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125 lines
5.0 KiB
125 lines
5.0 KiB
#-*- conding: utf-8 -*-
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import os
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import warnings
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import logging
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logger = logging.getLogger('RMD_READER')
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from pelican import readers
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from pelican import signals
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from pelican import settings
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KNITR = None
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RMD = False
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FIG_PATH = None
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R_STARTED = False
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def startr():
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global KNITR, R_OBJECTS, R_STARTED
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if R_STARTED:
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return
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logger.debug('STARTING R')
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with warnings.catch_warnings():
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warnings.simplefilter("ignore")
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import rpy2.rinterface
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rpy2.rinterface.set_initoptions((b'rpy2', b'--no-save', b'--vanilla', b'--quiet'))
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import rpy2.robjects as R_OBJECTS
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from rpy2.robjects.packages import importr
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KNITR = importr('knitr')
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logger.debug('R STARTED')
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R_STARTED = True
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def initsignal(pelicanobj):
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global RMD, FIG_PATH
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try:
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startr()
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R_OBJECTS.r('Sys.setlocale("LC_ALL", "C")')
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R_OBJECTS.r('Sys.setlocale("LC_NUMERIC", "C")')
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R_OBJECTS.r('Sys.setlocale("LC_MESSAGES", "C")')
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idx = KNITR.opts_knit.names.index('set')
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path = pelicanobj.settings.get('PATH','%s/content' % settings.DEFAULT_CONFIG.get('PATH'))
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logger.debug("RMD_READER PATH = %s", path)
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KNITR.opts_knit[idx](**{'base.dir': path})
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knitroptsknit = pelicanobj.settings.get('RMD_READER_KNITR_OPTS_KNIT', None)
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if knitroptsknit:
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KNITR.opts_knit[idx](**{str(k): v for k,v in knitroptsknit.items()})
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idx = KNITR.opts_chunk.names.index('set')
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knitroptschunk = pelicanobj.settings.get('RMD_READER_KNITR_OPTS_CHUNK', None)
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if knitroptschunk:
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FIG_PATH = knitroptschunk['fig.path'] if 'fig.path' in knitroptschunk else 'figure/'
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KNITR.opts_chunk[idx](**{str(k): v for k,v in knitroptschunk.items()})
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RMD = True
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except ImportError as ex:
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RMD = False
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class RmdReader(readers.BaseReader):
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file_extensions = ['Rmd', 'rmd']
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@property
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def enabled():
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return RMD
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# You need to have a read method, which takes a filename and returns
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# some content and the associated metadata.
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def read(self, filename):
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"""Parse content and metadata of markdown files"""
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QUIET = self.settings.get('RMD_READER_KNITR_QUIET', True)
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ENCODING = self.settings.get('RMD_READER_KNITR_ENCODING', 'UTF-8')
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CLEANUP = self.settings.get('RMD_READER_CLEANUP', True)
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RENAME_PLOT = self.settings.get('RMD_READER_RENAME_PLOT', 'chunklabel')
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if type(RENAME_PLOT) is bool:
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logger.error("RMD_READER_RENAME_PLOT takes a string value (either chunklabel or directory), please see the readme.")
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if RENAME_PLOT:
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RENAME_PLOT = 'chunklabel'
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logger.error("Defaulting to chunklabel")
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else:
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RENAME_PLOT = 'disabled'
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logger.error("Disabling plot renaming")
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logger.debug("RMD_READER_KNITR_QUIET = %s", QUIET)
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logger.debug("RMD_READER_KNITR_ENCODING = %s", ENCODING)
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logger.debug("RMD_READER_CLEANUP = %s", CLEANUP)
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logger.debug("RMD_READER_RENAME_PLOT = %s", RENAME_PLOT)
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# replace single backslashes with double backslashes
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filename = filename.replace('\\', '\\\\')
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# parse Rmd file - generate md file
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md_filename = filename.replace('.Rmd', '.aux').replace('.rmd', '.aux')
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if RENAME_PLOT == 'chunklabel' or RENAME_PLOT == 'directory':
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if RENAME_PLOT == 'chunklabel':
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chunk_label = os.path.splitext(os.path.basename(filename))[0]
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logger.debug('Chunk label: %s', chunk_label)
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elif RENAME_PLOT == 'directory':
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chunk_label = 'unnamed-chunk'
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PATH = self.settings.get('PATH','%s/content' % settings.DEFAULT_CONFIG.get('PATH'))
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src_name = os.path.splitext(os.path.relpath(filename, PATH))[0]
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idx = KNITR.opts_chunk.names.index('set')
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knitroptschunk = { 'fig.path': '%s-' % os.path.join(FIG_PATH, src_name) }
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KNITR.opts_chunk[idx](**{str(k): v for k,v in knitroptschunk.items()})
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logger.debug('Figures path: %s, chunk label: %s', knitroptschunk['fig.path'], chunk_label)
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R_OBJECTS.r('''
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opts_knit$set(unnamed.chunk.label="{unnamed_chunk_label}")
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render_markdown()
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hook_plot <- knit_hooks$get('plot')
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knit_hooks$set(plot=function(x, options) hook_plot(paste0("{{filename}}/", x), options))
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'''.format(unnamed_chunk_label=chunk_label))
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with warnings.catch_warnings():
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warnings.simplefilter("ignore")
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KNITR.knit(filename, md_filename, quiet=QUIET, encoding=ENCODING)
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# read md file - create a MarkdownReader
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md_reader = readers.MarkdownReader(self.settings)
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content, metadata = md_reader.read(md_filename)
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# remove md file
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if CLEANUP:
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os.remove(md_filename)
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return content, metadata
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def add_reader(readers):
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readers.reader_classes['rmd'] = RmdReader
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def register():
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signals.readers_init.connect(add_reader)
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signals.initialized.connect(initsignal)
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