Arch Linux User Repository

@JP-Ellis

Papis has this dependency on "python-bibtexparser", https://aur.archlinux.org/packages/python-bibtexparser

But "python-bibtexparser" is, an AUR dependency, is out of date and was ... orphaned ??? ...

I'm not very confortable with too may AUR dependencies, if they are not properly watched.

My naive question is:

Is there any way to "replace" this "python-bibtexparser" dependency for "papis" ? Could some sort of "replacement" from from the official Arch repos be used ?

I noticed this one,

extra/python-pybtex 0.24.0-5
    A BibTeX-compatible bibliography processor written in Python

Or is it really impossible to find a substitute, and this is really a mandatory thing for "papis" ?

@JP-Ellis

How are you yourself or other Arch users using "papis" ? Or some other text oriented or command line tool in this field ? Did you commmit to using it for a long time (years) ?

Can you recommend me some blog posts, personal experiences, wiki pages etc, from people describing their (academic) workflow using papis or some other command line bib manager ?

I cant find a place where Arch users, academics or not, share their experiences in this field. The "Arch way".That is, similar related simple tools, preferably cli, working in tandem with other simple tools.

I'm having a lot of trouble finding time tested, "real world" experiences, that last a life long. There is a lot of stuff on the Internet. And I personally know a lot of academic people that need to work with this on a dailly basis. But they are not Linux users. And they couldnt care less about using big bloated tools. They would never touch a command line or use a text oriented workflow.

I know papis from some years now. Read all the README's and wiki pages. Same thing for similar tools like "cobib" "pubs" etc. I'm trying to compare them. Cant decide which one to invest time in learning it properly. Zotero, Jabref, Calibre and all that. But I never commited to using one long term.

I have a distaste for propietary tools, GUI's, and browser based workflows . Spent too much time finding the tools, but have not yet decided where to invest my time. I am a power command line user, but I have never managed to integrate all of this in stable workflow.

Recently, for personal reasons, I've been amassing a ton of pdf's and bib references in a humanities field. I'm overwhelmed. I'm loosing control of my files and references collections.

I feel overloaded with information, and I am loosing stuff and redownloading pdf's. Also need to integrate with Zotero and all. I guess it is not so much a matter of the right tool, but more a matter of finding the right workflow.

Yeap, can confirm "python-pip" seems to solve the problem. I left the feed back on the "python-habanero" page.

@m040601 Thank you for the feedback and the debugging efforts! Much appreciated.

With regards to the difficulty of the PKGBUILD, it is actually a fairly standard Python package PKGBUILD, although it does have quite a few dependencies.

Regarding the Habanero dependencies, it looks like it is ultimately due to the python-pip package not being installed. As mentioned over in the python-habanero package, would you mind installing python-pip as a dependency, and letting me know whether it resolves your issue? I don't think papis itself will require a rebuild if the habanero dependency is fixed.

Thanks to the maintainer of this PKGBUILD for his work.

It is not an easy job I guess.

Could you please respond to the comments, and confirm that this PKGBUILD is actually currently building without errors and working properly on your system ?

This is such a complicated PKGBUILD with loootz of dependencies on the official packages and AUR packages. And a troublesome history of failing because of it. It is therefore necessary to constantl keep an an eye on papis itself, but also its dependencies.

I'm having trouble and cant get it to build. Already tried all standard procedures, clean AUR root etc.

Currently getting some errors, something about "python-habanero", https://aur.archlinux.org/packages/python-habanero ,

    Habanero is a low level client for working with Crossref's search API.

I'm not an expert, neither in python nor PKGBUILDs. But I did tried to build "python-habanero" alone, and it indeed fails. So that seems, I guess, to be the culprit. Already left a message there.

I also tried "papis-git" and it is the same error In the middle of the long build,

   $   File "/usr/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1135, in best_match
    return self.obtain(req, installer)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1147, in obtain
    return installer(requirement)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/setuptools/installer.py", line 98, in _fetch_build_egg_no_warn
    raise DistutilsError(str(e)) from e
distutils.errors.DistutilsError: Command '['/usr/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpqpm7hi5b', '--quiet', 'setuptools_scm']' returned non-zero exit status 1.
==> ERROR: A failure occurred in build().
    Aborting...
 -> Failed to install layer, rolling up to next layer.error:error making: python-habanero - exit status 4

Later at the end,

checking dependencies...

Package (4)             Old Version  Net Change

python-pyproject-hooks  1.0.0-5       -0.09 MiB
python-build            0.10.0-4      -0.68 MiB
python-installer        0.7.0-3       -0.82 MiB
python-wheel            0.40.0-3      -0.28 MiB

Total Removed Size:  1.87 MiB

:: Do you want to remove these packages? [Y/n]
:: Processing package changes...
(1/4) removing python-installer                    [------------------] 100%
(2/4) removing python-build                        [------------------] 100%
(3/4) removing python-pyproject-hooks              [------------------] 100%
(4/4) removing python-wheel                        [------------------] 100%
:: Running post-transaction hooks...
(1/1) Arming ConditionNeedsUpdate...
 -> Failed to install the following packages. Manual intervention is require
d:
python-habanero - exit status 4
papis - exit status 8

And I still end up with a messed system. Because, even though it failed to install, it installed these dependencies and failed to remove them (roll back)

Package (4)          New Version  Net Change

python-arxiv2bib     1.0.8-1        0.05 MiB
python-bibtexparser  1.4.0-1        0.42 MiB
python-doi           0.2.0-1        0.02 MiB
python-isbnlib       3.10.14-2      0.47 MiB

Lastly I checked if I could use pipx

pipx install papis

And that option did work. You end up with an isolated virtual environment of 50 Mega in your ~/.local/pipx because of all the papis dependencies.

I would never use "pip install papis", as they say in the papis README , because I dont want more mess in my system

python-certifi should be added to the dependencies, or getting errors:

Error while loading entrypoint 'EntryPoint(name='bibtex', value='papis.bibtex:Importer', group='papis.importer')': No module named 'certifi'.
Error while loading entrypoint 'EntryPoint(name='dblp', value='papis.dblp:Importer', group='papis.importer')': No module named 'certifi'.
Error while loading entrypoint 'EntryPoint(name='isbn', value='papis.isbn:Importer', group='papis.importer')': The 'certifi>=2017.4.17' distribution was not found and is required by requests.
Error while loading entrypoint 'EntryPoint(name='addto', value='papis.commands.addto:cli', group='papis.command')': No module named 'certifi'.
Error while loading entrypoint 'EntryPoint(name='bibtex', value='papis.bibtex:exporter', group='papis.exporter')': No module named 'certifi'.
Error while loading entrypoint 'EntryPoint(name='bibtex', value='papis.bibtex:explorer', group='papis.explorer')': No module named 'certifi'.
Error while loading entrypoint 'EntryPoint(name='dblp', value='papis.dblp:explorer', group='papis.explorer')': No module named 'certifi'.
Error while loading entrypoint 'EntryPoint(name='isbn', value='papis.isbn:explorer', group='papis.explorer')': The 'certifi>=2017.4.17' distribution was not found and is required by requests.
Error while loading entrypoint 'EntryPoint(name='bibtex', value='papis.commands.bibtex:cli', group='papis.command')': No module named 'certifi'.

Getting this error:

ModuleNotFoundError: No module named 'colorama'

Adding the package manually using pacman -S python-colorama resolved the issue.

Might want to add python-colorama to the dependencies.