Merge branch 'main' of github.com:pubs/pubs

2021-11-29 09:51:18 +01:00 · 2021-11-29 09:51:18 +01:00 · dfc332006e
commit dfc332006e
parent 9856193952 4ec4ba0390
41 changed files with 405 additions and 320 deletions
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@ -0,0 +1,60 @@
+name: Pubs tests
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 8 * * *'
+
+
+jobs:
+  unit-test:
+    name: Run unit tests
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r dev_requirements.txt
+      - name: Configure git author (fix issue with environment variable)
+        run: |
+          # Manually sets some git user and email to avoid failure of the test
+          # (For some reason the environment variables set in the test are not
+          # taken into account by git on the runner.)
+          git config --global user.name "Pubs test"
+          git config --global user.email "unittest@pubs.org"
+      - name: Test with pytest (mock API mode)
+        env:
+          PUBS_TESTS_MODE: MOCK
+        run: pytest
+      - name: Test with pytest (online API mode)
+        env:
+          PUBS_TESTS_MODE: COLLECT
+        run: pytest
+
+  install-test:
+    name: Test installation
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    if: github.event_name == 'schedule'
+
+    steps:
+      - uses: actions/setup-python@v2
+      - name: install test
+        run: |
+          pip install -U pip
+          pip install pubs
+          pubs --help
+          pip uninstall -y pubs
--- a/.travis.yml
+++ b/.travis.yml
@ -1,105 +0,0 @@
-# list of environments to test
-matrix:
-  include:
-
-    # Full tests (with online API)
-    - os: linux
-      language: python
-      python: 2.7
-      env:
-        - TO_TEST=TEST_FULL
-    - os: linux
-      language: python
-      python: 3.7
-      dist: xenial
-      sudo: true
-      env:
-        - TO_TEST=TEST_FULL
-    - os: osx
-      language: generic
-      python: 2.7
-      env:
-        - TO_TEST=TEST_FULL
-      # before_install:
-      #   - python2 --version
-      #   - pip2 install -U virtualenv
-      #   - virtualenv env -p python2
-      #   - source env/bin/activate
-    - os: osx
-      language: generic
-      python: ">=3.6"
-      env:
-        - TO_TEST=TEST_FULL
-      before_install:
-        - brew outdated python3 || brew install python3 || brew upgrade python3
-        - python3 -m venv env
-        - source env/bin/activate
-
-    # Mock tests (with mock API)
-    - os: linux
-      language: python
-      python: 3.3
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      python: 3.4
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      python: 3.5
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      python: 3.6
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      dist: xenial
-      python: 3.7
-      sudo: true
-      env:
-        - TO_TEST=TEST_MOCK
-
-
-    # Install tests
-    - os: linux
-      language: python
-      python: 2.7
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-    - os: linux
-      language: python
-      dist: xenial
-      sudo: true
-      python: 3.7
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-    - os: osx
-      language: generic
-      python: 2.7
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-    - os: osx
-      language: generic
-      python: ">=3.6"
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-
-  allow_failures:
-    - python: 3.3
-
-# command to run tests
-script:
-  - python --version
-  - if [ "$TO_TEST" = "TEST_MOCK" ] ||
-       [ "$TO_TEST" = "TEST_FULL" ]; then PUBS_TESTS_MODE=MOCK    python setup.py test; fi
-  - if [ "$TO_TEST" = "TEST_FULL" ]; then PUBS_TESTS_MODE=COLLECT python setup.py test; fi
-  - if [ "$TO_TEST" = "INSTALL" ]; then pip install -U pip && pip install pubs && pubs --help && pip uninstall -y pubs; fi
--- a/changelog.md
+++ b/changelog.md
@ -5,8 +5,24 @@

 [Full Changelog](https://github.com/pubs/pubs/compare/v0.8.3...master)

+### Implemented enhancements
+
+- 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))
+- The number of displayed authors in listings is now configurable, as the `max_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225))
+- More explicit add command dialogs when copying and moving documents.
+- Empty tags are not added to papers anymore.
+
 ### Fixed bugs

+- Fixed collision when entry uses `type` field ([#252](https://github.com/pubs/pubs/pull/252))
+- Note on comma in alias descriptions ([#240](https://github.com/pubs/pubs/pull/240) [StanczakDominik](https://github.com/StanczakDominik))
+- Note path correctly expand user '~' ([#250](https://github.com/pubs/pubs/pull/250))
+- Tests don't run on python 2.7 or <=3.4. They may still work, but support will not be tested and will eventually be dropped. ([#223](https://github.com/pubs/pubs/pull/223))
+- Fixed the reported number of paper with a tag in the statistic command ([#232](https://github.com/pubs/pubs/pull/232)  by [beuerle](https://github.com/beuerle))
+- Fixed a crash when resolving citekeys introduced by [#225](https://github.com/pubs/pubs/pull/225) ([#233](https://github.com/pubs/pubs/pull/233)  by [beuerle](https://github.com/beuerle))
+

 ## [v0.8.3](https://github.com/pubs/pubs/compare/v0.8.2...v0.8.3) (2019-08-12)

@ -38,7 +54,6 @@ A hotfix release. All users of 0.8.0 are urged to upgrade.
 ### Fixed bugs

 - Fix adding paper with DOIs, ISBNs or arXiv references. [(#165)](https://github.com/pubs/pubs/pull/165)
-
 - Fix statistics command when there is not yet any paper in the repository. [(#164)](https://github.com/pubs/pubs/pull/164)


@ -49,69 +64,39 @@ A long overdue feature release. Add supports for arXiv bibtex fetching, and many
 ### Implemented enhancements

 - Adds `move`, and `link` options for handling of documents during `import` (copy being the default). Makes `copy` the default for document handling during `add`. [(#159)](https://github.com/pubs/pubs/pull/159)
-
 - Support for downloading arXiv reference from their ID ([#146](https://github.com/pubs/pubs/issues/146) by [joe-antognini](https://github.com/joe-antognini))
-
 - Better feedback when an error is encountered while adding a reference from a DOI, ISBN or arXiv ID [#155](https://github.com/pubs/pubs/issues/155)
-
 - Better dialog after editing paper [(#142)](https://github.com/pubs/pubs/issues/142)
-
 - Add a command to open urls ([#139](https://github.com/pubs/pubs/issues/139) by [ksunden](https://github.com/ksunden))
-
 - More robust cache on version change [(#138)](https://github.com/pubs/pubs/issues/138)
-
 - Allow utf8 citekeys [(#133)](https://github.com/pubs/pubs/issues/133)
-
 - Adds tag list completion in `pubs add -t ` [(#130)](https://github.com/pubs/pubs/issues/130)
-
 - Wider Travis coverage ([#107](https://github.com/pubs/pubs/issues/107) and [#108](https://github.com/pubs/pubs/issues/108))
-
 - Uses bibtexparser bwriter instead of internal encoder and adds `--ignore-fields` option to export. [(#106)](https://github.com/pubs/pubs/issues/106)
-
 - Configurable alias descriptions ([#104](https://github.com/pubs/pubs/issues/104) by [wflynny](https://github.com/wflynny))
-
 - Support year ranges in query [(#102)](https://github.com/pubs/pubs/issues/102)
-
 - Tests can now be run with `python setup.py test` [#155](https://github.com/pubs/pubs/issues/155)

 ### Fixed bugs

 - [[#144]](https://github.com/pubs/pubs/issues/144) More robust handling of the `doc_add` options [(#159)](https://github.com/pubs/pubs/pull/159)
-
 - [[#149]](https://github.com/pubs/pubs/issues/149) More robust handling of parsing and citekey errors [(#87)](https://github.com/pubs/pubs/pull/87)
-
 - [[#148]](https://github.com/pubs/pubs/issues/148) Fix compatibility with Pyfakefs 3.7 [(#151)](https://github.com/pubs/pubs/pull/151)
-
 - [[#95]](https://github.com/pubs/pubs/issues/95) Error message when editor is missing [(#141)](https://github.com/pubs/pubs/issues/141)
-
 - Fixes tests for printing help on `--help` and without argument. [(#137)](https://github.com/pubs/pubs/issues/137)
-
 - [[#126]](https://github.com/pubs/pubs/issues/126) Removes journal customization [(#127)](https://github.com/pubs/pubs/issues/127)
-
 - Fixes Travis failure on installing python3 for OSX [(#125)](https://github.com/pubs/pubs/issues/125)
-
 - [[#119]](https://github.com/pubs/pubs/issues/119) Removes link and DOI customization. [(#124)](https://github.com/pubs/pubs/issues/124)
-
 - [[#122]](https://github.com/pubs/pubs/issues/122) Fixes common strings [(#123)](https://github.com/pubs/pubs/issues/123)
-
 - [[#28]](https://github.com/pubs/pubs/issues/28) allow utf8 in citekeys [(#120)](https://github.com/pubs/pubs/issues/120)
-
 - Fixes field orders to use 'url' and fixes broken test. [(#118)](https://github.com/pubs/pubs/issues/118)
-
 - [[#25]](https://github.com/pubs/pubs/issues/25) Fix bibtex testcase [(#117)](https://github.com/pubs/pubs/issues/117)
-
 - [[#103]](https://github.com/pubs/pubs/issues/103) Fixes unicode comparison [(#116)](https://github.com/pubs/pubs/issues/116)
-
 - [[#95]](https://github.com/pubs/pubs/issues/95) robust handling of DOIs ([#105](https://github.com/pubs/pubs/issues/105) by [wflynny](https://github.com/wflynny))
-
 - [[#99]](https://github.com/pubs/pubs/issues/99) Print help when no subcommand is provided ([#100](https://github.com/pubs/pubs/issues/100) by [wflynny](https://github.com/wflynny))
-
 - Fix defaults not used in config. [(#97)](https://github.com/pubs/pubs/issues/97)
-
 - Fixes content not read from urls because of call to `os.abspath` [(#96)](https://github.com/pubs/pubs/issues/96)
-
 - [[#93]](https://github.com/pubs/pubs/issues/93) actually save the modifications on `edit -m`. [(#94)](https://github.com/pubs/pubs/issues/94)
-
 - [[#88]](https://github.com/pubs/pubs/issues/88) Adds proper escaping for
 arguments in alias plugin. [(#91)](https://github.com/pubs/pubs/issues/91)

--- a/dev_requirements.txt
+++ b/dev_requirements.txt
@ -20,6 +20,6 @@ six
 # those are the additional packages required to run the tests
 pyfakefs
 certifi
-ddt
+ddt>=1.4.1
 mock
-pytest # optional (python setup.py test works without it), but possible nonetheless
+pytest
--- a/pubs/bibstruct.py
+++ b/pubs/bibstruct.py
@ -16,7 +16,7 @@ from .p3 import ustr, uchr

 # Citekey stuff

-TYPE_KEY = 'type'
+TYPE_KEY = 'ENTRYTYPE'

 CONTROL_CHARS = ''.join(map(uchr, list(range(0, 32)) + list(range(127, 160))))
 CITEKEY_FORBIDDEN_CHARS = '@\'\\,#}{~%/ '  # '/' is OK for bibtex but forbidden
--- a/pubs/color.py
+++ b/pubs/color.py
@ -144,7 +144,7 @@ def setup(conf, force_colors=False):


 # undye
-undye_re = re.compile('\x1b\[[;\d]*[A-Za-z]')
+undye_re = re.compile('\x1b\\[[;\\d]*[A-Za-z]')

 def undye(s):
    """Purge string s of color"""
--- a/pubs/commands/add_cmd.py
+++ b/pubs/commands/add_cmd.py
@ -6,6 +6,7 @@ from .. import p3
 from .. import bibstruct
 from .. import content
 from .. import repo
+from .. import color
 from .. import paper
 from .. import templates
 from .. import apis
@ -150,15 +151,17 @@ def command(conf, args):
        doc_add = conf['main']['doc_add']

    rp.push_paper(p)
-    ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p)))
+    ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])))
    if docfile is not None:
-        rp.push_doc(p.citekey, docfile, copy=(doc_add in ('copy', 'move')))
-        if doc_add == 'move' and content.content_type(docfile) != 'url':
-            content.remove_file(docfile)
+        rp.push_doc_paper(p, docfile, copy=(doc_add in ('copy', 'move')))

-        if doc_add == 'move':
-            ui.message('{} was moved to the pubs repository.'.format(docfile))
-        elif doc_add == 'copy':
-                ui.message('{} was copied to the pubs repository.'.format(docfile))
+        if doc_add in ('move', 'copy'):
+            if doc_add == 'move' and content.content_type(docfile) != 'url':
+                content.remove_file(docfile)
+
+            docpath = content.system_path(rp.databroker.real_docpath(p.docpath))
+            verb = 'moved' if doc_add == 'move' else 'copied'
+            ui.message('{} was {} to {} inside the pubs repository.'.format(color.dye_out(docfile, 'filepath'), verb,
+                                                                            color.dye_out(docpath, 'filepath')))

    rp.close()
--- a/pubs/commands/doc_cmd.py
+++ b/pubs/commands/doc_cmd.py
@ -34,7 +34,7 @@ def parser(subparsers, conf):
                            ).completer = CiteKeyCompletion(conf)
    add_exclusives = add_parser.add_mutually_exclusive_group()
    add_exclusives.add_argument(
-        '-L', '--link', action='store_false', dest='link', default=False,
+        '-L', '--link', action='store_true', dest='link', default=False,
        help='do not copy document files, just create a link')
    add_exclusives.add_argument(
        '-M', '--move', action='store_true', dest='move', default=False,
@ -71,7 +71,7 @@ def command(conf, args):
    # ui.exit()

    if args.action == 'add':
-        citekey = resolve_citekey(rp, args.citekey[0], ui=ui, exit_on_fail=True)
+        citekey = resolve_citekey(rp, conf, args.citekey[0], ui=ui, exit_on_fail=True)
        paper = rp.pull_paper(citekey)

        if paper.docpath is not None and not args.force:
@ -92,13 +92,14 @@ def command(conf, args):
        if not args.link and args.move:
            content.remove_file(document)

+        # FIXME: coherence with add command, the destination location should be given when copying/moving.
        ui.message('{} added to {}'.format(
            color.dye_out(document, 'filepath'),
            color.dye_out(paper.citekey, 'citekey')))

    elif args.action == 'remove':

-        for key in resolve_citekey_list(rp, args.citekeys, ui=ui, exit_on_fail=True):
+        for key in resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True):
            paper = rp.pull_paper(key)

            # if there is no document (and the user cares) -> inform + continue
@ -126,7 +127,7 @@ def command(conf, args):
                color.dye_err(args.path[0], 'filepath')))
            ui.exit(1)

-        for key in resolve_citekey_list(rp, args.citekeys, ui=ui, exit_on_fail=True):
+        for key in resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True):
            try:
                paper = rp.pull_paper(key)
                doc = paper.docpath
@ -143,7 +144,7 @@ def command(conf, args):

    elif args.action == 'open':
        with_command = args.cmd
-        citekey = resolve_citekey(rp, args.citekey[0], ui=ui, exit_on_fail=True)
+        citekey = resolve_citekey(rp, conf, args.citekey[0], ui=ui, exit_on_fail=True)
        paper = rp.pull_paper(citekey)

        if paper.docpath is None:
--- a/pubs/commands/edit_cmd.py
+++ b/pubs/commands/edit_cmd.py
@ -2,6 +2,7 @@ from __future__ import unicode_literals

 from ..paper import Paper
 from .. import repo
+from .. import color

 from ..uis import get_ui
 from ..endecoder import EnDecoder
@ -29,7 +30,7 @@ def command(conf, args):
    meta = args.meta

    rp = repo.Repository(conf)
-    citekey = resolve_citekey(rp, args.citekey, ui=ui, exit_on_fail=True)
+    citekey = resolve_citekey(rp, conf, args.citekey, ui=ui, exit_on_fail=True)
    paper = rp.pull_paper(citekey)

    coder = EnDecoder()
@ -55,17 +56,18 @@ def command(conf, args):
                new_paper = Paper(paper.citekey, paper.bibdata,
                                  metadata=content)
                rp.push_paper(new_paper, overwrite=True, event=False)
-                ui.info(('The metadata of paper `{}`  was successfully '
-                         'edited.'.format(citekey)))
+                ui.info(("The metadata of paper '{}' was successfully "
+                         "edited.".format(color.dye_out(citekey, 'citekey'))))
            else:
                new_paper = Paper.from_bibentry(content,
                                                metadata=paper.metadata)
                if rp.rename_paper(new_paper, old_citekey=paper.citekey):
-                    ui.info(('Paper `{}` was successfully edited and renamed '
-                             'as `{}`.'.format(citekey, new_paper.citekey)))
+                    ui.info(("Paper '{}' was successfully edited and renamed "
+                             "as '{}'.".format(color.dye_out(citekey, 'citekey'),
+                                               color.dye_out(new_paper.citekey, 'citekey'))))
                else:
-                    ui.info(('Paper `{}` was successfully edited.'.format(
-                        citekey)))
+                    ui.info(("Paper '{}' was successfully edited.".format(
+                             color.dye_out(citekey, 'citekey'))))
            break

        except coder.BibDecodingError:
@ -84,7 +86,7 @@ def command(conf, args):
                break
            elif choice == 'overwrite':
                paper = rp.push_paper(paper, overwrite=True)
-                ui.info(('Paper `{}` was overwritten.'.format(citekey)))
+                ui.info(('Paper `{}` was overwritten.'.format(color.dye_out(citekey, 'citekey'))))
                break
            # else edit again
        # Also handle malformed bibtex and metadata
--- a/pubs/commands/export_cmd.py
+++ b/pubs/commands/export_cmd.py
@ -46,7 +46,7 @@ def command(conf, args):
    if len(args.citekeys) < 1:
        papers = rp.all_papers()
    else:
-        for key in resolve_citekey_list(repo=rp, citekeys=args.citekeys, ui=ui, exit_on_fail=True):
+        for key in resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True):
            papers.append(rp.pull_paper(key))

    bib = {}
--- a/pubs/commands/list_cmd.py
+++ b/pubs/commands/list_cmd.py
@ -54,7 +54,7 @@ def command(conf, args):
        papers = sorted(papers, key=date_added)
    if len(papers) > 0:
        ui.message('\n'.join(
-            pretty.paper_oneliner(p, citekey_only=args.citekeys)
+            pretty.paper_oneliner(p, citekey_only=args.citekeys, max_authors=conf['main']['max_authors'])
            for p in papers))

    rp.close()
--- a/pubs/commands/note_cmd.py
+++ b/pubs/commands/note_cmd.py
@ -23,7 +23,7 @@ def command(conf, args):

    ui = get_ui()
    rp = repo.Repository(conf)
-    citekey = resolve_citekey(rp, args.citekey, ui=ui, exit_on_fail=True)
+    citekey = resolve_citekey(rp, conf, args.citekey, ui=ui, exit_on_fail=True)
    notepath = rp.databroker.real_notepath(citekey, rp.conf['main']['note_extension'])
    if args.append is None:
        ui.edit_file(notepath, temporary=False)
--- a/pubs/commands/remove_cmd.py
+++ b/pubs/commands/remove_cmd.py
@ -2,6 +2,7 @@ from __future__ import unicode_literals

 from .. import repo
 from .. import color
+from .. import pretty
 from ..uis import get_ui
 from ..utils import resolve_citekey_list
 from ..p3 import ustr, u_maybe
@ -24,12 +25,16 @@ def command(conf, args):
    force = args.force
    rp = repo.Repository(conf)

-    keys = resolve_citekey_list(repo=rp, citekeys=args.citekeys, ui=ui, exit_on_fail=True)
+    keys = resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True)
+    plural = 's' if len(keys) > 1 else ''

    if force is None:
-        are_you_sure = (("Are you sure you want to delete the publication(s) [{}]"
-            " (this will also delete associated documents)?")
-            .format(', '.join([color.dye_out(c, 'citekey') for c in args.citekeys])))
+        to_remove_str = '\n'.join(pretty.paper_oneliner(rp.pull_paper(key),
+                                                        max_authors=conf['main']['max_authors'])
+                                  for key in keys)
+        are_you_sure = (("Are you sure you want to delete the following publication{}"
+            " (this will also delete associated documents)?:\n{}\n")
+            .format(plural, to_remove_str))
        sure = ui.input_yn(question=are_you_sure, default='n')
    if force or sure:
        failed = False  # Whether something failed
@ -42,11 +47,12 @@ def command(conf, args):
        if failed:
            ui.exit()  # Exit with nonzero error code
        else:
-            ui.message('The publication(s) [{}] were removed'.format(
+
+            ui.message('The publication{} {} were removed'.format(plural,
                ', '.join([color.dye_out(c, 'citekey') for c in keys])))

        # FIXME: print should check that removal proceeded well.
    else:
-        ui.message('The publication(s) [{}] were {} removed'.format(
+        ui.message('The publication{} {} were {} removed'.format(plural,
            ', '.join([color.dye_out(c, 'citekey') for c in keys]),
            color.dye_out('not','bold')))
--- a/pubs/commands/rename_cmd.py
+++ b/pubs/commands/rename_cmd.py
@ -26,7 +26,7 @@ def command(conf, args):
    rp = repo.Repository(conf)

    # TODO: here should be a test whether the new citekey is valid
-    key = resolve_citekey(repo=rp, citekey=args.citekey, ui=ui, exit_on_fail=True)
+    key = resolve_citekey(rp, conf, args.citekey, ui=ui, exit_on_fail=True)
    paper = rp.pull_paper(key)
    rp.rename_paper(paper, args.new_citekey)
    ui.message("The '{}' citekey has been renamed into '{}'".format(
--- a/pubs/commands/statistics_cmd.py
+++ b/pubs/commands/statistics_cmd.py
@ -22,7 +22,7 @@ def command(conf, args):
    else:
        doc_count = sum([0 if p.docpath is None else 1 for p in papers])
        tag_count = len(list(rp.get_tags()))
-        papers_with_tags = sum([0 if p.tags else 1 for p in papers])
+        papers_with_tags = sum([1 if p.tags else 0 for p in papers])

        ui.message(color.dye_out('Repository statistics:', 'bold'))
        ui.message('Total papers: {}, {} ({}) have a document attached'.format(
--- a/pubs/commands/tag_cmd.py
+++ b/pubs/commands/tag_cmd.py
@ -55,7 +55,9 @@ def _parse_tag_seq(s):
            if last != 0:
                raise ValueError('could not match tag expression')
        else:
-            tags.append(s[last:(m.start())])
+            tag = s[last:(m.start())]
+            if len(tag) > 0:
+                tags.append(s[last:(m.start())])
        last = m.start()
    if last == len(s):
        raise ValueError('could not match tag expression')
@ -89,7 +91,7 @@ def command(conf, args):
    else:
        not_citekey = False
        try:
-            citekeyOrTag = resolve_citekey(repo=rp, citekey=citekeyOrTag, ui=ui, exit_on_fail=True)
+            citekeyOrTag = resolve_citekey(rp, conf, citekeyOrTag, ui=ui, exit_on_fail=True)
        except SystemExit:
            not_citekey = True
        if not not_citekey:
@ -117,7 +119,7 @@ def command(conf, args):
                    len(p.tags.intersection(excluded)) == 0):
                    papers_list.append(p)

-            ui.message('\n'.join(pretty.paper_oneliner(p)
+            ui.message('\n'.join(pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])
                                 for p in papers_list))

        rp.close()
--- a/pubs/commands/url_cmd.py
+++ b/pubs/commands/url_cmd.py
@ -22,7 +22,7 @@ def command(conf, args):
    ui = get_ui()
    rp = repo.Repository(conf)

-    for key in resolve_citekey_list(rp, args.citekey, ui=ui, exit_on_fail=False):
+    for key in resolve_citekey_list(rp, conf, args.citekey, ui=ui, exit_on_fail=False):
        try:
            paper = rp.pull_paper(key)
            url = paper.bibdata['url']
--- a/pubs/config/spec.py
+++ b/pubs/config/spec.py
@ -27,6 +27,10 @@ edit_cmd = string(default='')
 # Which default extension to use when creating a note file.
 note_extension = string(default='txt')

+# How many authors to display when displaying a citation. If there are more
+# authors, only the first author is diplayed followed by 'et al.'.
+max_authors = integer(default=3)
+
 # If true debug mode is on which means exceptions are not catched and
 # the full python stack is printed.
 debug = boolean(default=False)
@ -115,6 +119,9 @@ active = force_list(default=list('alias'))
 # command = !pubs list -k | wc -l
 # description = lists number of pubs in repo

+# To use commas in the description, wrap them in a "" string. For example:
+# description = "lists number of pubs in repo, greets the user afterward"
+
 [[git]]
 # The git plugin will commit changes to the repository in a git repository
 # created at the root of the pubs directory. All detected changes will be
--- a/pubs/content.py
+++ b/pubs/content.py
@ -114,7 +114,7 @@ def write_file(filepath, data, mode='w'):

 def content_type(path):
    parsed = urlparse(path)
-    if parsed.scheme == 'http':
+    if parsed.scheme in ('http', 'https'):
        return 'url'
    else:
        return 'file'
--- a/pubs/endecoder.py
+++ b/pubs/endecoder.py
@ -51,7 +51,6 @@ def customizations(record):
    """

    # record = bp.customization.convert_to_unicode(record) # transform \& into & ones, messing-up latex
-    record = bp.customization.type(record)
    record = bp.customization.author(record)
    record = bp.customization.editor(record)
    record = bp.customization.keyword(record)
@ -119,18 +118,18 @@ class EnDecoder(object):
                keyword for keyword in entry['keyword'])
        return entry

-    def decode_bibdata(self, bibdata):
+    def decode_bibdata(self, bibstr):
        """Decodes bibdata from string.

        If the decoding fails, returns a BibDecodingError.
        """
-        if len(bibdata) == 0:
+        if len(bibstr) == 0:
            error_msg = 'parsing error: the provided string has length zero.'
-            raise self.BibDecodingError(error_msg, bibdata)
+            raise self.BibDecodingError(error_msg, bibstr)
        try:
            entries = bp.bparser.BibTexParser(
-                bibdata, common_strings=True, customization=customizations,
-                homogenize_fields=True).get_entry_dict()
+                bibstr, common_strings=True, customization=customizations,
+                homogenize_fields=True, ignore_nonstandard_types=False).get_entry_dict()
            # Remove id from bibtexparser attribute which is stored as citekey
            for e in entries:
                entries[e].pop(BP_ID_KEY)
@ -147,13 +146,13 @@ class EnDecoder(object):
                return entries
            else:
                raise self.BibDecodingError(('no valid entry found in the provided data: '
-                                            ' {}').format(bibdata), bibdata)
+                                            ' {}').format(bibstr), bibstr)
        except (pyparsing.ParseException, pyparsing.ParseSyntaxException) as e:
            error_msg = self._format_parsing_error(e)
-            raise self.BibDecodingError(error_msg, bibdata)
+            raise self.BibDecodingError(error_msg, bibstr)
        except bibtexparser.bibdatabase.UndefinedString as e:
            error_msg = 'parsing error: undefined string in provided data: {}'.format(e)
-            raise self.BibDecodingError(error_msg, bibdata)
+            raise self.BibDecodingError(error_msg, bibstr)

    @classmethod
    def _format_parsing_error(cls, e):
--- a/pubs/filebroker.py
+++ b/pubs/filebroker.py
@ -16,7 +16,7 @@ def filter_filename(filename, ext):
    """ Return the filename without the extension if the extension matches ext.
        Otherwise return None
    """
-    pattern = '.*\{}$'.format(ext)
+    pattern = '.*\\{}$'.format(ext)
    if re.match(pattern, filename) is not None:
        return u_maybe(filename[:-len(ext)])

@ -154,7 +154,7 @@ class DocBroker(object):

    def __init__(self, directory, scheme='docsdir', subdir='doc'):
        self.scheme = scheme
-        self.docdir = os.path.join(directory, subdir)
+        self.docdir = os.path.expanduser(os.path.join(directory, subdir))
        if not check_directory(self.docdir, fail=False):
            os.mkdir(system_path(self.docdir))

--- a/pubs/plugs/git/git.py
+++ b/pubs/plugs/git/git.py
@ -16,11 +16,13 @@ GITIGNORE = """# files or directories for the git plugin to ignore


 class GitPlugin(PapersPlugin):
-    """The git plugin creates a git repository in the pubs directory and commit the changes
-    to the pubs repository everytime a paper is modified.
+    """Make the pubs repository also a git repository.

-    It also add the `pubs git` subcommand, so git commands can be executed in the git repository
-    from the command line.
+    The git plugin creates a git repository in the pubs directory
+    and commit the changes to the pubs repository.
+
+    It also add the `pubs git` subcommand, so git commands can be executed
+    in the git repository from the command line.
    """

    name = 'git'
@ -28,10 +30,10 @@ class GitPlugin(PapersPlugin):

    def __init__(self, conf, ui):
        self.ui = ui
-        self.pubsdir     = os.path.expanduser(conf['main']['pubsdir'])
-        self.manual      = conf['plugins'].get('git', {}).get('manual', False)
+        self.pubsdir = os.path.expanduser(conf['main']['pubsdir'])
+        self.manual = conf['plugins'].get('git', {}).get('manual', False)
        self.force_color = conf['plugins'].get('git', {}).get('force_color', True)
-        self.quiet   = conf['plugins'].get('git', {}).get('quiet', True)
+        self.quiet = conf['plugins'].get('git', {}).get('quiet', True)
        self.list_of_changes = []
        self._gitinit()

@ -72,17 +74,18 @@ class GitPlugin(PapersPlugin):
        """
        colorize = ' -c color.ui=always' if self.force_color else ''
        git_cmd = 'git -C {}{} {}'.format(self.pubsdir, colorize, cmd)
-        #print(git_cmd)
        p = Popen(git_cmd, stdin=PIPE, stdout=PIPE, stderr=STDOUT, shell=True)
        output, err = p.communicate(input_stdin)
        p.wait()

        if p.returncode != 0:
-            raise RuntimeError('The git plugin encountered an error when running the git command:\n' +
-                '{}\n\nReturned output:\n{}\n'.format(git_cmd, output.decode('utf-8')) +
-                'If needed, you may fix the state of the {} git repository '.format(self.pubsdir) +
-                'manually.\nIf relevant, you may submit a bug report at ' +
-                'https://github.com/pubs/pubs/issues')
+            raise RuntimeError((
+                'The git plugin encountered an error when running the git command:\n'
+                '{}\n\n'
+                'Returned output:\n{}\n'
+                'If needed, you may fix the state of the {} git repository manually.\n'
+                'If relevant, you may submit a bug report at https://github.com/pubs/pubs/issues'
+            ).format(git_cmd, output.decode('utf-8'), self.pubsdir))
        elif command:
            self.ui.message(output.decode('utf-8'), end='')
        elif not self.quiet:
@ -97,10 +100,11 @@ def paper_change_event(event):
        git = GitPlugin.get_instance()
        if not git.manual:
            event_desc = event.description
-            for a, b in [('\\','\\\\'), ('"','\\"'), ('$','\\$'), ('`','\\`')]:
+            for a, b in [('\\', '\\\\'), ('"', '\\"'), ('$', '\\$'), ('`', '\\`')]:
                event_desc = event_desc.replace(a, b)
            git.list_of_changes.append(event_desc)

+
@PostCommandEvent.listen()
 def git_commit(event):
    if GitPlugin.is_loaded():
--- a/pubs/pretty.py
+++ b/pubs/pretty.py
@ -23,19 +23,24 @@ def person_repr(p):
        ' '.join(p.lineage(abbr=True))] if s)


-def short_authors(bibdata):
+def short_authors(bibdata, max_authors=3):
+    """
+    :param max_authors:  number of authors to display completely. Additional authors will be
+                       represented by 'et al.'.
+    """
    try:
        authors = [p for p in bibdata['author']]
-        if len(authors) < 3:
-            return ' and '.join(authors)
+        if 0 < max_authors < len(authors):
+            authors_str = '{} et al.'.format(authors[0])
        else:
-            return authors[0] + (' et al.' if len(authors) > 1 else '')
+            authors_str = ' and '.join(authors)
+        return authors_str
    except KeyError:  # When no author is defined
        return ''


-def bib_oneliner(bibdata):
-    authors = short_authors(bibdata)
+def bib_oneliner(bibdata, max_authors=3):
+    authors = short_authors(bibdata, max_authors=max_authors)
    journal = ''
    if 'journal' in bibdata:
        journal = ' ' + bibdata['journal']
@ -60,11 +65,11 @@ def bib_desc(bib_data):
    return s


-def paper_oneliner(p, citekey_only=False):
+def paper_oneliner(p, citekey_only=False, max_authors=3):
    if citekey_only:
        return p.citekey
    else:
-        bibdesc = bib_oneliner(p.get_unicode_bibdata())
+        bibdesc = bib_oneliner(p.get_unicode_bibdata(), max_authors=max_authors)
        doc_str = ''
        if p.docpath is not None:
            doc_extension = os.path.splitext(p.docpath)[1]
--- a/pubs/repo.py
+++ b/pubs/repo.py
@ -182,17 +182,22 @@ class Repository(object):
            events.RenameEvent(paper, old_citekey).send()
            return True

+
    def push_doc(self, citekey, docfile, copy=None):
        p = self.pull_paper(citekey)
+        return self.push_doc_paper(p, docfile, copy=copy)
+
+    def push_doc_paper(self, paper, docfile, copy=None):
+        """Same as push_doc, only the Paper instance is provided rather than the citekey"""
        if copy is None:
            copy = self.conf['main']['doc_add'] in ('copy', 'move')
        if copy:
-            docfile = self.databroker.add_doc(citekey, docfile)
+            docfile = self.databroker.add_doc(paper.citekey, docfile)
        else:
            docfile = system_path(docfile)
-        p.docpath = docfile
-        self.push_paper(p, overwrite=True, event=False)
-        events.DocAddEvent(citekey).send()
+        paper.docpath = docfile
+        self.push_paper(paper, overwrite=True, event=False)
+        events.DocAddEvent(paper.citekey).send()

    def unique_citekey(self, base_key, bibentry):
        """Create a unique citekey for a given base key.
--- a/pubs/uis.py
+++ b/pubs/uis.py
@ -3,6 +3,7 @@ from __future__ import print_function, unicode_literals
 import os
 import sys
 import shlex
+import errno
 import locale
 import codecs
 import tempfile
@ -237,7 +238,7 @@ class InputUI(PrintUI):
        try:
            subprocess.call(cmd)
        except OSError as e:
-            if e.errno == os.errno.ENOENT:
+            if e.errno == errno.ENOENT:
                self.error(("Error while calling editor '{}'. The editor may "
                            "not be present. You can change the text editor "
                            "that pubs uses by setting the $EDITOR environment "
--- a/pubs/utils.py
+++ b/pubs/utils.py
@ -7,7 +7,7 @@ from . import color
 from . import pretty


-def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
+def resolve_citekey(repo, conf, citekey, ui=None, exit_on_fail=True):
    """Check that a citekey exists, or autocompletes it if not ambiguous.
        :returns found citekey
    """
@ -29,22 +29,23 @@ def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
    elif citekey not in citekeys:
        if ui is not None:
            citekeys = sorted(citekeys)
-            ui.error("Be more specific; '{}' matches multiples "
-                     "citekeys:".format(citekey))
+            msg = ["Be more specific; '{}' matches multiples citekeys:".format(citekey)]
            for c in citekeys:
                p = repo.pull_paper(c)
-                ui.message('    {}'.format(pretty.paper_oneliner(p)))
+                paper_str = pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])
+                msg.append('    {}'.format(paper_str))
+            ui.error('\n'.join(msg))
            if exit_on_fail:
                ui.exit()
    return citekey


-def resolve_citekey_list(repo, citekeys, ui=None, exit_on_fail=True):
+def resolve_citekey_list(repo, conf, citekeys, ui=None, exit_on_fail=True):
    shutdown = False
    keys = []
    for key in citekeys:
        try:
-            keys.append(resolve_citekey(repo, key, ui, exit_on_fail))
+            keys.append(resolve_citekey(repo, conf, key, ui=ui, exit_on_fail=exit_on_fail))
        except SystemExit:
            shutdown = exit_on_fail

@ -73,11 +74,11 @@ def standardize_doi(doi):
    """

    doi_regexes = (
-        '(10\.\d{4,9}/[-._;()/:A-z0-9\>\<]+)',
-        '(10.1002/[^\s]+)',
-        '(10\.\d{4}/\d+-\d+X?(\d+)\d+<[\d\w]+:[\d\w]*>\d+.\d+.\w+;\d)',
-        '(10\.1021/\w\w\d+\+)',
-        '(10\.1207/[\w\d]+\&\d+_\d+)')
+        r'(10\.\d{4,9}/[-._;()/:A-z0-9\>\<]+)',
+        r'(10.1002/[^\s]+)',
+        r'(10\.\d{4}/\d+-\d+X?(\d+)\d+<[\d\w]+:[\d\w]*>\d+.\d+.\w+;\d)',
+        r'(10\.1021/\w\w\d+\+)',
+        r'(10\.1207/[\w\d]+\&\d+_\d+)')
    doi_pattern = re.compile('|'.join(doi_regexes))

    match = doi_pattern.search(doi)
--- a/readme.md
+++ b/readme.md
@ -15,24 +15,24 @@ correct bugs, but have no short-term plans to add major features to it. Pubs doe
 is supposed to do: help us do science, so now we are mostly doing that.

 **Notice:** pubs is relatively stable but comes with no warranty; do keep backups of your data.
-**Notice:** pubs currently works with Python 2.7, but support will be dropped as soon as maintaining it becomes tedious.
+**Notice:** pubs currently works with Python 2.7, but support is being dropped (tests are not run anymore).

 ## Installation

 You can install the latest stable version of `pubs` through Pypi, with:
-  ```
+  ```shell
  pip install pubs
  ```

 Alternatively, you can:

  - install the latest development version with pip:
-    ```
+    ```shell
    pip install --upgrade git+https://github.com/pubs/pubs
    ```

  - clone the repository and install it manually:
-    ```
+    ```shell
    git clone https://github.com/pubs/pubs
    cd pubs
    python setup.py install [--user]
@ -44,32 +44,32 @@ Arch Linux users can also use the [pubs-git](https://aur.archlinux.org/packages/
 ## Getting started

 Create your library (by default, goes to `~/.pubs/`).
-  ```
+  ```shell
  pubs init
  ```

 Import existing data from bibtex (pubs will try to automatically copy documents defined as 'file' in bibtex):
-  ```
+  ```shell
  pubs import path/to/collection.bib
  ```

 or for a .bib file containing a single reference:
-  ```
+  ```shell
  pubs add reference.bib -d article.pdf
  ```

 pubs can also automatically retrieve the bibtex from a doi:
-  ```
+  ```shell
  pubs add -D 10.1007/s00422-012-0514-6 -d article.pdf
  ```

 or an ISBN (dashes are ignored):
-  ```
+  ```shell
  pubs add -I 978-0822324669 -d article.pdf
  ```

 or an arXiv id (automatically downloading arXiv article is in the works):
-  ```
+  ```shell
  pubs add -X math/9501234 -d article.pdf
  ```

@ -79,7 +79,7 @@ or an arXiv id (automatically downloading arXiv article is in the works):
 If you use latex, you can automatize references, by running `pubs export > references.bib` each time you update your library, which also fits well as a `makefile` rule.

 This ensures that your reference file is always up-to-date; you can cite a paper in your manuscript a soon as you add it in pubs. This means that if you have, for instance, a DOI on a webpage, you only need to do:
-  ```
+  ```shell
  pubs add -D 10.1007/s00422-012-0514-6
  ```

@ -89,12 +89,12 @@ and then add `\cite{Loeb_2012}` in your manuscript. After exporting the bibliogr
 ## Document management

 You can attach a document to a reference:
-  ```
+  ```shell
  pubs doc add Loeb2012_downloaded.pdf Loeb_2012
  ```

 And open your documents automatically from the command line:
-  ```
+  ```shell
  pubs doc open Loeb_2012
  pubs doc open --with lp Loeb_2012  # Opens the document with `lp` to actually print it.
  ```
@ -111,21 +111,21 @@ Pubs comes with a git plugin that automatically commits your changes. You only n
 You can then also conveniently interact with the git repository by using `pubs git <regular git commands>`.


-## Multiple pubs Repository
+## Multiple pubs Repositories

 You may want to have different pubs repositories, for different projects. To create an alternate repository:
-  ```
+  ```shell
  pubs --config /path/to/config init --pubsdir /path/to/desired_repository_directory
  ```
 The configuration file and repository will be automatically created.

 Then you can add papers to the new repository:
-  ```
+  ```shell
  pubs --config /path/to/config add -D 10.1007/s00422-012-0514-6
  ```

 A useful thing might be to define an alias in your shell:
-  ```
+  ```shell
  alias pubs2="pubs --config /path/to/config"
  ```
 and then use `pubs2` as you would use `pubs` directly.  Note that you cannot use the alias plugin below to do this.
@ -141,13 +141,13 @@ You can add custom commands to pubs by defining aliases in your configuration fi
  count = !pubs list -k "$@" | wc -l
  ```

-The first command defines a new subcommand: `pubs open --with evince` will be executed when `pubs evince` is typed.
-The second starts with a bang: `!`, and is treated as a shell command. If other arguments are provided they are passed to the shell command as in a script. In the example above the `count` alias can take arguments that are be passed to the `pubs list -k` command, hence enabling filters like `pubs count year:2012`.
+The first configuration line defines a new subcommand: `pubs open --with evince` will be executed when `pubs evince` is typed.
+The second starts with a bang: `!`, which means that it is treated as a shell command. If other arguments are provided they are passed to the shell command as in a script. In the example above the `count` alias can take arguments that are passed over to the `pubs list -k` command, hence enabling filters like `pubs count year:2012`.


 ## Autocompletion

-For autocompletion to work, you need the [argcomplete](https://argcomplete.readthedocs.io) Python package, and Bash 4.2 or newer. For activating *bash* or *tsch* completion, consult the [argcomplete documentation](https://argcomplete.readthedocs.io/en/latest/#global-completion).
+For autocompletion to work, you need the [argcomplete](https://kislyuk.github.io/argcomplete) Python package, and Bash 4.2 or newer. For activating *bash* or *tsch* completion, consult the [argcomplete documentation](https://kislyuk.github.io/argcomplete/#global-completion).

 For *zsh* completion, the global activation is not supported but bash completion compatibility can be used for pubs. For that, add the following to your `.zshrc`:
  ```shell
@ -183,3 +183,7 @@ You can access the self-documented configuration by using `pubs conf`, and all t
 - [Shane Stone](https://github.com/shanewstone)
 - [Amlesh Sivanantham](http://github.com/zamlz)
 - [DV Klopfenstein](http://github.com/dvklopfenstein)
+- [beuerle](https://github.com/beuerle)
+- [Jonáš Kulhánek](https://github.com/jkulhanek)
+- [Dominik Stańczak](https://github.com/StanczakDominik)
+- [Gustavo José de Sousa](https://github.com/guludo)
--- a/setup.py
+++ b/setup.py
@ -45,23 +45,22 @@ setup(
        },

    include_package_data=True,
-
    install_requires=['pyyaml', 'bibtexparser>=1.0', 'python-dateutil', 'six',
                      'requests', 'configobj', 'beautifulsoup4', 'feedparser'],
    extras_require={'autocompletion': ['argcomplete'],
                    },

+    python_requires='>=3.6',
    classifiers=[
        'Development Status :: 4 - Beta',
        'License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)',
-        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3',
        'Intended Audience :: Developers',
        'Intended Audience :: Science/Research',
    ],

    test_suite='tests',
-    tests_require=['pyfakefs>=3.4', 'mock', 'ddt', 'certifi'],
+    tests_require=['pyfakefs>=3.4', 'mock', 'ddt>=1.4.1', 'certifi', 'pytest'],

    # in order to avoid 'zipimport.ZipImportError: bad local file header'
    zip_safe=False,
--- a/tests/data/three_articles.bib
+++ b/tests/data/three_articles.bib
--- a/tests/data_non_standard/non_standard_collection.bib
+++ b/tests/data_non_standard/non_standard_collection.bib
@ -0,0 +1,9 @@
+@collection{Geometric_phases,
+ title = {Geometric phases in physics},
+ editor = {Shapere, Alfred and Wilczek, Frank},
+ year = {1989},
+ series = {Advanced Series in Mathematical Physics},
+ volume = {5},
+ publisher = {World Scientific},
+ isbn = {9789971506216}
+}
--- a/tests/data_non_standard/non_standard_software.bib
+++ b/tests/data_non_standard/non_standard_software.bib
@ -0,0 +1,7 @@
+@software{hadoop,
+  author = {{Apache Software Foundation}},
+  title = {Hadoop},
+  url = {https://hadoop.apache.org},
+  version = {0.20.2},
+  date = {2010-02-19},
+}
--- a/tests/fake_env.py
+++ b/tests/fake_env.py
@ -9,7 +9,7 @@ import dotdot

 from pyfakefs import fake_filesystem, fake_filesystem_unittest

-from pubs.p3 import input, _fake_stdio, _get_fake_stdio_ucontent
+from pubs.p3 import input
 from pubs import content, filebroker, uis

 # code for fake fs
@ -29,29 +29,6 @@ original_exception_handler = uis.InputUI.handle_exception
 locale.setlocale(locale.LC_ALL, '')


-# capture output
-
-def capture(f, verbose=False):
-    """Capture the stdout and stderr output.
-
-    Useful for comparing the output with the expected one during tests.
-
-    :param f:        The function to capture output from.
-    :param verbose:  If True, print call will still display their outputs.
-                     If False, they will be silenced.
-
-    """
-    def newf(*args, **kwargs):
-        old_stderr, old_stdout = sys.stderr, sys.stdout
-        sys.stdout = _fake_stdio(additional_out=old_stderr if verbose else None)
-        sys.stderr = _fake_stdio(additional_out=old_stderr if False else None)
-        try:
-            return f(*args, **kwargs), _get_fake_stdio_ucontent(sys.stdout), _get_fake_stdio_ucontent(sys.stderr)
-        finally:
-            sys.stderr, sys.stdout = old_stderr, old_stdout
-    return newf
-
-
 # Test helpers

 # automating input
--- a/tests/str_fixtures.py
+++ b/tests/str_fixtures.py
@ -1,7 +1,7 @@
 from __future__ import unicode_literals


-bibtex_external0 = """
+bibtex_external0 = r"""
@techreport{Page99,
     number = {1999-66},
      month = {November},
@ -17,7 +17,7 @@ institution = {Stanford InfoLab},
 }
 """

-bibtex_external_alt = """
+bibtex_external_alt = r"""
@techreport{Page99,
     number = {1999-66},
      month = {November},
@ -33,7 +33,7 @@ institution = {Stanford InfoLab},
 }
 """

-bibtex_raw0 = """@techreport{
+bibtex_raw0 = r"""@techreport{
    Page99,
    author = "Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry",
    publisher = "Stanford InfoLab",
@ -50,12 +50,12 @@ bibtex_raw0 = """@techreport{

 """

-metadata_raw0 = """docfile: docsdir://Page99.pdf
+metadata_raw0 = r"""docfile: docsdir://Page99.pdf
 tags: [search, network]
 added: '2013-11-14 13:14:20'
 """

-turing_bib = """@article{turing1950computing,
+turing_bib = r"""@article{turing1950computing,
  title={Computing machinery and intelligence},
  author={Turing, Alan M},
  journal={Mind},
@ -75,7 +75,7 @@ added: '2013-11-14 13:14:20'
 """

 # Should not parse (see #113)
-bibtex_no_citekey = """@Manual{,
+bibtex_no_citekey = r"""@Manual{,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
@ -85,7 +85,7 @@ bibtex_no_citekey = """@Manual{,
 }
 """

-bibtex_month = """@inproceedings{Goyal2017,
+bibtex_month = r"""@inproceedings{Goyal2017,
 author = {Goyal, Anirudh and Sordoni, Alessandro and C{\^{o}}t{\'{e}}, Marc-Alexandre and Ke, Nan Rosemary and Bengio, Yoshua},
 title = {Z-Forcing: Training Stochastic Recurrent Networks},
 year = {2017},
@ -94,15 +94,15 @@ bibtex_month = """@inproceedings{Goyal2017,
 }
 """

-not_bibtex = """@misc{this looks,
+not_bibtex = r"""@misc{this looks,
  like = a = bibtex file but
    , is not a real one!

 """

-bibtex_with_latex = """@article{kjaer2018large,
+bibtex_with_latex = r"""@article{kjaer2018large,
  title={A large impact crater beneath Hiawatha Glacier in northwest Greenland},
-  author={Kj{\\ae}r, Kurt H and Larsen, Nicolaj K and Binder, Tobias and Bj{\\o}rk, Anders A and Eisen, Olaf and Fahnestock, Mark A and Funder, Svend and Garde, Adam A and Haack, Henning and Helm, Veit and others},
+  author={Kj{\ae}r, Kurt H and Larsen, Nicolaj K and Binder, Tobias and Bj{\o}rk, Anders A and Eisen, Olaf and Fahnestock, Mark A and Funder, Svend and Garde, Adam A and Haack, Henning and Helm, Veit and others},
  journal={Science advances},
  volume={4},
  number={11},
--- a/tests/test_endecoder.py
+++ b/tests/test_endecoder.py
@ -57,6 +57,12 @@ class TestEnDecode(unittest.TestCase):

        self.assertEqual(bibraw1, bibraw2)

+    def test_decode_bibtex_preserves_type_field(self):
+        """Test that multiple encode/decode step preserve data"""
+        decoder = endecoder.EnDecoder()
+        entry = decoder.decode_bibdata(bibtex_raw0)
+        self.assertEqual(entry['Page99']['type'], "Technical Report")
+
    def test_endecode_bibtex_BOM(self):
        """Test that bibtexparser if fine with BOM-prefixed data"""
        decoder = endecoder.EnDecoder()
--- a/tests/test_filebroker.py
+++ b/tests/test_filebroker.py
@ -71,6 +71,16 @@ class TestFileBroker(fake_env.TestFakeFs):

 class TestDocBroker(fake_env.TestFakeFs):

+    def test_expanduser(self):
+        """Test that real_docpath expand the user ~"""
+
+        self.fs.add_real_directory(os.path.join(self.rootpath, 'data'), read_only=False)
+        fb = filebroker.FileBroker('~/testrepo', create = True)
+        docb = filebroker.DocBroker('~/testrepo')
+        self.assertTrue(os.path.isabs(docb.docdir))
+        self.assertTrue(os.path.isabs(docb.real_docpath('docsdir://abc')))
+
+
    def test_doccopy(self):

        self.fs.add_real_directory(os.path.join(self.rootpath, 'data'), read_only=False)
--- a/tests/test_git.py
+++ b/tests/test_git.py
@ -1,5 +1,6 @@
-import unittest
+import os
 import subprocess
+import unittest

 import sand_env

@ -16,11 +17,20 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):

    def setUp(self, nsec_stat=True):
        super(TestGitPlugin, self).setUp()
+        # Backup environment variables and set git author
+        self.env_backup = os.environ.copy()
+        os.environ['GIT_AUTHOR_NAME'] = "Pubs test"
+        os.environ['GIT_AUTHOR_EMAIL'] = "unittest@pubs.org"
+        # Setup pubs repository
        self.execute_cmds([('pubs init',)])
        conf = config.load_conf(path=self.default_conf_path)
        conf['plugins']['active'] = ['git']
        config.save_conf(conf, path=self.default_conf_path)

+    def tearDown(self):
+        super().tearDown()
+        os.environ = self.env_backup
+
    def test_git(self):
        self.execute_cmds([('pubs add data/pagerank.bib',)])
        hash_a = git_hash(self.default_pubs_dir)
@ -31,7 +41,7 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
        self.execute_cmds([('pubs rename Page99a ABC',)])
        hash_c = git_hash(self.default_pubs_dir)

-        self.execute_cmds([('pubs remove ABC', ['y']),])
+        self.execute_cmds([('pubs remove ABC', ['y'])])
        hash_d = git_hash(self.default_pubs_dir)

        self.execute_cmds([('pubs doc add testrepo/doc/Page99.pdf Page99',)])
@ -72,6 +82,7 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
        # self.assertEqual(hash_i, hash_j)

    def test_manual(self):
+        print(self.default_pubs_dir)
        conf = config.load_conf(path=self.default_conf_path)
        conf['plugins']['active'] = ['git']
        conf['plugins']['git']['manual'] = True
@ -101,6 +112,5 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
        self.assertNotEqual(hash_l, hash_m)


-
 if __name__ == '__main__':
    unittest.main()
--- a/tests/test_note_append.py
+++ b/tests/test_note_append.py
@ -46,7 +46,7 @@ class TestNoteAppend(DataCommandTestCase):
        #   * Pass the command split into a command and its args to
        #     execute_cmdsplit, which is called by execute_cmds:
        cmd_split = ['pubs', 'note', 'Page99', '-a', 'xxx yyy']
-        self.execute_cmdsplit(cmd_split, expected_out=None, expected_err=None)
+        self.execute_cmd_capture(cmd_split, expected_out=None, expected_err=None)
        note_lines.append('xxx yyy')
        self.assertFileContentEqual(fin_notes, self._get_note_content(note_lines))

--- a/tests/test_plug_alias.py
+++ b/tests/test_plug_alias.py
@ -1,7 +1,7 @@
 import shlex
 import unittest
-
 import dotdot
+import argparse

 import pubs
 from pubs import config
@ -61,6 +61,19 @@ class AliasTestCase(unittest.TestCase):
            shlex.split(self.subprocess.called.splitlines()[-1])[1:],
            args)

+    def testShellAliasNamedArguments(self):
+        parser = argparse.ArgumentParser()
+        parser.add_argument('--test2')
+        subparsers = parser.add_subparsers(title='commands', dest='command')
+
+        alias = Alias.create_alias('test', '!echo "$@"')
+        alias.parser(subparsers)
+        args = ['test', '2', '--option', '3']
+        args = parser.parse_args(args)
+
+        self.assertEqual(args.command, 'test')
+        self.assertListEqual(args.arguments, ['2', '--option', '3'])
+

 class AliasPluginTestCase(unittest.TestCase):

--- a/tests/test_pretty.py
+++ b/tests/test_pretty.py
@ -28,5 +28,15 @@ class TestPretty(unittest.TestCase):
        line = 'Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web."'
        self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'])), line)

+    def test_oneliner_max_authors(self):
+        decoder = endecoder.EnDecoder()
+        bibdata = decoder.decode_bibdata(bibtex_raw0)
+        for max_authors in [1, 2, 3]:
+            line = 'Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999)'
+            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], max_authors=max_authors)), line)
+        for max_authors in [-1, 0, 4, 5, 10]:
+            line = 'Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry "The PageRank Citation Ranking: Bringing Order to the Web." (1999)'
+            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], max_authors=max_authors)), line)
+
 if __name__ == '__main__':
    unittest.main()
--- a/tests/test_queries.py
+++ b/tests/test_queries.py
@ -200,8 +200,8 @@ class TestFilterPaper(unittest.TestCase):

    def test_latex_enc(self):
        latexenc_paper = doe_paper.deepcopy()
-        latexenc_paper.bibentry['Doe2013']['title'] = "{E}l Ni{\~n}o"
-        latexenc_paper.bibentry['Doe2013']['author'][0] = "Erd\H{o}s, Paul"
+        latexenc_paper.bibentry['Doe2013']['title'] = r"{E}l Ni{\~n}o"
+        latexenc_paper.bibentry['Doe2013']['author'][0] = r"Erd\H{o}s, Paul"
        self.assertTrue(get_paper_filter(['title:El'])(latexenc_paper))
        self.assertTrue(get_paper_filter(['title:Niño'])(latexenc_paper))
        self.assertTrue(get_paper_filter(['author:erdős'])(latexenc_paper))
@ -209,12 +209,12 @@ class TestFilterPaper(unittest.TestCase):

    def test_normalize_unicode(self):
        latexenc_paper = doe_paper.deepcopy()
-        latexenc_paper.bibentry['Doe2013']['title'] = "{E}l Ni{\~n}o"
+        latexenc_paper.bibentry['Doe2013']['title'] = r"{E}l Ni{\~n}o"
        self.assertTrue(get_paper_filter(['title:Nin\u0303o'])(latexenc_paper))

    def test_strict(self):
        latexenc_paper = doe_paper.deepcopy()
-        latexenc_paper.bibentry['Doe2013']['title'] = "El Ni{\~n}o"
+        latexenc_paper.bibentry['Doe2013']['title'] = r"El Ni{\~n}o"
        self.assertFalse(get_paper_filter(
            ['title:Nin\u0303o'], strict=True)(latexenc_paper))

--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@ -12,11 +12,13 @@ import ddt
 import certifi
 import mock
 from pyfakefs.fake_filesystem import FakeFileOpen
+import pytest

 import dotdot
 import fake_env
 import mock_requests

+
 from pubs import pubs_cmd, color, content, uis, p3, endecoder
 from pubs.config import conf

@ -25,7 +27,7 @@ import fixtures


 # makes the tests very noisy
-PRINT_OUTPUT   = False
+PRINT_OUTPUT   = True #False
 CAPTURE_OUTPUT = True


@ -118,14 +120,12 @@ class CommandTestCase(fake_env.TestFakeFs):
                input.as_global()
                try:
                    if capture_output:
-                        actual_out = self.execute_cmdsplit(
-                            actual_cmd.split(), expected_out, expected_err)
+                        actual_out = self.execute_cmd_capture(actual_cmd.split(), expected_out, expected_err)
                        outs.append(color.undye(actual_out))
                    else:
                        pubs_cmd.execute(actual_cmd.split())
                except fake_env.FakeInput.UnexpectedInput:
-                    self.fail('Unexpected input asked by command: {}.'.format(
-                        actual_cmd))
+                    self.fail('Unexpected input asked by command: {}.'.format(actual_cmd))
            return outs
        except SystemExit as exc:
            exc_class, exc, tb = sys.exc_info()
@ -145,27 +145,39 @@ class CommandTestCase(fake_env.TestFakeFs):
            pass
        return s

-    def execute_cmdsplit(self, actual_cmdlist, expected_out, expected_err):
-        """Run a single command, which has been split into a list containing cmd and args"""
-        capture_wrap = fake_env.capture(pubs_cmd.execute,
-                                        verbose=PRINT_OUTPUT)
-        _, stdout, stderr = capture_wrap(actual_cmdlist)
-        actual_out = self.normalize(stdout)
-        actual_err = self.normalize(stderr)
-        if expected_out is not None:
-            self.assertEqual(p3.u_maybe(actual_out), p3.u_maybe(expected_out))
-        if expected_err is not None:
-            self.assertEqual(p3.u_maybe(actual_err), p3.u_maybe(expected_err))
-        return actual_out
+    def execute_cmd_capture(self, cmd, expected_out, expected_err):
+        """Run a single command, captures the output and and stderr and compare it to the expected ones"""
+        sys_stdout, sys_stderr = sys.stdout, sys.stderr
+        sys.stdout = p3._fake_stdio(additional_out=sys_stdout if PRINT_OUTPUT else None)
+        sys.stderr = p3._fake_stdio(additional_out=sys_stderr if PRINT_OUTPUT else None)
+
+        try:
+            pubs_cmd.execute(cmd)
+        finally:
+            # capturing output even if exception was raised.
+            self.captured_stdout = self.normalize(p3._get_fake_stdio_ucontent(sys.stdout))
+            self.captured_stderr = self.normalize(p3._get_fake_stdio_ucontent(sys.stderr))
+            sys.stderr, sys.stdout = sys_stderr, sys_stdout
+
+        if expected_out is not None:
+            self.assertEqual(p3.u_maybe(self.captured_stdout), p3.u_maybe(expected_out))
+        if expected_err is not None:
+            self.assertEqual(p3.u_maybe(self.captured_stderr), p3.u_maybe(expected_err))
+        return self.captured_stdout
+
+    def update_config(self, config_update, path=None):
+        """Allow to set the config parameters. Must have done a `pubs init` beforehand."""
+        if path is None:
+            path = self.default_conf_path
+        cfg = conf.load_conf(path=path)
+        for section, section_update in config_update.items():
+            cfg[section].update(section_update)
+        conf.save_conf(cfg, path=path)

-    def tearDown(self):
-        pass


 class DataCommandTestCase(CommandTestCase):
-    """Abstract TestCase intializing the fake filesystem and
-    copying fake data.
-    """
+    """Abstract TestCase intializing the fake filesystem and copying fake data."""

    def setUp(self, nsec_stat=True):
        super(DataCommandTestCase, self).setUp(nsec_stat=nsec_stat)
@ -182,8 +194,7 @@ class DataCommandTestCase(CommandTestCase):


 class URLContentTestCase(DataCommandTestCase):
-    """Mocks access to online files by using files in data directory.
-    """
+    """Mocks access to online files by using files in data directory."""

    def setUp(self):
        super(URLContentTestCase, self).setUp()
@ -209,6 +220,8 @@ class URLContentTestCase(DataCommandTestCase):
        content.url_exists = self._original_url_exist


+
+
 # Actual tests

 class TestAlone(CommandTestCase):
@ -615,6 +628,7 @@ class TestTag(DataCommandTestCase):
        with self.assertRaises(FakeSystemExit):
            self.execute_cmds(cmds)

+
 class TestURL(DataCommandTestCase):

    def setUp(self):
@ -720,7 +734,7 @@ class TestUsecase(DataCommandTestCase):
    def test_first(self):
        correct = ['Initializing pubs in /paper_first\n',
                   'added to pubs:\n[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
-                   'data/pagerank.pdf was copied to the pubs repository.\n',
+                   'data/pagerank.pdf was copied to /paper_first/doc/Page99.pdf inside the pubs repository.\n',
                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] \n',
                   '\n',
                   '',
@ -1072,14 +1086,31 @@ class TestUsecase(DataCommandTestCase):
                              target_path=os.path.join('data', 'no-ext'))
        correct = ['Initializing pubs in /pubs\n',
                   'added to pubs:\n[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
-                   'data/no-ext was copied to the pubs repository.\n',
+                   'data/no-ext was copied to /pubs/doc/Page99 inside the pubs repository.\n',
                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [NOEXT] \n',
                  ]
        cmds = ['pubs init -p /pubs',
                'pubs add -d data/no-ext data/pagerank.bib',
                'pubs list',
               ]
-        self.assertEqual(correct, self.execute_cmds(cmds, capture_output=True))
+        actual = self.execute_cmds(cmds, capture_output=True)
+        self.assertEqual(correct, actual)
+
+    def test_add_non_standard(self):
+        """Test that non-standard bibtex are correctly added"""
+        self.fs.add_real_directory(os.path.join(self.rootpath, 'data_non_standard'), read_only=False)
+        correct = ['Initializing pubs in /pubs\n',
+                   'added to pubs:\n[Geometric_phases]  "Geometric phases in physics" (1989) \n',
+                   'added to pubs:\n[hadoop] Foundation, Apache Software "Hadoop" \n',
+                  ]
+        cmds = ['pubs init -p /pubs',
+                'pubs add data_non_standard/non_standard_collection.bib',
+                'pubs add data_non_standard/non_standard_software.bib',
+                # 'pubs list',
+               ]
+        actual = self.execute_cmds(cmds, capture_output=True)
+        self.assertEqual(correct, actual)
+

    @mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
    def test_readme(self, reqget):
@ -1089,7 +1120,7 @@ class TestUsecase(DataCommandTestCase):
        self.fs.add_real_file(os.path.join(self.rootpath, 'data/pagerank.pdf'), target_path='data/Knuth1995.pdf')

        cmds = ['pubs init',
-                'pubs import data/collection.bib',
+                'pubs import data/three_articles.bib',
                'pubs add data/pagerank.bib -d data/pagerank.pdf',
                #'pubs add -D 10.1007/s00422-012-0514-6 -d data/pagerank.pdf',
                'pubs add -I 978-0822324669 -d data/oyama2000the.pdf',
@ -1100,6 +1131,21 @@ class TestUsecase(DataCommandTestCase):
        self.execute_cmds(cmds, capture_output=True)
 #        self.assertEqual(correct, self.execute_cmds(cmds, capture_output=True))

+    def test_ambiguous_citekey(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib',
+                'pubs add data/pagerank.bib', # now we have Page99 and Page99a
+                'pubs edit Page',
+                ]
+        output = '\n'.join(["error: Be more specific; 'Page' matches multiples citekeys:",
+                            "    [Page99] Page, Lawrence et al. \"The PageRank Citation Ranking: Bringing Order to the Web.\" (1999) ",
+                            "    [Page99a] Page, Lawrence et al. \"The PageRank Citation Ranking: Bringing Order to the Web.\" (1999) \n"])
+
+        with self.assertRaises(FakeSystemExit):
+            self.execute_cmds(cmds)
+
+        self.assertEqual(self.captured_stderr, output)
+


@ddt.ddt
@ -1145,5 +1191,23 @@ class TestCache(DataCommandTestCase):
        self.assertEqual(line1, out[4])


+class TestConfigChange(DataCommandTestCase):
+
+    def test_max_authors_default(self):
+        line_al   = '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
+        line_full = '[Page99] Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
+
+        self.execute_cmds(['pubs init', 'pubs add data/pagerank.bib'])
+
+        for max_authors in [1, 2, 3]:
+            self.update_config({'main': {'max_authors': max_authors}})
+            self.execute_cmds([('pubs list', None, line_al, None)])
+
+        for max_authors in [-1, 0, 4, 5, 10]:
+            self.update_config({'main': {'max_authors': max_authors}})
+            self.execute_cmds([('pubs list', None, line_full, None)])
+
+
+
 if __name__ == '__main__':
    unittest.main(verbosity=2)