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Merge pubs updates

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This commit is contained in:
Jonas Kulhanek 2022-02-15 10:03:12 +01:00
commit f7cfe22bf6
13 changed files with 102 additions and 16 deletions
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2
changelog.md
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@ -7,6 +7,8 @@
### Implemented enhancements
- Possibily to exclude bibtext field when adding references ([#273](https://github.com/pubs/pubs/pull/273) by [Mitsuhiro Nakamura](https://github.com/m15a))
- Less ambiguous tag display for tags with space ([#265](https://github.com/pubs/pubs/pull/265) by [Florian Richoux](https://github.com/richoux))
- Migration from Travis CI to Github actions ([#260](https://github.com/pubs/pubs/pull/260))
- Allow passing named arguments to custom commands ([#241](https://github.com/pubs/pubs/pull/241) by [jkulhanek](https://github.com/jkulhanek))
- Added support for non-standard bibtex types, e.g. @collection, @software, etc. ([#226](https://github.com/pubs/pubs/pull/226))

3
pubs/commands/add_cmd.py
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@ -116,6 +116,9 @@ def command(conf, args):
if bibentry is None:
ui.error('invalid bibfile {}.'.format(bibfile))
# exclude bibtex fields if specified
utils.remove_bibtex_fields(bibentry, conf['main']['exclude_bibtex_fields'])
# citekey
citekey = args.citekey

5
pubs/commands/edit_cmd.py
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@ -6,7 +6,7 @@ from .. import color
from ..uis import get_ui
from ..endecoder import EnDecoder
from ..utils import resolve_citekey
from ..utils import resolve_citekey, remove_bibtex_fields
from ..completion import CiteKeyCompletion
from ..events import ModifyEvent
@ -59,6 +59,9 @@ def command(conf, args):
ui.info(("The metadata of paper '{}' was successfully "
"edited.".format(color.dye_out(citekey, 'citekey'))))
else:
# exclude bibtex fields if specified
remove_bibtex_fields(content, conf['main']['exclude_bibtex_fields'])
new_paper = Paper.from_bibentry(content,
metadata=paper.metadata)
if rp.rename_paper(new_paper, old_citekey=paper.citekey):

5
pubs/commands/export_cmd.py
View File

@ -5,7 +5,7 @@ import argparse
from .. import repo
from ..uis import get_ui
from .. import endecoder
from ..utils import resolve_citekey_list
from ..utils import resolve_citekey_list, remove_bibtex_fields
from ..endecoder import BIBFIELD_ORDER
from ..completion import CiteKeyCompletion, CommaSeparatedListCompletion
@ -53,6 +53,9 @@ def command(conf, args):
for p in papers:
bib[p.citekey] = p.bibdata
# exclude bibtex fields if specified
remove_bibtex_fields(bib, conf['main']['exclude_bibtex_fields'])
exporter = endecoder.EnDecoder()
bibdata_raw = exporter.encode_bibdata(bib, args.ignore_fields)
ui.message(bibdata_raw)

14
pubs/commands/import_cmd.py
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@ -11,6 +11,7 @@ from .. import content
from ..paper import Paper
from ..uis import get_ui
from ..content import system_path, read_text_file
from ..utils import remove_bibtex_fields
from ..command_utils import add_doc_copy_arguments
@ -21,7 +22,7 @@ _IGNORING_MSG = " Ignoring it."
def parser(subparsers, conf):
parser = subparsers.add_parser(
'import',
help='import paper(s) to the repository.')
help='import paper(s) to the repository')
parser.add_argument(
'bibpath',
help=("path to bibtex, bibtexml or bibyaml file, or a directory "
@ -40,7 +41,7 @@ def parser(subparsers, conf):
return parser
def many_from_path(ui, bibpath, ignore=False):
def many_from_path(ui, bibpath, exclude_bibtex_fields=[], ignore=False):
"""Extract list of papers found in bibliographic files in path.
The behavior is to:
@ -62,7 +63,10 @@ def many_from_path(ui, bibpath, ignore=False):
biblist = []
for filepath in all_files:
try:
biblist.append(coder.decode_bibdata(read_text_file(filepath)))
bibentry = coder.decode_bibdata(read_text_file(filepath))
# exclude bibtex fields if specified
remove_bibtex_fields(bibentry, exclude_bibtex_fields)
biblist.append(bibentry)
except coder.BibDecodingError:
error = "Could not parse bibtex at {}.".format(filepath)
if ignore:
@ -100,7 +104,9 @@ def command(conf, args):
rp = repo.Repository(conf)
# Extract papers from bib
papers = many_from_path(ui, bibpath, ignore=args.ignore_malformed)
papers = many_from_path(ui, bibpath,
exclude_bibtex_fields=conf['main']['exclude_bibtex_fields'],
ignore=args.ignore_malformed)
keys = args.keys or papers.keys()
for k in keys:
p = papers[k]

2
pubs/commands/statistics_cmd.py
View File

@ -6,7 +6,7 @@ from .. import color
def parser(subparsers, conf):
parser = subparsers.add_parser(
'statistics',
help="show statistics on the repository.")
help="show statistics on the repository")
return parser

4
pubs/commands/tag_cmd.py
View File

@ -87,7 +87,7 @@ def command(conf, args):
rp = Repository(conf)
if citekeyOrTag is None:
ui.message(color.dye_out(' '.join(sorted(rp.get_tags())), 'tag'))
ui.message(color.dye_out(', '.join(sorted(rp.get_tags())), 'tag'))
else:
not_citekey = False
try:
@ -97,7 +97,7 @@ def command(conf, args):
if not not_citekey:
p = rp.pull_paper(citekeyOrTag)
if tags is None:
ui.message(color.dye_out(' '.join(sorted(p.tags)), 'tag'))
ui.message(color.dye_out(', '.join(sorted(p.tags)), 'tag'))
else:
add_tags, remove_tags = _tag_groups(_parse_tag_seq(tags))
for tag in add_tags:

5
pubs/config/spec.py
View File

@ -56,6 +56,11 @@ normalize_citekey = boolean(default=False)
#
citekey_format = string(default='{{author_last_name:l}}{{year}}{{short_title:l}}')
# which bibliographic fields to exclude from bibtex files. By default, none.
# Please note that excluding critical fields such as `title` or `author`
# will break many commands of pubs.
exclude_bibtex_fields = force_list(default=list())
[formating]
# Enable bold formatting, if the terminal supports it.

2
pubs/pretty.py
View File

@ -78,7 +78,7 @@ def paper_oneliner(p, citekey_only=False, max_authors=3):
else 'NOEXT'),
'tag')
tags = '' if len(p.tags) == 0 else '| {}'.format(
','.join(color.dye_out(t, 'tag') for t in sorted(p.tags)))
', '.join(color.dye_out(t, 'tag') for t in sorted(p.tags)))
return '[{citekey}] {descr}{doc} {tags}'.format(
citekey=color.dye_out(p.citekey, 'citekey'),
descr=bibdesc, tags=tags, doc=doc_str)

6
pubs/utils.py
View File

@ -87,3 +87,9 @@ def standardize_doi(doi):
new_doi = match.group(0)
return new_doi
def remove_bibtex_fields(bibentry, fields):
for item in bibentry.values():
for field in fields:
if field in item:
del item[field]

2
readme.md
View File

@ -187,3 +187,5 @@ You can access the self-documented configuration by using `pubs conf`, and all t
- [Jonáš Kulhánek](https://github.com/jkulhanek)
- [Dominik Stańczak](https://github.com/StanczakDominik)
- [Gustavo José de Sousa](https://github.com/guludo)
- [Florian Richoux](https://github.com/richoux)
- [Mitsuhiro Nakamura](https://github.com/m15a)

3
tests/str_fixtures.py
View File

@ -138,6 +138,9 @@ edit_cmd = "vim"
# the full python stack is printed.
debug = False
# which bibliographic fields to exclude from bibtex files.
exclude_bibtex_fields =
[formating]
# Enable bold formatting, if the terminal supports it.

65
tests/test_usecase.py
View File

@ -437,6 +437,18 @@ class TestAdd(URLContentTestCase):
self.execute_cmds(cmds)
self.assertEqual(cm.exception.code, 1)
def test_add_excludes_bibtex_fields(self):
self.execute_cmds(['pubs init'])
config = conf.load_conf()
config['main']['exclude_bibtex_fields'] = ['abstract', 'publisher']
conf.save_conf(config)
self.execute_cmds(['pubs add data/pagerank.bib'])
with FakeFileOpen(self.fs)(self.default_pubs_dir + '/bib/Page99.bib', 'r') as buf:
out = endecoder.EnDecoder().decode_bibdata(buf.read())
for bib in out.values():
self.assertFalse('abstract' in bib or 'publisher' in bib)
self.assertTrue('title' in bib and 'author' in bib)
class TestList(DataCommandTestCase):
@ -590,7 +602,7 @@ class TestTag(DataCommandTestCase):
'pubs list',
]
correct = ['',
'[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | network,search\n' +
'[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | network, search\n' +
'[Turing1950] Turing, Alan M "Computing machinery and intelligence" Mind (1950) \n',
]
out = self.execute_cmds(cmds)
@ -738,9 +750,9 @@ class TestUsecase(DataCommandTestCase):
'[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] \n',
'\n',
'',
'network search\n',
'network, search\n',
'info: Assuming search to be a tag.\n'
'[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] | network,search\n',
'[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] | network, search\n',
]
cmds = ['pubs init -p /paper_first',
@ -785,7 +797,7 @@ class TestUsecase(DataCommandTestCase):
'',
'',
'',
'search network\n',
'search, network\n',
]
cmds = ['pubs init -p paper_first/',
@ -798,7 +810,7 @@ class TestUsecase(DataCommandTestCase):
out = self.execute_cmds(cmds)
def clean(s):
return set(s.strip().split(' '))
return set(s.strip().split(', '))
self.assertEqual(clean(correct[2]), clean(out[2]))
self.assertEqual(clean(correct[4]), clean(out[4]))
@ -829,6 +841,22 @@ class TestUsecase(DataCommandTestCase):
]
self.execute_cmds(cmds)
def test_editor_excludes_bibtex_field(self):
cmds = ['pubs init',
'pubs add data/pagerank.bib',
]
self.execute_cmds(cmds)
config = conf.load_conf()
config['main']['exclude_bibtex_fields'] = ['author']
conf.save_conf(config)
cmds = [('pubs edit Page99', ['@misc{Page99, title="TTT", author="auth"}', 'n'])]
self.execute_cmds(cmds)
with FakeFileOpen(self.fs)(self.default_pubs_dir + '/bib/Page99.bib', 'r') as buf:
out = endecoder.EnDecoder().decode_bibdata(buf.read())
for bib in out.values():
self.assertFalse('author' in bib)
self.assertTrue('title' in bib)
def test_add_aborts(self):
with self.assertRaises(FakeSystemExit):
cmds = ['pubs init',
@ -879,7 +907,7 @@ class TestUsecase(DataCommandTestCase):
meta = str_fixtures.turing_meta
line = '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
line1 = re.sub('\n', '| AI,computer\n', line)
line1 = re.sub('\n', '| AI, computer\n', line)
cmds = ['pubs init',
'pubs add data/pagerank.bib',
@ -908,6 +936,19 @@ class TestUsecase(DataCommandTestCase):
fixtures.page_bibentry, ignore_fields=['author', 'title'])
self.assertEqual(outs[2], expected + os.linesep)
def test_export_excludes_bibtex_field(self):
cmds = ['pubs init',
'pubs add data/pagerank.bib'
]
self.execute_cmds(cmds)
config = conf.load_conf()
config['main']['exclude_bibtex_fields'] = ['url']
conf.save_conf(config)
outs = self.execute_cmds(['pubs export Page99'])
for bib in endecoder.EnDecoder().decode_bibdata(outs[0]).values():
self.assertFalse('url' in bib)
self.assertTrue('title' in bib and 'author' in bib)
def test_import(self):
cmds = ['pubs init',
'pubs import data/',
@ -970,6 +1011,18 @@ class TestUsecase(DataCommandTestCase):
outs = self.execute_cmds(cmds)
self.assertEqual(1 + 1, len(outs[-1].split('\n')))
def test_import_excludes_bibtex_field(self):
self.execute_cmds(['pubs init'])
config = conf.load_conf()
config['main']['exclude_bibtex_fields'] = ['abstract']
conf.save_conf(config)
self.execute_cmds(['pubs import data/ Page99'])
with FakeFileOpen(self.fs)(self.default_pubs_dir + '/bib/Page99.bib', 'r') as buf:
out = endecoder.EnDecoder().decode_bibdata(buf.read())
for bib in out.values():
self.assertFalse('abstract' in bib)
self.assertTrue('title' in bib and 'author' in bib)
def test_update(self):
cmds = ['pubs init',
'pubs add data/pagerank.bib',