Sourcery Starbot ⭐ refactored sidphbot/Auto-Research #3
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SourceryAI
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Dec 10, 2023
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| st.sidebar.image(Image.open('logo_landscape.png'), use_column_width = 'always') | ||
| st.title('Auto-Research') | ||
| st.write('#### A no-code utility to generate a detailed well-cited survey with topic clustered sections' | ||
| '(draft paper format) and other interesting artifacts from a single research query or a curated set of papers(arxiv ids).') | ||
| st.write('##### Data Provider: arXiv Open Archive Initiative OAI') | ||
| st.write('##### GitHub: https://github.com/sidphbot/Auto-Research') | ||
| download_placeholder = st.container() | ||
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| with st.sidebar.form(key="survey_keywords_form"): | ||
| session_data = sp.pydantic_input(key="keywords_input_model", model=KeywordsModel) | ||
| st.write('or') | ||
| session_data.update(sp.pydantic_input(key="arxiv_ids_input_model", model=ArxivIDsModel)) | ||
| submit = st.form_submit_button(label="Submit") | ||
| st.sidebar.write('#### execution log:') | ||
|
|
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| run_kwargs = {'surveyor':get_surveyor_instance(_print_fn=st.sidebar.write, _survey_print_fn=st.write), | ||
| 'download_placeholder':download_placeholder} | ||
| if submit: | ||
| if session_data['research_keywords'] != '': | ||
| run_kwargs.update({'research_keywords':session_data['research_keywords'], | ||
| 'max_search':session_data['max_search'], | ||
| 'num_papers':session_data['num_papers']}) | ||
| elif session_data['arxiv_ids'] != '': | ||
| run_kwargs.update({'arxiv_ids':[id.strip() for id in session_data['arxiv_ids'].split(',')]}) | ||
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|
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| run_survey(**run_kwargs) | ||
| st.sidebar.image(Image.open('logo_landscape.png'), use_column_width = 'always') | ||
| st.title('Auto-Research') | ||
| st.write('#### A no-code utility to generate a detailed well-cited survey with topic clustered sections' | ||
| '(draft paper format) and other interesting artifacts from a single research query or a curated set of papers(arxiv ids).') | ||
| st.write('##### Data Provider: arXiv Open Archive Initiative OAI') | ||
| st.write('##### GitHub: https://github.com/sidphbot/Auto-Research') | ||
| download_placeholder = st.container() | ||
|
|
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| with st.sidebar.form(key="survey_keywords_form"): | ||
| session_data = sp.pydantic_input(key="keywords_input_model", model=KeywordsModel) | ||
| st.write('or') | ||
| session_data.update(sp.pydantic_input(key="arxiv_ids_input_model", model=ArxivIDsModel)) | ||
| submit = st.form_submit_button(label="Submit") | ||
| st.sidebar.write('#### execution log:') | ||
|
|
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| run_kwargs = {'surveyor':get_surveyor_instance(_print_fn=st.sidebar.write, _survey_print_fn=st.write), | ||
| 'download_placeholder':download_placeholder} | ||
| if submit: | ||
| if session_data['research_keywords'] != '': | ||
| run_kwargs.update({'research_keywords':session_data['research_keywords'], | ||
| 'max_search':session_data['max_search'], | ||
| 'num_papers':session_data['num_papers']}) | ||
| elif session_data['arxiv_ids'] != '': | ||
| run_kwargs['arxiv_ids'] = [ | ||
| id.strip() for id in session_data['arxiv_ids'].split(',') | ||
| ] | ||
|
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| run_survey(**run_kwargs) |
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Lines 76-101 refactored with the following changes:
- Add single value to dictionary directly rather than using update() (
simplify-dictionary-update)
| author_entry = [s, match.group(1), ''] | ||
| elif mtype == 'name-prefix-name': | ||
| s = '{} {}'.format(match.group(2), match.group(3)) | ||
| s = f'{match.group(2)} {match.group(3)}' |
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Function _parse_author_affil_split refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| else: | ||
| parts.append(pt) | ||
| last = pt | ||
| parts.append(pt) | ||
| last = pt |
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Function _remove_double_commas refactored with the following changes:
- Remove unnecessary else after guard condition (
remove-unnecessary-else)
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| def _collaboration_at_start(names: List[str]) \ | ||
| -> Tuple[List[str], List[List[str]], int]: | ||
| def _collaboration_at_start(names: List[str]) -> Tuple[List[str], List[List[str]], int]: | ||
| """Perform special handling of collaboration at start.""" | ||
| author_list = [] | ||
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| back_propagate_affiliations_to = 0 | ||
| while len(names) > 0: | ||
| while names: |
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Function _collaboration_at_start refactored with the following changes:
- Simplify sequence length comparison (
simplify-len-comparison) - Replace multiple comparisons of same variable with
inoperator (merge-comparisons)
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| def _enum_collaboration_at_end(author_line: str)->Dict: | ||
| def _enum_collaboration_at_end(author_line: str) -> Dict: |
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Function _enum_collaboration_at_end refactored with the following changes:
- Use named expression to simplify assignment and conditional (
use-named-expression)
This removes the following comments ( why? ):
# Now expect `1) affil1 ', discard if no match
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| log.info('Searching "{}"...'.format(globber)) | ||
| log.info('Found: {} pdfs'.format(len(pdffiles))) | ||
| log.info(f'Searching "{globber}"...') | ||
| log.info(f'Found: {len(pdffiles)} pdfs') |
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Function convert_directory refactored with the following changes:
- Replace call to format with f-string [×3] (
use-fstring-for-formatting)
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| log.info('Searching "{}"...'.format(globber)) | ||
| log.info('Found: {} pdfs'.format(len(pdffiles))) | ||
| log.info(f'Searching "{globber}"...') | ||
| log.info(f'Found: {len(pdffiles)} pdfs') |
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Function convert_directory_parallel refactored with the following changes:
- Replace call to format with f-string [×2] (
use-fstring-for-formatting)
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| log.error('File conversion failed for {}: {}'.format(pdffile, e)) | ||
| log.error(f'File conversion failed for {pdffile}: {e}') |
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Function convert_safe refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| raise RuntimeError('No such path: %s' % path) | ||
| raise RuntimeError(f'No such path: {path}') |
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Function convert refactored with the following changes:
- Replace interpolated string formatting with f-string (
replace-interpolation-with-fstring)
| if 'txt' in f: | ||
| out.append(os.path.join(root, f)) | ||
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| out.extend(os.path.join(root, f) for f in files if 'txt' in f) |
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Function all_articles refactored with the following changes:
- Replace a for append loop with list extend (
for-append-to-extend)
SourceryAI
commented
Dec 10, 2023
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| log.info('Completed {} articles'.format(i)) | ||
| log.info(f'Completed {i} articles') | ||
| try: | ||
| refs = extract_references(article) | ||
| cites[path_to_id(article)] = refs | ||
| except: | ||
| log.error("Error in {}".format(article)) | ||
| log.error(f"Error in {article}") |
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Function citation_list_inner refactored with the following changes:
- Replace call to format with f-string [×2] (
use-fstring-for-formatting)
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| log.info('Calculating citation network for {} articles'.format(len(articles))) | ||
| log.info(f'Calculating citation network for {len(articles)} articles') |
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Function citation_list_parallel refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| log.info('Saving to "{}"'.format(filename)) | ||
| log.info(f'Saving to "{filename}"') |
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Function save_to_default_location refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| if response.status_code == 503: | ||
| secs = int(response.headers.get('Retry-After', 20)) * 1.5 | ||
| log.info('Requested to wait, waiting {} seconds until retry...'.format(secs)) | ||
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| time.sleep(secs) | ||
| return get_list_record_chunk(resumptionToken=resumptionToken) | ||
| else: | ||
| if response.status_code != 503: | ||
| raise Exception( | ||
| 'Unknown error in HTTP request {}, status code: {}'.format( | ||
| response.url, response.status_code | ||
| ) | ||
| f'Unknown error in HTTP request {response.url}, status code: {response.status_code}' | ||
| ) | ||
| secs = int(response.headers.get('Retry-After', 20)) * 1.5 | ||
| log.info(f'Requested to wait, waiting {secs} seconds until retry...') | ||
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| time.sleep(secs) | ||
| return get_list_record_chunk(resumptionToken=resumptionToken) |
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Function get_list_record_chunk refactored with the following changes:
- Swap if/else branches (
swap-if-else-branches) - Remove unnecessary else after guard condition (
remove-unnecessary-else) - Replace call to format with f-string [×2] (
use-fstring-for-formatting)
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| item = elm.find('arXiv:{}'.format(name), OAI_XML_NAMESPACES) | ||
| item = elm.find(f'arXiv:{name}', OAI_XML_NAMESPACES) |
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Function _record_element_text refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| logger.info('Requesting "{}" (costs money!)'.format(filename)) | ||
| logger.info(f'Requesting "{filename}" (costs money!)') | ||
| request = requests.get(url, stream=True) | ||
| response_iter = request.iter_content(chunk_size=chunk_size) | ||
| logger.info("\t Writing {}".format(outfile)) | ||
| logger.info(f"\t Writing {outfile}") | ||
| with gzip.open(outfile, 'wb') as fout: | ||
| for i, chunk in enumerate(response_iter): | ||
| for chunk in response_iter: | ||
| fout.write(chunk) | ||
| md5.update(chunk) | ||
| else: | ||
| logger.info('Requesting "{}" (free!)'.format(filename)) | ||
| logger.info("\t Writing {}".format(outfile)) | ||
| logger.info(f'Requesting "{filename}" (free!)') | ||
| logger.info(f"\t Writing {outfile}") |
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Function download_file refactored with the following changes:
- Replace call to format with f-string [×4] (
use-fstring-for-formatting) - Remove unnecessary calls to
enumeratewhen the index is not used (remove-unused-enumerate)
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| def _tar_to_filename(filename): | ||
| return os.path.join(DIR_PDFTARS, os.path.basename(filename)) + '.gz' | ||
| return f'{os.path.join(DIR_PDFTARS, os.path.basename(filename))}.gz' |
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Function _tar_to_filename refactored with the following changes:
- Use f-string instead of string concatenation (
use-fstring-for-concatenation)
| msg = "MD5 '{}' does not match expected '{}' for file '{}'".format( | ||
| md5_downloaded, md5_expected, filename | ||
| ) | ||
| msg = f"MD5 '{md5_downloaded}' does not match expected '{md5_expected}' for file '{filename}'" |
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Function download_check_tarfile refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| if dryrun: | ||
| logger.info(cmd) | ||
| return 0 | ||
| else: | ||
| if not dryrun: | ||
| return subprocess.check_call( | ||
| shlex.split(cmd), stderr=None if debug else open(os.devnull, 'w') | ||
| ) | ||
| logger.info(cmd) | ||
| return 0 |
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Function call refactored with the following changes:
- Swap if/else branches (
swap-if-else-branches) - Remove unnecessary else after guard condition (
remove-unnecessary-else)
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| msg = 'Tarfile from manifest not found {}, skipping...'.format(outname) | ||
| msg = f'Tarfile from manifest not found {outname}, skipping...' |
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Function process_tarfile_inner refactored with the following changes:
- Replace call to format with f-string [×5] (
use-fstring-for-formatting)
SourceryAI
commented
Dec 10, 2023
| return | ||
|
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| logger.info('Processing tar "{}" ...'.format(filename)) | ||
| logger.info(f'Processing tar "{filename}" ...') |
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Function process_tarfile refactored with the following changes:
- Replace call to format with f-string [×2] (
use-fstring-for-formatting)
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| logger.info("Indexing {}...".format(name)) | ||
| logger.info(f"Indexing {name}...") | ||
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| tarname = os.path.join(DIR_PDFTARS, os.path.basename(name))+'.gz' | ||
| tarname = f'{os.path.join(DIR_PDFTARS, os.path.basename(name))}.gz' |
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Function generate_tarfile_indices refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting) - Use f-string instead of string concatenation (
use-fstring-for-concatenation)
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| logger.info("Checking {}...".format(tar)) | ||
| logger.info(f"Checking {tar}...") |
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Function check_missing_txt_files refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
|
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| for tar, names in sort: | ||
| logger.info("Running {} ({} to do)...".format(tar, len(names))) | ||
| logger.info(f"Running {tar} ({len(names)} to do)...") |
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Function rerun_missing refactored with the following changes:
- Replace identity comprehension with call to collection constructor (
identity-comprehension) - Replace call to format with f-string (
use-fstring-for-formatting)
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| return '{}/{}.pdf'.format(ym, n) | ||
| return f'{ym}/{n}.pdf' | ||
| else: | ||
| ym = n.split('/')[1][:4] | ||
| return '{}/{}.pdf'.format(ym, n.replace('/', '')) | ||
| return f"{ym}/{n.replace('/', '')}.pdf" |
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Function id_to_tarpdf refactored with the following changes:
- Replace call to format with f-string [×2] (
use-fstring-for-formatting)
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| joblib.dump(papers, dump_dir + 'papers_selected_pdf_route.dmp') | ||
| joblib.dump(papers, f'{dump_dir}papers_selected_pdf_route.dmp') |
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Function Surveyor.fetch_papers refactored with the following changes:
- Use f-string instead of string concatenation (
use-fstring-for-concatenation)
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| file = open(filename, 'w+') | ||
| if query is None: | ||
| query = 'Internal(existing) research' | ||
| self.survey_print_fn("#### Generated_survey:") | ||
| file.write("----------------------------------------------------------------------") | ||
| file.write("Title: A survey on " + query) | ||
| self.survey_print_fn("") | ||
| self.survey_print_fn("----------------------------------------------------------------------") | ||
| self.survey_print_fn("Title: A survey on " + query) | ||
| file.write("Author: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| self.survey_print_fn("Author: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| file.write("Dev: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| self.survey_print_fn("Dev: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| file.write("Disclaimer: This survey is intended to be a research starter. This Survey is Machine-Summarized, "+ | ||
| "\nhence some sentences might be wrangled or grammatically incorrect. However all sentences are "+ | ||
| "\nmined with proper citations. As All of the text is practically quoted texted, hence to "+ | ||
| "\nimprove visibility, all the papers are duly cited in the Bibiliography section. as bibtex "+ | ||
| "\nentries(only to avoid LaTex overhead). ") | ||
| self.survey_print_fn("Disclaimer: This survey is intended to be a research starter. This Survey is Machine-Summarized, "+ | ||
| "\nhence some sentences might be wrangled or grammatically incorrect. However all sentences are "+ | ||
| "\nmined with proper citations. As All of the text is practically quoted texted, hence to "+ | ||
| "\nimprove visibility, all the papers are duly cited in the Bibiliography section. as bibtex "+ | ||
| "\nentries(only to avoid LaTex overhead). ") | ||
| file.write("----------------------------------------------------------------------") | ||
| self.survey_print_fn("----------------------------------------------------------------------") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write('ABSTRACT') | ||
| self.survey_print_fn('ABSTRACT') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(research_sections['abstract']) | ||
| self.survey_print_fn(research_sections['abstract']) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write('INTRODUCTION') | ||
| self.survey_print_fn('INTRODUCTION') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(research_sections['introduction']) | ||
| self.survey_print_fn(research_sections['introduction']) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| for k, v in research_sections.items(): | ||
| if k not in ['abstract', 'introduction', 'conclusion']: | ||
| file.write(k.upper()) | ||
| self.survey_print_fn(k.upper()) | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(v) | ||
| self.survey_print_fn(v) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write('CONCLUSION') | ||
| self.survey_print_fn('CONCLUSION') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(research_sections['conclusion']) | ||
| self.survey_print_fn(research_sections['conclusion']) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
|
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| file.write('REFERENCES') | ||
| self.survey_print_fn('REFERENCES') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| for entry in bibentries: | ||
| file.write(entry) | ||
| self.survey_print_fn(entry) | ||
| with open(filename, 'w+') as file: | ||
| if query is None: | ||
| query = 'Internal(existing) research' | ||
| self.survey_print_fn("#### Generated_survey:") | ||
| file.write("----------------------------------------------------------------------") | ||
| file.write(f"Title: A survey on {query}") | ||
| self.survey_print_fn("") | ||
| self.survey_print_fn("----------------------------------------------------------------------") | ||
| self.survey_print_fn(f"Title: A survey on {query}") | ||
| file.write("Author: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| self.survey_print_fn("Author: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| file.write("Dev: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| self.survey_print_fn("Dev: Auto-Research (github.com/sidphbot/Auto-Research)") | ||
| file.write("Disclaimer: This survey is intended to be a research starter. This Survey is Machine-Summarized, "+ | ||
| "\nhence some sentences might be wrangled or grammatically incorrect. However all sentences are "+ | ||
| "\nmined with proper citations. As All of the text is practically quoted texted, hence to "+ | ||
| "\nimprove visibility, all the papers are duly cited in the Bibiliography section. as bibtex "+ | ||
| "\nentries(only to avoid LaTex overhead). ") | ||
| self.survey_print_fn("Disclaimer: This survey is intended to be a research starter. This Survey is Machine-Summarized, "+ | ||
| "\nhence some sentences might be wrangled or grammatically incorrect. However all sentences are "+ | ||
| "\nmined with proper citations. As All of the text is practically quoted texted, hence to "+ | ||
| "\nimprove visibility, all the papers are duly cited in the Bibiliography section. as bibtex "+ | ||
| "\nentries(only to avoid LaTex overhead). ") | ||
| file.write("----------------------------------------------------------------------") | ||
| self.survey_print_fn("----------------------------------------------------------------------") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write('ABSTRACT') | ||
| self.survey_print_fn('ABSTRACT') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(research_sections['abstract']) | ||
| self.survey_print_fn(research_sections['abstract']) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write('INTRODUCTION') | ||
| self.survey_print_fn('INTRODUCTION') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(research_sections['introduction']) | ||
| self.survey_print_fn(research_sections['introduction']) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| for k, v in research_sections.items(): | ||
| if k not in ['abstract', 'introduction', 'conclusion']: | ||
| file.write(k.upper()) | ||
| self.survey_print_fn(k.upper()) | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(v) | ||
| self.survey_print_fn(v) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write('CONCLUSION') | ||
| self.survey_print_fn('CONCLUSION') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| file.write(research_sections['conclusion']) | ||
| self.survey_print_fn(research_sections['conclusion']) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| self.survey_print_fn("========================XXX=========================") | ||
| file.write("========================XXX=========================") | ||
| file.close() | ||
|
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| file.write('REFERENCES') | ||
| self.survey_print_fn('REFERENCES') | ||
| self.survey_print_fn("=================================================") | ||
| file.write("=================================================") | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| for entry in bibentries: | ||
| file.write(entry) | ||
| self.survey_print_fn(entry) | ||
| file.write("") | ||
| self.survey_print_fn("") | ||
| self.survey_print_fn("========================XXX=========================") | ||
| file.write("========================XXX=========================") |
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Function Surveyor.build_doc refactored with the following changes:
- Use
withwhen opening file to ensure closure (ensure-file-closed) - Use f-string instead of string concatenation [×2] (
use-fstring-for-concatenation)
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| res = set([str(sent) for sent in list(res.sents)]) | ||
| summtext = ''.join([line for line in res]) | ||
| res = {str(sent) for sent in list(res.sents)} | ||
| summtext = ''.join(list(res)) |
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Function Surveyor.build_basic_blocks refactored with the following changes:
- Replace list(), dict() or set() with comprehension (
collection-builtin-to-comprehension) - Replace unneeded comprehension with generator (
comprehension-to-generator) - Replace identity comprehension with call to collection constructor (
identity-comprehension)
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| res = set([str(sent) for sent in list(res.sents)]) | ||
| summtext = ''.join([line for line in res]) | ||
| #self.print_fn("abstractive summary type:" + str(type(summary))) | ||
| return summtext | ||
| res = {str(sent) for sent in list(res.sents)} | ||
| return ''.join(list(res)) |
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Function Surveyor.abstractive_summary refactored with the following changes:
- Replace list(), dict() or set() with comprehension (
collection-builtin-to-comprehension) - Replace unneeded comprehension with generator (
comprehension-to-generator) - Inline variable that is immediately returned (
inline-immediately-returned-variable) - Replace identity comprehension with call to collection constructor (
identity-comprehension)
This removes the following comments ( why? ):
#self.print_fn("abstractive summary type:" + str(type(summary)))
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| abstext = k + '. ' + v.replace('\n', ' ') | ||
| abstext = f'{k}. ' + v.replace('\n', ' ') |
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Function Surveyor.get_corpus_lines refactored with the following changes:
- Use f-string instead of string concatenation (
use-fstring-for-concatenation)
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