first working version

.gitignore

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+config.py
+library/
+storage.*
+.idea/
+*.egg-info
+__pycache__/

example.py

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+import os
+import sys
+import posixpath
+
+import click
+
+
+class Repo(object):
+
+    def __init__(self, home):
+        self.home = home
+        self.config = {}
+        self.verbose = False
+
+    def set_config(self, key, value):
+        self.config[key] = value
+        if self.verbose:
+            click.echo('  config[%s] = %s' % (key, value), file=sys.stderr)
+
+    def __repr__(self):
+        return '<Repo %r>' % self.home
+
+
+pass_repo = click.make_pass_decorator(Repo)
+
+
+@click.group()
+@click.option('--repo-home', envvar='REPO_HOME', default='.repo',
+              metavar='PATH', help='Changes the repository folder location.')
+@click.option('--config', nargs=2, multiple=True,
+              metavar='KEY VALUE', help='Overrides a config key/value pair.')
+@click.option('--verbose', '-v', is_flag=True,
+              help='Enables verbose mode.')
+@click.version_option('1.0')
+@click.pass_context
+def cli(ctx, repo_home, config, verbose):
+    """Repo is a command line tool that showcases how to build complex
+    command line interfaces with Click.
+
+    This tool is supposed to look like a distributed version control
+    system to show how something like this can be structured.
+    """
+    # Create a repo object and remember it as as the context object.  From
+    # this point onwards other commands can refer to it by using the
+    # @pass_repo decorator.
+    ctx.obj = Repo(os.path.abspath(repo_home))
+    ctx.obj.verbose = verbose
+    for key, value in config:
+        ctx.obj.set_config(key, value)
+
+
+@cli.command()
+@click.argument('src')
+@click.argument('dest', required=False)
+@click.option('--shallow/--deep', default=False,
+              help='Makes a checkout shallow or deep.  Deep by default.')
+@click.option('--rev', '-r', default='HEAD',
+              help='Clone a specific revision instead of HEAD.')
+@pass_repo
+def clone(repo, src, dest, shallow, rev):
+    """Clones a repository.
+
+    This will clone the repository at SRC into the folder DEST.  If DEST
+    is not provided this will automatically use the last path component
+    of SRC and create that folder.
+    """
+    if dest is None:
+        dest = posixpath.split(src)[-1] or '.'
+    click.echo('Cloning repo %s to %s' % (src, os.path.abspath(dest)))
+    repo.home = dest
+    if shallow:
+        click.echo('Making shallow checkout')
+    click.echo('Checking out revision %s' % rev)
+
+
+@cli.command()
+@click.confirmation_option()
+@pass_repo
+def delete(repo):
+    """Deletes a repository.
+
+    This will throw away the current repository.
+    """
+    click.echo('Destroying repo %s' % repo.home)
+    click.echo('Deleted!')
+
+
+@cli.command()
+@click.option('--username', prompt=True,
+              help='The developer\'s shown username.')
+@click.option('--email', prompt='E-Mail',
+              help='The developer\'s email address')
+@click.password_option(help='The login password.')
+@pass_repo
+def setuser(repo, username, email, password):
+    """Sets the user credentials.
+
+    This will override the current user config.
+    """
+    repo.set_config('username', username)
+    repo.set_config('email', email)
+    repo.set_config('password', '*' * len(password))
+    click.echo('Changed credentials.')
+
+
+@cli.command()
+@click.option('--message', '-m', multiple=True,
+              help='The commit message.  If provided multiple times each '
+                   'argument gets converted into a new line.')
+@click.argument('files', nargs=-1, type=click.Path())
+@pass_repo
+def commit(repo, files, message):
+    """Commits outstanding changes.
+
+    Commit changes to the given files into the repository.  You will need to
+    "repo push" to push up your changes to other repositories.
+
+    If a list of files is omitted, all changes reported by "repo status"
+    will be committed.
+    """
+    if not message:
+        marker = '# Files to be committed:'
+        hint = ['', '', marker, '#']
+        for file in files:
+            hint.append('#   U %s' % file)
+        message = click.edit('\n'.join(hint))
+        if message is None:
+            click.echo('Aborted!')
+            return
+        msg = message.split(marker)[0].rstrip()
+        if not msg:
+            click.echo('Aborted! Empty commit message')
+            return
+    else:
+        msg = '\n'.join(message)
+    click.echo('Files to be committed: %s' % (files,))
+    click.echo('Commit message:\n' + msg)
+
+
+@cli.command(short_help='Copies files.')
+@click.option('--force', is_flag=True,
+              help='forcibly copy over an existing managed file')
+@click.argument('src', nargs=-1, type=click.Path())
+@click.argument('dst', type=click.Path())
+@pass_repo
+def copy(repo, src, dst, force):
+    """Copies one or multiple files to a new location.  This copies all
+    files from SRC to DST.
+    """
+    for fn in src:
+        click.echo('Copy from %s -> %s' % (fn, dst))

main.py

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+import math
+
+import ads
+import ads.config
+import click
+import peewee
+import requests
+from peewee import Model
+
+import config
+from models import Author, Keyword, Publication, Doctype, Paper, PaperAuthors, PaperKeywords, db
+
+ads.config.token = config.ads_token
+
+
+@click.group()
+@click.version_option('1.0')
+@click.pass_context
+def cli(ctx):
+    pass
+    # print("bla")
+
+
+cli = cli  # type:click.core.Group
+
+
+@cli.command()
+def init():
+    print("initializing")
+    db.create_tables([Author, Keyword, Publication, Doctype, Paper, PaperAuthors, PaperKeywords])
+
+
+# @cli.command()
+# @click.argument('file', type=click.Path(exists=True, readable=True))
+# @click.option('-p', '--python_file', is_flag=True)
+# def add(file, python_file):
+#     fo = Files(filename=file, pythonfile=python_file)
+#     fo.save()
+#     print(file, python_file)
+#     pass
+
+@cli.command()
+@click.argument("search_query")
+@click.option("-a", "--author")
+@click.option("-t", "--title")
+def add(search_query, author, title):
+    fl = ['id', 'author', 'first_author', 'bibcode', 'id', 'year', 'title', 'abstract', 'doi', 'pubdate', "pub",
+          "doctype", "identifier"]
+    if author:
+        search_query += "author:" + author
+    if title:
+        search_query += "title:" + title
+    papers = list(ads.SearchQuery(q=search_query, fl=fl))
+    if len(papers) == 0:
+        selection = ads.search.Article
+        exit()
+    elif len(papers) == 1:
+        selection = papers[0]  # type:ads.search.Article
+    else:
+        # first_ten = itertools.islice(papers, 10)
+        first_ten = papers[:10]
+        single_paper: ads.search.Article
+        for index, single_paper in enumerate(first_ten):
+            print(index, single_paper.title[0])
+        selected_index = click.prompt('select paper', type=int)
+        selection = papers[selected_index]  # type:ads.search.Article
+
+    assert len(selection.doi) == 1
+    doi = selection.doi[0]
+
+    try:
+
+        paper = Paper.get(Paper.doi == doi)
+        print("this paper has already been added")
+        exit(1)
+
+    except peewee.DoesNotExist:
+        pass
+
+    print("fetching bibcode")
+    q = ads.ExportQuery([selection.bibcode])
+    bibtex = q.execute()
+
+    print("saving in db")
+
+    paper = Paper()
+    assert len(selection.title) == 1
+    paper.doi = doi
+    paper.title = selection.title[0]
+    paper.abstract = selection.abstract
+    paper.bibcode = selection.bibcode
+    paper.year = selection.year
+    paper.pubdate = selection.pubdate
+    paper.pdf_downloaded = False
+    authors = [Author.get_or_create(name=name)[0] for name in selection.author]
+    paper.first_author = Author.get_or_create(name=selection.first_author)[0]
+    paper.publication = Publication.get_or_create(name=selection.pub)[0]
+    paper.doctype = Doctype.get_or_create(name=selection.doctype)[0]
+    paper.arxiv_identifier = [ident for ident in selection.identifier if "arXiv:" in ident][0].split("arXiv:")[-1]
+    paper.bibtex = bibtex
+    paper.save()
+    for author in db.batch_commit(authors, 100):
+        PaperAuthors.create(author=author, paper=paper)
+    print("fetching PDF")
+    arxiv_url = "https://arxiv.org/pdf/{id}".format(id=paper.arxiv_identifier)
+    r = requests.get(arxiv_url, stream=True)
+    print(arxiv_url)
+    with open('library/{filename}.pdf'.format(filename=paper.id), 'wb') as f:
+        chunk_size = 1024  # bytes
+        file_size = int(r.headers.get('content-length', 0))
+        progress_length = math.ceil(file_size // chunk_size)
+        with click.progressbar(r.iter_content(chunk_size=20), length=progress_length) as progress_chunks:
+            for chunk in progress_chunks:
+                f.write(chunk)
+    paper.pdf_downloaded = True
+    paper.save()
+
+
+if __name__ == '__main__':
+    cli()

models.py

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+from peewee import Model, CharField, SqliteDatabase, BooleanField, TextField, \
+    ForeignKeyField, DateField
+
+db = SqliteDatabase('storage.db', pragmas={
+    'journal_mode': 'wal',
+    'cache_size': -1 * 64000,  # 64MB
+    'foreign_keys': 1,
+    'ignore_check_constraints': 0})
+
+db.connect()
+
+
+class BaseModel(Model):
+    class Meta:
+        database = db
+
+
+class Author(BaseModel):
+    name = CharField(unique=True)
+    affiliation = CharField(null=True)
+    orcid_id = CharField(null=True)
+
+
+class Keyword(BaseModel):
+    keyword = CharField(unique=True)
+
+
+class Publication(BaseModel):
+    name = CharField(unique=True)
+
+
+class Doctype(BaseModel):
+    name = CharField(unique=True)
+
+
+class Paper(BaseModel):
+    title = TextField()
+    abstract = TextField()
+    doi = CharField(unique=True)
+    bibtex = TextField()
+    first_author = ForeignKeyField(Author)
+    publication = ForeignKeyField(Publication)
+    doctype = ForeignKeyField(Doctype)
+    arxiv_identifier = CharField(unique=True)
+    bibcode = CharField(unique=True)
+    year = CharField()
+    pubdate = DateField()
+    pdf_downloaded = BooleanField()
+
+
+class PaperAuthors(BaseModel):
+    paper = ForeignKeyField(Paper)
+    author = ForeignKeyField(Author)
+
+
+class PaperKeywords(BaseModel):
+    paper = ForeignKeyField(Paper)
+    keyword = ForeignKeyField(Keyword)

requirements.txt

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+ads==0.12.3
+certifi==2018.11.29
+chardet==3.0.4
+Click==7.0
+click-example-repo==0.1
+httpretty==0.8.10
+idna==2.8
+mock==2.0.0
+pbr==5.1.1
+peewee==3.8.0
+requests==2.21.0
+six==1.12.0
+urllib3==1.24.1
+Werkzeug==0.14.1

setup.py

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+from setuptools import setup
+
+setup(
+    name='click-example-repo',
+    version='0.1',
+    py_modules=['repo'],
+    include_package_data=True,
+    install_requires=[
+        'click',
+    ],
+    entry_points='''
+        [console_scripts]
+        repo=example:cli
+        paperlibrary=main:cli
+    ''',
+)