Merge pull request #59 from dvklopfenstein/dvk

Pytest; get_indexs fnc; summarize_papers; Copyright cleanup; Add QUERY to summary prints

.github/workflows/build.yml

@@ -29,5 +29,5 @@ jobs:
 
       - name: Test with pytest
         run: |
-          pip install pytest pytest-cov
+          pip install pytest coverage
           make pytest

CITATION.cff

@@ -1,5 +1,5 @@
 cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
+message: "If you use this project, please cite it as below."
 authors:
 - family-names: "Klopfenstein"
   given-names: "DV"
@@ -11,6 +11,7 @@ title: "pmidcite"
 version: 0.0.18
 doi: 10.5281/zenodo.5172712
 keywords: 
+  - "Google Scholar"
   - CitedBy
   - PubMed
   - PMID
@@ -19,6 +20,7 @@ keywords:
   - "forward snowball"
   - "backward snowball"
   - "literature review"
+  - "literature search"
   - "citation downloader"
 contact:
   - email: dvklopfenstein@protonmail.com
@@ -36,22 +38,28 @@ preferred-citation:
     given-names: "Will"
   doi: "10.1002/jrsm.1456"
   journal: "Research Synthesis Methods"
+  publisher: "Wiley"
   month: 3
   start: 126 # First page number
   end: 135 # Last page number
   title: "Commentary to Gusenbauer and Haddaway 2020: Evaluating retrieval qualities of Google Scholar and PubMed"
   issue: 2
   volume: 12
   year: 2021
+  pmid:33031632
+  eprint:33031632
+  eprinttype:pubmed
   keywords: 
     - CitedBy
     - PubMed
     - PMID
+    - "Google Scholar"
     - "forward citation"
     - "backward citation"
     - "forward snowball"
     - "backward snowball"
     - "literature review"
+    - "literature search"
     - "citation downloader"
   contact:
     - email: dvklopfenstein@protonmail.com

doc/example_cfg/.pmidciterc

@@ -49,10 +49,10 @@ tool = scripts
 #
 #  # PMID 33031632 is a new (-1) research (R) paper discussing humans (H)
 #  # with 2 citations and 18 references that is authored by 2 (au[02]) people with
-#  # the first author being DV Klopfenstein.
+#  # the first author being DV Klopfenstein, PhD.
 #  #
 #  $ icite 33031632
-#  TOP 33031632 R. H....  -1 i 2021     2  0  18 au[02](D V Klopfenstein) Commentary ...
+#  TOP 33031632 R. H....  -1 i 2021     2  0  18 au[02](D V Klopfenstein, PhD) Commentary ...
 #
 # Thousands of NIH citation files may be downloaded for a literature search
 # on a single subject. It is not necessary to save the NIH citation data and I

makefile

@@ -45,7 +45,8 @@ pylint:
 
 pytest:
 	make clobber_tmp
-	python3 --version; python3 -m pytest --cov=pmidcite -v src/tests | tee pytest.log
+	coverage run -m pytest -v src/tests --log-file=pytest.log
+	#python3 --version; python3 -m pytest --cov=pmidcite -v src/tests | tee pytest.log
 	#### python3 -m pytest $(TESTS)
 
 ver:
@@ -76,7 +77,7 @@ vim_md:
 build:
 	# python3 -m pip install -U pip
 	# python3 -m pip install --user --upgrade setuptools wheel
-	make clean_dist
+	make clean_build
 	$(PYTHON) setup.py sdist
 	$(PYTHON) setup.py bdist_wheel --universal
 	ls -lh dist
@@ -95,7 +96,7 @@ upgrade:
 	$(PYTHON) -m pip install --upgrade setuptools wheel twine
 	$(PYTHON) -m pip install --upgrade distutils
 
-clean_dist:
+clean_build:
 	rm -rf dist build 
 
 pyc:
@@ -121,11 +122,11 @@ clean:
 	rm -rf notebooks/icite
 	rm -rf src/tests/icite
 	make clobber_tmp
-	make clean_dist
+	make clean_build
 
 clobber_tmp:
 	rm -rf ./icite
 	rm -rf ./src/tests/icite
 
 clobber:
-	make -f makefile clobber_tmp clean_dist
+	make -f makefile clobber_tmp clean_build

setup.py

@@ -51,7 +51,7 @@ def get_long_description():
     entry_points={
         'console_scripts':[
             'icite=pmidcite.scripts.icite:main',
-            'summarize_papers=pmidcite.scripts.icite:summarize_papers',
+            'sumpaps=pmidcite.scripts.summarize_papers:main',
         ],
     },
     # https://pypi.org/classifiers/

src/bin/dnld_pmids.py

@@ -32,7 +32,7 @@ def main():
     #   $ src/bin/dnld_pmids.py -2
     #
     obj = PubMedQueryToICite(force_dnld=True)
-    dnld_idx = obj.get_index(sys.argv)
+    dnld_idx = obj.get_index(sys.argv, queries)
     obj.run(queries, dnld_idx)
 
 

src/bin/icite.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 """Given a PubMed ID (PMID), return a list of citing publications"""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved."
-__author__ = "DV Klopfenstein, PhD, PhD"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 from pmidcite.cli.icite import NIHiCiteCli  # get_argparser
 from pmidcite.cfg import get_cfgparser
@@ -16,4 +16,4 @@ def main():
 if __name__ == '__main__':
     main()
 
-# Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved.
+# Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved.

src/bin/summarize_papers.py

@@ -1,18 +1,13 @@
 #!/usr/bin/env python3
 """Summarize NIH citation data for requested papers from the commandline or in files"""
 
-__copyright__ = "Copyright (C) 2022-present, DV Klopfenstein, PhD, PhD. All rights reserved."
-__author__ = "DV Klopfenstein, PhD, PhD"
+__copyright__ = "Copyright (C) 2022-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
-from pmidcite.cli.summarize_papers import SummarizePapersCli # get_argparser
-from pmidcite.cfg import get_cfgparser
+from pmidcite.scripts.summarize_papers import main
 
 
-def main():
-    """Summarize NIH citation data for requested papers from the commandline or in files"""
-    SummarizePapersCli(get_cfgparser(prt=None)).cli()
-
 if __name__ == '__main__':
     main()
 
-# Copyright (C) 2022-present, DV Klopfenstein, PhD, PhD. All rights reserved.
+# Copyright (C) 2022-present, DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/__init__.py

@@ -1,7 +1,7 @@
 """Code to access NIH's iCite API"""
 
-__copyright__ = 'Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved'
-__author__ = 'DV Klopfenstein, PhD, PhD'
+__copyright__ = 'Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved'
+__author__ = 'DV Klopfenstein, PhD.'
 
 
-# Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved
+# Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved

src/pmidcite/__version__.py

@@ -1,7 +1,7 @@
 """Version of pmidcite project"""
 
-__copyright__ = 'Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved'
-__author__ = ' DV Klopfenstein, PhD, PhD'
+__copyright__ = 'Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved'
+__author__ = ' DV Klopfenstein, PhD.
 __version__ = '0.0.45'
 
-# Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved
+# Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved

src/pmidcite/cfg.py

@@ -1,7 +1,7 @@
 """Manage pmidcite Configuration"""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved."
-__author__ = "DV Klopfenstein, PhD, PhD"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 from os import environ
 from os import getcwd
@@ -229,4 +229,4 @@ def _init_cfgfilename(self, prt=None):
 
 
 
-# Copyright (C) 2019-present DV Klopfenstein, PhD, PhD. All rights reserved.
+# Copyright (C) 2019-present DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/citation.py

@@ -0,0 +1,41 @@
+"""Cite the pmidcite project"""
+
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
+
+
+CITATION = """
+If you use pmidcite in your research or literature search,
+please cite the publication in any papers, pre-prints or reports.
+The proper citation information for pmidcite appears below.
+
+Reference:
+==========
+
+Klopfenstein, D.V., & Dampier, W. (2021).
+Commentary to Gusenbauer and Haddaway 2020: Evaluating retrieval qualities of Google Scholar and PubMed.
+Research Synthesis Methods, 12(2), 126–135. https://doi.org/10.1002/jrsm.1456
+
+
+bibtex:
+=======
+
+@article{Klopfenstein_2021,
+  author = {Klopfenstein, DV and Dampier, Will},
+  doi = {10.1002/jrsm.1456},
+  pmid = {33031632},
+  eprint = {33031632},
+  eprinttype = {pubmed},
+  url = {https://onlinelibrary.wiley.com/doi/10.1002/jrsm.1456}
+  journal = {Research Synthesis Methods},
+  publisher = {{Wiley}},
+  month = {mar},
+  number = {2},
+  pages = {126--135},
+  title = {{Commentary to Gusenbauer and Haddaway 2020: Evaluating retrieval qualities of Google Scholar and PubMed}},
+  volume = {12},
+  year = {2021}
+}
+"""
+
+# Copyright (C) 2019-present DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/cli/dnldpubmed.py

@@ -1,7 +1,7 @@
 """Given PMIDs, download PubMed entries into a text file"""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved."
-__author__ = "DV Klopfenstein, PhD, PhD"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 import argparse
 
@@ -65,4 +65,4 @@ def _get_pmids(args, argparser):
         return pmids
 
 
-# Copyright (C) 2019-present DV Klopfenstein, PhD, PhD. All rights reserved.
+# Copyright (C) 2019-present DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/cli/icite.py

@@ -1,12 +1,14 @@
 """Manage args for NIH iCite run for one PubMed ID (PMID)"""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD, PhD. All rights reserved."
-__author__ = "DV Klopfenstein, PhD, PhD"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 from sys import stdout
-import argparse
+from sys import exit as sys_exit
+from argparse import ArgumentParser
 
 from pmidcite.eutils.cmds.pubmed import PubMed
+from pmidcite.citation import CITATION
 from pmidcite.cfgini import prt_rcfile
 from pmidcite.cli.utils import get_outfile
 from pmidcite.cli.utils import get_pmids
@@ -29,7 +31,7 @@ def __init__(self, cfg):
 
     def get_argparser(self):
         """Argument parser for Python wrapper of NIH's iCite given PubMed IDs"""
-        parser = argparse.ArgumentParser(
+        parser = ArgumentParser(
             description="Run NIH's iCite given PubMed IDs",
             add_help=False)
         cfg = self.cfg
@@ -42,6 +44,9 @@ def get_argparser(self):
         parser.add_argument(
             '-h', '--help', action='store_true',
             help='print this help message and exit (also --help)')
+        parser.add_argument(
+            '--cite', action='store_true',
+            help='publication citation for the pmidcite project')
         parser.add_argument(
             'pmids', metavar='PMID', type=int, nargs='*',
             help='PubMed IDs (PMIDs)')
@@ -91,17 +96,15 @@ def get_argparser(self):
             help='Download PubMed entry containing title, abstract, authors, journal, MeSH, etc.')
         self.cfg.get_nihgrouper().add_arguments(parser)
         # - directories ----------------------------------------------------------------------
-        # pylint: disable=line-too-long
         parser.add_argument(
             '--dir_icite_py', default=dflt_dir_icite_py,
-            help='Write PMID iCite information into directory which contains temporary working files (default={D})'.format(
-                D=dflt_dir_icite_py))
+            help=f'Write PMID iCite information into directory which contains temporary working files (default={dflt_dir_icite_py})')
         parser.add_argument(
             '--dir_icite', default=dflt_dir_icite,
-            help='Write PMID icite reports into directory (default={D})'.format(D=dflt_dir_icite))
+            help=f'Write PMID icite reports into directory (default={dflt_dir_icite})')
         parser.add_argument(
             '--dir_pubmed_txt', default=dflt_dir_pubmed_txt,
-            help='Write PubMed entry into directory (default={D})'.format(D=dflt_dir_pubmed_txt))
+            help=f'Write PubMed entry into directory (default={dflt_dir_pubmed_txt})')
         # ------------------------------------------------------------------------------------
         parser.add_argument(
             '--md', action='store_true',
@@ -120,21 +123,24 @@ def cli(self):
         """Run iCite/PubMed using command-line interface"""
         argparser = self.get_argparser()
         args = self._get_args(argparser)
-        ##print('ICITE ARGS ../pmidcite/src/pmidcite/cli/icite.py', args)
+        ## print('ICITE ARGS ../pmidcite/src/pmidcite/cli/icite.py', args)
         self._run(args, argparser)
 
     def _run(self, args, argparser):
         """Run iCite/PubMed using command-line interface"""
         if args.help:
             argparser.print_help()
             print('\nHelp message printed because: -h or --help == True')
-            exit()
+            sys_exit()
+        if args.cite:
+            print(CITATION)
+            sys_exit()
         self.prt_info(args)
         # Get a list of researcher-specified PMIDs
         pmids = get_pmids(args.pmids, args.infile)
         if pmids:
             if len(pmids) > 10:
-                print('PROCESSING {N:,} PMIDs'.format(N=len(pmids)))
+                print(f'PROCESSING {len(pmids):,} PMIDs')
             dnldr = self._get_downloader(args)
             pmid2icitepaper = dnldr.get_pmid2paper(pmids, None)
             ## print('XXXXXXXXXXXXXXXXXXXXXXXXXXXX pmid2icitepaper', pmid2icitepaper)
@@ -193,7 +199,6 @@ def _get_args(self, argparser):
             args.load_references = True
         return args
 
-    # pylint: disable=too-many-arguments
     def run_icite(self, pmid2icitepaper_all, dnldr, args, argparser):
         """Run iCite/PubMed"""
         pmid2icitepaper_cur = self.run_icite_pre(pmid2icitepaper_all, args, argparser)
@@ -225,7 +230,7 @@ def _prt_infiles(infiles):
         """Print input files"""
         if infiles:
             for fin in infiles:
-                print('**ERROR: NO PMIDs found in: {F}'.format(F=fin))
+                print(f'**ERROR: NO PMIDs found in: {fin}')
 
     @staticmethod
     def run_icite_wr(pmid2icitepaper, args, dnldr):
@@ -246,19 +251,18 @@ def run_icite_wr(pmid2icitepaper, args, dnldr):
     def _wr_papers(self, pmid2icitepaper, dnldr, print_header):
         """Write one icite report per PMID into dir_icite/PMID.txt"""
         for pmid, paper in pmid2icitepaper.items():
-            fout_txt = self.cfg.get_fullname_icite('{PMID}.txt'.format(PMID=pmid))
-            with open(fout_txt, 'w') as prt:
+            fout_txt = self.cfg.get_fullname_icite(f'{pmid}.txt')
+            with open(fout_txt, 'w', encoding='utf8') as prt:
                 if print_header:
                     prt_hdr(prt)
                 dnldr.prt_papers({pmid:paper}, prt)
-                print('  WROTE: {TXT}'.format(TXT=fout_txt))
+                print(f'  WROTE: {fout_txt}')
 
     @staticmethod
     def _prt_no_icite(pmids):
         if not pmids:
             return
-        print('**NOTE: No NIH iCite papers found for: {Ps}'.format(
-            Ps=' '.join(str(p) for p in pmids)))
+        print('**NOTE: No NIH iCite papers found for: {" ".join(str(p) for p in pmids)}')
 
 
-# Copyright (C) 2019-present DV Klopfenstein, PhD, PhD. All rights reserved.
+# Copyright (C) 2019-present DV Klopfenstein, PhD. All rights reserved.