diff options
Diffstat (limited to 'papis/commands/bibtex.py')
| -rw-r--r-- | papis/commands/bibtex.py | 149 |
1 files changed, 98 insertions, 51 deletions
diff --git a/papis/commands/bibtex.py b/papis/commands/bibtex.py index 7ec7db10..b266eff8 100644 --- a/papis/commands/bibtex.py +++ b/papis/commands/bibtex.py @@ -6,12 +6,6 @@ This command helps to interact with `bib` files in your LaTeX projects. Examples ^^^^^^^^ -:: - - papis bibtex \ - read new_papers.bib \ # Read bib file - cmd 'papis add --from-doi {doc[doi]}' # For every entry run the command - I use it for opening some papers for instance :: @@ -37,7 +31,65 @@ or if I update some information in my papis ``yaml`` files then I can do update -f \ # Update what has been read from papis library save new_papers.bib # save everything to new_papers.bib, overwriting -Maybe this is also interesting for you guys! +Local configuration file +^^^^^^^^^^^^^^^^^^^^^^^^ + +If you are working in a local folder where you have +a bib file called ``main.bib``, you'll grow sick and tired +of writing always ``read main.bib`` and ``save main.bib``, so you can +write a local configuration file ``.papis.config`` for ``papis bibtex`` +to read and write automatically + +:: + + [bibtex] + default-read-bibfile = main.bib + default-save-bibfile = main.bib + auto-read = True + +with this setup, you can just do + +:: + + papis bibtex add einstein save + +Check references quality +^^^^^^^^^^^^^^^^^^^^^^^^ + +When you're collaborating with someone, you might come across malformed +or incomplete references. Most journals want to have all the ``doi``s +and urls available. You can automate this diagnostic with + +For this you kan use the command ``doctor`` + +:: + + papis bibtex read mybib.bib doctor + +Mostly I want to have only the references in my project's bib file +that are actually cited in the latex file, you can check +which references are not cited in the tex files by doing + + +:: + + papis bibtex iscited -f main.tex -f chapter-2.tex + +and you can then filter them out using the command ``filter-cited``. + +To monitor the health of the bib project's file, I mostly have a +target in the project's ``Makefile`` like + +.. code:: make + + .PHONY: check-bib + check-bib: + papis bibtex iscited -f main.tex doctor + +it does not solve all problems under the sun, but it is really better than no +check! + + Vim integration ^^^^^^^^^^^^^^^ @@ -67,15 +119,18 @@ And use like such: |asciicast| Cli ^^^ -.. click:: papis.commands.add:cli - :prog: papis add +.. click:: papis.commands.bibtex:cli + :prog: papis bibtex """ import os import re +import click +import logging +from typing import List, Optional + import papis.api import papis.cli -import click import papis.config as config import papis.utils import papis.tui.utils @@ -86,10 +141,7 @@ import papis.commands.edit import papis.commands.browse import papis.commands.export import papis.bibtex -import logging -import colorama -from typing import List, Optional logger = logging.getLogger('papis:bibtex') @@ -116,14 +168,14 @@ def cli(ctx: click.Context, no_auto_read: bool) -> None: ctx.obj = {'documents': []} if no_auto_read: - logger.info('Setting auto-read to False') + logger.info("Setting 'auto-read' to False") config.set('auto-read', 'False', section='bibtex') bibfile = config.get('default-read-bibfile', section='bibtex') - if (bool(config.getboolean('auto-read', section='bibtex')) and - bibfile and - os.path.exists(bibfile)): - logger.info("auto reading {0}".format(bibfile)) + if (bool(config.getboolean('auto-read', section='bibtex')) + and bibfile + and os.path.exists(bibfile)): + logger.info("Auto-reading '%s'", bibfile) explorer_mgr['bibtex'].plugin.callback(bibfile) @@ -136,7 +188,7 @@ cli.add_command(explorer_mgr['bibtex'].plugin, 'read') @papis.cli.all_option() @click.pass_context def _add(ctx: click.Context, query: str, _all: bool) -> None: - """Add a refrence to the bibtex file""" + """Add a reference to the bibtex file""" docs = papis.api.get_documents_in_lib(search=query) if not _all: docs = list(papis.api.pick_doc(docs)) @@ -176,17 +228,15 @@ def _update(ctx: click.Context, _all: bool, libdoc = papis.utils.locate_document_in_lib(doc) except IndexError as e: logger.info( - '{c.Fore.YELLOW}{0}:' - '\n\t{c.Back.RED}{doc: <80.80}{c.Style.RESET_ALL}' - .format(e, doc=papis.document.describe(doc), c=colorama) - ) + '{c.Fore.YELLOW}%s:' + '\n\t{c.Back.RED}%-80.80s{c.Style.RESET_ALL}', + e, papis.document.describe(doc)) else: if fromdb: logger.info( 'Updating \n\t{c.Fore.GREEN}' - '{c.Back.BLACK}{doc: <80.80}{c.Style.RESET_ALL}' - .format(doc=papis.document.describe(doc), c=colorama) - ) + '{c.Back.BLACK}%-80.80s{c.Style.RESET_ALL}', + papis.document.describe(doc)) if keys: docs[j].update( {k: libdoc.get(k) for k in keys if libdoc.has(k)}) @@ -283,7 +333,7 @@ def _save(ctx: click.Context, bibfile: str, force: bool) -> None: print('Not saving..') return with open(bibfile, 'w+') as fd: - logger.info('Saving {1} documents in {0}..'.format(bibfile, len(docs))) + logger.info("Saving %d documents in '%s'", len(docs), bibfile) fd.write(papis.commands.export.run(docs, to_format='bibtex')) @@ -334,18 +384,18 @@ def _unique(ctx: click.Context, key: str, o: Optional[str]) -> None: if doc.get(key) == bottle.get(key): indices.append(i) duplis_docs.append(bottle) - logger.info('{}. repeated {} ⇒ {}' - .format(len(duplis_docs), key, doc.get(key))) + logger.info( + '%d repeated %s -> %s', + len(duplis_docs), key, doc.get(key)) docs = [d for (i, d) in enumerate(docs) if i not in indices] - logger.info("Unique : {}".format(len(unique_docs))) - logger.info("Discarded: {}".format(len(duplis_docs))) + logger.info("Unique : %d", len(unique_docs)) + logger.info("Discarded: %d", len(duplis_docs)) ctx.obj['documents'] = unique_docs if o: with open(o, 'w+') as f: - logger.info('Saving {1} documents in {0}..' - .format(o, len(duplis_docs))) + logger.info("Saving %d documents in '%s'", len(duplis_docs), o) f.write(papis.commands.export.run(duplis_docs, to_format='bibtex')) @@ -360,19 +410,18 @@ def _unique(ctx: click.Context, key: str, o: Optional[str]) -> None: def _doctor(ctx: click.Context, key: List[str]) -> None: """ Check bibfile for correctness, missing keys etc. - e.g. papis bibtex -k title -k url -k doi + e.g. papis bibtex doctor -k title -k url -k doi """ - logger.info("Checking for existence of %s", ", ".join(key)) + logger.info("Checking for existence of keys %s", ", ".join(key)) failed = [(d, keys) for d, keys in [(d, [k for k in key if not d.has(k)]) for d in ctx.obj['documents']] if keys] for j, (doc, keys) in enumerate(failed): - logger.info('{} {c.Back.BLACK}{c.Fore.RED}{doc: <80.80}' - '{c.Style.RESET_ALL}' - .format(j, doc=papis.document.describe(doc), c=colorama)) + logger.info('%s {c.Back.BLACK}{c.Fore.RED}%-80.80s{c.Style.RESET_ALL}', + j, papis.document.describe(doc)) for k in keys: logger.info('\tmissing: %s', k) @@ -425,9 +474,8 @@ def _iscited(ctx: click.Context, _files: List[str]) -> None: logger.info('%s documents not cited', len(unfound)) for j, doc in enumerate(unfound): - logger.info('{} {c.Back.BLACK}{c.Fore.RED}{doc: <80.80}' - '{c.Style.RESET_ALL}' - .format(j, doc=papis.document.describe(doc), c=colorama)) + logger.info('%s {c.Back.BLACK}{c.Fore.RED}%-80.80s{c.Style.RESET_ALL}', + j, papis.document.describe(doc)) @cli.command('import') @@ -456,29 +504,28 @@ def _import(ctx: click.Context, out: Optional[str], _all: bool) -> None: fileValue = None filepaths = [] for k in ["file", "FILE"]: - logger.info('{} {c.Back.BLACK}{c.Fore.YELLOW}{doc: <80.80}' - '{c.Style.RESET_ALL}' - .format(j, doc=papis.document.describe(doc), - c=colorama)) + logger.info( + '%s {c.Back.BLACK}{c.Fore.YELLOW}%-80.80s' + '{c.Style.RESET_ALL}', + j, papis.document.describe(doc)) if doc.has(k): fileValue = doc[k] - logger.info("\tkey '%s' exists", k) + logger.info("\tKey '%s' exists", k) break if not fileValue: logger.info("\t" "{c.Back.YELLOW}{c.Fore.BLACK}" - "no pdf files will be imported" - "{c.Style.RESET_ALL}".format(c=colorama)) + "No pdf files will be imported" + "{c.Style.RESET_ALL}") else: filepaths = [f for f in fileValue.split(":") if os.path.exists(f)] if not filepaths and fileValue is not None: logger.info("\t" "{c.Back.BLACK}{c.Fore.RED}" - "I could not find a valid file in \n" - "{value}{c.Style.RESET_ALL}" - .format(value=fileValue, c=colorama)) + "No valid file in \n%s{c.Style.RESET_ALL}", + fileValue) else: logger.info("\tfound %s file(s)", len(filepaths)) |