diff --git a/.gitignore b/.gitignore index d5c63d4..f0d1478 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ .coverage +.cache __pycache__ experimental wiki @@ -12,3 +13,11 @@ images build/ dist/ .eggs/ +.idea +pytest.ini +venv +sandbox +pandoc-* + +# internal script for development +convert_testcases.sh diff --git a/.jupyter/jupyter_notebook_config.py b/.jupyter/jupyter_notebook_config.py new file mode 100644 index 0000000..af08e00 --- /dev/null +++ b/.jupyter/jupyter_notebook_config.py @@ -0,0 +1,526 @@ +#--- nbextensions configuration --- +import sys +#--- nbextensions configuration --- +# Configuration file for jupyter-notebook. + +#------------------------------------------------------------------------------ +# Configurable configuration +#------------------------------------------------------------------------------ + +#------------------------------------------------------------------------------ +# SingletonConfigurable configuration +#------------------------------------------------------------------------------ + +# A configurable that only allows one instance. +# +# This class is for classes that should only have one instance of itself or +# *any* subclass. To create and retrieve such a class use the +# :meth:`SingletonConfigurable.instance` method. + +#------------------------------------------------------------------------------ +# Application configuration +#------------------------------------------------------------------------------ + +# This is an application. + +# Set the log level by value or name. +# c.Application.log_level = 30 + +# The date format used by logging formatters for %(asctime)s +# c.Application.log_datefmt = '%Y-%m-%d %H:%M:%S' + +# The Logging format template +# c.Application.log_format = '[%(name)s]%(highlevel)s %(message)s' + +#------------------------------------------------------------------------------ +# JupyterApp configuration +#------------------------------------------------------------------------------ + +# Base class for Jupyter applications + +# Full path of a config file. +# c.JupyterApp.config_file = '' + +# Generate default config file. +# c.JupyterApp.generate_config = False + +# Answer yes to any prompts. +# c.JupyterApp.answer_yes = False + +# Specify a config file to load. +# c.JupyterApp.config_file_name = '' + +#------------------------------------------------------------------------------ +# NotebookApp configuration +#------------------------------------------------------------------------------ + +# Use a regular expression for the Access-Control-Allow-Origin header +# +# Requests from an origin matching the expression will get replies with: +# +# Access-Control-Allow-Origin: origin +# +# where `origin` is the origin of the request. +# +# Ignored if allow_origin is set. +# c.NotebookApp.allow_origin_pat = '' + +# Set the Access-Control-Allow-Credentials: true header +# c.NotebookApp.allow_credentials = False + +# Whether to trust or not X-Scheme/X-Forwarded-Proto and X-Real-Ip/X-Forwarded- +# For headerssent by the upstream reverse proxy. Necessary if the proxy handles +# SSL +# c.NotebookApp.trust_xheaders = False + +# Reraise exceptions encountered loading server extensions? +# c.NotebookApp.reraise_server_extension_failures = False + +# Hashed password to use for web authentication. +# +# To generate, type in a python/IPython shell: +# +# from notebook.auth import passwd; passwd() +# +# The string should be of the form type:salt:hashed-password. +# c.NotebookApp.password = '' + +# Specify what command to use to invoke a web browser when opening the notebook. +# If not specified, the default browser will be determined by the `webbrowser` +# standard library module, which allows setting of the BROWSER environment +# variable to override it. +# c.NotebookApp.browser = '' + +# DEPRECATED use base_url +# c.NotebookApp.base_project_url = '/' + +# The port the notebook server will listen on. +# c.NotebookApp.port = 8888 + +# The base URL for the notebook server. +# +# Leading and trailing slashes can be omitted, and will automatically be added. +# c.NotebookApp.base_url = '/' + +# Supply extra arguments that will be passed to Jinja environment. +# c.NotebookApp.jinja_environment_options = traitlets.Undefined + +# Supply overrides for the tornado.web.Application that the IPython notebook +# uses. +# c.NotebookApp.tornado_settings = traitlets.Undefined + +# The random bytes used to secure cookies. By default this is a new random +# number every time you start the Notebook. Set it to a value in a config file +# to enable logins to persist across server sessions. +# +# Note: Cookie secrets should be kept private, do not share config files with +# cookie_secret stored in plaintext (you can read the value from a file). +# c.NotebookApp.cookie_secret = b'' + +# The url for MathJax.js. +# c.NotebookApp.mathjax_url = '' + +# extra paths to look for Javascript notebook extensions +# c.NotebookApp.extra_nbextensions_path = traitlets.Undefined + +# The session manager class to use. +# c.NotebookApp.session_manager_class = + +# The full path to an SSL/TLS certificate file. +# c.NotebookApp.certfile = '' + +# Python modules to load as notebook server extensions. This is an experimental +# API, and may change in future releases. +# c.NotebookApp.server_extensions = traitlets.Undefined + +# The kernel manager class to use. +# c.NotebookApp.kernel_manager_class = + +# The IP address the notebook server will listen on. +# c.NotebookApp.ip = 'localhost' + +# DISABLED: use %pylab or %matplotlib in the notebook to enable matplotlib. +# c.NotebookApp.pylab = 'disabled' + +# The full path to a private key file for usage with SSL/TLS. +# c.NotebookApp.keyfile = '' + +# DEPRECATED, use tornado_settings +# c.NotebookApp.webapp_settings = traitlets.Undefined + +# Set the Access-Control-Allow-Origin header +# +# Use '*' to allow any origin to access your server. +# +# Takes precedence over allow_origin_pat. +# c.NotebookApp.allow_origin = '' + +# The notebook manager class to use. +# c.NotebookApp.contents_manager_class = + +# The config manager class to use +# c.NotebookApp.config_manager_class = + +# Whether to enable MathJax for typesetting math/TeX +# +# MathJax is the javascript library IPython uses to render math/LaTeX. It is +# very large, so you may want to disable it if you have a slow internet +# connection, or for offline use of the notebook. +# +# When disabled, equations etc. will appear as their untransformed TeX source. +# c.NotebookApp.enable_mathjax = True + +# The kernel spec manager class to use. Should be a subclass of +# `jupyter_client.kernelspec.KernelSpecManager`. +# +# The Api of KernelSpecManager is provisional and might change without warning +# between this version of IPython and the next stable one. +# c.NotebookApp.kernel_spec_manager_class = + +# The number of additional ports to try if the specified port is not available. +# c.NotebookApp.port_retries = 50 + +# Extra paths to search for serving jinja templates. +# +# Can be used to override templates from notebook.templates. +# c.NotebookApp.extra_template_paths = traitlets.Undefined + +# Whether to open in a browser after starting. The specific browser used is +# platform dependent and determined by the python standard library `webbrowser` +# module, unless it is overridden using the --browser (NotebookApp.browser) +# configuration option. +# c.NotebookApp.open_browser = True + +# The default URL to redirect to from `/` +# c.NotebookApp.default_url = '/tree' + +# The file where the cookie secret is stored. +# c.NotebookApp.cookie_secret_file = '' + +# The directory to use for notebooks and kernels. +# c.NotebookApp.notebook_dir = '' + +# Extra paths to search for serving static files. +# +# This allows adding javascript/css to be available from the notebook server +# machine, or overriding individual files in the IPython +# c.NotebookApp.extra_static_paths = traitlets.Undefined + +# The base URL for websockets, if it differs from the HTTP server (hint: it +# almost certainly doesn't). +# +# Should be in the form of an HTTP origin: ws[s]://hostname[:port] +# c.NotebookApp.websocket_url = '' + +# The logout handler class to use. +# c.NotebookApp.logout_handler_class = + +# Extra variables to supply to jinja templates when rendering. +# c.NotebookApp.jinja_template_vars = traitlets.Undefined + +# Supply SSL options for the tornado HTTPServer. See the tornado docs for +# details. +# c.NotebookApp.ssl_options = traitlets.Undefined + +# +# c.NotebookApp.file_to_run = '' + +# The login handler class to use. +# c.NotebookApp.login_handler_class = + +#------------------------------------------------------------------------------ +# LoggingConfigurable configuration +#------------------------------------------------------------------------------ + +# A parent class for Configurables that log. +# +# Subclasses have a log trait, and the default behavior is to get the logger +# from the currently running Application. + +#------------------------------------------------------------------------------ +# ConnectionFileMixin configuration +#------------------------------------------------------------------------------ + +# Mixin for configurable classes that work with connection files + +# JSON file in which to store connection info [default: kernel-.json] +# +# This file will contain the IP, ports, and authentication key needed to connect +# clients to this kernel. By default, this file will be created in the security +# dir of the current profile, but can be specified by absolute path. +# c.ConnectionFileMixin.connection_file = '' + +# set the iopub (PUB) port [default: random] +# c.ConnectionFileMixin.iopub_port = 0 + +# set the control (ROUTER) port [default: random] +# c.ConnectionFileMixin.control_port = 0 + +# set the stdin (ROUTER) port [default: random] +# c.ConnectionFileMixin.stdin_port = 0 + +# set the heartbeat port [default: random] +# c.ConnectionFileMixin.hb_port = 0 + +# set the shell (ROUTER) port [default: random] +# c.ConnectionFileMixin.shell_port = 0 + +# +# c.ConnectionFileMixin.transport = 'tcp' + +# Set the kernel's IP address [default localhost]. If the IP address is +# something other than localhost, then Consoles on other machines will be able +# to connect to the Kernel, so be careful! +# c.ConnectionFileMixin.ip = '' + +#------------------------------------------------------------------------------ +# KernelManager configuration +#------------------------------------------------------------------------------ + +# Manages a single kernel in a subprocess on this host. +# +# This version starts kernels with Popen. + +# DEPRECATED: Use kernel_name instead. +# +# The Popen Command to launch the kernel. Override this if you have a custom +# kernel. If kernel_cmd is specified in a configuration file, Jupyter does not +# pass any arguments to the kernel, because it cannot make any assumptions about +# the arguments that the kernel understands. In particular, this means that the +# kernel does not receive the option --debug if it given on the Jupyter command +# line. +# c.KernelManager.kernel_cmd = traitlets.Undefined + +# Should we autorestart the kernel if it dies. +# c.KernelManager.autorestart = False + +#------------------------------------------------------------------------------ +# Session configuration +#------------------------------------------------------------------------------ + +# Object for handling serialization and sending of messages. +# +# The Session object handles building messages and sending them with ZMQ sockets +# or ZMQStream objects. Objects can communicate with each other over the +# network via Session objects, and only need to work with the dict-based IPython +# message spec. The Session will handle serialization/deserialization, security, +# and metadata. +# +# Sessions support configurable serialization via packer/unpacker traits, and +# signing with HMAC digests via the key/keyfile traits. +# +# Parameters ---------- +# +# debug : bool +# whether to trigger extra debugging statements +# packer/unpacker : str : 'json', 'pickle' or import_string +# importstrings for methods to serialize message parts. If just +# 'json' or 'pickle', predefined JSON and pickle packers will be used. +# Otherwise, the entire importstring must be used. +# +# The functions must accept at least valid JSON input, and output *bytes*. +# +# For example, to use msgpack: +# packer = 'msgpack.packb', unpacker='msgpack.unpackb' +# pack/unpack : callables +# You can also set the pack/unpack callables for serialization directly. +# session : bytes +# the ID of this Session object. The default is to generate a new UUID. +# username : unicode +# username added to message headers. The default is to ask the OS. +# key : bytes +# The key used to initialize an HMAC signature. If unset, messages +# will not be signed or checked. +# keyfile : filepath +# The file containing a key. If this is set, `key` will be initialized +# to the contents of the file. + +# Threshold (in bytes) beyond which a buffer should be sent without copying. +# c.Session.copy_threshold = 65536 + +# The digest scheme used to construct the message signatures. Must have the form +# 'hmac-HASH'. +# c.Session.signature_scheme = 'hmac-sha256' + +# The UUID identifying this session. +# c.Session.session = '' + +# The name of the packer for serializing messages. Should be one of 'json', +# 'pickle', or an import name for a custom callable serializer. +# c.Session.packer = 'json' + +# The maximum number of digests to remember. +# +# The digest history will be culled when it exceeds this value. +# c.Session.digest_history_size = 65536 + +# path to file containing execution key. +# c.Session.keyfile = '' + +# The maximum number of items for a container to be introspected for custom +# serialization. Containers larger than this are pickled outright. +# c.Session.item_threshold = 64 + +# Threshold (in bytes) beyond which an object's buffer should be extracted to +# avoid pickling. +# c.Session.buffer_threshold = 1024 + +# Debug output in the Session +# c.Session.debug = False + +# The name of the unpacker for unserializing messages. Only used with custom +# functions for `packer`. +# c.Session.unpacker = 'json' + +# execution key, for signing messages. +# c.Session.key = b'' + +# Metadata dictionary, which serves as the default top-level metadata dict for +# each message. +# c.Session.metadata = traitlets.Undefined + +# Username for the Session. Default is your system username. +# c.Session.username = 'sturm' + +#------------------------------------------------------------------------------ +# MultiKernelManager configuration +#------------------------------------------------------------------------------ + +# A class for managing multiple kernels. + +# The name of the default kernel to start +# c.MultiKernelManager.default_kernel_name = 'python3' + +# The kernel manager class. This is configurable to allow subclassing of the +# KernelManager for customized behavior. +# c.MultiKernelManager.kernel_manager_class = 'jupyter_client.ioloop.IOLoopKernelManager' + +#------------------------------------------------------------------------------ +# MappingKernelManager configuration +#------------------------------------------------------------------------------ + +# A KernelManager that handles notebook mapping and HTTP error handling + +# +# c.MappingKernelManager.root_dir = '' + +#------------------------------------------------------------------------------ +# ContentsManager configuration +#------------------------------------------------------------------------------ + +# Base class for serving files and directories. +# +# This serves any text or binary file, as well as directories, with special +# handling for JSON notebook documents. +# +# Most APIs take a path argument, which is always an API-style unicode path, and +# always refers to a directory. +# +# - unicode, not url-escaped +# - '/'-separated +# - leading and trailing '/' will be stripped +# - if unspecified, path defaults to '', +# indicating the root path. + +# Python callable or importstring thereof +# +# To be called on a contents model prior to save. +# +# This can be used to process the structure, such as removing notebook outputs +# or other side effects that should not be saved. +# +# It will be called as (all arguments passed by keyword):: +# +# hook(path=path, model=model, contents_manager=self) +# +# - model: the model to be saved. Includes file contents. +# Modifying this dict will affect the file that is stored. +# - path: the API path of the save destination +# - contents_manager: this ContentsManager instance +# c.ContentsManager.pre_save_hook = None + +# +# c.ContentsManager.checkpoints = traitlets.Undefined + +# The base name used when creating untitled notebooks. +# c.ContentsManager.untitled_notebook = 'Untitled' + +# The base name used when creating untitled files. +# c.ContentsManager.untitled_file = 'untitled' + +# +# c.ContentsManager.checkpoints_kwargs = traitlets.Undefined + +# +# c.ContentsManager.checkpoints_class = + +# The base name used when creating untitled directories. +# c.ContentsManager.untitled_directory = 'Untitled Folder' + +# Glob patterns to hide in file and directory listings. +# c.ContentsManager.hide_globs = traitlets.Undefined + +#------------------------------------------------------------------------------ +# FileContentsManager configuration +#------------------------------------------------------------------------------ + +# DEPRECATED, use post_save_hook +# c.FileContentsManager.save_script = False + +# +# c.FileContentsManager.root_dir = '' + +# Python callable or importstring thereof +# +# to be called on the path of a file just saved. +# +# This can be used to process the file on disk, such as converting the notebook +# to a script or HTML via nbconvert. +# +# It will be called as (all arguments passed by keyword):: +# +# hook(os_path=os_path, model=model, contents_manager=instance) +# +# - path: the filesystem path to the file just written - model: the model +# representing the file - contents_manager: this ContentsManager instance +# c.FileContentsManager.post_save_hook = None + +#------------------------------------------------------------------------------ +# NotebookNotary configuration +#------------------------------------------------------------------------------ + +# A class for computing and verifying notebook signatures. + +# The file where the secret key is stored. +# c.NotebookNotary.secret_file = '' + +# The secret key with which notebooks are signed. +# c.NotebookNotary.secret = b'' + +# The number of notebook signatures to cache. When the number of signatures +# exceeds this value, the oldest 25% of signatures will be culled. +# c.NotebookNotary.cache_size = 65535 + +# The hashing algorithm used to sign notebooks. +# c.NotebookNotary.algorithm = 'sha256' + +# The sqlite file in which to store notebook signatures. By default, this will +# be in your Jupyter runtime directory. You can set it to ':memory:' to disable +# sqlite writing to the filesystem. +# c.NotebookNotary.db_file = '' + +#------------------------------------------------------------------------------ +# KernelSpecManager configuration +#------------------------------------------------------------------------------ + +# Whitelist of allowed kernel names. +# +# By default, all installed kernels are allowed. +# c.KernelSpecManager.whitelist = traitlets.Undefined + +c.NotebookApp.server_extensions.append('ipyparallel.nbextension') + +c.NotebookApp.contents_manager_class = 'ipymd.IPymdContentsManager' +c.IPymdContentsManager.format = 'rmarkdown' + +c.NotebookApp.iopub_data_rate_limit = 1e8 diff --git a/Makefile b/Makefile index f487e3c..53c7924 100644 --- a/Makefile +++ b/Makefile @@ -1,11 +1,18 @@ +VENV=venv/bin +PIP=$(VENV)/pip +PYTHON=$(VENV)/python + help: @echo "clean - remove all build, test, coverage and Python artifacts" @echo "clean-build - remove build artifacts" @echo "clean-pyc - remove Python file artifacts" + @echo "clean-venv - remove Python virtual environment" + @echo "python - create Python virtual environment and install all required packages" @echo "lint - check style with flake8" @echo "test - run tests quickly with the default Python" + @echo "jupyter - run jupyter notebook in a virtual environment with ipymd" -clean: clean-build clean-pyc +clean: clean-build clean-pyc clean-venv clean-build: rm -fr build/ @@ -18,8 +25,37 @@ clean-pyc: find . -name '*~' -exec rm -f {} + find . -name '__pycache__' -exec rm -fr {} + -lint: - flake8 ipymd setup.py --exclude=ipymd/ext/six.py,ipymd/core/contents_manager.py --ignore=E226,E265,F401,F403,F811 +clean-venv: + rm -rf venv/ + +lint: | $(PYTHON) + $(VENV)/flake8 ipymd setup.py --exclude=ipymd/ext/six.py,ipymd/core/contents_manager.py,ipymd/formats/tests/test_rmarkdown.py --ignore=E226,E265,F401,F403,F811 + +test: lint | $(PYTHON) + $(PYTHON) setup.py test + +jupyter: | $(PYTHON) + ./venv/bin/jupyter notebook --config=./.jupyter/jupyter_notebook_config.py + +################################################################################ +# Setup python virtual environment +################################################################################ + +.PHONY: python +python: $(PYTHON) + +venv: + virtualenv venv -p /usr/bin/python3 + +$(PIP): | venv + $(PIP) install --upgrade pip + +venv/.installed: requirements-dev.txt | venv + $(PIP) install -Ur requirements-dev.txt + $(PIP) install -e . + $(PYTHON) -c 'import pypandoc; pypandoc.download_pandoc(version="1.19.1")' + echo "pip install successful" > $@ + +$(PYTHON): | $(PIP) venv/.installed + -test: lint - python setup.py test diff --git a/README.md b/README.md index e96f004..966c451 100644 --- a/README.md +++ b/README.md @@ -1,143 +1,183 @@ [![Build Status](https://travis-ci.org/rossant/ipymd.svg?branch=travis)](https://travis-ci.org/rossant/ipymd) [![Coverage Status](https://coveralls.io/repos/rossant/ipymd/badge.svg)](https://coveralls.io/r/rossant/ipymd) -# Replace .ipynb with .md in the IPython Notebook - -The goal of ipymd is to replace `.ipynb` notebook files like: - -```json -{ - "cells": [ - { - "cell_type": "markdown", - "source": [ - "Here is some Python code:" - ] - }, - { - "cell_type": "code", - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Hello world!\n" - ] - } - ], - "source": [ - "print(\"Hello world!\")" - ] - } - ... - ] -} -``` - -with: - - Here is some Python code: - - ```python - >>> print("Hello world!") - Hello world! - ``` - -The JSON `.ipynb` are removed from the equation, and the conversion happens on the fly. The IPython Notebook becomes an interactive Markdown text editor! +# Store Jupyter notebooks in markdown format. +This package provides an alternative content manager for jupyter. +It allows to store notebooks in text-based formats, replacing the native json-based `.ipynb`. -A drawback is that you lose prompt numbers and images (for now). +This combines the advantages of a simple, text-based format (vi and git-friendly) with jupyter's powerful UI for interactively editing code and text. -This is useful when you write technical documents, blog posts, books, etc. -![image](https://cloud.githubusercontent.com/assets/1942359/5570181/f656a484-8f7d-11e4-8ec2-558d022b13d3.png) +## Overview of formats +Ipymd currently supports the following formats: -## Installation +| Format | Extension | vi | git | images | +| ------------ | ------------------ | -- | --- | ------ | +| [notebook](#ipython-notebook-ipynb) | `.ipynb` | | | ✔ | +| [rmarkdown](#rmarkdown-rmd--rnotebook-nbhtml) | `.Rmd`, `.nb.html` | ✔ | ✔ | ✔ | +| [markdown]() | `.md` | ✔ | (✔) | | +| [atlas](#oreilly-atlas-md) | `.md` | ✔ | (✔) | | +| [opendocument](#opendocument-odt) | `.odt` | | | | +| [python](#python-py) | `.py` | ✔ | (✔) | | -1. Install ipymd: +✔ works; (✔) works with limitations - To install the latest release version: - ```shell - pip install ipymd - ``` +## Usage +Ipymd hooks into jupyter, enabling to open the files directly in jupyter notebook. - Alternatively, to install the development version: +Alternatively, you can use ipymd to convert between the formats from command line: - ```shell - pip install git+https://github.com/rossant/ipymd - ``` +``` +ipymd my_notebook.ipynb --from notebook --to markdown +``` -2. **Optional:** - To interact with `.ipynb` files: +Additional options: +``` + -h, --help show this help message and exit + --output OUTPUT output folder + --extension EXTENSION + output file extension + --overwrite overwrite target file if it exists (false by default) +``` - ```shell - pip install jupyter ipython - ``` - To interact with `.odt` files: +## Installation +There are two possibilities to use ipymd: +1. **Within a virtual environment, for testing and developing** ```shell - pip install git+https://github.com/eea/odfpy + git clone https://github.com/rossant/ipymd + make jupyter ``` + will setup a virtual environment and run a `jupyter notebook` instance with ipymd activated. -3. Open your `jupyter_notebook_config.py`. Here's how to find it: - - - ``` - jupyter notebook --generate-config # generate a default config file - jupyter --config-dir # find out the path to the config file + You can choose the format by editing `.jupyter/jupyter_notebook_config.py`: + ```python + c.IPymdContentsManager.format = 'rmarkdown' # choose the format here ``` -4. Add the following in `jupyter_notebook_config.py`: - ```python - c.NotebookApp.contents_manager_class = 'ipymd.IPymdContentsManager' - ``` +2. **Integrated into your local jupyter installation** + * Install ipymd + ```shell + pip install ipymd + ``` -5. Now, you can open `.md` files in the Notebook. + * Open your `jupyter_notebook_config.py`. Here's how to find it: + ``` + jupyter notebook --generate-config # generate a default config file + jupyter --config-dir # find out the path to the config file + ``` -## Why? + * Add the following in `jupyter_notebook_config.py`: + ```python + c.NotebookApp.contents_manager_class = 'ipymd.IPymdContentsManager' + c.IPymdContentsManager.format = 'rmarkdown' # choose the format here + ``` -### IPython Notebook + * (re)start jupyter -Pros: +**Optional:** +To interact with `.odt` files: -* Excellent UI for executing code interactively *and* writing text +```shell +pip install git+https://github.com/eea/odfpy +``` -Cons: +## Caveats -* `.ipynb` not git-friendly -* Cannot easily edit in a text editor -* Cannot easily edit on GitHub's web interface +**WARNING**: use this library at your own risks, backup your data, and version-control your notebooks and Markdown files! +* Renaming doesn't work yet (issue #4) +* New notebook doesn't work yet (issue #5) +* Only nbformat v4 is supported currently (IPython 3.0) -### Markdown -Pros: -* Simple ASCII/Unicode format to write code and text -* Can easily edit in a text editor -* Can easily edit on GitHub's web interface -* Git-friendly +## Formats +### IPython notebook (`.ipynb`) +Jupyter's default notebook format. It stores cells as json-objects. +The main downsides of this format are +* not git-friendly +* cannot easily edit in a text editor +* cannot easily edit on GitHub's web interface -Cons: +[Format documentation](http://nbformat.readthedocs.io/en/latest/) -* No UI to execute code interactively +### RMarkdown (`.Rmd`) / RNotebook (`.nb.html`) +RMarkdown is propagated by rstudio and widely adopted within the R community. +Unlike the name suggests, it can very well be used with python. +The clue about this format is, that it strictly separates source code from output. +This makes it the format of choice when working with version control. -### ipymd +While the source code is stored as markdown in a `.Rmd` file, the results go into a +`.nb.html` file which can also be viewed in a browser. -All pros of IPython Notebook and Markdown, no cons! +[Format documentation](http://rmarkdown.rstudio.com/r_notebooks.html) -## How it works +#### Known issues +See [grst/ipymd/issues](https://github.com/grst/ipymd/issues) for issues related to rmarkdown. Major issues: +* HTML formatting can be improved +* Some output is not compatible with rstudio -* Write in Markdown in `document.md` - * Either in a text editor (convenient when working on text) - * Or in the Notebook (convenient when writing code examples) -* Markdown cells, code cells and (optionally) notebook metadata are saved in - the file -* Collaborators can work on the Markdown document using GitHub's web interface. +#### Implementation of `.Rmd` format +* markdown cells are saved as plain markdown +* code cells are saved as code chunks, separated by a newline + ~~~ + ```{python, some="meta", data=True} + print("Hello World!") + ``` + ~~~ + Note the curly braced `{}` which distinguish an executed code chunk from + a code chunk within markdown. +* metadata is saved as chunk options. + * Both python and R literals are supported (`NULL`, `None`, `TRUE`, `True`, `FALSE`, `False`), + but always saved as R literals to maintain compatibility with rstudio. + * Both single and double quoted strings are supported. + * We try to parse unquoted options as literal, then as integer, then as float. If all three fail a `TypeError` is raised. + +#### Implementation of `nb.html` format. +* This format stores the outputs of the notebook in a way that + * the outputs can be read from jupyter + * the entire notebook can be viewed from a browser +* a html templated is used, which is filled using `jinja2`. +* markdown cells are saved within `...` tags +* code cells are saved within `chunk` tags: + ``` + + + 
...
+ + + ... + + + + + + ``` +* tags cannot be nested +* a `chunk` may hold an arbitrary number of `outputs` +* tags hold data as base64 encoded json dictionaries as follows: + * rnb-source-begin: + ~~~ + {'data': '```python\n chunk as markdown```'} + ~~~ + * rnb-output-begin/rnb-plot-begin + ~~~ + {'data': '', # fallback for rstudio + 'ipymd.data': {'text/plain': ..., # output['data'] from jupyter nbformat + 'image/png': ..., + ... }, + 'ipymd.metadata': {}, # output['metadata'] from jupyter nbformat + 'ipymd.output_type': 'display_data'} # output['output_type'] from jupyter nbformat + ~~~ + + +### Markdown (`.md`) * By convention, a **notebook code cell** is equivalent to a **Markdown code block with explicit `python` syntax highlighting**: ``` @@ -194,26 +234,23 @@ All pros of IPython Notebook and Markdown, no cons! * Text output and standard output are combined into a single text output (stdout lines first, output lines last) -## Caveats -**WARNING**: use this library at your own risks, backup your data, and version-control your notebooks and Markdown files! +### O'Reilly Atlas (`.md`) +* `.md` with special HTML tags for code and mathematical equations +[Format documentation](http://odewahn.github.io/publishing-workflows-for-jupyter/#1) ( -* Renaming doesn't work yet (issue #4) -* New notebook doesn't work yet (issue #5) -* Only nbformat v4 is supported currently (IPython 3.0) +### Python (`.py`) +* code cells are delimited by double line breaks. +* Markdown cells = Python comments. +* [TODO: this doesn't work well, see #28 and #31] +### Opendocument (`.odt`). +* You need to install the [development version of odfpy](https://github.com/eea/odfpy/). -## Formats -ipymd uses a modular architecture that lets you define new formats. The following formats are currently implemented, and can be selected by modifying `~/.ipython/profile_/ipython_notebook_config.py`: -* IPython notebook (`.ipynb`) -* Markdown (`.md`) - * `c.IPymdContentsManager.format = 'markdown'` -* [O'Reilly Atlas](http://odewahn.github.io/publishing-workflows-for-jupyter/#1) (`.md` with special HTML tags for code and mathematical equations) - * `c.IPymdContentsManager.format = 'atlas'` -* Python (`.py`): code cells are delimited by double line breaks. Markdown cells = Python comments. [TODO: this doesn't work well, see #28 and #31] -* Opendocument (`.odt`). You need to install the [development version of odfpy](https://github.com/eea/odfpy/). +## Implementing your own format +ipymd uses a modular architecture that lets you define new formats. The following formats are currently implemented, and can be selected by modifying `~/.ipython/profile_/ipython_notebook_config.py`: You can convert from any supported format to any supported format. This works by converting to an intermediate format that is basically a list of notebook cells. diff --git a/examples/ex5.notebook.ipynb b/examples/ex5.notebook.ipynb new file mode 100644 index 0000000..9def03b --- /dev/null +++ b/examples/ex5.notebook.ipynb @@ -0,0 +1,86 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Header\n", + "\n", + "A paragraph.\n", + "\n", + "test" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "foo = 'bar'" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Python code:" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Hello world!\n" + ] + } + ], + "source": [ + "print(\"Hello world!\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "JavaScript code:\n", + "\n", + "```javascript\n", + "console.log(\"Hello world!\");\n", + "```\n", + "\n", + "test" + ] + } + ], + "metadata": { + "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": "3.6.2" + }, + "output": "html_notebook", + "title": "Example 5" + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ex5.rmarkdown.Rmd b/examples/ex5.rmarkdown.Rmd new file mode 100644 index 0000000..2d0b0be --- /dev/null +++ b/examples/ex5.rmarkdown.Rmd @@ -0,0 +1,42 @@ +--- +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: 3.6.2 +output: html_notebook +title: Example 5 +--- + +# Header + +A paragraph. + +test + +```{python, collapsed=TRUE} +foo = 'bar' +``` + +Python code: + +```{python} +print("Hello world!") +``` + +JavaScript code: + +```javascript +console.log("Hello world!"); +``` + +test diff --git a/examples/ex5.rmarkdown.nb.html b/examples/ex5.rmarkdown.nb.html new file mode 100644 index 0000000..273fec5 --- /dev/null +++ b/examples/ex5.rmarkdown.nb.html @@ -0,0 +1,243 @@ + + + + + + + + + + + + + +Example 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + +

Header

+

A paragraph.

+

test

+ + + +
foo = 'bar'
+ + + +

Python code:

+ + + +
print("Hello world!")
+ + +
Hello world!
+ + + +

JavaScript code:

+
console.log("Hello world!");
+

test

+ + + +
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
+ + + +
+ + + + + + + + diff --git a/examples/ex5.rmarkdown.rstudio.Rmd b/examples/ex5.rmarkdown.rstudio.Rmd new file mode 100644 index 0000000..2d0b0be --- /dev/null +++ b/examples/ex5.rmarkdown.rstudio.Rmd @@ -0,0 +1,42 @@ +--- +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: 3.6.2 +output: html_notebook +title: Example 5 +--- + +# Header + +A paragraph. + +test + +```{python, collapsed=TRUE} +foo = 'bar' +``` + +Python code: + +```{python} +print("Hello world!") +``` + +JavaScript code: + +```javascript +console.log("Hello world!"); +``` + +test diff --git a/examples/ex5.rmarkdown.rstudio.nb.html b/examples/ex5.rmarkdown.rstudio.nb.html new file mode 100644 index 0000000..f1f0058 --- /dev/null +++ b/examples/ex5.rmarkdown.rstudio.nb.html @@ -0,0 +1,244 @@ + + + + + + + + + + + + + +Example 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
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
+ + + +
+ + + + + + + + diff --git a/examples/ex6.notebook.ipynb b/examples/ex6.notebook.ipynb new file mode 100644 index 0000000..ddb744e --- /dev/null +++ b/examples/ex6.notebook.ipynb @@ -0,0 +1,271 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Python notebook tests\n", + "\n", + "Some literal python which is not evaluated: \n", + "\n", + "```python\n", + "print(\"Hello World!\")\n", + "```\n", + "\n", + "## Advanved Markdown\n", + "\n", + "Foo bar kk\n", + "\n", + "$\\sum_{i=1}^n 2^i$\n", + "\n", + "## Special characters, text output" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "ä'<>$& 0\n", + "ä'<>$& 1\n", + "ä'<>$& 2\n", + "ä'<>$& 3\n", + "ä'<>$& 4\n", + "ä'<>$& 5\n", + "ä'<>$& 6\n", + "ä'<>$& 7\n", + "ä'<>$& 8\n", + "ä'<>$& 9\n" + ] + } + ], + "source": [ + "for i in range(10):\n", + " print(\"ä'<>$& \" + str(i))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Multiple images in the same output" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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5T58rJuSDDzJPn/7vbITUVOZt25g//JC5alU5tkoV5h9+MCO34gxSU5nHj2cu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\nzDcsk6vwBlAnAtjBzB+blic7EFEpX9Y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mPn2umJAPPsg8ffq/sxFSU5m3bWP+8EPmqlXl2CpVmH/4wYzcijNITWUeP565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\n/m+55YrvXxVAcDADd90lO93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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 = 256\n", + "X = np.linspace(-np.pi,np.pi,n,endpoint=True)\n", + "Y = np.sin(2*X)\n", + "\n", + "fig, ax = plt.subplots( nrows=1, ncols=1 )\n", + "ax.plot (X, Y+1, color='blue', alpha=1.00)\n", + "ax.plot (X, Y-1, color='blue', alpha=1.00)\n", + "plt.show()\n", + "\n", + "fig, ax = plt.subplots( nrows=1, ncols=1 )\n", + "ax.plot (X, Y+1, color='red', alpha=1.00)\n", + "ax.plot (X, Y-1, color='red', alpha=1.00)\n", + "plt.show()" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "collapsed": true + }, + "source": [ + "## A table" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " x y\n", + "0 0 0\n", + "1 1 2\n", + "2 2 4\n", + "3 3 6\n", + "4 4 8\n", + "5 5 10\n", + "6 6 12\n", + "7 7 14\n", + "8 8 16\n", + "9 9 18" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas as pd\n", + "df = pd.DataFrame().assign(x=range(10), y=range(0, 20, 2))\n", + "df" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## An Error" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "ename": "SyntaxError", + "evalue": "invalid syntax (, line 3)", + "output_type": "error", + "traceback": [ + "\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m3\u001b[0m\n\u001b[0;31m knitr::knit_engines$set(python = reticulate::eng_python)\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n" + ] + } + ], + "source": [ + "library(knitr)\n", + "library(reticulate)\n", + "knitr::knit_engines$set(python = reticulate::eng_python)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.3" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/ex6.rmarkdown.Rmd b/examples/ex6.rmarkdown.Rmd new file mode 100644 index 0000000..f1ea095 --- /dev/null +++ b/examples/ex6.rmarkdown.Rmd @@ -0,0 +1,74 @@ +--- +kernelspec: + display_name: Python 3 + language: python + name: python3 +language_info: + codemirror_mode: + name: ipython + version: 3 + file_extension: .py + mimetype: text/x-python + name: python + nbconvert_exporter: python + pygments_lexer: ipython3 + version: 3.6.3 +--- + +# Python notebook tests + +Some literal python which is not evaluated: + +```python +print("Hello World!") +``` + +## Advanved Markdown + +Foo bar kk + +$\sum_{i=1}^n 2^i$ + +## Special characters, text output + +```{python} +for i in range(10): + print("ä'<>$& " + str(i)) +``` + +## Multiple images in the same output + +```{python} +import numpy as np +import matplotlib.pyplot as plt + +n = 256 +X = np.linspace(-np.pi,np.pi,n,endpoint=True) +Y = np.sin(2*X) + +fig, ax = plt.subplots( nrows=1, ncols=1 ) +ax.plot (X, Y+1, color='blue', alpha=1.00) +ax.plot (X, Y-1, color='blue', alpha=1.00) +plt.show() + +fig, ax = plt.subplots( nrows=1, ncols=1 ) +ax.plot (X, Y+1, color='red', alpha=1.00) +ax.plot (X, Y-1, color='red', alpha=1.00) +plt.show() +``` + +## A table + +```{python} +import pandas as pd +df = pd.DataFrame().assign(x=range(10), y=range(0, 20, 2)) +df +``` + +## An Error + +```{python} +library(knitr) +library(reticulate) +knitr::knit_engines$set(python = reticulate::eng_python) +``` diff --git a/examples/ex6.rmarkdown.nb.html b/examples/ex6.rmarkdown.nb.html new file mode 100644 index 0000000..84ef3cd --- /dev/null +++ b/examples/ex6.rmarkdown.nb.html @@ -0,0 +1,821 @@ + + + + + + + + + + + + + +IPYMD Notebook + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + +

Python notebook tests

+

Some literal python which is not evaluated:

+
print("Hello World!")
+

Advanved Markdown

+

Foo bar kk

+

$\sum_{i=1}^n 2^i$

+

Special characters, text output

+ + + +
for i in range(10):
+    print("ä'<>$& " + str(i))
+ + +
ä'<>$& 0
+ä'<>$& 1
+ä'<>$& 2
+ä'<>$& 3
+ä'<>$& 4
+ä'<>$& 5
+ä'<>$& 6
+ä'<>$& 7
+ä'<>$& 8
+ä'<>$& 9
+ + + +

Multiple images in the same output

+ + + +
import numpy as np
+import matplotlib.pyplot as plt
+
+n = 256
+X = np.linspace(-np.pi,np.pi,n,endpoint=True)
+Y = np.sin(2*X)
+
+fig, ax = plt.subplots( nrows=1, ncols=1 )
+ax.plot (X, Y+1, color='blue', alpha=1.00)
+ax.plot (X, Y-1, color='blue', alpha=1.00)
+plt.show()
+
+fig, ax = plt.subplots( nrows=1, ncols=1 )
+ax.plot (X, Y+1, color='red', alpha=1.00)
+ax.plot (X, Y-1, color='red', alpha=1.00)
+plt.show()
+ + +

+ +

+ + +

A table

+ + + +
import pandas as pd
+df = pd.DataFrame().assign(x=range(10), y=range(0, 20, 2))
+df
+ + +['
\n', '\n', '\n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', ' \n', '
xy
000
112
224
336
448
5510
6612
7714
8816
9918
\n', '
'] + + +

An Error

+ + + +
library(knitr)
+library(reticulate)
+knitr::knit_engines$set(python = reticulate::eng_python)
+ + +
  File "", line 3
+    knitr::knit_engines$set(python = reticulate::eng_python)
+          ^
+SyntaxError: invalid syntax
+ + + + +
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+ + + +
+ + + + + + + + diff --git a/examples/ex7.notebook.ipynb b/examples/ex7.notebook.ipynb new file mode 100644 index 0000000..992fd9b --- /dev/null +++ b/examples/ex7.notebook.ipynb @@ -0,0 +1,103 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": "## R notebook with R kernel\n\nSome literal R code which should not be evaluated\n```r\nstop(\"not evaluated\")\n```" + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "trusted": true + }, + "outputs": [ + { + "data": { + "text/plain": "Loading tidyverse: ggplot2\nLoading tidyverse: tibble\nLoading tidyverse: tidyr\nLoading tidyverse: readr\nLoading tidyverse: purrr\nLoading tidyverse: dplyr\nConflicts with tidy packages ---------------------------------------------------\nfilter(): dplyr, stats\nlag(): dplyr, stats" + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": "library(tidyverse)" + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "trusted": true + }, + "outputs": [ + { + "data": { + "text/html": "
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\n20 20 40 " + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": "df = tibble(x=1:20, data=data)\ndf" + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "trusted": true + }, + "outputs": [ + { + "data": { + "image/png": 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AORvEwAIiGSgUheJgCREMlAJC8TgEiI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\nkQAKgEgABfj/eVKPyALu1jYAAAAASUVORK5CYII=", + "text/plain": "plot without title" + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": "ggplot(df, aes(x=x, y=data)) + geom_bar(stat='identity')" + } + ], + "metadata": { + "kernelspec": { + "display_name": "R", + "language": "R", + "name": "ir" + }, + "language_info": { + "codemirror_mode": "r", + "file_extension": ".r", + "mimetype": "text/x-r-source", + "name": "R", + "pygments_lexer": "r", + "version": "3.4.2" + }, + "output": "html_notebook" + }, + "nbformat": 4, + "nbformat_minor": 2 +} \ No newline at end of file diff --git a/examples/ex7.rmarkdown.Rmd b/examples/ex7.rmarkdown.Rmd new file mode 100644 index 0000000..ce04613 --- /dev/null +++ b/examples/ex7.rmarkdown.Rmd @@ -0,0 +1,39 @@ +--- +kernelspec: + display_name: R + language: R + name: ir +language_info: + codemirror_mode: r + file_extension: .r + mimetype: text/x-r-source + name: R + pygments_lexer: r + version: 3.4.2 +output: html_notebook +--- + +## R notebook with R kernel + +Some literal R code which should not be evaluated +```r +stop("not evaluated") +``` + +```{R, trusted=TRUE} +library(tidyverse) +``` + +```{R, trusted=TRUE} +data = 1:20 * 2 +data +``` + +```{R, trusted=TRUE} +df = tibble(x=1:20, data=data) +df +``` + +```{R, trusted=TRUE} +ggplot(df, aes(x=x, y=data)) + geom_bar(stat='identity') +``` diff --git a/examples/ex7.rmarkdown.nb.html b/examples/ex7.rmarkdown.nb.html new file mode 100644 index 0000000..23e45cd --- /dev/null +++ b/examples/ex7.rmarkdown.nb.html @@ -0,0 +1,509 @@ + + + + + + + + + + + + + +IPYMD Notebook + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + +

R notebook with R kernel

+

Some literal R code which should not be evaluated

+
stop("not evaluated")
+ + + +
library(tidyverse)
+ + +
Loading tidyverse: ggplot2
+Loading tidyverse: tibble
+Loading tidyverse: tidyr
+Loading tidyverse: readr
+Loading tidyverse: purrr
+Loading tidyverse: dplyr
+Conflicts with tidy packages ---------------------------------------------------
+filter(): dplyr, stats
+lag():    dplyr, stats
+ + + + +
data = 1:20 * 2
+data
+ + +
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+ + + + +
df = tibble(x=1:20, data=data)
+df
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
xdata
1 2
2 4
3 6
4 8
510
612
714
816
918
1020
1122
1224
1326
1428
1530
1632
1734
1836
1938
2040
+ + + + +
ggplot(df, aes(x=x, y=data)) + geom_bar(stat='identity')
+ + +

+ + + +
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
+ + + +
+ + + + + + + + diff --git a/ipymd/core/contents_manager.py b/ipymd/core/contents_manager.py index dda1591..a475681 100644 --- a/ipymd/core/contents_manager.py +++ b/ipymd/core/contents_manager.py @@ -9,6 +9,8 @@ import io import os import os.path as op +import notebook.transutils + from tornado import web diff --git a/ipymd/core/format_manager.py b/ipymd/core/format_manager.py index 66b5a20..71f9849 100644 --- a/ipymd/core/format_manager.py +++ b/ipymd/core/format_manager.py @@ -12,6 +12,7 @@ import os.path as op import glob import json +import notebook.transutils from pkg_resources import iter_entry_points, DistributionNotFound @@ -252,6 +253,18 @@ def convert(self, if to_kwargs is None: to_kwargs = {} + if from_ == 'rmarkdown' or to == 'rmarkdown': + # TODO: HACK: do rmarkdown conversion in external function. + # As Rmarkdown uses jupyter nbformat as internal format instead of + # ipymd cells, the usual 'conversion' scheme does not work. + # atm, I cannot think of an elegant solution which does not require + # to change a good deal of the ipymd code. + # + # The jupyter format was chosen as internal format to enable + # more complex outputs (i.e. multiple outputs per cell, including + # multiple images). + return convert_rmarkdown(from_, to, contents) + if reader is None: reader = (self.create_reader(from_, **from_kwargs) if from_ is not None else None) @@ -334,3 +347,19 @@ def format_manager(): def convert(*args, **kwargs): """Alias for format_manager().convert().""" return format_manager().convert(*args, **kwargs) + + +def convert_rmarkdown(from_, to, contents): + from ..formats.rmarkdown import RmarkdownReader, RmarkdownWriter + if to == 'rmarkdown' and from_ == 'notebook': + writer = RmarkdownWriter() + writer.write_contents(contents) + return writer.contents + + elif to == 'notebook' and from_ == 'rmarkdown': + reader = RmarkdownReader() + return reader.read(contents) + + else: + raise RuntimeError("Rmarkdown conversion is only possible between" + " 'notebook' and 'rmarkdown' format. ") diff --git a/ipymd/formats/markdown.py b/ipymd/formats/markdown.py index 20828a3..332adb4 100644 --- a/ipymd/formats/markdown.py +++ b/ipymd/formats/markdown.py @@ -116,7 +116,8 @@ def __init__(self): def _new_paragraph(self): self._output.write('\n\n') - def meta(self, source, is_notebook=False): + @staticmethod + def meta(source, is_notebook=False): if source is None: return '' @@ -139,6 +140,11 @@ def meta(self, source, is_notebook=False): return meta + @staticmethod + def format_code(code, lang="python"): + return '```{lang}\n{code}\n```'.format(lang=lang, + code=code.rstrip()) + def append_markdown(self, source, metadata): source = _ensure_string(source) self._output.write(self.meta(metadata) + source.rstrip()) @@ -243,7 +249,7 @@ def __init__(self, prompt=None): def append_code(self, input, output=None, metadata=None): code = self._prompt.from_cell(input, output) - wrapped = '```python\n{code}\n```'.format(code=code.rstrip()) + wrapped = self.format_code(code) self._output.write(self.meta(metadata) + wrapped) diff --git a/ipymd/formats/notebook.py b/ipymd/formats/notebook.py index 02ed0ab..142632e 100644 --- a/ipymd/formats/notebook.py +++ b/ipymd/formats/notebook.py @@ -19,44 +19,7 @@ from ..lib.python import PythonFilter from ..ext.six import string_types from ..utils.utils import _ensure_string - - -#------------------------------------------------------------------------------ -# Utility functions -#------------------------------------------------------------------------------ - -def _cell_input(cell): - """Return the input of an ipynb cell.""" - return _ensure_string(cell.get('source', [])) - - -def _cell_output(cell): - """Return the output of an ipynb cell.""" - outputs = cell.get('outputs', []) - # Add stdout. - stdout = ('\n'.join(_ensure_string(output.get('text', '')) - for output in outputs)).rstrip() - # Add text output. - text_outputs = [] - for output in outputs: - out = output.get('data', {}).get('text/plain', []) - out = _ensure_string(out) - # HACK: skip outputs. - if out.startswith('' + r'([\s\S]+?)' + r'' + ) + + def_chunk_element = re.compile( + r'' + r'([\s\S]+?)' + r'' + ) + + def_image_element = re.compile( + r'' + ) + + def __init__(self): + self._nb = nbf.v4.new_notebook() + self._count = 1 + + def read(self, html): + if html is not None: + for block_type, block_content in self._parse_html(html): + if block_type == 'text': + self._nb['cells'].append(self._text_cell(block_content)) + else: + self._nb['cells'].append(self._chunk_cell(block_content)) + + return self._nb + + def _parse_html(self, html): + """ get a list of rnb-text and rnb-chunks""" + for start_tag, contents, end_tag in ( + self.def_text_or_chunk.findall(html)): + assert start_tag == end_tag, \ + "text and chunk blocks must not be nested." + yield start_tag, contents.strip() + + def _parse_image(self, html): + try: + mime, data = next(iter(self.def_image_element.findall(html))) + except StopIteration: + mime = 'text/plain' + data = 'IPYMD: Error reading image.' + return mime, data + + @staticmethod + def _text_cell(text_block): + # new markdown cell will be filled with html. The corresponding + # source is found in .Rmd file. + return nbf.v4.new_markdown_cell(text_block) + + def _chunk_cell(self, chunk_block): + """parse an rnb-chunk consisting of source/plot/...""" + # A chunk block can be divided in multiple sub-blocks, namely + # + # "source", "plot", "output", + # "warning", "error", "message" + cell = HtmlNbChunkCell(self._count) + self._count += 1 + + for start_tag, b64, contents, end_tag in ( + self.def_chunk_element.findall(chunk_block)): + assert start_tag == end_tag, \ + "different chunk elements must not be nested. " + b64 = b64.strip() + contents = contents.strip() + if start_tag == 'source': + # we ignore the source as we obtain it from .Rmd + pass + elif start_tag in ['output', 'warning', 'message']: + assert cell is not None, "output without source" + cell.new_output(start_tag, b64) + elif start_tag == 'error': + assert cell is not None, "error without source" + cell.new_error(b64) + elif start_tag == 'plot': + assert cell is not None, "plot without source" + mime, data = self._parse_image(contents) + cell.new_plot(mime, data, b64) + + return cell.cell + + +class RmarkdownWriter(object): + """Write R notebook (combine .Rmd and .nb.html) """ + + DEFAULT_LANGUAGE = "python" # if, for whatever reason, no metadata is set + + def __init__(self): + self._language = self.DEFAULT_LANGUAGE + self.rmd_writer = RmdWriter(self) + self.nb_html_writer = NbHtmlWriter(self) + + def write_contents(self, nb): + """convert a jupyter notebook dict to rmarkdown""" + # Parsing the notebook using nbf will get rid of the + # multi line strings. + # nb = nbf.from_dict(nb) + assert nb['nbformat'] >= 4 + + try: + self._language = nb['metadata']['kernelspec']['language'] + except KeyError: + pass + + self.write_notebook_metadata(nb['metadata']) + for cell in nb['cells']: + self.write(cell) + + def write(self, cell): + self.rmd_writer.write(cell) + self.nb_html_writer.write(cell) + + def write_notebook_metadata(self, metadata): + self.rmd_writer.write_notebook_metadata(metadata) + self.nb_html_writer.write_notebook_metadata(metadata) + + def close(self): + self.rmd_writer.close() + + @property + def kernel_lang(self): + """get the kernel language""" + return self._language + + @property + def contents(self): + return { + 'rmd': self.rmd_writer.contents, + 'html': self.nb_html_writer.contents + } + + def __del__(self): + self.close() + + +class RmdWriter(BaseMarkdownWriter): + """.Rmd writer""" + + def __init__(self, rmarkdown_writer): + super(RmdWriter, self).__init__() + self._rmarkdown_writer = rmarkdown_writer + + def append_code(self, input, output=None, metadata=None): + input = _ensure_string(input) + self._output.write(self._code_block(input, metadata)) + + def _code_block(self, code, meta): + return '```{{{meta}}}\n{code}\n```'.format( + meta=self._encode_metadata(meta), code=code.rstrip()) + + def append_markdown(self, source, metadata): + source = _ensure_string(source) + if metadata is not None and len(metadata) > 0: + print("WARNING: Metadata for markdown cells is currently " + "not supported.") + + self._output.write(source.rstrip()) + + def _encode_metadata(self, metadata): + def encode_option(key, value): + return "{}={}".format(key, _option_value_str(value)) + + metadata = {} if metadata is None else metadata + + lang = metadata.pop('lang', self._rmarkdown_writer.kernel_lang) + name = metadata.pop('name', None) + options = ", ".join(encode_option(k, v) + for k, v in metadata.items()) + + out = [lang] + if name is not None: + out.append(" " + name) + if len(options): + out.append(", " + options) + + return "".join(out) + + def write(self, cell): + """Write a ipynb cell to markdown""" + metadata = cell.get('metadata', None) + if cell['cell_type'] == 'markdown': + self.append_markdown(cell['source'], metadata) + elif cell['cell_type'] == 'code': + # output is not handled by RmdReader + self.append_code(cell['source'], output=None, metadata=metadata) + self._new_paragraph() + + @property + def contents(self): + return self._output.getvalue().rstrip() + '\n' # end of file \n + + +class NbHtmlWriter(object): + """ Write R notebook .nb.html """ + def __init__(self, rmarkdown_writer): + """ + + Parameters + ---------- + rmarkdown_writer: RmarkdownWriter + a reference to the parent RmarkdownWriter + """ + self._rmarkdown_writer = rmarkdown_writer + self._rmd_writer = rmarkdown_writer.rmd_writer + self._output = StringIO() + self._metadata = {} + + @property + def template(self): + """ Load the jinja2 template from the package resources. """ + env = Environment( + loader=PackageLoader('ipymd', 'ressources'), + autoescape=select_autoescape(['html', 'xml']) + ) + return env.get_template('r_notebook.template.html') + + def append_markdown(self, markdown, metadata): + markdown = _ensure_string(markdown) + html = pypandoc.convert_text(markdown, 'html', format='md') + # ignore metadata, not supported. + self._output.write(self._create_tag('text', html) + "\n") + + def append_code(self, source, outputs, metadata): + source = _ensure_string(source) + + # Markdown representation of code is given as b64 in nb.html + lang = metadata.get('lang', self._rmarkdown_writer.kernel_lang) + source_as_markdown = BaseMarkdownWriter.format_code(source, lang) + + child_tags = [] + child_tags.append( + self._create_tag('source', + tag_content=self._format_source(source, lang), + tag_meta={'data': source_as_markdown}) + ) + for output in outputs: + child_tags.extend(self._create_output_tag(output)) + + self._output.write( + self._create_tag('chunk', "\n".join(child_tags) + "\n") + "\n" + ) + + def _create_output_tag(self, output): + """yield tags such as + tag_meta: dict + meta-dictionary which can be added to the tag. + Will be base64 encoded. Example + tag_content: + html content which will be enclosed in the `begin` and `end` tags. + + Returns + ------- + str + \n + + """ + meta_b64 = "" if tag_meta is None or tag_meta == {} else _b64_encode( + json.dumps(tag_meta, sort_keys=True)) + return "\n" \ + "{contents}" \ + "".format(tag=tag_name, b64=meta_b64, + contents=tag_content) + + def write(self, cell): + metadata = cell.get('metadata', None) + if cell['cell_type'] == 'markdown': + self.append_markdown(cell['source'], metadata) + elif cell['cell_type'] == 'code': + self.append_code(cell['source'], cell['outputs'], metadata) + + def write_notebook_metadata(self, metadata): + self._metadata = metadata + + @property + def contents(self): + base64_rmd = _b64_encode(self._rmd_writer.contents) + html_nb = Markup(self._output.getvalue().rstrip() + '\n') + # TODO is the filename in javascript necessary for anything_ + # TODO set title (-> filename) + # the writer does not know anything about the filename + # therefore we use a hardcoded filename as workaround. + filename = self._metadata.get("filename", "notebook.Rmd") + title = self._metadata.get("title", "IPYMD Notebook") + return self.template.render(filename=filename, + title=title, + html_nb=html_nb, + base64_rmd=base64_rmd) + + +def load_rmarkdown(path): + """ + Read .Rmd and the corresponding .html.nb + If .html.nb is not available, outputs will be empty. + """ + html_path = _get_nb_html_path(path) + return { + 'rmd': _read_text(path), + 'html': _read_text(html_path) if os.path.isfile(html_path) else None + } + + +def save_rmarkdown(path, contents): + """ + store cells to .Rmd and outputs to .html.nb + """ + html_path = _get_nb_html_path(path) + _write_text(path, contents['rmd']) + if contents['html'] is not None: + _write_text(html_path, contents['html']) + + +RMD_FORMAT = dict( + reader=RmarkdownReader, + writer=RmarkdownWriter, + file_extension='.Rmd', + load=load_rmarkdown, + save=save_rmarkdown, +) diff --git a/ipymd/formats/tests/test_markdown.py b/ipymd/formats/tests/test_markdown.py index f40ab29..66d6691 100644 --- a/ipymd/formats/tests/test_markdown.py +++ b/ipymd/formats/tests/test_markdown.py @@ -10,6 +10,7 @@ from ...utils.utils import _diff, _show_outputs from ._utils import (_test_reader, _test_writer, _exec_test_file, _read_test_file) +from ..markdown import MarkdownReader, MarkdownWriter #------------------------------------------------------------------------------ @@ -87,3 +88,32 @@ def test_decorator(): markdown_bis = convert(cells, to='markdown') assert _diff(markdown, markdown_bis.replace('python', '')) == '' + + +def test_md_notebook_metadata(): + """Test that reading and writing complex notebook metadata + results in the identity. """ + mock_metadata = '\n'.join(('---', + 'author: John Doe', + 'date: 2017-05-07', + 'output:', + ' html_document:', + ' - --title-prefix', + ' - Foo', + ' - --id-prefix', + ' - Bar', + ' toc: true', + ' toc_float:', + ' collapsed: false', + ' smooth_scroll: false', + 'title: Habits', + '---', + '')) + + mdreader = MarkdownReader() + cells = mdreader.read(mock_metadata) + + mdwriter = MarkdownWriter() + mdwriter.write_notebook_metadata(cells[0]['metadata']) + + assert mdwriter.contents == mock_metadata diff --git a/ipymd/formats/tests/test_notebook.py b/ipymd/formats/tests/test_notebook.py index 167edb7..21c9683 100644 --- a/ipymd/formats/tests/test_notebook.py +++ b/ipymd/formats/tests/test_notebook.py @@ -7,7 +7,7 @@ #------------------------------------------------------------------------------ from ...core.format_manager import format_manager, convert -from ..notebook import _compare_notebooks +from ...lib.notebook import _assert_notebooks_equal from ...utils.utils import _diff, _show_outputs from ._utils import (_test_reader, _test_writer, _exec_test_file, _read_test_file) @@ -23,21 +23,24 @@ def _test_notebook_reader(basename): assert converted == expected -def _test_notebook_writer(basename): +def _test_notebook_writer(basename, check_outputs=True): """Check that (test nb) and (test cells ==> nb) are the same. """ converted, expected = _test_writer(basename, 'notebook') - assert _compare_notebooks(converted, expected) + _assert_notebooks_equal(converted, expected, check_notebook_metadata=False, + check_cell_outputs=check_outputs) -def _test_notebook_notebook(basename): + +def _test_notebook_notebook(basename, check_outputs=True): """Check that the double conversion is the identity.""" contents = _read_test_file(basename, 'notebook') cells = convert(contents, from_='notebook') converted = convert(cells, to='notebook') - assert _compare_notebooks(contents, converted) + _assert_notebooks_equal(contents, converted, check_notebook_metadata=False, + check_cell_outputs=check_outputs) def test_notebook_reader(): @@ -48,11 +51,13 @@ def test_notebook_reader(): def test_notebook_writer(): _test_notebook_writer('ex1') - _test_notebook_writer('ex2') + # Ex2 contains an image, which is not supported by ipymd internal format + _test_notebook_writer('ex2', check_outputs=False) _test_notebook_writer('ex3') def test_notebook_notebook(): _test_notebook_notebook('ex1') - _test_notebook_notebook('ex2') + # Ex2 contains an image, which is not supported by ipymd internal format + _test_notebook_notebook('ex2', check_outputs=False) _test_notebook_notebook('ex3') diff --git a/ipymd/formats/tests/test_rmarkdown.py b/ipymd/formats/tests/test_rmarkdown.py new file mode 100644 index 0000000..9e8118a --- /dev/null +++ b/ipymd/formats/tests/test_rmarkdown.py @@ -0,0 +1,533 @@ +# -*- coding: utf-8 -*- + +"""Test Markdown parser and reader.""" + +# ------------------------------------------------------------------------------ +# Imports +# ------------------------------------------------------------------------------ + +from ipymd.core.format_manager import convert, format_manager +from ._utils import _read_test_file +from ...utils.utils import _full_diff +from ...lib.notebook import _assert_notebooks_equal, _assert_cell_outputs_equal +from ipymd.formats.rmarkdown import HtmlNbChunkCell, RmarkdownWriter, \ + RmarkdownReader, RmdWriter, RmdReader, NbHtmlWriter, HtmlNbReader, \ + RMD_FORMAT +import pytest + +from collections import OrderedDict +import json + + +# ------------------------------------------------------------------------------ +# Test Rmarkdown classes and helper functions +# ------------------------------------------------------------------------------ + +def test_htmlnb_parse_html(): + html = """ + + text contents + + + + + """ + htmlnbreader = HtmlNbReader() + result = list(htmlnbreader._parse_html(html)) + assert result == [('text', 'text contents'), + ('chunk', '')] + + +def test_htmlnb_parse_image(): + htmlnbreader = HtmlNbReader() + + html = '

' + mime, data = list(htmlnbreader._parse_image(html)) + assert mime == 'image/png' + assert data == "iVBORw0KGgoAAAANSUhEUgAAAjwAAAFhCAMAAABDKYAcAAACT" \ + "FBMVEUAAAA\nBAQEJCQ...==" + + html = ('\n' + '

\n' + '') + mime, data = list(htmlnbreader._parse_image(html)) + assert mime == 'image/png' + assert data == "iVBORw0KGgoAAAANSUhEUgAAAWQAAAD8CAYAAABAWd66AAAABHNCSV" \ + "QICAgIfAhkiAAAAAlwSFlz\n" \ + "AAALEgAACxIB0t1+/AAACDBJREFUeJzt3c2LnWcZx/Hf1RmlScW" \ + "XklJwWpzKiCUIUglSLbiwLnxD\n" + + html = """

some other html

""" + mime, data = list(htmlnbreader._parse_image(html)) + assert mime == 'text/plain' + assert data == 'IPYMD: Error reading image.' + + +def test_htmlnb_parse_error(): + error_output = { + "ename": "SyntaxError", + "evalue": "invalid syntax (, line 3)", + "output_type": "error", + "traceback": ["\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m3\u001b" + "[0m\n\u001b[0;31m knitr::knit_engines$set(python =" + " reticulate::eng_python)\u001b[0m\n\u001b[0m " + "^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b" + "[0;31m:\u001b[0m invalid syntax\n"] + } + rmarkdown_writer = RmarkdownWriter() + nb_html_writer = NbHtmlWriter(rmarkdown_writer) + nb_html_reader = HtmlNbReader() + html_chunk = "".join(nb_html_writer._create_output_tag(error_output)) + + cell = nb_html_reader._chunk_cell(html_chunk) + + assert cell.outputs[0] == error_output + + +def test_htmlnb_chunk_cell(): + html = """ + + + 
ggplot(data.frame(x=1:10), aes(y=x, x=x)) + geom_point()
+ + +

+ + """ + + htmlnbreader = HtmlNbReader() + assert htmlnbreader._chunk_cell(html) == { + "cell_type": "code", + "execution_count": 1, + "source": HtmlNbChunkCell.NO_CODE_FROM_HTMLNB, + "metadata": {}, + "outputs": [{ + # list of output dicts (described below) + "execution_count": 1, + "output_type": "execute_result", + "metadata": {}, + "data": {'image/png': "iVBORw0KGgoAAAANSUhEUgAAAjwAAAFhCAMAAABD" + "KYAcAAACTFBMVEUAAAABAQEJCQ...=="} + }] + } + + +def test_htmlnb_chunk_cell2(): + html = """ + + 
print(1:10)
+ + + 
 [1]  1  2  3  4  5  6  7  8  9 10
+ + """ + + htmlnbreader = HtmlNbReader() + assert htmlnbreader._chunk_cell(html) == { + "cell_type": "code", + "execution_count": 1, + "source": HtmlNbChunkCell.NO_CODE_FROM_HTMLNB, + "metadata": {}, + "outputs": [{ + # list of output dicts (described below) + "execution_count": 1, + "output_type": "execute_result", + "metadata": {}, + "data": {'text/plain': " [1] 1 2 3 4 5 6 7 8 9 10\n"} + }] + } + + +def test_rmd_read_cell_metadata(): + """test that metadata from chunk options is correctly read. """ + chunk1 = "```{r test, str_type=\"foo\", str_single_quote='bar', " \ + "int_type=42, bool_type=TRUE, null_type=NULL}\n\n```" + chunk2 = "```{python, str_type=\"foo\", str_single_quote='bar', " \ + "int_type=42, bool_type=TRUE, null_type=NULL}\n\n```""" + chunk_meta = OrderedDict([('str_type', 'foo'), + ('str_single_quote', 'bar'), + ('int_type', 42), + ('bool_type', True), + ('null_type', None)]) + + rmdreader = RmdReader() + cell1 = rmdreader.read(chunk1)[0] + cell2 = rmdreader.read(chunk2)[0] + assert cell1['lang'] == 'r' + assert cell2['lang'] == 'python' + assert cell1['metadata'] == chunk_meta + assert cell2['metadata'] == chunk_meta + + +def test_rmd_read_notebook_metadata(): + """test that notebook metadata is properly read.""" + rmd = """---\ntitle: "R Notebook"\noutput: html_notebook\n---""" + + rmdreader = RmdReader() + nb_metadata = rmdreader.read(rmd)[0] + assert nb_metadata['metadata'] == { + "title": "R Notebook", + "output": "html_notebook" + } + + +def test_rmarkdown_read_notebook_metadata(): + """test that notebook metadata is properly read.""" + contents = { + "rmd": """---\ntitle: "R Notebook"\noutput: html_notebook\n---""", + "html": None + } + + reader = RmarkdownReader() + nb = reader.read(contents) + assert nb['metadata'] == { + "title": "R Notebook", + "output": "html_notebook" + } + + +def test_nbhtml_write_output(): + """test that output is correctly read and written. """ + + rmarkdown_writer = RmarkdownWriter() + nb_html_writer = NbHtmlWriter(rmarkdown_writer) + nb_html_reader = HtmlNbReader() + + text_output = { + "data": { + "text/plain": "some text" + }, + "output_type": "execute_result", + "metadata": {}, + 'execution_count': 1 + } + + html_chunk = "".join(nb_html_writer._create_output_tag(text_output)) + cell = nb_html_reader._chunk_cell(html_chunk) + _assert_cell_outputs_equal(cell.outputs[0], text_output) + assert text_output['data']['text/plain'] in html_chunk + + # should write the image to html, not the plain text! + image_output = { + "data": { + "text/plain": ["some image"], + "image/png": "base64 data" + }, + "output_type": "display_data", + "metadata": {"x": "y"} + } + + html_chunk = "".join(nb_html_writer._create_output_tag(image_output)) + cell = nb_html_reader._chunk_cell(html_chunk) + _assert_cell_outputs_equal(cell.outputs[0], image_output) + # test that image is part of html + assert image_output['data']['image/png'] in html_chunk + + unknown_output = { + "data": { + "foo/bar": "should raise an error. " + }, + "output_type": "execute_result", + "metadata": {}, + 'execution_count': 2 + } + + with pytest.raises(RuntimeError): + "".join(nb_html_writer._create_output_tag(unknown_output)) + + # should write the html to html, not the plain text. + html_output = { + "data": { + "text/plain": "should raise an error. ", + "text/html": "Hello World!" + }, + "output_type": "execute_result", + "metadata": {}, + 'execution_count': 3 + } + + html_chunk = "".join(nb_html_writer._create_output_tag(html_output)) + cell = nb_html_reader._chunk_cell(html_chunk) + _assert_cell_outputs_equal(cell.outputs[0], html_output) + # test that image is part of html + assert html_output['data']['text/html'] in html_chunk + + text_output_with_additional_data = { + "data": { + "text/plain": "some data", + "foo/bar": "will not appear in html, but should be preserved" + "in base64" + }, + "output_type": "execute_result", + "metadata": {}, + 'execution_count': 4 + } + + html_chunk = "".join(nb_html_writer._create_output_tag( + text_output_with_additional_data)) + cell = nb_html_reader._chunk_cell(html_chunk) + _assert_cell_outputs_equal(cell.outputs[0], + text_output_with_additional_data) + # test that image is part of html + assert text_output_with_additional_data['data']['text/plain'] in html_chunk + + +def test_rmarkdown_merge_cells(): + """test that source and output are correctly merged. """ + contents = { + "rmd": """```{r}\nprint(1:10)\n```""", + "html": """ + + + 
print(1:10)
+ + + 
 [1]  1  2  3  4  5  6  7  8  9 10
+ + + """ + } + + reader = RmarkdownReader() + nb = reader.read(contents) + cell = nb['cells'][0] + assert cell['source'] == 'print(1:10)' + assert cell['outputs'] == [{ + "output_type": "execute_result", + 'metadata': {}, + 'data': {"text/plain": " [1] 1 2 3 4 5 6 7 8 9 10\n"}, + "execution_count": 1 + }] + + +def test_rmarkdown_merge_cells_inconsistent_input(): + """test that source and output are not merged when the sources + are inconsistent. """ + contents = { + "rmd": """```{r}\nprint(1:10)\n```\n\n```{r}\nprint(1:10)\n```""", + "html": """ + + + 
print(1:10)
+ + + 
 [1]  1  2  3  4  5  6  7  8  9 10
+ + + """ + } + + reader = RmarkdownReader() + nb = reader.read(contents) + assert (nb['cells'][0]['source'] == nb['cells'][1]['source'] == + 'print(1:10)') + assert nb['cells'][0]['outputs'] == nb['cells'][0]['outputs'] == [] + + +def test_rmd_write_cell_metadata(): + """test that cell metadata is properly encoded.""" + expected = "r test, str_type=\"foo\", str_single_quote='bar'," \ + " int_type=42, bool_type=TRUE, null_type=NULL" + chunk_meta = OrderedDict([('lang', 'r'), + ('name', 'test'), + ('str_type', 'foo'), + ('str_single_quote', 'bar'), + ('int_type', 42), + ('bool_type', True), + ('null_type', None)]) + + rmdreader = RmdWriter(RmarkdownWriter()) + result = rmdreader._encode_metadata(chunk_meta) + # we know that all strings will be double-quoted. + expected = expected.replace("'", '"') + assert expected == result + + +# ------------------------------------------------------------------------------ +# Test Format +# ------------------------------------------------------------------------------ + +""" +Testing reading and writing of Rmd notebooks. + +We have the issue that we cannot *exactly* reproduce the HTML +generated by rstudio (and there is no point in trying hard +to do so, as this might also change over time). + +Therefore, an assertion for *writing* exactly the same .nb.html is futile. +We circumvent this problem by splitting up the test files in +*.rstudio.{rmd,nb.html} and *.{rmd,nb.html}. + +While the reader should be able to correctly read both of the file formats +(i.e. nb.html as generated by rstudio and ipymd), the writer only has +to be consistent with the ipymd version. + +## The round-trip-conversion test +By checking that rmarkdown can be correctly converted to rmarkdown +we ensure that no information is lost. + +By checking that a notebook can be correctly converted to a notebook +and back, we ensure that a notebook can be represented +in rmarkdown without any information loss, i.e. rmarkdown is a +full replacement for .ipynb. + +## Compatibility with rstudio +While we can ensure automatically, that reading rmarkdown generated +with rstudio works, we cannot test (easily) that rstudio correctly +reads rmarkdown generated by ipymd. This would require to implement +tests in R instead of python. +""" + +# register rstudio rmarkdown dialect to the format manager. +_fm = format_manager() +_fm.register(name='rmarkdown.rstudio', **RMD_FORMAT) +# ipymd only makes sense with verbose metadata +_fm.verbose_metadata = True + + +def _test_rmarkdown_reader(basename): + """Check that reading Rmarkdown (.Rmd + .nb.html) results + in the correct notebook (.ipynb). + """ + contents = _read_test_file(basename, 'rmarkdown') + expected = _read_test_file(basename, 'notebook') + converted = convert(contents, from_='rmarkdown', to='notebook') + + # for ipymd rmd notebook, metadata must be equal + _assert_notebooks_equal(expected, converted, check_cell_metadata=True, + check_notebook_metadata=True) + + +def _test_rmarkdown_reader_rstudio(basename): + """Check that reading Rmarkdown (.Rmd + .nb.html) generated + by rstudio results in the correct notebook (.ipynb) + ignoring metadata""" + contents_rstudio = _read_test_file(basename, 'rmarkdown.rstudio') + expected = _read_test_file(basename, 'notebook') + converted_rstudio = convert(contents_rstudio, from_='rmarkdown', + to='notebook') + + # we must be able to correctly read an Rmd created by rstudio, + # but we cannot expect all metadata to be there + _assert_notebooks_equal(expected, converted_rstudio, + check_cell_metadata=False, + check_notebook_metadata=False) + + +def _test_rmarkdown_writer(basename): + """Check that writing a notebook (.ipynb) to Rmarkdown results + in the correct .Rmd + .nb.html files""" + contents = _read_test_file(basename, 'notebook') + expected = _read_test_file(basename, 'rmarkdown') + converted = convert(contents, to='rmarkdown', from_='notebook') + + # The writer must produce exactly the rmd/html we want + assert converted['rmd'] == expected['rmd'] + assert converted['html'].strip() == expected['html'].strip() + + +def _diff_rmarkdown_writer_rstudio(basename): + """print a diff to the Rmd/.nb.html generated by rstudio + + We cannot expect to generate exactly the same result + as rstudio (minor things like markdown->HTML conversion. + Therefore, we do not use a test here. + + We want to have a diff for development purposes, though + """ + contents = _read_test_file(basename, 'notebook') + expected_rstudio = _read_test_file(basename, 'rmarkdown.rstudio') + converted = convert(contents, to='rmarkdown', from_='notebook') + + print("\n\n" + "#########################################################\n" + "Diff converted Rmd with {}.rmarkdown.rstudio.Rmd\n" + "#########################################################" + "\n\n".format(basename)) + print(_full_diff(converted['rmd'], expected_rstudio['rmd'])) + print('\n\n') + + print("\n\n" + "#########################################################\n" + "Diff converted nb.html with {}.rmarkdown.rstudio.nb.html\n" + "#########################################################" + "\n\n".format(basename)) + print(_full_diff(converted['html'], expected_rstudio['html'])) + print('\n\n') + + +def _test_rmarkdown_rmarkdown(basename): + """Check that the double conversion is the identity.""" + contents = _read_test_file(basename, 'rmarkdown') + notebook = convert(contents, from_='rmarkdown', to='notebook') + notebook_dict = json.loads(json.dumps(notebook)) + converted = convert(notebook_dict, from_='notebook', to='rmarkdown') + + assert converted['rmd'] == contents['rmd'] + assert converted['html'].strip() == contents['html'].strip() + + +def _test_notebook_notebook(basename): + """check that converting a notebook to Rmarkdown and back + is the identity""" + contents = _read_test_file(basename, 'notebook') + rmarkdown = convert(contents, from_='notebook', to='rmarkdown') + converted = convert(rmarkdown, from_='rmarkdown', to='notebook') + + _assert_notebooks_equal(contents, converted, check_notebook_metadata=True, + check_cell_metadata=True) + + +def test_ex5_reader(): + _test_rmarkdown_reader('ex5') + _test_rmarkdown_reader_rstudio('ex5') + + +def test_ex5_writer(): + _test_rmarkdown_writer('ex5') + _diff_rmarkdown_writer_rstudio('ex5') + + +def test_ex5_rmarkdown_rmarkdown(): + _test_rmarkdown_rmarkdown('ex5') + + +def test_ex5_notebook_notebook(): + _test_notebook_notebook('ex5') + + +def test_ex6_reader(): + _test_rmarkdown_reader('ex6') + + +def test_ex6_writer(): + _test_rmarkdown_writer('ex6') + + +def test_ex6_rmarkdown_rmarkdown(): + _test_rmarkdown_rmarkdown('ex6') + + +def test_ex6_notebook_notebook(): + _test_notebook_notebook('ex6') + + +def test_ex7_reader(): + _test_rmarkdown_reader('ex7') + + +def test_ex7_writer(): + _test_rmarkdown_writer('ex7') + + +def test_ex7_rmarkdown_rmarkdown(): + _test_rmarkdown_rmarkdown('ex7') + + +def test_ex7_notebook_notebook(): + _test_notebook_notebook('ex7') diff --git a/ipymd/lib/markdown.py b/ipymd/lib/markdown.py index 2d7ea24..0d0de34 100644 --- a/ipymd/lib/markdown.py +++ b/ipymd/lib/markdown.py @@ -68,7 +68,8 @@ class BlockGrammar(object): newline = re.compile(r'^\n+') block_code = re.compile(r'^( {4}[^\n]+\n*)+') fences = re.compile( - r'^ *(`{3,}|~{3,}) *(\S+)? *\n' # ```lang + # ```lang | ```{lang, option1=foo, option2='bar'} + r'^ *(`{3,}|~{3,}) *(\S+|\{.+\})? *\n' r'([\s\S]+?)\s*' r'\1 *(?:\n+|$)' # ``` ) @@ -654,7 +655,7 @@ def _filter_markdown(source, filters): class MarkdownFilter(object): - """Filter Marakdown contents by keeping a subset of the contents. + """Filter Markdown contents by keeping a subset of the contents. Parameters ---------- diff --git a/ipymd/lib/notebook.py b/ipymd/lib/notebook.py new file mode 100644 index 0000000..0dcc116 --- /dev/null +++ b/ipymd/lib/notebook.py @@ -0,0 +1,107 @@ +"""Test helper functions for comparing ipynb notebooks. """ +from ipymd.utils.utils import _ensure_string + + +def _cell_source(cell): + """Return the input of an ipynb cell.""" + return _ensure_string(cell.get('source', [])) + + +def _cell_outputs(cell): + """Return the output of an ipynb cell.""" + outputs = cell.get('outputs', []) + return outputs + + +def _stream_output_to_result(output): + """Convert a 'stream' output cell to an 'execute_result' cell. """ + if output['output_type'] == 'stream': + return { + 'output_type': 'execute_result', + 'metadata': {}, + 'data': {'text/plain': _ensure_string(output['text']).rstrip()}, + 'execution_count': None + } + else: + return output + + +def _output_ensure_string(*args): + """make sure that strings split up as a list are coerced into a + single string. """ + for output in args: + for mime, out in output.get('data', {}).items(): + output['data'][mime] = _ensure_string(out) + + +def _assert_dict_key_equals(field, dict0, dict1): + """assert that a field does either not exist in both + dictionaries or is equal""" + KEY_DOESNT_EXIST = object() + assert dict0.get(field, KEY_DOESNT_EXIST) \ + == dict1.get(field, KEY_DOESNT_EXIST) + + +def _assert_cell_outputs_equal(output_0, output_1, check_metadata=True): + output_0 = _stream_output_to_result(output_0) + output_1 = _stream_output_to_result(output_1) + _output_ensure_string(output_0, output_1) + + fields_to_check = ['output_type', 'data', 'ename', 'evalue', 'traceback'] + if check_metadata: + fields_to_check.append('metadata') + + for field in fields_to_check: + _assert_dict_key_equals(field, output_0, output_1) + + if 'execution_count' in (set(output_0) | set(output_1)): + assert output_0['execution_count'] == output_1['execution_count'] or \ + output_1['execution_count'] is None or \ + output_0['execution_count'] is None + + +def _assert_cells_equal(cell_0, cell_1, check_metadata=True, + check_outputs=True): + assert cell_0['cell_type'] == cell_1['cell_type'] + assert _cell_source(cell_0) == _cell_source(cell_1) + if check_outputs: + outputs_0 = _cell_outputs(cell_0) + outputs_1 = _cell_outputs(cell_1) + assert len(outputs_0) == len(outputs_1) + for output_0, output_1 in zip(outputs_0, outputs_1): + _assert_cell_outputs_equal(output_0, output_1, + check_metadata=check_metadata) + + +def _assert_notebooks_equal(nb_0, nb_1, check_notebook_metadata=True, + check_cell_metadata=True, + check_cell_outputs=True): + if check_notebook_metadata: + assert nb_0['metadata'] == nb_1['metadata'] + assert len(nb_0['cells']) == len(nb_1['cells']) + for cell_0, cell_1 in zip(nb_0['cells'], nb_1['cells']): + _assert_cells_equal(cell_0, cell_1, check_metadata=check_cell_metadata, + check_outputs=check_cell_outputs) + + +def _cell_input(cell): + """Return the input of an ipynb cell.""" + return _ensure_string(cell.get('source', [])) + + +def _cell_output(cell): + """Return the output of an ipynb cell.""" + outputs = cell.get('outputs', []) + # Add stdout. + stdout = ('\n'.join(_ensure_string(output.get('text', '')) + for output in outputs)).rstrip() + # Add text output. + text_outputs = [] + for output in outputs: + out = output.get('data', {}).get('text/plain', []) + out = _ensure_string(out) + # HACK: skip outputs. + if out.startswith('([^,=]+ *)= *(".*"|\'.*\'|[^,=}]+))' + ARG = r'(?P\w+)' + OPEN = r'(?P{ *)' + DELIM = r'(?P *, *)' + CLOSE = r'(?P})' + BLANK = r'(?P\s+)' + + master_pat = re.compile('|'.join([KWARG, ARG, OPEN, DELIM, + CLOSE, BLANK])) + + def generate_tokens(pat, text): + scanner = pat.scanner(text) + for m in iter(scanner.match, None): + yield Token(m.lastgroup, m.group(m.lastgroup)) + + tok = list(generate_tokens(master_pat, options_line)) + return tok + + +def _parse_option_value(value): + """Parse a value given as string to the appropriate data type. """ + value = value.strip() + if value in str_to_literal: + # special value + return str_to_literal[value] + elif value.startswith('"') and value.endswith('"'): + # double quoted string + return value.strip('"') + elif value.startswith("'") and value.endswith("'"): + # single quoted string + return value.strip("'") + else: + try: + # Number: int + return int(value) + except ValueError: + try: + # Number: float + return float(value) + except ValueError: + # something else + raise TypeError( + "Unknown data type in chunk option: {}".format(value)) + + +def _option_value_str(value): + """Convert an option value to the corresponding string""" + try: + return literal_to_str[value] + except KeyError: + # quote a string + if isinstance(value, string_types): + return '"{}"'.format(value) + else: + return str(value) + + +def _process_cell_metadata(kwargs): + """process kwargs such as foo='bar', cat="gold", horse=9, bool_val=TRUE""" + def process_kwarg(kwarg): + key, value = kwarg.split("=") + return key, _parse_option_value(value) + + return OrderedDict([process_kwarg(kwarg) for kwarg in kwargs]) + + +def _is_code_chunk(chunk_lang): + """determine from ```... if the chunk is executable code + or documentation code (markdown) """ + return chunk_lang.startswith('{') and chunk_lang.endswith('}') + + +def _parse_chunk_meta(meta_string): + """Process a string in the form + {r chunk_name, foo='bar', cat="gold", horse=9, bool_val=TRUE}""" + tokens = _tokenize_chunk_options(meta_string) + args = [] + kwargs = [] + for kind, value in tokens: + if kind == "ARG": + args.append(value) + elif kind == "KWARG": + kwargs.append(value) + + lang = args[0] + name = None if len(args) <= 1 else args[1] + meta = _process_cell_metadata(kwargs) + + return lang, name, meta + + +def _read_rmd_b64(b64): + decoded = base64.b64decode(b64).decode('utf-8') + return json.loads(decoded, encoding='utf-8') + + +def _get_nb_html_path(rmd_path): + assert rmd_path.endswith(".Rmd"), "invalid file extension" + return re.sub(r"\.Rmd$", ".nb.html", rmd_path) + + +def _merge_consecutive_markdown_cells(cells): + """Merge consecutive cells with cell_type == 'markdown'. + + Parameters + ---------- + cells : a list of jupyter notebook cells. + """ + merged = [] + tmp_cell = None + + def done_merging(): + """execute, when switching back from a series of markdown + cells to other cell types""" + nonlocal merged, tmp_cell + if tmp_cell is not None: + merged.append(tmp_cell) + tmp_cell = None + + for cell in cells: + if cell['cell_type'] == 'markdown': + if tmp_cell is None: + tmp_cell = cell + else: + if 'source' in cell: + tmp_cell['source'] = (tmp_cell.get('source', "") + "\n\n" + + cell['source']) + if 'metadata' in cell: + tmp_cell['metadata'] = (tmp_cell.get('metadata', {}) + .update(cell['metadata'])) + else: + done_merging() + merged.append(cell) + + done_merging() + + return merged + + +def html_escape(s): + """escape HTML and double quotes only. """ + return _html_escape(s, quote=False).replace('"', """) + + +class HtmlNbChunkCell(object): + NO_CODE_FROM_HTMLNB = "Code is not parsed from .html.nb. " \ + "Use code provided by *.Rmd instead. " + NO_META_FROM_HTMLNB = "Cell metadata is not parsed from .html.nb. " \ + "Use metadata provided by *.Rmd instead. " + + def __init__(self, execution_count): + self._count = execution_count + self._cell = nbf.v4.new_code_cell(self.NO_CODE_FROM_HTMLNB, + execution_count=self._count) + + def new_output(self, tag, b64): + b64_data = _read_rmd_b64(b64) + + # fallback for rstudio + data = b64_data.get('ipymd.data', {'text/plain': b64_data['data']}) + + self._new_generic_output(b64_data, data) + + def new_plot(self, mime, data, b64): + b64_data = {} if not b64 else _read_rmd_b64(b64) + + # fallback for rstudio + data = b64_data.get('ipymd.data', {mime: data}) + + self._new_generic_output(b64_data, data) + + def _new_generic_output(self, b64_data, data): + """ + + Parameters + ---------- + b64_data: data read from base64 string + data: data dictionary passed to the output = {'data' : {...} } + + """ + metadata = b64_data.get('ipymd.metadata', {}) + output_type = b64_data.get('ipymd.output_type', "execute_result") + + kwargs = {} + if output_type == "execute_result": + kwargs['execution_count'] = self._count + + self._cell.outputs.append( + nbf.v4.new_output(output_type, + data, + metadata=metadata, + **kwargs) + ) + + def new_error(self, b64): + err_dict = {} if not b64 else _read_rmd_b64(b64) + traceback = [str(x) for x in err_dict.get("traceback", [])] + ename = err_dict.get("ename", "") + evalue = err_dict.get("evalue", "") + self._cell.outputs.append( + nbf.v4.new_output('error', + traceback=traceback, + ename=ename, + evalue=evalue) + ) + + @property + def cell(self): + return self._cell diff --git a/ipymd/lib/tests/test_notebook_utils.py b/ipymd/lib/tests/test_notebook_utils.py new file mode 100644 index 0000000..eee5002 --- /dev/null +++ b/ipymd/lib/tests/test_notebook_utils.py @@ -0,0 +1,67 @@ +"""Test the notebook utils. """ +from ..notebook import _assert_cell_outputs_equal, _assert_notebooks_equal +from ipymd.formats.tests._utils import _read_test_file +import pytest + + +def test_cell_outputs_equal(): + out1 = { + "execution_count": 1, + "output_type": "execute_result", + "metadata": {'output_type': 'output'}, + "data": {'text/plain': "[1] 1 2 3 4 5 6 7 8 9 10"} + } + # execution_count modified + out2 = { + "execution_count": 2, + "output_type": "execute_result", + "metadata": {'output_type': 'output'}, + "data": {'text/plain': "[1] 1 2 3 4 5 6 7 8 9 10"} + } + # execution_count None + out3 = { + "execution_count": None, + "output_type": "execute_result", + "metadata": {'output_type': 'output'}, + "data": {'text/plain': "[1] 1 2 3 4 5 6 7 8 9 10"} + } + # stream + out4 = { + "output_type": "stream", + "name": 'stdout', + "text": "[1] 1 2 3 4 5 6 7 8 9 10" + } + # differing metadata + out5 = { + "execution_count": 1, + "output_type": "execute_result", + "metadata": {'foo': 'bar'}, + "data": {'text/plain': "[1] 1 2 3 4 5 6 7 8 9 10"} + } + # output split up as list. + out6 = { + "execution_count": 1, + "output_type": "execute_result", + "metadata": {'output_type': 'output'}, + "data": {'text/plain': ["[1] 1 2 3 4 5 6 7 8 9 10"]} + } + _assert_cell_outputs_equal(out1, out1) + with pytest.raises(AssertionError): + _assert_cell_outputs_equal(out1, out2) + _assert_cell_outputs_equal(out1, out3) + _assert_cell_outputs_equal(out1, out4, check_metadata=False) + _assert_cell_outputs_equal(out1, out5, check_metadata=False) + with pytest.raises(AssertionError): + _assert_cell_outputs_equal(out1, out5) + _assert_cell_outputs_equal(out1, out6) + + +def test_assert_notebook_equals(): + ex1 = _read_test_file('ex1', 'notebook') + ex4 = _read_test_file('ex4', 'notebook') + _assert_notebooks_equal(ex1, ex1) + _assert_notebooks_equal(ex4, ex4) + with pytest.raises(AssertionError): + _assert_notebooks_equal(ex1, ex4) + with pytest.raises(AssertionError): + _assert_notebooks_equal(ex4, ex1) diff --git a/ipymd/lib/tests/test_rmarkdown.py b/ipymd/lib/tests/test_rmarkdown.py new file mode 100644 index 0000000..8b8e8f8 --- /dev/null +++ b/ipymd/lib/tests/test_rmarkdown.py @@ -0,0 +1,83 @@ +"""Test rmarkdown helper functions. """ + + +from ipymd.lib.rmarkdown import _merge_consecutive_markdown_cells, \ + _read_rmd_b64, _option_value_str, \ + _parse_option_value, _parse_chunk_meta +from collections import OrderedDict + + +def test_merge_consecutive_markdown_cells(): + """Test that consecutive markdown cells are correctly merged. """ + cells = [ + {'cell_type': 'notebook_metadata'}, + {'cell_type': 'markdown', 'source': '1'}, + {'cell_type': 'markdown', 'source': '2', 'x': 'a'}, + {'cell_type': 'markdown'}, + {'cell_type': 'code', 'source': '1'}, + {'cell_type': 'markdown', 'source': '1'}, + {'cell_type': 'markdown'}, + ] + + assert _merge_consecutive_markdown_cells(cells) == [ + {'cell_type': 'notebook_metadata'}, + {'cell_type': 'markdown', 'source': '1\n\n2'}, + {'cell_type': 'code', 'source': '1'}, + {'cell_type': 'markdown', 'source': '1'} + ] + + +def test_merge_consecutive_markdown_cells_2(): + """Test, that consecutive code cells are not merged. """ + cells = [ + {'cell_type': 'notebook_metadata'}, + {'cell_type': 'code', 'source': '1'}, + {'cell_type': 'code', 'source': '2', 'x': 'a'}, + {'cell_type': 'code'}, + {'cell_type': 'code', 'source': '1'}, + {'cell_type': 'markdown', 'source': '1'}, + {'cell_type': 'markdown'}, + ] + + assert _merge_consecutive_markdown_cells(cells) == [ + {'cell_type': 'notebook_metadata'}, + {'cell_type': 'code', 'source': '1'}, + {'cell_type': 'code', 'source': '2', 'x': 'a'}, + {'cell_type': 'code'}, + {'cell_type': 'code', 'source': '1'}, + {'cell_type': 'markdown', 'source': '1'} + ] + + +def test_read_rmd_base64(): + expected = {"data": "```python\nfoo = 'bar'\n```"} + b64 = "eyJkYXRhIjoiYGBgcHl0aG9uXG5mb28gPSAnYmFyJ1xuYGBgIn0=" + assert _read_rmd_b64(b64) == expected + + +def test_parse_chunk_meta(): + chunk_meta = \ + """{r chunk_name, foo='bar', cat="gold", horse=9, bool_val=TRUE}""" + lang, name, meta = _parse_chunk_meta(chunk_meta) + assert lang == 'r' + assert name == 'chunk_name' + assert meta == OrderedDict([ + ('foo', 'bar'), ('cat', 'gold'), ('horse', 9), ('bool_val', True) + ]) + + +def test_option_value_str(): + assert _option_value_str(True) == "TRUE" + assert _option_value_str("foo") == '"foo"' + assert _option_value_str(42) == "42" + assert _option_value_str(None) == "NULL" + + +def test_parse_option_value(): + assert _parse_option_value("'True'") == "True" + assert _parse_option_value('"TRUE"') == "TRUE" + assert _parse_option_value("True") + assert _parse_option_value("TRUE") + assert type(_parse_option_value("42")) == int + assert type(_parse_option_value("42.")) == float + assert type(_parse_option_value("42")) == int diff --git a/ipymd/ressources/r_notebook.template.html b/ipymd/ressources/r_notebook.template.html new file mode 100644 index 0000000..c9c5b68 --- /dev/null +++ b/ipymd/ressources/r_notebook.template.html @@ -0,0 +1,217 @@ + + + + + + + + + + + + + +{{ title }} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + +{{ html_nb }} + +
{{ base64_rmd }}
+ + + +
+ + + + + + + + diff --git a/ipymd/utils/utils.py b/ipymd/utils/utils.py index d249809..f4b6f57 100644 --- a/ipymd/utils/utils.py +++ b/ipymd/utils/utils.py @@ -98,6 +98,13 @@ def _diff(text_0, text_1): return _diff_removed_lines(diff) +def _full_diff(text_0, text_1): + """Return a full diff between two strings""" + diff = difflib.ndiff(text_0.splitlines(keepends=True), + text_1.splitlines(keepends=True)) + return "".join(diff) + + def _show_outputs(*outputs): for output in outputs: print() @@ -105,6 +112,10 @@ def _show_outputs(*outputs): pprint(output) +def _get_cell_types(cells): + return [cell['cell_type'] for cell in cells] + + #------------------------------------------------------------------------------ # Reading/writing files from/to disk #------------------------------------------------------------------------------ diff --git a/requirements-dev.txt b/requirements-dev.txt index 6aa7fcf..630835b 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -4,3 +4,4 @@ https://github.com/eea/odfpy/archive/master.zip pytest pytest-cov python-coveralls +jupyter diff --git a/setup.py b/setup.py index 09a4261..e79490b 100644 --- a/setup.py +++ b/setup.py @@ -77,6 +77,7 @@ def run_tests(self): 'ipymd=ipymd.core.scripts:main', ], 'ipymd.format': [ + 'rmarkdown=ipymd.formats.rmarkdown:RMD_FORMAT', 'markdown=ipymd.formats.markdown:MARKDOWN_FORMAT', 'atlas=ipymd.formats.atlas:ATLAS_FORMAT', 'notebook=ipymd.formats.notebook:NOTEBOOK_FORMAT', @@ -84,7 +85,7 @@ def run_tests(self): 'python=ipymd.formats.python:PYTHON_FORMAT', ] }, - install_requires=['pyyaml'], + install_requires=['pyyaml', 'jinja2', 'pypandoc'], extras_require={ 'odf': ['odfpy'], },