def run_asm_stats(assembly, out_file):
os.environ["FASTA_FILE"] = assembly
notebook = read(open("masmvaliweb/notebooks/assembly-stats.ipynb"), 'json')
r = NotebookRunner(notebook)
r.run_notebook()
os.remove(assembly)
exportHTML = HTMLExporter(config=Config({'HTMLExporter': {'default_template': 'basic'}}))
with open(out_file, 'w') as of:
of.write(exportHTML.from_notebook_node(r.nb)[0])
def convert_nb_html(nb):
"""
Convert a notebooks output to HTML
"""
nb = run_notebook(nb)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exportHtml = HTMLExporter(config=config)
html, resources = exportHtml.from_notebook_node(nb)
soup = BeautifulSoup(html)
return ''.join(map(str, soup.findAll("div", {"class": ["output", "text_cell_render border-box-sizing rendered_html"]})))
def convert_nb_html(nb):
"""
Convert a notebooks output to HTML
"""
nb = run_notebook(nb)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exportHtml = HTMLExporter(config=config)
html, resources = exportHtml.from_notebook_node(nb)
soup = BeautifulSoup(html)
filters = ["output", "text_cell_render border-box-sizing rendered_html"]
return ''.join(map(str, soup.findAll("div", {"class": filters})))
def html_conversion(nbjson, template=None):
"""
Input template file .tpl as string.
Provisionnally use the templates in class ezmarkdown.template.
e.g. 'ezmarkdown.template.TEMPLATE_OUTPUT_CELLS_ONLY'.
"""
tpl_loader = jinja2.FileSystemLoader(TEMPLATE_DIR)
html_config = Config({"HTMLExporter": {"default_template": 'full'}})
if template:
html_config = Config({"HTMLExporter": {"template_file": template}})
html_exporter = HTMLExporter(config=html_config, extra_loaders=[tpl_loader])
html, resources = html_exporter.from_notebook_node(nbjson)
return html
def export_unit_to_html(unit):
"""Export unit into html format."""
path = os.path.dirname(os.path.realpath(__file__))
cfg = Config({'HTMLExporter':{'template_file':'basic_reduced',
'template_path':['.',path],
'filters':{'markdown2html':
markdown2html_pandoc}}})
exportHtml = HTMLExporter(config=cfg)
(body, resources) = exportHtml.from_notebook_node(unit)
body = re.sub(r'\\begin\{ *equation *\}', '\[', body)
body = re.sub(r'\\end\{ *equation *\}', '\]', body)
return body
def display(user, path):
full_path = os.path.join('/home', user, 'notebooks', path + '.ipynb')
if not os.path.exists(full_path):
return "No such notebook", 404
mtime = str(os.stat(full_path).st_mtime)
key = cache_key(user, path, mtime)
cached = redis.get(key)
if cached:
return cached
exportHtml = HTMLExporter(config=Config({'HTMLExporter':{'default_template':'basic'}}))
notebook = nbformat.reads_json(open(full_path).read())
body, res = exportHtml.from_notebook_node(notebook)
redis.set(key, body)
redis.expire(key, app.config['REDIS_EXPIRY_SECONDS'])
return body
def export_html(nb, dest_path=None, image_dir=None, image_rel_dir=None):
"""Convert notebook to HTML.
Optionally saves HTML to dest_path.
"""
c = Config({'ExtractOutputPreprocessor': {'enabled': True}})
exporter = HTMLExporter(template_file='full', config=c)
output, resources = exporter.from_notebook_node(nb)
header = output.split('<head>', 1)[1].split('</head>', 1)[0]
body = output.split('<body>', 1)[1].split('</body>', 1)[0]
# Monkeypatch CSS
header = header.replace('<style', '<style scoped="scoped"')
header = header.replace(
'body {\n overflow: visible;\n padding: 8px;\n}\n', '')
header = header.replace("code,pre{", "code{")
# Filter out styles that conflict with the sphinx theme.
bad_anywhere = [
'navbar', 'body{', 'alert{', 'uneditable-input{', 'collapse{'
]
bad_anywhere.extend(['h%s{' % (i + 1) for i in range(6)])
bad_beginning = ['pre{', 'p{margin']
header_lines = [
x for x in header.split('\n')
if (not any(x.startswith(s)
for s in bad_beginning) and not any(s in x
for s in bad_anywhere))
]
header = '\n'.join(header_lines)
# Concatenate raw html lines
lines = ['<div class="ipynotebook">']
lines.append(header)
lines.append(body)
lines.append('</div>')
html_out = '\n'.join(lines)
if image_dir is not None and image_rel_dir is not None:
html_out = export_images(resources, image_dir, image_rel_dir, html_out)
if dest_path is not None:
with io.open(dest_path, 'w', encoding='utf-8') as f:
f.write(html_out)
return html_out
def export_html(nb, dest_path=None, image_dir=None, image_rel_dir=None):
"""Convert notebook to HTML.
Optionally saves HTML to dest_path.
"""
c = Config({'ExtractOutputPreprocessor': {'enabled': True}})
exporter = HTMLExporter(template_file='full', config=c)
output, resources = exporter.from_notebook_node(nb)
header = output.split('<head>', 1)[1].split('</head>', 1)[0]
body = output.split('<body>', 1)[1].split('</body>', 1)[0]
# Monkeypatch CSS
header = header.replace('<style', '<style scoped="scoped"')
header = header.replace(
'body {\n overflow: visible;\n padding: 8px;\n}\n', '')
header = header.replace("code,pre{", "code{")
# Filter out styles that conflict with the sphinx theme.
bad_anywhere = ['navbar',
'body{',
'alert{',
'uneditable-input{',
'collapse{']
bad_anywhere.extend(['h%s{' % (i+1) for i in range(6)])
bad_beginning = ['pre{', 'p{margin']
header_lines = [x for x in header.split('\n')
if (not any(x.startswith(s) for s in bad_beginning)
and not any(s in x for s in bad_anywhere))]
header = '\n'.join(header_lines)
# Concatenate raw html lines
lines = ['<div class="ipynotebook">']
lines.append(header)
lines.append(body)
lines.append('</div>')
html_out = '\n'.join(lines)
if image_dir is not None and image_rel_dir is not None:
html_out = export_images(resources, image_dir, image_rel_dir, html_out)
if dest_path is not None:
with open(dest_path, 'w') as f:
f.write(html_out)
return html_out
def parse(path):
source = read_text_file(path)
if path.endswith('.rst'):
doctree = publish_doctree(source)
docinfos = doctree.traverse(nodes.docinfo)
docinfo = {c.tagname: str(c.children[0])
for i in docinfos for c in i.children}
parts = publish_parts(source, writer_name='html')
return {'body': parts['body'],
'date': docinfo.get('date'),
'title': parts['title']}
elif path.endswith('.ipynb'):
notebook = nbformat.reads_json(source)
exporter = HTMLExporter(config=None, extra_loaders=[dl])
body, resources = exporter.from_notebook_node(notebook)
return {'body': body,
'date': notebook['metadata']['date'],
'title': notebook['metadata']['name']}
def Viewer(nburl=None, showcode=False, render='html'):
from IPython.nbformat import reader as nbformat
from IPython.nbconvert import exporters
# Get url or file path
if nburl:
if nburl.startswith("http"):
import requests
response = requests.get(nburl)
notebook = nbformat.reads_json(response.content)
else:
notebook = nbformat.read(fp=file(nburl))
else:
notebook = ''
# Get rendering template
if showcode:
if render == 'html':
template = 'full'
else:
if render == 'html':
template = 'full2'
import IPython.nbconvert
from IPython.config import Config
from IPython.nbconvert import HTMLExporter
## I use `basic` here to have less boilerplate and headers in the HTML.
## we'll see later how to pass config to exporters.
exportHtml = HTMLExporter(
config=Config({'HTMLExporter': {
'template_file': template
}}))
(body, resources) = exportHtml.from_filename(nburl)
return body
def article_of(notebook_txt, HTMLExporter):
notebook = nbformat.reads(notebook_txt)
hide, meta = article_meta(notebook)
for ix in sorted(hide, reverse=True):
del notebook.cells[ix]
for n, v in meta:
yield '%s: %s\n' % (n, v)
yield '\n'
exportHtml = HTMLExporter(config=Config({'HTMLExporter':
{'default_template': 'basic'}}))
body, resources = exportHtml.from_notebook_node(notebook)
# [txt[:100] for txt in resources['inlining']['css']]
yield body
def article_of(notebook_txt, HTMLExporter):
notebook = nbformat.reads(notebook_txt)
hide, meta = article_meta(notebook)
for ix in sorted(hide, reverse=True):
del notebook.cells[ix]
for n, v in meta:
yield '%s: %s\n' % (n, v)
yield '\n'
exportHtml = HTMLExporter(
config=Config({'HTMLExporter': {
'default_template': 'basic'
}}))
body, resources = exportHtml.from_notebook_node(notebook)
# [txt[:100] for txt in resources['inlining']['css']]
yield body
def convert_to_html(notebook, resources, target_directory):
"""Return a list of strings representing the rst of the given notebook."""
exporter = HTMLExporter(
template_file='gallery_page',
template_path=[os.path.dirname(__file__)],
config={'ExtractOutputPreprocessor': {
'enabled': True
}})
resources.update({'output_files_dir': 'notebook_output'})
html, resources = exporter.from_notebook_node(notebook, resources)
# Convert linked resources (such as images) into actual files in the
# source directory.
for name, data in resources.get('outputs', {}).items():
name = os.path.join(target_directory, name)
if not os.path.exists(os.path.dirname(name)):
os.makedirs(os.path.dirname(name))
with io.open(name, 'wb') as f:
f.write(data)
return html, resources.get('outputs', {}).keys()
def _parse_ipynb(self):
notebook = nbformat.reads_json(self.source)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exporter = HTMLExporter(config=config)
body, resources = exporter.from_notebook_node(notebook)
body = body[body.index('\n<div class="cell'):-36] # excise template
body = self._decapitate(body)
body = body.replace('\n</pre>', '</pre>')
self.add_mathjax = r'\(' in body
fields = notebook['metadata']
if 'date' in fields:
self.date = datetime.strptime(fields['date'], '%d %B %Y').date()
else:
self.date = datetime.now().date()
self.tags = set()
if 'tags' in fields:
self.tags.update('-'.join(tag.strip().lower().split())
for tag in fields['tags'].split(','))
if self.date and self.tags:
heading = ':Date: {}\n:Tags: {}\n'.format(
self.date.strftime('%d %B %Y').lstrip('0'),
', '.join(sorted(self.tags)),
)
parts = parse_rst(heading)
body = parts['docinfo'] + body
self.add_disqus = fields.get('add_disqus', False)
self.body_html = body
self.next_link = None
self.previous_link = None
self.add_title = True
def _parse_ipynb(self):
notebook = nbformat.reads_json(self.source)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exporter = HTMLExporter(config=config)
body, resources = exporter.from_notebook_node(notebook)
body = body[body.index('\n<div class="cell'):-36] # excise template
body = self._decapitate(body)
body = body.replace('\n</pre>', '</pre>')
self.add_mathjax = r'\(' in body
fields = notebook['metadata']
if 'date' in fields:
self.date = datetime.strptime(fields['date'], '%d %B %Y').date()
else:
self.date = datetime.now().date()
self.tags = set()
if 'tags' in fields:
self.tags.update('-'.join(tag.strip().lower().split())
for tag in fields['tags'].split(','))
if self.date and self.tags:
heading = ':Date: {}\n:Tags: {}\n'.format(
self.date.strftime('%d %B %Y').lstrip('0'),
', '.join(sorted(self.tags)),
)
parts = parse_rst(heading)
body = parts['docinfo'] + body
self.add_disqus = fields.get('add_disqus', False)
self.body_html = body
self.next_link = None
self.previous_link = None
self.add_title = True
def inner():
# run MUMmer
mummer_cmd = "echo RUNNING NUCMER && bash -x ~/github/metassemble/scripts/validate/nucmer/run-nucmer.sh test/references/Mircea_07102013_selected_refs.fasta {0} /tmp/nucmer && echo SUCCESS!".format(save_path)
#mummer_cmd = "echo fakka"
proc = subprocess.Popen(mummer_cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
while True:
char = proc.stdout.read(1)
if char:
if str(char) != '\n':
yield str(char)
else:
yield '<br />\n'
else:
break
#TODO: not working, points to relative dir
yield '<a href="/tmp/nucmer/nucmer.coords">nucmer.coords</a>\n'
notebook = read(open("masmvaliweb/notebooks/mgcov-comparison-mpld3.ipynb"), 'json')
r = NotebookRunner(notebook)
r.run_notebook()
exportHTML = HTMLExporter(config=Config({'HTMLExporter': {'default_template': 'basic'}}))
yield exportHTML.from_notebook_node(r.nb)[0]
def parse(path):
source = read_text_file(path)
if path.endswith('.rst'):
doctree = publish_doctree(source)
docinfos = doctree.traverse(nodes.docinfo)
docinfo = {
c.tagname: str(c.children[0])
for i in docinfos for c in i.children
}
parts = publish_parts(source, writer_name='html')
return {
'body': parts['body'],
'date': docinfo.get('date'),
'title': parts['title']
}
elif path.endswith('.ipynb'):
notebook = nbformat.reads_json(source)
exporter = HTMLExporter(config=None, extra_loaders=[dl])
body, resources = exporter.from_notebook_node(notebook)
return {
'body': body,
'date': notebook['metadata']['date'],
'title': notebook['metadata']['name']
}
def parse(path):
source = read_text_file(path)
result = {}
if path.endswith('.html'):
if utils.detect_blogofile(source):
heading, info, other_html = utils.convert_blogofile(source)
parts = utils.parse_rst(heading)
body_html = parts['docinfo'] + other_html
body_html = utils.pygmentize_pre_blocks(body_html)
body_html = body_html.replace('\n</pre>', '</pre>')
result['title'] = utils.html_parser.unescape(parts['title'])
result['needs_disqus'] = True
result['date'] = info['date']
result['tags'] = info['tags']
else:
result['title'] = utils.find_title_in_html(source)
body_html = SimpleTemplate(source)
result['needs_disqus'] = False
result['date'] = None
result['tags'] = ()
result['body'] = body_html
result['next_link'] = None
result['previous_link'] = None
elif path.endswith('.rst'):
if utils.detect_blogofile(source):
heading, info, body = utils.convert_blogofile(source)
source = heading + body
result['title'] = info['title']
del heading, info, body
result['needs_disqus'] = True
else:
result['needs_disqus'] = False
doctree = publish_doctree(source)
docinfos = doctree.traverse(nodes.docinfo)
docinfo = {c.tagname: str(c.children[0])
for i in docinfos for c in i.children}
parts = utils.parse_rst(source)
# parts = publish_from_doctree(source, writer_name='html',
# settings_overrides={'initial_header_level': 2})
body = parts['docinfo'] + utils.pygmentize_pre_blocks(parts['fragment'])
result['body'] = body
result['date'] = datetime.strptime(
docinfo.get('date'), '%d %B %Y').date()
if 'title' not in result:
result['title'] = parts['title']
elif path.endswith('.ipynb'):
notebook = nbformat.reads_json(source)
docinfo = utils.build_docinfo_block_for_notebook(notebook)
exporter = HTMLExporter(config=None, extra_loaders=[dl],
filters=filters)
body, resources = exporter.from_notebook_node(notebook)
body = body.replace('\n</pre>', '</pre>')
body = body.replace('</h1>', '</h1>\n' + docinfo.rstrip())
date = notebook['metadata']['date']
if date is not None:
date = datetime.strptime(date, '%d %B %Y').date()
result['body'] = body
result['date'] = date
result['needs_disqus'] = notebook['metadata'].get('needs_disqus')
result['title'] = (notebook['metadata']['name']
or utils.find_title_in_html(body))
return result
def _generate_html(self, node, substitutions): # pragma: no cover
exporter = HTMLExporter()
exporter.register_preprocessor(
Substitute(self.nbversion, substitutions))
html, _ = exporter.from_notebook_node(node)
return html
def _generate_html(self, node, substitutions): # pragma: no cover
exporter = HTMLExporter()
exporter.register_preprocessor(Substitute(self.nbversion,
substitutions))
html,_ = exporter.from_notebook_node(node)
return html
parser.add_argument('title', type=str, help=strings_help[2])
parser.add_argument('file', type=str, help=strings_help[5])
parser.add_argument('--url', '-u', type=str, help=strings_help[3], nargs='?', default="", required=False)
parser.add_argument('--directory', '-d', type=str, help=strings_help[4], nargs='?', default=default.directory, required=False)
parser.add_argument('--author', '-a', type=str, help=strings_help[1], nargs='?', default=default.author, required=False)
parser.add_argument('--rsakey', '-k', type=str, help=strings_help[6], nargs='?', default=default.private_key_path, required=False)
parser.add_argument('--category', '-c', type=str, help=strings_help[10], nargs='?', default=default.category, required=False)
parser.add_argument('--year', type=int, help=strings_help[7], nargs='?',default=datetime.datetime.now().year, required=False)
parser.add_argument('--month', type=int, help=strings_help[8], nargs='?', default=datetime.datetime.now().month, required=False)
parser.add_argument('--day', type=int, help=strings_help[9], nargs='?', default=datetime.datetime.now().day, required=False)
args = parser.parse_args()
host = default.host + "/blog"
exportHtml = HTMLExporter(config=Config({'HTMLExporter':{'default_template':'basic'}}))
f = open(args.rsakey,'r')
private_key = RSA.importKey(f.read())
signer = PKCS1_v1_5.new(private_key)
url = args.url
if url == "":
url = '-'.join((args.title).lower().split(" "))
notebook = nbformat.reads_json(open(os.path.join(args.directory, args.file), "r").read())
(body,resources) = exportHtml.from_notebook_node(notebook)
content = ((body.split("</body>")[0]).split('<div class="container" id="notebook-container">')[1])[0:-16]
category = ""
if args.title == "root":
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import glob
from IPython.config import Config
from IPython.nbconvert import HTMLExporter
c = Config({'ExecutePreprocessor': {'enabled': True}})
exporter = HTMLExporter(config=c)
for filename in glob.glob("example-notebooks/*.ipynb"):
print(filename)
exporter.from_filename(filename)
def publish(notebook_name,
url_path,
page_title,
page_description,
ignore_last_n_cells=2,
uses_plotly_offline=False,
thumbnail=DEFAULT_THUMBNAIL_URL,
**kwargs):
'''
Convert an IPython notebook into an HTML file that can be consumed
by GitHub pages in plotly's documentation repo.
Arguments:
- notebook_name: The name of the notebook to convert.
Used as input arg to nbconvert, nowhere else.
- url_path: e.g. /python/offline
- page_title: The <title> of the page.
- page_description: So, what's this page about?
Sell it in 160 characters or less.
This is the <meta name="description"> tag.
- ignore_last_n_cells: When converting to HTML, don't convert the
ignore_last_n_cells number of cells.
This is usually the cell that runs this `publish`
command and the blank output cell that is always
included.
- uses_plotly_offline: If this was created with plotly.offline, then set
this to True. This will include an extra lib
(jquery) that is included in ipython notebook,
but not included in gh-pages
- thumbnail: Used as a thumbnail image on the notebook splash
(if applicable) and as the image when sharing the
notebook as a tweet, a facebook post, etc.
Can be relative to the repo, eg '/images/static-image'
or absolute, e.g. http://i.imgur.com/j0Uiy0n.jpg
- language: Not sure what this is used for.
Example:
publish('Plotly Offline',
'/python/offline',
'Plotly Offline for IPython Notebooks',
'How to use Plotly offline inside IPython notebooks with Plotly Offline',
uses_plotly_offline=True)
'''
# backwards compatability
if 'thumbnail_url' in kwargs and kwargs[
'thumbnail'] == DEFAULT_THUMBNAIL_URL:
kwargs['thumbnail'] = kwargs['thumbnail_url']
warnings.warn('Did you "Save" this notebook before running this command? '
'Remember to save, always save.')
parts = url_path.split('/')
if len(parts) > 3:
warnings.warn('Your URL has more than 2 parts... are you sure?')
if url_path[-1] == '/':
url_path = url_path[:-1]
if len(page_description) > 160:
raise Exception("Shorten up that page_description! "
"Your description was {} characters, "
"and it's gotta be <= than 160.".format(
len(page_description)))
if thumbnail == DEFAULT_THUMBNAIL_URL:
has_thumbnail = 'false'
else:
has_thumbnail = 'true'
if '.ipynb' not in notebook_name:
notebook_name += '.ipynb'
fn = notebook_name
tmpfn = 'temp-{}'.format(fn)
nbjson = json.load(open(fn))
if 'cells' in nbjson:
nbjson['cells'] = nbjson['cells'][:-ignore_last_n_cells]
elif 'worksheets' in nbjson:
if len(nbjson['worksheets']) != 1:
raise Exception('multiple worksheets?')
elif 'cells' in nbjson['worksheets'][0]:
nbjson['worksheets'][0]['cells'] = nbjson['worksheets'][0][
'cells'][:-ignore_last_n_cells]
else:
raise Exception('cells not in worksheets[0]?')
else:
raise Exception('unknown ipython notebook format')
with open(tmpfn, 'w') as f:
f.write(json.dumps(nbjson))
exporter = HTMLExporter(template_file='basic')
html = exporter.from_filename(tmpfn)[0]
kwargs.setdefault('layout', 'user-guide')
kwargs.setdefault('page_type', 'u-guide')
kwargs.setdefault('language', 'python')
with open('2015-06-30-' + fn.replace('.ipynb', '.html'), 'w') as f:
f.write('\n'.join([
''
'---', 'permalink: ' + url_path,
'description: ' + page_description.replace(':', ':'),
'name: ' + page_title.replace(':', ':'),
'has_thumbnail: ' + has_thumbnail, 'thumbnail: ' + thumbnail,
'\n'.join(['{}: {}'.format(k, v)
for k, v in kwargs.iteritems()]), '---', '{% raw %}'
]))
if uses_plotly_offline:
f.write(
'<script type="text/javascript" '
' src="https://code.jquery.com/jquery-2.1.4.min.js">'
'</script>')
f.write(html.encode('utf8'))
f.write('{% endraw %}')
os.remove(tmpfn)
def publish(notebook_name, url_path, page_title, page_description,
ignore_last_n_cells=2, uses_plotly_offline=False,
thumbnail=DEFAULT_THUMBNAIL_URL, **kwargs):
'''
Convert an IPython notebook into an HTML file that can be consumed
by GitHub pages in plotly's documentation repo.
Arguments:
- notebook_name: The name of the notebook to convert.
Used as input arg to nbconvert, nowhere else.
- url_path: e.g. /python/offline
- page_title: The <title> of the page.
- page_description: So, what's this page about?
Sell it in 160 characters or less.
This is the <meta name="description"> tag.
- ignore_last_n_cells: When converting to HTML, don't convert the
ignore_last_n_cells number of cells.
This is usually the cell that runs this `publish`
command and the blank output cell that is always
included.
- uses_plotly_offline: If this was created with plotly.offline, then set
this to True. This will include an extra lib
(jquery) that is included in ipython notebook,
but not included in gh-pages
- thumbnail: Used as a thumbnail image on the notebook splash
(if applicable) and as the image when sharing the
notebook as a tweet, a facebook post, etc.
Can be relative to the repo, eg '/images/static-image'
or absolute, e.g. http://i.imgur.com/j0Uiy0n.jpg
- language: Not sure what this is used for.
Example:
publish('Plotly Offline',
'/python/offline',
'Plotly Offline for IPython Notebooks',
'How to use Plotly offline inside IPython notebooks with Plotly Offline',
uses_plotly_offline=True)
'''
# backwards compatability
if 'thumbnail_url' in kwargs and kwargs['thumbnail'] == DEFAULT_THUMBNAIL_URL:
kwargs['thumbnail'] = kwargs['thumbnail_url']
warnings.warn('Did you "Save" this notebook before running this command? '
'Remember to save, always save.')
parts = url_path.split('/')
if len(parts) > 3:
warnings.warn('Your URL has more than 2 parts... are you sure?')
#if url_path[-1] == '/':
# url_path = url_path[:-1]
if len(page_description) > 160:
raise Exception("Shorten up that page_description! "
"Your description was {} characters, "
"and it's gotta be <= than 160."
.format(len(page_description)))
if thumbnail == DEFAULT_THUMBNAIL_URL:
has_thumbnail = 'false'
else:
has_thumbnail = 'true'
if '.ipynb' not in notebook_name:
notebook_name += '.ipynb'
fn = notebook_name
tmpfn = 'temp-{}'.format(fn)
nbjson = json.load(open(fn))
if 'cells' in nbjson:
nbjson['cells'] = nbjson['cells'][:-ignore_last_n_cells]
elif 'worksheets' in nbjson:
if len(nbjson['worksheets']) != 1:
raise Exception('multiple worksheets?')
elif 'cells' in nbjson['worksheets'][0]:
nbjson['worksheets'][0]['cells'] = nbjson['worksheets'][0]['cells'][:-ignore_last_n_cells]
else:
raise Exception('cells not in worksheets[0]?')
else:
raise Exception('unknown ipython notebook format')
with open(tmpfn, 'w') as f:
f.write(json.dumps(nbjson))
exporter = HTMLExporter(template_file='basic')
html = exporter.from_filename(tmpfn)[0]
kwargs.setdefault('layout', 'user-guide')
kwargs.setdefault('page_type', 'u-guide')
kwargs.setdefault('language', 'python')
with open('2015-06-30-' + fn.replace('.ipynb', '.html'), 'w') as f:
f.write('\n'.join([''
'---',
'permalink: ' + url_path,
'description: ' + page_description.replace(':', ':'),
'name: ' + page_title.replace(':', ':'),
'has_thumbnail: ' + has_thumbnail,
'thumbnail: ' + thumbnail,
'\n'.join(['{}: {}'.format(k, v) for k, v in kwargs.iteritems()]),
'---',
'{% raw %}'
]))
if uses_plotly_offline:
f.write(
'<script type="text/javascript" '
' src="https://code.jquery.com/jquery-2.1.4.min.js">'
'</script>'
)
f.write(html.encode('utf8'))
f.write('{% endraw %}')
os.remove(tmpfn)
def post(args, debug=False):
"""
Inserts a file as a post to a blog.
"""
title, suffix = os.path.splitext(os.path.basename(args.file))
# Need to add mathJax header in front of html
mathJaxFile = os.path.join(os.path.dirname(__file__), 'mathJax.html')
with open(mathJaxFile, 'r') as htmlFile:
mathJax = htmlFile.read()
# Read file to post
if suffix in ('.html', '.htm'):
with open(args.file, 'r') as htmlFile:
html = mathJax + htmlFile.read()
elif suffix in '.ipynb':
exportHtml = HTMLExporter(template_file='basic')
html = mathJax + exportHtml.from_filename(args.file)[0]
else:
print args.file, 'has an unrecognized suffix. Stopping.'
return
# Labels for post
if args.label is None: labels = None
else: labels = args.label
if args.title is not None: title = args.title
# Start communications with blogger
service, http = authenticate(args)
# Retrieve the list of Blogs this user has write privileges on
blogs = service.blogs()
if debug: print 'blogs =', blogs
# Find blog by URL
request = blogs.getByUrl(url=args.url)
if debug: print 'blogs.getByUrl(url=args.url) =', request.to_json()
response = request.execute()
if debug: print 'response =', json.dumps(response, indent=2)
#response = blogs.getByUrl(url=args.url).execute()
# Get blogId
blogId = response['id']
if debug: print 'blogId =', blogId
# posts instance
posts = service.posts()
if debug: print 'posts =', posts
# Build body of post
# Check post doesn't already exist
existingPost = getPostByTitle(posts,
blogId,
title,
status='draft',
debug=False)
if existingPost == None:
existingPost = getPostByTitle(posts,
blogId,
title,
status='scheduled',
debug=False)
if existingPost == None:
existingPost = getPostByTitle(posts,
blogId,
title,
status='live',
debug=False)
if existingPost != None:
if args.update:
existingPost['content'] = html
if labels != None: existingPost['labels'] = labels
postId = existingPost['id']
request = posts.update(blogId=blogId,
postId=postId,
body=existingPost)
if debug: print 'posts().update() =', request.to_json()
response = request.execute()
if debug: print 'response =', json.dumps(response, indent=2)
else:
print 'Post "' + title + '" already exists!'
else:
# Insert new post
body = {}
body['kind'] = 'blogger#post'
body['title'] = title
body['content'] = html
body['blog'] = {'id': blogId}
body['labels'] = labels
request = posts.insert(blogId=blogId, body=body, isDraft=True)
if debug: print 'posts().insert() =', request.to_json()
response = request.execute()
if debug: print 'response =', json.dumps(response, indent=2)
def post(args, debug=False):
"""
Inserts a file as a post to a blog.
"""
title, suffix = os.path.splitext( os.path.basename(args.file) )
# Need to add mathJax header in front of html
mathJaxFile = os.path.join(os.path.dirname(__file__),'mathJax.html')
with open (mathJaxFile, 'r') as htmlFile:
mathJax = htmlFile.read()
# Read file to post
if suffix in ('.html','.htm'):
with open (args.file, 'r') as htmlFile:
html = mathJax + htmlFile.read()
elif suffix in '.ipynb':
exportHtml = HTMLExporter(template_file='basic')
html = mathJax + exportHtml.from_filename(args.file)[0]
else:
print args.file,'has an unrecognized suffix. Stopping.'
return
# Labels for post
if args.label is None: labels = None
else: labels = args.label
if args.title is not None: title = args.title
# Start communications with blogger
service, http = authenticate(args)
# Retrieve the list of Blogs this user has write privileges on
blogs = service.blogs()
if debug: print 'blogs =',blogs
# Find blog by URL
request = blogs.getByUrl(url=args.url)
if debug: print 'blogs.getByUrl(url=args.url) =',request.to_json()
response = request.execute()
if debug: print 'response =',json.dumps(response, indent=2)
#response = blogs.getByUrl(url=args.url).execute()
# Get blogId
blogId = response['id']
if debug: print 'blogId =',blogId
# posts instance
posts = service.posts()
if debug: print 'posts =',posts
# Build body of post
# Check post doesn't already exist
existingPost = getPostByTitle(posts, blogId, title, status='draft', debug=False)
if existingPost == None:
existingPost = getPostByTitle(posts, blogId, title, status='scheduled', debug=False)
if existingPost == None:
existingPost = getPostByTitle(posts, blogId, title, status='live', debug=False)
if existingPost != None:
if args.update:
existingPost['content'] = html
if labels != None: existingPost['labels'] = labels
postId = existingPost['id']
request = posts.update(blogId=blogId, postId=postId, body=existingPost)
if debug: print 'posts().update() =',request.to_json()
response = request.execute()
if debug: print 'response =',json.dumps(response, indent=2)
else:
print 'Post "'+title+'" already exists!'
else:
# Insert new post
body = {}
body['kind'] = 'blogger#post'
body['title'] = title
body['content'] = html
body['blog'] = {'id': blogId}
body['labels'] = labels
request = posts.insert(blogId=blogId, body=body, isDraft=True)
if debug: print 'posts().insert() =',request.to_json()
response = request.execute()
if debug: print 'response =',json.dumps(response, indent=2)
def build_gallery(examples_directory, target_directory):
notebook_fnames = list(notebooks_in_directory(examples_directory))
examples_dir_name = 'examples'
examples_directory = os.path.join(target_directory, examples_dir_name)
if not os.path.isdir(examples_directory):
os.makedirs(examples_directory)
gallery_page_fname = os.path.join(target_directory, 'gallery.html')
exporter = HTMLExporter(template_file='gallery',
template_path=[os.path.dirname(__file__)])
exporter._load_template()
exporter = exporter.template
sections = []
notebook_keywords = {}
for notebook_fname in notebook_fnames:
notebook = read_notebook(notebook_fname)
notebook_keywords[notebook_fname] = notebook['metadata'].get(
'keywords', [])
notebooks_by_keyword = {}
for notebook_fname, keywords in notebook_keywords.items():
for keyword in keywords:
notebooks_by_keyword.setdefault(keyword, []).append(notebook_fname)
import collections
Section = collections.namedtuple('Section', ['name', 'examples'])
Example = collections.namedtuple('Example',
['name', 'url', 'keywords', 'outputs'])
examples_by_fname = {}
for fname in notebook_fnames:
name = os.path.splitext(os.path.basename(fname))[0]
page_content_fname = os.path.join(examples_directory, name + '.html')
refname = 'gallery-{}'.format(name.replace('_', '-'))
with open(page_content_fname, 'w') as fh:
html, outputs = notebook_html(fname, refname, examples_directory)
fh.write(html.encode('utf-8'))
images = []
for output in outputs:
thumb_path = examples_dir_name + '/' + 'notebook_output_thumbs' + '/' + os.path.basename(
output)
thumb_fname = os.path.join(target_directory, thumb_path)
orig_fname = os.path.join(examples_directory, output)
if not os.path.exists(os.path.dirname(thumb_fname)):
os.makedirs(os.path.dirname(thumb_fname))
import shutil
# TODO - resize these.
shutil.copy(orig_fname, thumb_fname)
images.append(thumb_path)
# outputs = [examples_dir_name + '/' + image for image in images]
example = Example(name, '{}/{}.html'.format(examples_dir_name, name),
notebook_keywords[fname], images)
examples_by_fname[fname] = example
break
for keyword, fnames in notebooks_by_keyword.items():
section = Section(keyword, [])
sections.append(section)
for fname in fnames:
name = os.path.splitext(os.path.basename(fname))[0]
if fname in examples_by_fname:
section.examples.append(examples_by_fname[fname])
with open(gallery_page_fname, 'w') as gallery_page:
gallery_page.write(exporter.render(title='Gallery', sections=sections))
(body,resources) = exporter.from_notebook_node(notebook)
with open(out_file,'w') as f:
f.write(body.encode('utf8'))
return out_file
config=Config({
'HTMLExporter':{
'template_file':'local',
'template_path': [os.path.join(root_dir,'scripts')]
},
})
exportHtmlA = HTMLExporter()
exportHtmlB = HTMLExporter(config=config)
exportHtmlB.register_preprocessor(LocalPreprocessor(root_dir), enabled=True)
out_files = set()
for file in args.files:
for exporter, suffix in ( (exportHtmlA,'-code'), (exportHtmlB,'')):
out_file = convert(exporter, file, suffix)
if out_file:
out_files.add(out_file)
