# -*- coding: utf-8 -*- # Author: Óscar Nájera # License: 3-clause BSD """ RST file generator ================== Generate the rst files for the examples by iterating over the python example files. Files that generate images should start with 'plot' """ # Don't use unicode_literals here (be explicit with u"..." instead) otherwise # tricky errors come up with exec(code_blocks, ...) calls from __future__ import division, print_function, absolute_import from time import time import ast import codecs import hashlib import os import re import shutil import subprocess import sys import traceback from distutils.version import LooseVersion # Try Python 2 first, otherwise load from Python 3 try: # textwrap indent only exists in python 3 from textwrap import indent except ImportError: def indent(text, prefix, predicate=None): """Adds 'prefix' to the beginning of selected lines in 'text'. If 'predicate' is provided, 'prefix' will only be added to the lines where 'predicate(line)' is True. If 'predicate' is not provided, it will default to adding 'prefix' to all non-empty lines that do not consist solely of whitespace characters. """ if predicate is None: def predicate(line): return line.strip() def prefixed_lines(): for line in text.splitlines(True): yield (prefix + line if predicate(line) else line) return ''.join(prefixed_lines()) from io import StringIO # make sure that the Agg backend is set before importing any # matplotlib import matplotlib matplotlib.use('agg') matplotlib_backend = matplotlib.get_backend() if matplotlib_backend != 'agg': mpl_backend_msg = ( "Sphinx-Gallery relies on the matplotlib 'agg' backend to " "render figures and write them to files. You are " "currently using the {} backend. Sphinx-Gallery will " "terminate the build now, because changing backends is " "not well supported by matplotlib. We advise you to move " "sphinx_gallery imports before any matplotlib-dependent " "import. Moving sphinx_gallery imports at the top of " "your conf.py file should fix this issue") raise ValueError(mpl_backend_msg.format(matplotlib_backend)) import matplotlib.pyplot as plt import sphinx from . import glr_path_static from . import sphinx_compatibility from .backreferences import write_backreferences, _thumbnail_div from .downloads import CODE_DOWNLOAD from .py_source_parser import split_code_and_text_blocks from .notebook import jupyter_notebook, save_notebook try: basestring except NameError: basestring = str unicode = str logger = sphinx_compatibility.getLogger('sphinx-gallery') ############################################################################### class MixedEncodingStringIO(StringIO): """Helper when both ASCII and unicode strings will be written""" def write(self, data): if not isinstance(data, unicode): data = data.decode('utf-8') StringIO.write(self, data) ############################################################################### # The following strings are used when we have several pictures: we use # an html div tag that our CSS uses to turn the lists into horizontal # lists. HLIST_HEADER = """ .. rst-class:: sphx-glr-horizontal """ HLIST_IMAGE_TEMPLATE = """ * .. image:: /%s :scale: 47 """ SINGLE_IMAGE = """ .. image:: /%s :align: center """ # This one could contain unicode CODE_OUTPUT = u""".. rst-class:: sphx-glr-script-out Out:: {0}\n""" SPHX_GLR_SIG = """\n.. rst-class:: sphx-glr-signature `Generated by Sphinx-Gallery `_\n""" def codestr2rst(codestr, lang='python', lineno=None): """Return reStructuredText code block from code string""" if lineno is not None: if LooseVersion(sphinx.__version__) >= '1.3': # Sphinx only starts numbering from the first non-empty line. blank_lines = codestr.count('\n', 0, -len(codestr.lstrip())) lineno = ' :lineno-start: {0}\n'.format(lineno + blank_lines) else: lineno = ' :linenos:\n' else: lineno = '' code_directive = "\n.. code-block:: {0}\n{1}\n".format(lang, lineno) indented_block = indent(codestr, ' ' * 4) return code_directive + indented_block def extract_intro(filename, docstring): """ Extract the first paragraph of module-level docstring. max:95 char""" # lstrip is just in case docstring has a '\n\n' at the beginning paragraphs = docstring.lstrip().split('\n\n') if len(paragraphs) > 1: first_paragraph = re.sub('\n', ' ', paragraphs[1]) first_paragraph = (first_paragraph[:95] + '...' if len(first_paragraph) > 95 else first_paragraph) else: raise ValueError( "Example docstring should have a header for the example title " "and at least a paragraph explaining what the example is about. " "Please check the example file:\n {}\n".format(filename)) return first_paragraph def get_md5sum(src_file): """Returns md5sum of file""" with open(src_file, 'rb') as src_data: src_content = src_data.read() src_md5 = hashlib.md5(src_content).hexdigest() return src_md5 def md5sum_is_current(src_file): """Checks whether src_file has the same md5 hash as the one on disk""" src_md5 = get_md5sum(src_file) src_md5_file = src_file + '.md5' if os.path.exists(src_md5_file): with open(src_md5_file, 'r') as file_checksum: ref_md5 = file_checksum.read() return src_md5 == ref_md5 return False def save_figures(image_path, fig_count, gallery_conf): """Save all open matplotlib figures of the example code-block Parameters ---------- image_path : str Path where plots are saved (format string which accepts figure number) fig_count : int Previous figure number count. Figure number add from this number gallery_conf : dict Contains the configuration of Sphinx-Gallery Returns ------- images_rst : str rst code to embed the images in the document fig_num : int number of figures saved """ figure_list = [] for fig_num in plt.get_fignums(): # Set the fig_num figure as the current figure as we can't # save a figure that's not the current figure. fig = plt.figure(fig_num) kwargs = {} to_rgba = matplotlib.colors.colorConverter.to_rgba for attr in ['facecolor', 'edgecolor']: fig_attr = getattr(fig, 'get_' + attr)() default_attr = matplotlib.rcParams['figure.' + attr] if to_rgba(fig_attr) != to_rgba(default_attr): kwargs[attr] = fig_attr current_fig = image_path.format(fig_count + fig_num) fig.savefig(current_fig, **kwargs) figure_list.append(current_fig) if gallery_conf.get('find_mayavi_figures', False): from mayavi import mlab e = mlab.get_engine() last_matplotlib_fig_num = fig_count + len(figure_list) total_fig_num = last_matplotlib_fig_num + len(e.scenes) mayavi_fig_nums = range(last_matplotlib_fig_num + 1, total_fig_num + 1) for scene, mayavi_fig_num in zip(e.scenes, mayavi_fig_nums): current_fig = image_path.format(mayavi_fig_num) mlab.savefig(current_fig, figure=scene) # make sure the image is not too large scale_image(current_fig, current_fig, 850, 999) figure_list.append(current_fig) mlab.close(all=True) return figure_rst(figure_list, gallery_conf['src_dir']) def figure_rst(figure_list, sources_dir): """Given a list of paths to figures generate the corresponding rst Depending on whether we have one or more figures, we use a single rst call to 'image' or a horizontal list. Parameters ---------- figure_list : list of str Strings are the figures' absolute paths sources_dir : str absolute path of Sphinx documentation sources Returns ------- images_rst : str rst code to embed the images in the document fig_num : int number of figures saved """ figure_paths = [os.path.relpath(figure_path, sources_dir) .replace(os.sep, '/').lstrip('/') for figure_path in figure_list] images_rst = "" if len(figure_paths) == 1: figure_name = figure_paths[0] images_rst = SINGLE_IMAGE % figure_name elif len(figure_paths) > 1: images_rst = HLIST_HEADER for figure_name in figure_paths: images_rst += HLIST_IMAGE_TEMPLATE % figure_name return images_rst, len(figure_list) def scale_image(in_fname, out_fname, max_width, max_height): """Scales an image with the same aspect ratio centered in an image with a given max_width and max_height if in_fname == out_fname the image can only be scaled down """ # local import to avoid testing dependency on PIL: try: from PIL import Image except ImportError: import Image img = Image.open(in_fname) width_in, height_in = img.size scale_w = max_width / float(width_in) scale_h = max_height / float(height_in) if height_in * scale_w <= max_height: scale = scale_w else: scale = scale_h if scale >= 1.0 and in_fname == out_fname: return width_sc = int(round(scale * width_in)) height_sc = int(round(scale * height_in)) # resize the image img.thumbnail((width_sc, height_sc), Image.ANTIALIAS) # insert centered thumb = Image.new('RGB', (max_width, max_height), (255, 255, 255)) pos_insert = ((max_width - width_sc) // 2, (max_height - height_sc) // 2) thumb.paste(img, pos_insert) thumb.save(out_fname) # Use optipng to perform lossless compression on the resized image if # software is installed if os.environ.get('SKLEARN_DOC_OPTIPNG', False): try: subprocess.call(["optipng", "-quiet", "-o", "9", out_fname]) except Exception: logger.warning( 'Install optipng to reduce the size of the generated images') def save_thumbnail(image_path_template, src_file, file_conf, gallery_conf): """Save the thumbnail image""" # read specification of the figure to display as thumbnail from main text thumbnail_number = file_conf.get('thumbnail_number', 1) if not isinstance(thumbnail_number, int): raise TypeError( 'sphinx_gallery_thumbnail_number setting is not a number.') thumbnail_image_path = image_path_template.format(thumbnail_number) thumb_dir = os.path.join(os.path.dirname(thumbnail_image_path), 'thumb') if not os.path.exists(thumb_dir): os.makedirs(thumb_dir) base_image_name = os.path.splitext(os.path.basename(src_file))[0] thumb_file = os.path.join(thumb_dir, 'sphx_glr_%s_thumb.png' % base_image_name) if src_file in gallery_conf['failing_examples']: broken_img = os.path.join(glr_path_static(), 'broken_example.png') scale_image(broken_img, thumb_file, 200, 140) elif os.path.exists(thumbnail_image_path): scale_image(thumbnail_image_path, thumb_file, 400, 280) elif not os.path.exists(thumb_file): # create something to replace the thumbnail default_thumb_file = os.path.join(glr_path_static(), 'no_image.png') default_thumb_file = gallery_conf.get("default_thumb_file", default_thumb_file) scale_image(default_thumb_file, thumb_file, 200, 140) def generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs): """Generate the gallery reStructuredText for an example directory""" with codecs.open(os.path.join(src_dir, 'README.txt'), 'r', encoding='utf-8') as fid: fhindex = fid.read() # Add empty lines to avoid bug in issue #165 fhindex += "\n\n" if not os.path.exists(target_dir): os.makedirs(target_dir) sorted_listdir = [fname for fname in sorted(os.listdir(src_dir)) if fname.endswith('.py')] entries_text = [] computation_times = [] build_target_dir = os.path.relpath(target_dir, gallery_conf['src_dir']) iterator = sphinx_compatibility.status_iterator( sorted_listdir, 'Generating gallery for %s ' % build_target_dir, length=len(sorted_listdir)) for fname in iterator: intro, amount_of_code, time_elapsed = generate_file_rst( fname, target_dir, src_dir, gallery_conf) computation_times.append((time_elapsed, fname)) new_fname = os.path.join(src_dir, fname) this_entry = _thumbnail_div(build_target_dir, fname, intro) + """ .. toctree:: :hidden: /%s\n""" % os.path.join(build_target_dir, fname[:-3]).replace(os.sep, '/') entries_text.append((amount_of_code, this_entry)) if gallery_conf['backreferences_dir']: write_backreferences(seen_backrefs, gallery_conf, target_dir, fname, intro) # sort to have the smallest entries in the beginning entries_text.sort() for _, entry_text in entries_text: fhindex += entry_text # clear at the end of the section fhindex += """.. raw:: html\n
\n\n""" return fhindex, computation_times def handle_exception(exc_info, src_file, block_vars, gallery_conf): etype, exc, tb = exc_info stack = traceback.extract_tb(tb) # Remove our code from traceback: if isinstance(exc, SyntaxError): # Remove one extra level through ast.parse. stack = stack[2:] else: stack = stack[1:] formatted_exception = 'Traceback (most recent call last):\n' + ''.join( traceback.format_list(stack) + traceback.format_exception_only(etype, exc)) logger.warning('%s failed to execute correctly: %s', src_file, formatted_exception) except_rst = codestr2rst(formatted_exception, lang='pytb') # Breaks build on first example error if gallery_conf['abort_on_example_error']: raise # Stores failing file gallery_conf['failing_examples'][src_file] = formatted_exception block_vars['execute_script'] = False return except_rst def execute_code_block(src_file, code_block, lineno, example_globals, block_vars, gallery_conf): """Executes the code block of the example file""" time_elapsed = 0 # If example is not suitable to run, skip executing its blocks if not block_vars['execute_script']: return '', time_elapsed plt.close('all') cwd = os.getcwd() # Redirect output to stdout and orig_stdout = sys.stdout src_file = block_vars['src_file'] # First cd in the original example dir, so that any file # created by the example get created in this directory my_stdout = MixedEncodingStringIO() os.chdir(os.path.dirname(src_file)) sys.stdout = my_stdout try: code_ast = ast.parse(code_block, src_file) ast.increment_lineno(code_ast, lineno - 1) t_start = time() # don't use unicode_literals at the top of this file or you get # nasty errors here on Py2.7 exec(compile(code_ast, src_file, 'exec'), example_globals) time_elapsed = time() - t_start except Exception: sys.stdout = orig_stdout except_rst = handle_exception(sys.exc_info(), src_file, block_vars, gallery_conf) code_output = u"\n{0}\n\n\n\n".format(except_rst) else: sys.stdout = orig_stdout os.chdir(cwd) my_stdout = my_stdout.getvalue().strip().expandtabs() if my_stdout: stdout = CODE_OUTPUT.format(indent(my_stdout, u' ' * 4)) logger.verbose('Output from %s', src_file, color='brown') logger.verbose(my_stdout) else: stdout = '' images_rst, fig_num = save_figures(block_vars['image_path'], block_vars['fig_count'], gallery_conf) block_vars['fig_count'] += fig_num code_output = u"\n{0}\n\n{1}\n\n".format(images_rst, stdout) finally: os.chdir(cwd) sys.stdout = orig_stdout return code_output, time_elapsed def clean_modules(): """Remove "unload" seaborn from the name space After a script is executed it can load a variety of setting that one does not want to influence in other examples in the gallery.""" # Horrible code to 'unload' seaborn, so that it resets # its default when is load # Python does not support unloading of modules # https://bugs.python.org/issue9072 for module in list(sys.modules.keys()): if 'seaborn' in module: del sys.modules[module] # Reset Matplotlib to default plt.rcdefaults() def generate_file_rst(fname, target_dir, src_dir, gallery_conf): """Generate the rst file for a given example. Returns ------- intro: str The introduction of the example amount_of_code : int character count of the corresponding python script in file time_elapsed : float seconds required to run the script """ src_file = os.path.normpath(os.path.join(src_dir, fname)) example_file = os.path.join(target_dir, fname) shutil.copyfile(src_file, example_file) file_conf, script_blocks = split_code_and_text_blocks(src_file) amount_of_code = sum([len(bcontent) for blabel, bcontent, lineno in script_blocks if blabel == 'code']) intro = extract_intro(fname, script_blocks[0][1]) if md5sum_is_current(example_file): return intro, amount_of_code, 0 image_dir = os.path.join(target_dir, 'images') if not os.path.exists(image_dir): os.makedirs(image_dir) base_image_name = os.path.splitext(fname)[0] image_fname = 'sphx_glr_' + base_image_name + '_{0:03}.png' build_image_dir = os.path.relpath(image_dir, gallery_conf['src_dir']) image_path_template = os.path.join(image_dir, image_fname) ref_fname = os.path.relpath(example_file, gallery_conf['src_dir']) ref_fname = ref_fname.replace(os.path.sep, '_') example_rst = """\n\n.. _sphx_glr_{0}:\n\n""".format(ref_fname) filename_pattern = gallery_conf.get('filename_pattern') execute_script = re.search(filename_pattern, src_file) and gallery_conf[ 'plot_gallery'] example_globals = { # A lot of examples contains 'print(__doc__)' for example in # scikit-learn so that running the example prints some useful # information. Because the docstring has been separated from # the code blocks in sphinx-gallery, __doc__ is actually # __builtin__.__doc__ in the execution context and we do not # want to print it '__doc__': '', # Examples may contain if __name__ == '__main__' guards # for in example scikit-learn if the example uses multiprocessing '__name__': '__main__', # Don't ever support __file__: Issues #166 #212 } # A simple example has two blocks: one for the # example introduction/explanation and one for the code is_example_notebook_like = len(script_blocks) > 2 time_elapsed = 0 block_vars = {'execute_script': execute_script, 'fig_count': 0, 'image_path': image_path_template, 'src_file': src_file} argv_orig = sys.argv[:] if block_vars['execute_script']: # We want to run the example without arguments. See # https://github.com/sphinx-gallery/sphinx-gallery/pull/252 # for more details. sys.argv[0] = src_file sys.argv[1:] = [] for blabel, bcontent, lineno in script_blocks: if blabel == 'code': code_output, rtime = execute_code_block(src_file, bcontent, lineno, example_globals, block_vars, gallery_conf) time_elapsed += rtime if not file_conf.get('line_numbers', gallery_conf.get('line_numbers', False)): lineno = None if is_example_notebook_like: example_rst += codestr2rst(bcontent, lineno=lineno) + '\n' example_rst += code_output else: example_rst += code_output if 'sphx-glr-script-out' in code_output: # Add some vertical space after output example_rst += "\n\n|\n\n" example_rst += codestr2rst(bcontent, lineno=lineno) + '\n' else: example_rst += bcontent + '\n\n' sys.argv = argv_orig clean_modules() # Writes md5 checksum if example has build correctly # not failed and was initially meant to run(no-plot shall not cache md5sum) if block_vars['execute_script']: with open(example_file + '.md5', 'w') as file_checksum: file_checksum.write(get_md5sum(example_file)) save_thumbnail(image_path_template, src_file, file_conf, gallery_conf) time_m, time_s = divmod(time_elapsed, 60) example_nb = jupyter_notebook(script_blocks) save_notebook(example_nb, example_file.replace('.py', '.ipynb')) with codecs.open(os.path.join(target_dir, base_image_name + '.rst'), mode='w', encoding='utf-8') as f: example_rst += "**Total running time of the script:**" \ " ({0: .0f} minutes {1: .3f} seconds)\n\n".format( time_m, time_s) example_rst += CODE_DOWNLOAD.format(fname, fname.replace('.py', '.ipynb')) example_rst += SPHX_GLR_SIG f.write(example_rst) if block_vars['execute_script']: logger.debug("%s ran in : %.2g seconds", src_file, time_elapsed) return intro, amount_of_code, time_elapsed