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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,126 +1,126 @@ | ||
| from shutil import copyfile | ||
| import os | ||
| from os.path import join | ||
|
|
||
| try: | ||
| import pypandoc | ||
| except Exception: | ||
| from pypandoc.pandoc_download import download_pandoc | ||
| download_pandoc() | ||
|
|
||
| from OrthoEvol.Tools.logit import LogIt | ||
|
|
||
|
|
||
| class PandocConverter(object): | ||
| """Convert files using the pypandoc wrapper. | ||
| :param infile: path to the input file | ||
| :param outfile_path: output path | ||
| """ | ||
| def __init__(self, infile, outfile_path): | ||
| self.infile = infile | ||
| self.outfile_path = outfile_path | ||
| self.pandoc_log = LogIt().default('pandoc converter', None) | ||
| self.md2rst() | ||
|
|
||
| def md2rst(self): | ||
| infile = str(self.infile) | ||
| filepath, ext = infile.split('.') | ||
| splitfilepath = filepath.split(os.sep) | ||
| initial_filename = splitfilepath[-1] | ||
| final_filename = str(splitfilepath[-2] + initial_filename).lower() | ||
| outfile = join(self.outfile_path, final_filename + ".rst") | ||
| if ext == 'md': | ||
| pypandoc.convert_file(infile, 'rst', outputfile=outfile) | ||
| self.pandoc_log.info('%s.md converted to %s.rst.' % | ||
| (infile, final_filename)) | ||
| else: | ||
| self.pandoc_log.error('%s not supported by this function.' % ext) | ||
|
|
||
|
|
||
| class CreateDocs(object): | ||
| def __init__(self): | ||
| """"Initialize this class.""" | ||
| self.createdocs_log = LogIt().default('create docs', None) | ||
| self.current_dir = os.path.dirname(os.path.realpath(__file__)) | ||
| self._docsdir = os.path.join(self.current_dir, 'docs') | ||
| self.up = '..' | ||
| self.docs_source = os.path.join(self._docsdir, 'source') | ||
| self.main_readme = self._pathtomainreadme() | ||
| self.readme2index() | ||
| self.packagename = 'OrthoEvol' | ||
| self.convertfiles() | ||
|
|
||
| def _append_toc_info(self): | ||
| """Write TOC info to the README.rst when copied as index.rst.""" | ||
| tocinfo = "\nContents\n" \ | ||
| "--------\n"\ | ||
| ".. toctree::\n " \ | ||
| ":maxdepth: 3\n\n " \ | ||
| "datasnakesreadme\n cookiesreadme\n managerreadme\n " \ | ||
| "orthologsreadme\n pipelinereadme\n toolsreadme\n" \ | ||
| "\nIndices and tables\n" \ | ||
| "==================\n" \ | ||
| "* :ref:`genindex`\n" \ | ||
| "* :ref:`modindex`\n" \ | ||
| "* :ref:`search`" | ||
|
|
||
| return tocinfo | ||
|
|
||
| def readme2index(self): | ||
| """Copy README.rst from the top level of your repo to docs source.""" | ||
| indexpath = os.path.join(self.docs_source, 'index.rst') | ||
| copyfile(self.main_readme, indexpath) | ||
| log_msg = '%s copied to %s.' % (self.main_readme, indexpath) | ||
| self.createdocs_log.info(log_msg) | ||
|
|
||
| with open(indexpath, 'a') as index: | ||
| toctree = self._append_toc_info() | ||
| index.write(toctree) | ||
| index.close() | ||
| self.createdocs_log.info('TOC written to index.rst') | ||
|
|
||
| def _pathtomainreadme(self): | ||
| """Return the path to the main README.rst.""" | ||
| os.chdir(self.current_dir) | ||
| os.chdir(self.up) | ||
| readmedir = os.getcwd() | ||
| main_readme = os.path.join(readmedir, 'README.rst') | ||
| os.chdir(self.current_dir) | ||
| return main_readme | ||
|
|
||
| def getfiles2convert(self): | ||
| """Get a list of files to convert.""" | ||
| os.chdir(self.current_dir) | ||
| os.chdir(self.up) | ||
| datasnakesdir = os.path.join(os.getcwd(), self.packagename) | ||
|
|
||
| # Skip these folders when looking for README.md | ||
| # Most of these are folders in the cookiecutter repository | ||
| skip = ['new_basic_project', 'new_repository', 'new_database_repo', | ||
| 'index', 'new_research', 'new_user', 'web', 'data', | ||
| 'new_website', 'config', 'utils'] | ||
|
|
||
| files2convert = [] | ||
|
|
||
| # Use os.walk to walk from the datasnakes/package directory and down | ||
| # to find README.md files in each main submodule. | ||
| for dirname, subdirlist, filelist in os.walk(datasnakesdir): | ||
| subdirlist[:] = [d for d in subdirlist if d not in skip] | ||
| for filename in filelist: | ||
| if filename == 'README.md': | ||
| file = os.path.join(dirname, filename) | ||
| files2convert.append(file) | ||
|
|
||
| return files2convert | ||
|
|
||
| def convertfiles(self): | ||
| """Convert a list of files from .md to .rst.""" | ||
| files2convert = self.getfiles2convert() | ||
| for file2convert in files2convert: | ||
| PandocConverter(file2convert, self.docs_source) | ||
| self.createdocs_log.info('Your docs were converted to .rst format.') | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| CreateDocs() | ||
| #from shutil import copyfile | ||
| #import os | ||
| #from os.path import join | ||
| # | ||
| #try: | ||
| # import pypandoc | ||
| #except Exception: | ||
| # from pypandoc.pandoc_download import download_pandoc | ||
| # download_pandoc() | ||
| # | ||
| #from OrthoEvol.Tools.logit import LogIt | ||
| # | ||
| # | ||
| #class PandocConverter(object): | ||
| # """Convert files using the pypandoc wrapper. | ||
| # | ||
| # :param infile: path to the input file | ||
| # :param outfile_path: output path | ||
| # """ | ||
| # def __init__(self, infile, outfile_path): | ||
| # self.infile = infile | ||
| # self.outfile_path = outfile_path | ||
| # self.pandoc_log = LogIt().default('pandoc converter', None) | ||
| # self.md2rst() | ||
| # | ||
| # def md2rst(self): | ||
| # infile = str(self.infile) | ||
| # filepath, ext = infile.split('.') | ||
| # splitfilepath = filepath.split(os.sep) | ||
| # initial_filename = splitfilepath[-1] | ||
| # final_filename = str(splitfilepath[-2] + initial_filename).lower() | ||
| # outfile = join(self.outfile_path, final_filename + ".rst") | ||
| # if ext == 'md': | ||
| # pypandoc.convert_file(infile, 'rst', outputfile=outfile) | ||
| # self.pandoc_log.info('%s.md converted to %s.rst.' % | ||
| # (infile, final_filename)) | ||
| # else: | ||
| # self.pandoc_log.error('%s not supported by this function.' % ext) | ||
| # | ||
| # | ||
| #class CreateDocs(object): | ||
| # def __init__(self): | ||
| # """"Initialize this class.""" | ||
| # self.createdocs_log = LogIt().default('create docs', None) | ||
| # self.current_dir = os.path.dirname(os.path.realpath(__file__)) | ||
| # self._docsdir = os.path.join(self.current_dir, 'docs') | ||
| # self.up = '..' | ||
| # self.docs_source = os.path.join(self._docsdir, 'source') | ||
| # self.main_readme = self._pathtomainreadme() | ||
| # self.readme2index() | ||
| # self.packagename = 'OrthoEvol' | ||
| # self.convertfiles() | ||
| # | ||
| # def _append_toc_info(self): | ||
| # """Write TOC info to the README.rst when copied as index.rst.""" | ||
| # tocinfo = "\nContents\n" \ | ||
| # "--------\n"\ | ||
| # ".. toctree::\n " \ | ||
| # ":maxdepth: 3\n\n " \ | ||
| # "datasnakesreadme\n cookiesreadme\n managerreadme\n " \ | ||
| # "orthologsreadme\n pipelinereadme\n toolsreadme\n" \ | ||
| # "\nIndices and tables\n" \ | ||
| # "==================\n" \ | ||
| # "* :ref:`genindex`\n" \ | ||
| # "* :ref:`modindex`\n" \ | ||
| # "* :ref:`search`" | ||
| # | ||
| # return tocinfo | ||
| # | ||
| # def readme2index(self): | ||
| # """Copy README.rst from the top level of your repo to docs source.""" | ||
| # indexpath = os.path.join(self.docs_source, 'index.rst') | ||
| # copyfile(self.main_readme, indexpath) | ||
| # log_msg = '%s copied to %s.' % (self.main_readme, indexpath) | ||
| # self.createdocs_log.info(log_msg) | ||
| # | ||
| # with open(indexpath, 'a') as index: | ||
| # toctree = self._append_toc_info() | ||
| # index.write(toctree) | ||
| # index.close() | ||
| # self.createdocs_log.info('TOC written to index.rst') | ||
| # | ||
| # def _pathtomainreadme(self): | ||
| # """Return the path to the main README.rst.""" | ||
| # os.chdir(self.current_dir) | ||
| # os.chdir(self.up) | ||
| # readmedir = os.getcwd() | ||
| # main_readme = os.path.join(readmedir, 'README.rst') | ||
| # os.chdir(self.current_dir) | ||
| # return main_readme | ||
| # | ||
| # def getfiles2convert(self): | ||
| # """Get a list of files to convert.""" | ||
| # os.chdir(self.current_dir) | ||
| # os.chdir(self.up) | ||
| # datasnakesdir = os.path.join(os.getcwd(), self.packagename) | ||
| # | ||
| # # Skip these folders when looking for README.md | ||
| # # Most of these are folders in the cookiecutter repository | ||
| # skip = ['new_basic_project', 'new_repository', 'new_database_repo', | ||
| # 'index', 'new_research', 'new_user', 'web', 'data', | ||
| # 'new_website', 'config', 'utils'] | ||
| # | ||
| # files2convert = [] | ||
| # | ||
| # # Use os.walk to walk from the datasnakes/package directory and down | ||
| # # to find README.md files in each main submodule. | ||
| # for dirname, subdirlist, filelist in os.walk(datasnakesdir): | ||
| # subdirlist[:] = [d for d in subdirlist if d not in skip] | ||
| # for filename in filelist: | ||
| # if filename == 'README.md': | ||
| # file = os.path.join(dirname, filename) | ||
| # files2convert.append(file) | ||
| # | ||
| # return files2convert | ||
| # | ||
| # def convertfiles(self): | ||
| # """Convert a list of files from .md to .rst.""" | ||
| # files2convert = self.getfiles2convert() | ||
| # for file2convert in files2convert: | ||
| # PandocConverter(file2convert, self.docs_source) | ||
| # self.createdocs_log.info('Your docs were converted to .rst format.') | ||
| # | ||
| # | ||
| #if __name__ == "__main__": | ||
| # CreateDocs() |