Merge pull request #44 from dvklopfenstein/dvk

v0.0.38 Move install to first make target; Add icite to console scripts

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Summary
 
 * [**Unreleased**](#unreleased)
+* [**Release 2022-11-26 v0.0.38**](#release-2022-11-26-v0038) Added instructions, and console_script to run script, icite
 * [**Release 2022-09-27 v0.0.37**](#release-2022-09-27-v0037) Remove unused package in setup.py
 * [**Release 2022-07-03 v0.0.36**](#release-2022-07-03-v0036) Change citation count on GitHub repo card
 * [**Release 2022-04-28 v0.0.35**](#release-2022-04-28-v0035) More detailed GitHub repo card (project summary image)
@@ -39,6 +40,11 @@
 
 ### Unreleased
 
+### release 2022-11-26 v0.0.38
+* ADDED instructions for loading locally to README.md [#43](https://github.com/dvklopfenstein/pmidcite/issues/43)
+* ADDED entry_points, console_scripts, icite to setup.py [#42](https://github.com/dvklopfenstein/pmidcite/issues/42)
+* CHANGED first make target to locally install pmidcite [#43](https://github.com/dvklopfenstein/pmidcite/issues/43)
+
 ### release 2022-09-03 v0.0.37
 FIXED: Remove unused package in setup.py (pmidcite.eutils.pubmed.mesh)
 

README.md

@@ -348,7 +348,16 @@ $ grep TOP log/icite/Osbourn_Anne.txt | awk '{print $7 " " $8}' | scatter.py
 
 ## Installation
 To install from [**PyPI**](https://pypi.org/project/pmidcite/)    
-```pip install pmidcite```
+```$ pip install pmidcite```
+
+To install locally
+```
+$ git clone https://github.com/dvklopfenstein/pmidcite.git
+$ cd ./pmidcite
+$ pip install .
+```
+
+
 
 ## Setup
 Save your literature search in a GitHub repo.

makefile

@@ -1,7 +1,18 @@
 PYTHON = python3
 
-findpy:
-	find src -regextype posix-extended -regex ".*[a-z]+.py"
+install:
+	pip install .
+
+py:
+	find src -name \*.py
+
+t:
+	find src/tests -regextype posix-extended -regex ".*[a-z]+.py"
+
+p:
+	find src/bin src/pmidcite -name \*.py
+
+d:
 	find src -regextype posix-extended -regex "[a-z./]*" -type d
 
 diff0:
@@ -17,6 +28,7 @@ pylint:
 	chmod 755 tmp_pylint
 	tmp_pylint
 
+
 #### TESTS := \
 ####     src/tests/test_cfg_icite.py
 
@@ -51,6 +63,7 @@ vim_md:
 #   Needs wheel package to run bdist_wheel: pip3 install wheel
 .PHONY: build
 build:
+	# python3 -m pip install -U pip
 	# python3 -m pip install --user --upgrade setuptools wheel
 	make clean_dist
 	$(PYTHON) setup.py sdist
@@ -95,6 +108,7 @@ clean:
 	rm -rf notebooks/icite
 	rm -rf src/tests/icite
 	make clobber_tmp
+	make clean_dist
 
 clobber_tmp:
 	rm -rf ./icite

setup.py

@@ -7,7 +7,6 @@
 from os.path import join
 # from distutils.core import setup
 from glob import glob
-from pathlib import PurePosixPath
 from setuptools import setup
 # import versioneer
 
@@ -26,7 +25,7 @@
     'pmidcite.plot',
 ]
 
-PACKAGE_DIRS = {p:join('src', PurePosixPath(*p.split('.'))) for p in PACKAGES}
+PACKAGE_DIRS = {p:join('src', *p.split('.')) for p in PACKAGES}
 
 def get_long_description():
     """Return the contents of the README.md as a string"""
@@ -38,14 +37,21 @@ def get_long_description():
 setup(
     name=NAME,
     ## version=versioneer.get_version(),
-    version='0.0.37',
-    author='DV Klopfenstein',
+    version='0.0.38',
+    author='DV Klopfenstein, PhD',
     author_email='[email protected]',
     ## cmdclass=versioneer.get_cmdclass(),
     packages=PACKAGES,
     package_dir=PACKAGE_DIRS,
     # https://stackoverflow.com/questions/18787036/difference-between-entry-points-console-scripts-and-scripts-in-setup-py
+    # https://stackoverflow.com/questions/45114076/python-setuptools-using-scripts-keyword-in-setup-py
+    # https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/#scripts
     scripts=glob('src/bin/*.py'),
+    entry_points={
+        'console_scripts':[
+            'icite=src.bin.icite:main',
+        ],
+    },
     # https://pypi.org/classifiers/
     classifiers=[
         'Programming Language :: Python',

src/pmidcite/__version__.py

@@ -1,3 +1,3 @@
 """Version of pmidcite project"""
 
-__version__ = '0.0.37'
+__version__ = '0.0.38'

src/pmidcite/cfg.py

@@ -107,7 +107,7 @@ def _get_fullname(self, filename, dir_key):
         dirname = self.cfgparser['pmidcite'][dir_key]
         if dirname is None or dirname == 'None':
             return filename
-        if exists(dirname):
+        if dirname is not None and exists(dirname):
             return join(dirname, filename)
         cwd = getcwd()
         print('**WARNING: DIR NOT EXIST {DIR_TYPE}({DIR_NAME}) RETURNING CWD({CWD})'.format(
@@ -159,7 +159,7 @@ def set_cfg(self, cfgfile=None):
 
     def rd_rc(self, prt=stdout, prt_fullname=True):
         """Read a configuration file"""
-        if exists(self.cfgfile):
+        if self.cfgfile is not None and exists(self.cfgfile):
             if prt:
                 cfgfile = self.cfgfile if prt_fullname else basename(self.cfgfile)
                 prt.write('  READ: {CFG}\n'.format(CFG=cfgfile))

src/pmidcite/icite/dnldr/pmid_dnlder_base.py

@@ -132,6 +132,8 @@ def get_pmid2paper(self, pmids_top, pmid2note=None):
         """Get one NIHiCitePaper object for each user-specified PMID"""
         if not self.details_cites_refs:
             return self._geticitepapers_wo_assc(pmids_top, pmid2note)
+        #print('PPPPPPPPPPPPPPPPPPP', pmids_top)
+        #print('PPPPPPPPPPPPPPPPPPP', pmid2note)
         return self._geticitepapers_w_assc(pmids_top, pmid2note)
         #### s_geticitepaper = self._geticitepaper
         #### papers = [s_geticitepaper(p, '', pmid2note) for p in pmids_top]
@@ -152,8 +154,12 @@ def _geticitepapers_w_assc(self, pmids_top, pmid2note=None):
         """Get one NIHiCitePaper object for each user-specified PMID w/cites and/or refs"""
         nihentries_top = self.get_icites(pmids_top)
         s_get_cites_refs = self.details_cites_refs
+        #print('AAAAAAAAAAAAAAAAAAAA', nihentries_top)
         top_n_assocs = [(e.pmid, e.get_assc_pmids(s_get_cites_refs)) for e in nihentries_top]
         # PMIDs that are associated with the top PMIDs (cited_by_clin, cited_by, references)
+        #print('AAAAAAAAAAAAAAAAAAAA', top_n_assocs)
+        #if not top_n_assocs:
+        #    return {}
         pmids_assoc = set.union(*list(zip(*top_n_assocs))[1])
         # Get associated PMIDs that were requested by the researcher
         nihentries_other = self.get_icites(pmids_assoc.difference(pmids_top))

src/pmidcite/pubmedqueryicite.py

@@ -7,7 +7,7 @@
 from collections import namedtuple
 from pmidcite.cfg import get_cfgparser
 from pmidcite.eutils.cmds.pubmed import PubMed
-from pmidcite.cli.utils import wr_pmids
+#### from pmidcite.cli.utils import wr_pmids
 from pmidcite.icite.downloader import get_downloader
 
 
@@ -53,14 +53,14 @@ def querypubmed_runicite(self, filename, query, details_cites_refs=None):
         #        https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
         pmids = self.pubmed.dnld_query_pmids(query, num_ids_p_epost=100000)
         ## print('PMIDCITE QQQQQQQQQQQQQQQQQ {N} PMIDs'.format(N=len(pmids)))
-        fout_pmids = self.cfg.get_fullname_pmids(filename)
+        ## fout_pmids = self.cfg.get_fullname_pmids(filename)
         fout_icite = self.cfg.get_fullname_icite(filename)
-        # 2) Write PubMed PMIDs into a simple text file, one PMID per line
-        if fout_pmids != fout_icite:
-            if pmids:
-                wr_pmids(fout_pmids, pmids)
-            else:
-                print('  0 PMIDs: NOT WRITING {TXT}'.format(TXT=fout_pmids))
+        ##### 2) Write PubMed PMIDs into a simple text file, one PMID per line
+        ####if fout_pmids != fout_icite:
+        ####    if pmids:
+        ####        wr_pmids(fout_pmids, pmids)
+        ####    else:
+        ####        print('  0 PMIDs: NOT WRITING {TXT}'.format(TXT=fout_pmids))
         # 3) Run NIH's iCite on the PMIDs and write the results into a file
         if pmids:
             return self._wr_icite(fout_icite, pmids, details_cites_refs)

src/tests/args_dflt.py

@@ -3,4 +3,4 @@
 from argparse import Namespace
 
 # pylint: disable=line-too-long
-ARGS = Namespace(O=False, append_outfile=None, dir_icite='./log/icite', dir_icite_py='None', dir_pubmed_txt='None', force_download=False, force_write=False, generate_rcfile=False, help=False, infile=None, load_citations=False, load_references=False, md=False, min1=2.1, min2=15.7, min3=70.0, min4=97.5, no_references=False, outfile=None, pmids=[1], print_header=False, print_keys=False, pubmed=False, verbose=False)
+ARGS = Namespace(O=False, append_outfile=None, dir_icite='./log/icite', dir_icite_py='None', dir_pubmed_txt='None', force_download=False, force_write=False, generate_rcfile=False, print_rcfile=False, help=False, infile=None, load_citations=False, load_references=False, md=False, min1=2.1, min2=15.7, min3=70.0, min4=97.5, no_references=False, outfile=None, pmids=[1], print_header=False, print_keys=False, pubmed=False, verbose=False)

src/tests/test_cli_icite.py

@@ -24,7 +24,7 @@
 def test_cli_icite():
     """Test the icite command-line options"""
     args = ARGS
-    print(args)
+    print('TEST ARGS test_cli_icite:', args)
 
     # icite
     # pylint: disable=protected-access