Merge pull request #29 from pcubillos/packaging

Packaging

CHANGELOG.txt

@@ -789,5 +789,23 @@ Added MANIFEST.in file.
 
 Bumped bibmanager version to 0.5.6.
 
+
+*****  Sat Jan 12 12:15:33 CET 2019  *****
+
+Refactored files and package structure to a standard package format.
+Fixed a few typos here and there.
+Updated docstring examples accordingly.
+
+*****
+
+Moved ads_token and ads_display loading into functions
+to update them at runtime.
+Removed unnecessary constants (url paths) from ads_manager.py
+
+*****
+
+Bumped bibmanager version to 0.6.0.
+This next merge closes #12
+
 *****
 

bibmanager/VERSION.py

@@ -3,5 +3,5 @@
 
 # bibmanager Version:
 BM_VER =  0  # Major version
-BM_MIN =  5  # Minor version
-BM_REV =  6  # Revision
+BM_MIN =  6  # Minor version
+BM_REV =  0  # Revision

bibmanager/__init__.py

@@ -1,12 +1,16 @@
 # Copyright (c) 2018-2019 Patricio Cubillos and contributors.
 # bibmanager is open-source software under the MIT license (see LICENSE).
 
-from . import VERSION as ver
-from .bib_manager import *
+__all__ = ["bib_manager", "config_manager", "latex_manager", "ads_manager",
+           "utils"]
 
-from .bib_manager import __all__ as bm_all
+from . import bib_manager
+from . import config_manager
+from . import latex_manager
+from . import ads_manager
+from . import utils
 
-__all__ = bm_all
+from . import VERSION as ver
 
 __version__ = f"{ver.BM_VER}.{ver.BM_MIN}.{ver.BM_REV}"
 

bibmanager/__main__.py

@@ -5,15 +5,15 @@
 import os
 import argparse
 import textwrap
+
 import prompt_toolkit
 
-sys.path.append(os.path.dirname(os.path.realpath(__file__)))
-import bibmanager as bm
-# FINDME: Temporary hack until setting BM as a package:
-import latex_manager  as lm
-import config_manager as cm
-import ads_manager    as am
-from utils import BOLD, END
+from . import bib_manager    as bm
+from . import latex_manager  as lm
+from . import config_manager as cm
+from . import ads_manager    as am
+from .utils import BOLD, END
+from .__init__ import __version__ as ver
 
 
 def cli_reset(args):
@@ -190,7 +190,7 @@ def main():
 
     parser.add_argument('-v', '--version', action='version',
         help="Show bibmanager's version.",
-        version=f'bibmanager version {bm.__version__}')
+        version=f'bibmanager version {ver}')
 
     # Parser Main Documentation:
     main_description = """

bibmanager/ads_manager/__init__.py

@@ -0,0 +1,14 @@
+# Copyright (c) 2018-2019 Patricio Cubillos and contributors.
+# bibmanager is open-source software under the MIT license (see LICENSE).
+
+from .ads_manager import *
+from .ads_manager import __all__
+
+
+# Clean up top-level namespace--delete everything that isn't in __all__
+# or is a magic attribute, and that isn't a submodule of this package
+for varname in dir():
+    if not ((varname.startswith('__') and varname.endswith('__')) or
+            varname in __all__ ):
+        del locals()[varname]
+del(varname)

bibmanager/ads_manager.py → bibmanager/ads_manager/ads_manager.py

@@ -7,29 +7,23 @@
 import os
 import re
 import json
-import requests
 import urllib
 import textwrap
 import pickle
 
-import bib_manager    as bm
-import config_manager as cm
-from utils import BM_CACHE, BOLD, END, BANNER, ignored, parse_name, get_authors
-
-
-# FINDME: Is to possible to check a token is valid?
-token = cm.get('ads_token')
-rows  = int(cm.get('ads_display'))
+import requests
 
-ADSQUERRY = "https://api.adsabs.harvard.edu/v1/search/query?"
-ADSEXPORT = "https://api.adsabs.harvard.edu/v1/export/bibtex"
-ADSURL    = "https://ui.adsabs.harvard.edu/\#abs/"
+from .. import bib_manager    as bm
+from .. import config_manager as cm
+from ..utils import BM_CACHE, BOLD, END, BANNER, ignored, parse_name, \
+                    get_authors
 
 
 def manager(querry=None):
   """
   A manager, it doesn't really do anything, it just delegates.
   """
+  rows  = int(cm.get('ads_display'))
   if querry is None and not os.path.exists(BM_CACHE):
       print("There are no more entries for this querry.")
       return
@@ -70,7 +64,7 @@ def search(querry, start=0, cache_rows=200, sort='pubdate+desc'):
      https://ui.adsabs.harvard.edu/
   start: Integer
      Starting index of entry to return.
-  rows: Integer
+  cache_rows: Integer
      Maximum number of entries to return.
   sort: String
      Sorting field and direction to use.
@@ -91,7 +85,7 @@ def search(querry, start=0, cache_rows=200, sort='pubdate+desc'):
 
   Examples
   --------
-  >>> import ads_manager as am
+  >>> import bibmanager.ads_manager as am
   >>> # Search entries by author (note the need for double quotes,
   >>> # otherwise, the search might produce bogus results):
   >>> querry = 'author:"cubillos, p"'
@@ -113,8 +107,11 @@ def search(querry, start=0, cache_rows=200, sort='pubdate+desc'):
   ValueError: Invalid ADS request:
   org.apache.solr.search.SyntaxError: org.apache.solr.common.SolrException: undefined field properties
   """
+  token = cm.get('ads_token')
   querry = urllib.parse.quote(querry)
-  r = requests.get(f'{ADSQUERRY}q={querry}&start={start}&rows={cache_rows}'
+
+  r = requests.get('https://api.adsabs.harvard.edu/v1/search/query?'
+                  f'q={querry}&start={start}&rows={cache_rows}'
                    f'&sort={sort}&fl=title,author,year,bibcode,pub',
                    headers={'Authorization': f'Bearer {token}'})
   resp = r.json()
@@ -153,7 +150,7 @@ def display(results, start, index, rows, nmatch, short=True):
 
   Examples
   --------
-  >>> import ads_manager as am
+  >>> import bibmanager.ads_manager as am
   >>> start = index = 0
   >>> querry = 'author:"^cubillos, p" property:refereed'
   >>> results, nmatch = am.search(querry, start=start)
@@ -165,7 +162,8 @@ def display(results, start, index, rows, nmatch, short=True):
       author_list = [parse_name(author) for author in result['author']]
       authors = textwrap.fill(f"Authors: {get_authors(author_list, short)}",
            **wrap_kw)
-      adsurl = f"adsurl: {ADSURL}{result['bibcode']}"
+      adsurl = ("adsurl: https://ui.adsabs.harvard.edu/\#abs/" +
+               f"{result['bibcode']}")
       bibcode = f"\n{BOLD}bibcode{END}: {result['bibcode']}"
       print(f"\n{title}\n{authors}\n{adsurl}{bibcode}")
   if index + rows < nmatch:
@@ -194,7 +192,7 @@ def add_bibtex(input_bibcodes, input_keys, update_keys=True):
 
   Examples
   --------
-  >>> import ads_manager as am
+  >>> import bibmanager.ads_manager as am
   >>> # A successful add call:
   >>> bibcodes = ['1925PhDT.........1P']
   >>> keys = ['Payne1925phdStellarAtmospheres']
@@ -213,6 +211,7 @@ def add_bibtex(input_bibcodes, input_keys, update_keys=True):
   >>> am.add_bibtex(bibcodes, keys)
   Warning: bibcode '1925PhDT.....X...1P' not found.
   """
+  token = cm.get('ads_token')
   # Keep the originals untouched (copies will be modified):
   bibcodes, keys = input_bibcodes.copy(), input_keys.copy()
 
@@ -336,7 +335,7 @@ def key_update(key, bibcode, alternate_bibcode):
 
   Examples
   --------
-  >>> import ads_manager as am
+  >>> import bibmanager.ads_manager as am
   >>> key = 'BeaulieuEtal2010arxivGJ436b'
   >>> bibcode           = '2011ApJ...731...16B'
   >>> alternate_bibcode = '2010arXiv1007.0324B'

bibmanager/bib_manager/__init__.py

@@ -0,0 +1,14 @@
+# Copyright (c) 2018-2019 Patricio Cubillos and contributors.
+# bibmanager is open-source software under the MIT license (see LICENSE).
+
+from .bib_manager import *
+from .bib_manager import __all__
+
+
+# Clean up top-level namespace--delete everything that isn't in __all__
+# or is a magic attribute, and that isn't a submodule of this package
+for varname in dir():
+    if not ((varname.startswith('__') and varname.endswith('__')) or
+            varname in __all__ ):
+        del locals()[varname]
+del(varname)

bibmanager/bib_manager.py → bibmanager/bib_manager/bib_manager.py

@@ -13,6 +13,7 @@
 import pickle
 import urllib
 import subprocess
+
 import numpy as np
 import prompt_toolkit
 from prompt_toolkit.formatted_text import PygmentsTokens
@@ -21,10 +22,8 @@
 from pygments.token import Token
 from pygments.lexers.bibtex import BibTeXLexer
 
-ROOT = os.path.realpath(os.path.dirname(__file__)) + '/'
-sys.path.append(ROOT)
-import config_manager as cm
-from utils import HOME, BM_DATABASE, BM_BIBFILE, BM_TMP_BIB, BANNER, \
+from .. import config_manager as cm
+from ..utils import ROOT, HOME, BM_DATABASE, BM_BIBFILE, BM_TMP_BIB, BANNER, \
     Sort_author, ordinal, count, cond_split, parse_name, \
     purify, initials, get_authors, get_fields, req_input, ignored
 
@@ -50,10 +49,10 @@ def __init__(self, entry):
       entry: String
          A bibliographic entry text.
 
-      Example
-      -------
-      >>> import bib_manager as bm
-      >>> from utils import Author
+      Examples
+      --------
+      >>> import bibmanager.bib_manager as bm
+      >>> from bibmanager.utils import Author
       >>> entry = '''@Misc{JonesEtal2001scipy,
                 author = {Eric Jones and Travis Oliphant and Pearu Peterson},
                 title  = {{SciPy}: Open source scientific tools for {Python}},
@@ -145,9 +144,9 @@ def __contains__(self, author):
       author: String
          An author name in a valid BibTeX format.
 
-      Example
-      -------
-      >>> import bibm as bm
+      Examples
+      --------
+      >>> import bibmanager.bib_manager as bm
       >>> bib = bm.Bib('''@ARTICLE{DoeEtal2020,
                       author = {{Doe}, J. and {Perez}, J. and {Dupont}, J.},
                        title = "What Have the Astromomers ever Done for Us?",
@@ -273,7 +272,7 @@ def display_bibs(labels, bibs):
 
   Examples
   --------
-  >>> import bibm as bm
+  >>> import bibmanager.bib_manager as bm
   >>> e1 = '''@Misc{JonesEtal2001scipy,
          author = {Eric Jones and Travis Oliphant and Pearu Peterson},
          title  = {{SciPy}: Open source scientific tools for {Python}},
@@ -425,8 +424,9 @@ def loadfile(bibfile=None, text=None):
 
   Examples
   --------
-  >>> import bibm as bm
-  >>> bibfile = "../examples/sample.bib"
+  >>> import bibmanager.bib_manager as bm
+  >>> import os
+  >>> bibfile = os.path.expanduser("~") + "/.bibmanager/examples/sample.bib"
   >>> bibs = bm.loadfile(bibfile)
   """
   entries = []  # Store Lists of bibtex entries
@@ -495,12 +495,11 @@ def merge(bibfile=None, new=None, take="old"):
 
   Examples
   --------
-  >>> import bib_manager as bm
-  >>> # Load bibmabager database (TBD: update with bm/examples/new.bib):
-  >>> newbib = (os.path.expanduser("~")
-                + "/Dropbox/latex/2018_hd209/current/hd209nuv.bib")
-  >>> new = bm.loadfile(newbib)
-  >>> # Merge new into database:
+  >>> import bibmanager.bib_manager as bm
+  >>> import os
+  >>> # TBD: Need to add sample2.bib into package.
+  >>> newbib = os.path.expanduser("~") + "/.bibmanager/examples/sample2.bib"
+  >>> # Merge newbib into database:
   >>> bm.merge(newbib, take='old')
   """
   bibs = load()
@@ -573,8 +572,8 @@ def save(entries):
 
   Examples
   --------
-  >>> import bibm as bm
-  >>> # [Load some entries]
+  >>> import bibmanager.bib_manager as bm
+  >>> # TBD: Load some entries
   >>> bm.save(entries)
   """
   # FINDME: Don't pickle-save the Bib() objects directly, but store them
@@ -594,7 +593,7 @@ def load():
 
   Examples
   --------
-  >>> import bibm as bm
+  >>> import bibmanager.bib_manager as bm
   >>> bibs = bm.load()
   """
   try:
@@ -647,10 +646,11 @@ def init(bibfile=BM_BIBFILE, reset_db=True, reset_config=False):
   reset_config: Bool
      If True, reset the config file.
 
-  Example
-  -------
-  >>> import bib_manager as bm
-  >>> bibfile = '../examples/sample.bib'
+  Examples
+  --------
+  >>> import bibmanager.bib_manager as bm
+  >>> import os
+  >>> bibfile = os.path.expanduser("~") + "/.bibmanager/examples/sample.bib"
   >>> bm.init(bibfile)
   """
   # First install ever:
@@ -764,7 +764,7 @@ def search(authors=None, year=None, title=None, key=None, bibcode=None):
 
   Examples
   --------
-  >>> import bib_manager as bm
+  >>> import bibmanager.bib_manager as bm
   >>> # Search by last name:
   >>> matches = bm.search(authors="Cubillos")
   >>> # Search by last name and initial:

bibmanager/config_manager/__init__.py

@@ -0,0 +1,14 @@
+# Copyright (c) 2018-2019 Patricio Cubillos and contributors.
+# bibmanager is open-source software under the MIT license (see LICENSE).
+
+from .config_manager import *
+from .config_manager import __all__
+
+
+# Clean up top-level namespace--delete everything that isn't in __all__
+# or is a magic attribute, and that isn't a submodule of this package
+for varname in dir():
+    if not ((varname.startswith('__') and varname.endswith('__')) or
+            varname in __all__ ):
+        del locals()[varname]
+del(varname)