble scripts! These will actually build the specification # in the repository into the image. {% for sd in assemble_script_directives -%} @@ -182,6 +190,21 @@ class BuildPack: "unzip", } + def get_build_env(self): + """ + Ordered list of environment variables to be set for this image. + + Ordered so that environment variables can use other environment + variables in their values. + + Expects tuples, with the first item being the environment variable + name and the second item being the value. + + These environment variables will be set prior to build. + Use .get_env() to set environment variables after build. + """ + return [] + def get_env(self): """ Ordered list of environment variables to be set for this image. @@ -191,6 +214,8 @@ class BuildPack: Expects tuples, with the first item being the environment variable name and the second item being the value. + + These variables will not be available to build. """ return [] @@ -225,6 +250,30 @@ class BuildPack: """ return {} + + @property + def stencila_manifest_dir(self): + """Find the stencila manifest dir if it exists""" + if hasattr(self, '_stencila_manifest_dir'): + return self._stencila_manifest_dir + + # look for a manifest.xml that suggests stencila could be used + # when we find one, stencila should be installed + # and set environment variables such that + # this file is located at: + # ${STENCILA_ARCHIVE_DIR}/${STENCILA_ARCHIVE}/manifest.xml + + self._stencila_manifest_dir = None + for root, dirs, files in os.walk("."): + if "manifest.xml" in files: + self._stencila_manifest_dir = root.split(os.path.sep, 1)[1] + self.log.info( + "Found stencila manifest.xml in %s", + self._stencila_manifest_dir, + ) + break + return self._stencila_manifest_dir + def get_build_scripts(self): """ Ordered list of shell script snippets to build the base image. @@ -322,6 +371,7 @@ class BuildPack: return t.render( packages=sorted(self.get_packages()), path=self.get_path(), + build_env=self.get_build_env(), env=self.get_env(), labels=self.get_labels(), build_script_directives=build_script_directives, @@ -388,11 +438,31 @@ class BuildPack: class BaseImage(BuildPack): - def get_env(self): + def get_build_env(self): + """Return env directives required for build""" return [ ("APP_BASE", "/srv") ] + def get_env(self): + """Return env directives to be set after build""" + env = [] + if self.stencila_manifest_dir: + # manifest_dir is the path containing the manifest.xml + # archive_dir is the directory containing archive directories (one level up) + # default archive is the name of the directory in the archive_dir + # such that + # ${STENCILA_ARCHIVE_DIR}/${STENCILA_ARCHIVE}/manifest.xml + # exists. + + archive_dir, archive = os.path.split(self.stencila_manifest_dir) + env.extend([ + ("STENCILA_ARCHIVE_DIR", "${HOME}/" + archive_dir), + ("STENCILA_ARCHIVE", archive), + ]) + return env + + def detect(self): return True @@ -425,6 +495,22 @@ class BaseImage(BuildPack): )) except FileNotFoundError: pass + if self.stencila_manifest_dir: + assemble_scripts.extend( + [ + ( + "${NB_USER}", + r""" + ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache https://github.com/stencila/py/archive/f6a245fd.tar.gz && \ + ${KERNEL_PYTHON_PREFIX}/bin/python -m stencila register && \ + ${NB_PYTHON_PREFIX}/bin/pip install --no-cache nbstencilaproxy==0.1.1 && \ + jupyter serverextension enable --sys-prefix --py nbstencilaproxy && \ + jupyter nbextension install --sys-prefix --py nbstencilaproxy && \ + jupyter nbextension enable --sys-prefix --py nbstencilaproxy + """, + ) + ] + ) return assemble_scripts def get_post_build_scripts(self): diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 17474bf1..1bd8a967 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -18,14 +18,14 @@ class CondaBuildPack(BaseImage): Uses miniconda since it is more lightweight than Anaconda. """ - def get_env(self): + def get_build_env(self): """Return environment variables to be set. We set `CONDA_DIR` to the conda install directory and the `NB_PYTHON_PREFIX` to the location of the jupyter binary. """ - env = super().get_env() + [ + env = super().get_build_env() + [ ('CONDA_DIR', '${APP_BASE}/conda'), ('NB_PYTHON_PREFIX', '${CONDA_DIR}'), ] diff --git a/repo2docker/buildpacks/julia.py b/repo2docker/buildpacks/julia.py index 86a54995..477d50c7 100644 --- a/repo2docker/buildpacks/julia.py +++ b/repo2docker/buildpacks/julia.py @@ -12,7 +12,7 @@ class JuliaBuildPack(CondaBuildPack): See https://github.com/JuliaPy/PyCall.jl/issues/410 """ - def get_env(self): + def get_build_env(self): """Get additional environment settings for Julia and Jupyter Returns: @@ -31,7 +31,7 @@ class JuliaBuildPack(CondaBuildPack): For example, a tuple may be `('JULIA_VERSION', '0.6.0')`. """ - return super().get_env() + [ + return super().get_build_env() + [ ('JULIA_PATH', '${APP_BASE}/julia'), ('JULIA_HOME', '${JULIA_PATH}/bin'), ('JULIA_PKGDIR', '${JULIA_PATH}/pkg'), diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index ebd5416b..57939bbd 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -82,7 +82,7 @@ class RBuildPack(PythonBuildPack): '/usr/lib/rstudio-server/bin/' ] - def get_env(self): + def get_build_env(self): """ Return environment variables to be set. @@ -90,7 +90,7 @@ class RBuildPack(PythonBuildPack): without needing root. This is set via the `R_LIBS_USER` environment variable, so we set that here. """ - return super().get_env() + [ + return super().get_build_env() + [ # This is the path where user libraries are installed ('R_LIBS_USER', '${APP_BASE}/rlibs') ] diff --git a/tests/stencila/basic/archive/py-jupyter/bibliography.bibtex b/tests/stencila/basic/archive/py-jupyter/bibliography.bibtex new file mode 100644 index 00000000..643df1dd --- /dev/null +++ b/tests/stencila/basic/archive/py-jupyter/bibliography.bibtex @@ -0,0 +1,21 @@ +@article{kluyver2016jupyter, + title={Jupyter Notebooks-a publishing format for reproducible computational workflows.}, + author={Kluyver, Thomas and Ragan-Kelley, Benjamin and P{\'e}rez, Fernando and Granger, Brian E and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica B and Grout, Jason and Corlay, Sylvain and others}, + journal={ELPUB}, + pages={87--90}, + year={2016} +} +@article{ragan2014jupyter, + title={The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication.}, + author={Ragan-Kelley, M and Perez, F and Granger, B and Kluyver, T and Ivanov, P and Frederic, J and Bussonnier, M}, + journal={AGU Fall Meeting Abstracts}, + year={2014} +} +@article{perez2015project, + title={Project Jupyter: Computational narratives as the engine of collaborative data science}, + author={Perez, Fernando and Granger, Brian E}, + journal={Retrieved September}, + volume={11}, + pages={207}, + year={2015} +} diff --git a/tests/stencila/basic/archive/py-jupyter/manifest.xml b/tests/stencila/basic/archive/py-jupyter/manifest.xml new file mode 100644 index 00000000..5bfbc6f8 --- /dev/null +++ b/tests/stencila/basic/archive/py-jupyter/manifest.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb b/tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb new file mode 100644 index 00000000..2a2f1835 --- /dev/null +++ b/tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb @@ -0,0 +1,195 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Introduction" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Jupyter notebooks ([@perez2015project; @kluyver2016jupyter; @ragan2014jupyter]) are one of the most popular platforms for doing reproducible research. Stencila supports importing of Jupyter Notebook `.ipynb` files. This allows you to work with collegues to refine a document for final publication while still retaining the code cells, and thus reprodubility of your the work. In the future we also plan to support exporting to `.ipynb` files. " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Markdown cells\n", + "\n", + "Most standard Markdown should be supported by the importer including inline `code`, headings etc (although the Stencila user interface do not currently support rendering of some elements e.g. math and lists).\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Code cells\n", + "\n", + "Code cells in notebooks are imported without loss. Stencila's user interface currently differs from Jupyter in that code cells are executed on update while you are typing. This produces a very reactive user experience but is inappropriate for more compute intensive, longer running code cells. We are currently working on improving this to allowing users to decide to execute cells explicitly (e.g. using `Ctrl+Enter`)." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'Hello this is Python 3.5 and it is Tue Feb 13 10:56:10 2018'" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import sys\n", + "import time\n", + "'Hello this is Python %s.%s and it is %s' % (sys.version_info[0], sys.version_info[1], time.strftime('%c'))\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Stencila also support Jupyter code cells that produce plots. The cell below produces a simple plot based on the example from [the Matplotlib website](https://matplotlib.org/examples/shapes_and_collections/scatter_demo.html). Try changing the code below (for example, the variable `N`)." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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8Uken0zFn4S2s+90/MlHfw1dJwtmSJkzm+C6H4wkh0JoMOBwOFQRGEIfDwRtv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\nIvwvXsTNLRZOFLWRlDIdg8FIrdXe52H4ivucO3e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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "\n", + "N = 50\n", + "N = min(N, 1000) # Prevent generation of too many numbers :)\n", + "x = np.random.rand(N)\n", + "y = np.random.rand(N)\n", + "colors = np.random.rand(N)\n", + "area = np.pi * (15 * np.random.rand(N))**2 # 0 to 15 point radii\n", + "\n", + "plt.scatter(x, y, s=area, c=colors, alpha=0.5)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We are currently working on supporting [Jupyter's magic commands](http://ipython.readthedocs.io/en/stable/interactive/magics.html) in Stencila via a bridge to Jupyter kernels." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Metadata\n", + "\n", + "To add some metadata about the document (such as authors, title, abstract and so on), In Jupyter, select `Edit -> Edit Notebook metadata` from the top menu. Add the title and abstract as JSON strings and authors and organisations metadata as [JSON arrays](https://www.w3schools.com/js/js_json_arrays.asp). Author `affiliation` identifiers (like `university-of-earth` below) must be unique and preferably use only lowercase characters and no spaces.\n", + " \n", + "For example," + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "```\n", + " \"authors\": [\n", + " {\n", + " \"given-names\": \"Your first name goes here\",\n", + " \"surname\": \"Your last name goes here\",\n", + " \"email\": \"your.email@your-organisation\",\n", + " \"corresponding\": \"yes / no\",\n", + " \"affiliation\": \"university-of-earth\"\n", + " }\n", + " ],\n", + " \n", + " \"organisations\": [ \n", + " {\n", + " \"university-of-earth\": {\n", + " \"institution\": \"Your organisation name\",\n", + " \"city\": \"Your city\",\n", + " \"country\": \"Your country\" \n", + " }\n", + " ],\n", + "\n", + " \"title\": \"Your title goes here\",\n", + " \"abstract\": \"This is a paper about lots of different interesting things\",\n", + " \n", + " ```\n", + " \n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Citations and references \n", + "\n", + "Stencila supports Pandoc style citations and reference lists within Jupyter notebook Markdown cells. Add a `bibliography` entry to the notebook's metadata which points to a file containing your list of references e.g.\n", + "\n", + "```json\n", + "\"bibliography\": \"my-bibliography.bibtex\"\n", + "```\n", + "\n", + "Then, within Markdown cells, you can insert citations inside square brackets and separated by semicolons. Each citation is represented using the `@` symbol followed by the citation identifier from the bibliography database e.g.\n", + "\n", + "```json\n", + "[@perez2015project; @kluyver2016jupyter]\n", + "```\n", + "\n", + "The [cite2c](https://github.com/takluyver/cite2c) Jupyter extension allows for easier, \"cite-while-you-write\" insertion of citations from a Zotero library. We're hoping to support conversion of cite2cstyle citations/references in the [future](https://github.com/stencila/convert/issues/14).\n" + ] + } + ], + "metadata": { + "anaconda-cloud": {}, + "authors": [ + { + "given-names": "Aleksandra", + "surname": "Pawlik" + } + ], + "bibliography": "bibliography.bibtex", + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.5.2" + }, + "title": "Jupyter and Stencila" + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb.jats.xml b/tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb.jats.xml new file mode 100644 index 00000000..38eac147 --- /dev/null +++ b/tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb.jats.xml @@ -0,0 +1,212 @@ + + +
+ + + + Jupyter and Stencila + + + + + Pawlik + Aleksandra + + + + +

An example of a Jupyter notebook converted into a JATS document for editing in Stencila.

+ + + + + + + Introduction +

Jupyter notebooks (1–3) are one of the most popular platforms for doing reproducible research. Stencila supports importing of Jupyter Notebook .ipynb files. This allows you to work with collegues to refine a document for final publication while still retaining the code cells, and thus reprodubility of your the work. In the future we also plan to support exporting to .ipynb files.

+ + + Markdown cells +

Most standard Markdown should be supported by the importer including inline code, headings etc (although the Stencila user interface do not currently support rendering of some elements e.g. math and lists).

+ + + Code cells +

Code cells in notebooks are imported without loss. Stencila’s user interface currently differs from Jupyter in that code cells are executed on update while you are typing. This produces a very reactive user experience but is inappropriate for more compute intensive, longer running code cells. We are currently working on improving this to allowing users to decide to execute cells explicitly (e.g. using Ctrl+Enter).

+ + import sys +import time +'Hello this is Python %s.%s and it is %s' % (sys.version_info[0], sys.version_info[1], time.strftime('%c')) + {} + + + +

Stencila also support Jupyter code cells that produce plots. The cell below produces a simple plot based on the example from the Matplotlib website. Try changing the code below (for example, the variable N).

+ + import numpy as np +import matplotlib.pyplot as plt + +N = 50 +N = min(N, 1000) # Prevent generation of too many numbers :) +x = np.random.rand(N) +y = np.random.rand(N) +colors = np.random.rand(N) +area = np.pi * (15 * np.random.rand(N))**2 # 0 to 15 point radii + +plt.scatter(x, y, s=area, c=colors, alpha=0.5) +plt.show() + {} + + + +

We are currently working on supporting Jupyter’s magic commands in Stencila via a bridge to Jupyter kernels.

+ + + Metadata +

To add some metadata about the document (such as authors, title, abstract and so on), In Jupyter, select Edit -> Edit Notebook metadata from the top menu. Add the title and abstract as JSON strings and authors and organisations metadata as JSON arrays. Author affiliation identifiers (like university-of-earth below) must be unique and preferably use only lowercase characters and no spaces.

+

For example,

+ "authors": [ + { + "given-names": "Your first name goes here", + "surname": "Your last name goes here", + "email": "your.email@your-organisation", + "corresponding": "yes / no", + "affiliation": "university-of-earth" + } + ], + + "organisations": [ + { + "university-of-earth": { + "institution": "Your organisation name", + "city": "Your city", + "country": "Your country" + } + ], + + "title": "Your title goes here", + "abstract": "This is a paper about lots of different interesting things", + + + + Citations and references +

Stencila supports Pandoc style citations and reference lists within Jupyter notebook Markdown cells. Add a bibliography entry to the notebook’s metadata which points to a file containing your list of references e.g.

+ "bibliography": "my-bibliography.bibtex" +

Then, within Markdown cells, you can insert citations inside square brackets and separated by semicolons. Each citation is represented using the @ symbol followed by the citation identifier from the bibliography database e.g.

+ [@perez2015project; @kluyver2016jupyter] +

The cite2c Jupyter extension allows for easier, “cite-while-you-write” insertion of citations from a Zotero library. We’re hoping to support conversion of cite2cstyle citations/references in the future.

+ + + + + + + + + Perez + Fernando + + + Granger + Brian E + + + Project jupyter: Computational narratives as the engine of collaborative data science + Retrieved September + 2015 + 11 + 207 + + + + + + + Kluyver + Thomas + + + Ragan-Kelley + Benjamin + + + Pérez + Fernando + + + Granger + Brian E + + + Bussonnier + Matthias + + + Frederic + Jonathan + + + Kelley + Kyle + + + Hamrick + Jessica B + + + Grout + Jason + + + Corlay + Sylvain + + + Others + + + Jupyter notebooks-a publishing format for reproducible computational workflows. + ELPUB + 2016 + 87 + + + + + + + Ragan-Kelley + M + + + Perez + F + + + Granger + B + + + Kluyver + T + + + Ivanov + P + + + Frederic + J + + + Bussonnier + M + + + The jupyter/ipython architecture: A unified view of computational research, from interactive exploration to communication and publication. + AGU Fall Meeting Abstracts + 2014 + + + + +
\ No newline at end of file diff --git a/tests/stencila/basic/archive/r-markdown/bibliography.bibtex b/tests/stencila/basic/archive/r-markdown/bibliography.bibtex new file mode 100644 index 00000000..bae49c05 --- /dev/null +++ b/tests/stencila/basic/archive/r-markdown/bibliography.bibtex @@ -0,0 +1,13 @@ +@article{baumer2014r, + title={R Markdown: Integrating a reproducible analysis tool into introductory statistics}, + author={Baumer, Ben and Cetinkaya-Rundel, Mine and Bray, Andrew and Loi, Linda and Horton, Nicholas J}, + journal={arXiv preprint arXiv:1402.1894}, + year={2014} +} + +@book{xie2016bookdown, + title={Bookdown: Authoring Books and Technical Documents with R Markdown}, + author={Xie, Yihui}, + year={2016}, + publisher={CRC Press} +} diff --git a/tests/stencila/basic/archive/r-markdown/manifest.xml b/tests/stencila/basic/archive/r-markdown/manifest.xml new file mode 100644 index 00000000..ac9d2942 --- /dev/null +++ b/tests/stencila/basic/archive/r-markdown/manifest.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd b/tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd new file mode 100644 index 00000000..fb9f13bb --- /dev/null +++ b/tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd @@ -0,0 +1,57 @@ +--- +title: RMarkdown and Stencila +author: + - surname: Bentley + given-names: Nokome + affiliation: stencila + - surname: Pawlik + given-names: Aleksandra + - surname: Aufrieter + given-names: Michael + affiliation: substance + - surname: Buchtala + given-names: Oliver + affiliation: substance +organisations: + - id: stencila + name: Stencila + city: Kaikoura + country: New Zealand + - id: substance + name: Substance GmbH + city: Linz + country: Austria +abstract: | + Stencila currently supports import of RMarkdown documents. This allows use cases like allowing collaborators to work on the same document using a WYSIWYG editing environment, or for you to put the final touches on a paper before final submission to a journal. +bibliography: bibliography.bibtex +--- + +# Introduction + +[RMarkdown](https://rmarkdown.rstudio.com/) is a popular format for reproducible research using the R programming language ([@baumer2014r],[@xie2016bookdown]). Stencila is a able to import RMarkdown documents. For example, the source for this example document is available on [Github](https://github.com/stencila/stencila/blob/more-examples/data/r-markdown/rmarkdown.Rmd). Eventually, we'll also support exporting to RMarkdown, allowing WYSIWYG editing of RMarkdown documents in Stencila. + +# Code chunks + +In RMarkdown, code "chunks" are written using "fenced" code blocks. Stencila converts these code "chunks" into Stencila code "cells" like this one: + +```{r} +n <- 500 +``` + +Stencila cells behave like functions having zero or more named `inputs` (like function arguments) and an optional `output` (like a assigning a function's return value). A cell's inputs and outputs are determined by analyzing the cell's code. The cell above has no inputs but produces an output variable named `n`. Stencila's execution engine uses this information to make code cells reactive. For instance, the cell below has `n` as an input i.e it is dependent on the first cell. So when you update the `n` in the cell above, the following plot will update. + +```{r} +s <- min(1000, n) +x <- runif(s) +y <- x + runif(s) +z <- y + rnorm(s) +plot(x, y, cex=z*2, col=rainbow(length(z), alpha=0.5)[rank(x+z)], pch=16) +``` + +# Figures + +In RMarkdown, code chunks can have various options. A common use for options is to set the caption and dimensions of figures. Stencila converts code chunks with the `fig.cap` option into JATS `` elements with a ``. This allows the user to edit the figure caption and for automatic figure numbering and referencing (although that is not working 100% right now). Other options are placed in a comment at the top of the cell so that they are preserved (and eventually will be used to apply those options within the R execution context). + +```{r fig.width=7,fig.height=6,fig.cap="Figure title"} +hist(z, breaks=40, col=hsv(0.6, 0.9, 1), xlab="Value", main="") +``` diff --git a/tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd.jats.xml b/tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd.jats.xml new file mode 100644 index 00000000..c7fc8e0e --- /dev/null +++ b/tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd.jats.xml @@ -0,0 +1,141 @@ + + +
+ + + + RMarkdown and Stencila + + + + + Bentley + Nokome + + + + + + Pawlik + Aleksandra + + + + + Aufrieter + Michael + + + + + + Buchtala + Oliver + + + + + + Stencila + Kaikoura + New Zealand + + + Substance GmbH + Linz + Austria + + +

Stencila currently supports import of RMarkdown documents. This allows use cases like allowing collaborators to work on the same document using a WYSIWYG editing environment, or for you to put the final touches on a paper before final submission to a journal.

+ + + + + + + Introduction +

RMarkdown is a popular format for reproducible research using the R programming language (1,2). Stencila is a able to import RMarkdown documents. For example, the source for this example document is available on Github. Eventually, we’ll also support exporting to RMarkdown, allowing WYSIWYG editing of RMarkdown documents in Stencila.

+ + + Code chunks +

In RMarkdown, code “chunks” are written using “fenced” code blocks. Stencila converts these code “chunks” into Stencila code “cells” like this one:

+ + n <- 500 + {} + + + +

Stencila cells behave like functions having zero or more named inputs (like function arguments) and an optional output (like a assigning a function’s return value). A cell’s inputs and outputs are determined by analyzing the cell’s code. The cell above has no inputs but produces an output variable named n. Stencila’s execution engine uses this information to make code cells reactive. For instance, the cell below has n as an input i.e it is dependent on the first cell. So when you update the n in the cell above, the following plot will update.

+ + s <- min(1000, n) +x <- runif(s) +y <- x + runif(s) +z <- y + rnorm(s) +plot(x, y, cex=z*2, col=rainbow(length(z), alpha=0.5)[rank(x+z)], pch=16) + {} + + + + + + Figures +

In RMarkdown, code chunks can have various options. A common use for options is to set the caption and dimensions of figures. Stencila converts code chunks with the fig.cap option into JATS <fig fig-type="repro-fig"> elements with a <caption>. This allows the user to edit the figure caption and for automatic figure numbering and referencing (although that is not working 100% right now). Other options are placed in a comment at the top of the cell so that they are preserved (and eventually will be used to apply those options within the R execution context).

+ + + Figure title + + + #: fig.width=7,fig.height=6 +hist(z, breaks=40, col=hsv(0.6, 0.9, 1), xlab="Value", main="") + {} + + + + + + + + + + + Baumer + Ben + + + Cetinkaya-Rundel + Mine + + + Bray + Andrew + + + Loi + Linda + + + Horton + Nicholas J + + + R markdown: Integrating a reproducible analysis tool into introductory statistics + arXiv preprint arXiv:1402.1894 + 2014 + + + + + + + Xie + Yihui + + + Bookdown: Authoring books and technical documents with r markdown + CRC Press + 2016 + + + + +
\ No newline at end of file diff --git a/tests/stencila/basic/verify b/tests/stencila/basic/verify new file mode 100755 index 00000000..0d9073c8 --- /dev/null +++ b/tests/stencila/basic/verify @@ -0,0 +1,4 @@ +#!/bin/sh + +jupyter serverextension list 2>&1 | grep nbstencilaproxy +jupyter nbextension list 2>&1 | grep nbstencilaproxy