python312Packages.papis: 0.13 -> 0.14 #354823

octvs · 2024-11-09T18:18:35Z

Papis had a recent minor release, the relevant parts of the 0.14 release
note are

Minimum required Python version bumped to 3.8
(#552).

Moved to pyproject.toml and removed setup.py completely. We use
hatchling as the build
backend.

Removed arxiv2bib in
favor of arxiv.py.

Removed tqdm dependency (using a progress
bar from prompt_toolkit instead).

Added platformdirs
dependency for platform-specific config locations.

I've added dependencies arxiv.py and sphinx-click which are mostly taken
from the upstream flake.

Initially I tried having fetchFromGithub on sphinx-click so in essence
having

diff --git a/pkgs/development/python-modules/sphinx-click/default.nix b/pkgs/development/python-modules/sphinx-click/default.nix
index 587618b5fcb5..6f02207abcf8 100644
--- a/pkgs/development/python-modules/sphinx-click/default.nix
+++ b/pkgs/development/python-modules/sphinx-click/default.nix
@@ -1,16 +1,18 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
+  fetchFromGithub,
   pbr,
 }:
 buildPythonPackage rec {
   pname = "sphinx-click";
   version = "5.1.0";
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-aBLC22LT+ucaSt2+WooKFsl+tJHzzWP+NLTtfgcjbzM=";
+  src = fetchFromGitHub {
+    owner = "click-contrib";
+    repo = pname;
+    rev = version;
+    hash = "sha256-XDzJjxzHGnMWS/C60hQvfQCX7veMcXklpUjqDcJetM0=";
   };
 
   propagatedBuildInputs = [ pbr ];

However this fails with

Error parsing
Traceback (most recent call last):
  File "/nix/store/5kg9855711f90m0vczaxdjgd5spzgjy9-python3.12-pbr-6.1.0/lib/python3.12/site-packages/pbr/core.py", line 105, in pbr
    attrs = util.cfg_to_args(path, dist.script_args)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/5kg9855711f90m0vczaxdjgd5spzgjy9-python3.12-pbr-6.1.0/lib/python3.12/site-packages/pbr/util.py", line 272, in cfg_to_args
    pbr.hooks.setup_hook(config)
  File "/nix/store/5kg9855711f90m0vczaxdjgd5spzgjy9-python3.12-pbr-6.1.0/lib/python3.12/site-packages/pbr/hooks/__init__.py", line 25, in setup_hook
    metadata_config.run()
  File "/nix/store/5kg9855711f90m0vczaxdjgd5spzgjy9-python3.12-pbr-6.1.0/lib/python3.12/site-packages/pbr/hooks/base.py", line 27, in run
    self.hook()
  File "/nix/store/5kg9855711f90m0vczaxdjgd5spzgjy9-python3.12-pbr-6.1.0/lib/python3.12/site-packages/pbr/hooks/metadata.py", line 25, in hook
    self.config['version'] = packaging.get_version(
                             ^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/5kg9855711f90m0vczaxdjgd5spzgjy9-python3.12-pbr-6.1.0/lib/python3.12/site-packages/pbr/packaging.py", line 866, in get_version
    raise Exception("Versioning for this project requires either an sdist"
Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name sphinx-click was given, but was not able to be found.
error in setup command: Error parsing /build/source/setup.cfg: Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name sphinx-click was given, but was not able to be found.

As far as I can find over
the internet
pbr tries to figure out the version, probably in nix environment it fails to
do so.

Asking this around on matrix room, I was advised to stick by fetchPypi.

Note: First time contributor, comments & feedback highly welcome!

Things done

Add a 👍 reaction to pull requests you find important.

pkgs/development/python-modules/arxiv/default.nix

octvs · 2024-11-13T16:18:14Z

Thanks for the feedback @steeleduncan.

no `with lib` #208242

Done on all three packages mentioned.

`refs/tags/${version}` is safer should there be a branch with the same name as the tag

Unfortunately there is none [1]. [1]: https://github.com/lukasschwab/arxiv.py/branches/all

…

-- octvs

steeleduncan · 2024-11-13T16:25:45Z

Unfortunately there is none [1]. [1]: https://github.com/lukasschwab/arxiv.py/branches/all

Understood, but if one were to be added in the future it would not be clear what rev would refer to. The derivation could break in the admittedly unlikely case that the branch and the tag were not on the same commit.

Specifying refs/tags/... is more precise, and leaves the derivation safe against such a change

octvs · 2024-11-13T16:50:07Z

Specifying `refs/tags/...` is more precise, and leaves the derivation safe against such a change

Oh, I understood this one just now. Checking how github forms download links for branches and tags, and then skimming over `fetchFromGitHub` source clarified [1]. Thanks, fixed! [1]: https://github.com/NixOS/nixpkgs/blob/4ac89e5e22d3e225057d90824618feeb7059947d/pkgs/build-support/fetchgithub/default.nix

octvs · 2024-11-15T18:59:32Z

Since sphinx-click was added via 57e033c, I dropped commit adding it. Also
inspired by it I enabled tests on arxiv package.

pkgs/development/python-modules/arxiv/default.nix

pkgs/development/python-modules/papis/default.nix

GaetanLepage

mis-approved previously.

octvs · 2024-11-16T16:02:56Z

```suggestion version = "2.1.0"; pyproject = true; ```

As far as I understand from arxiv repo, they use `setup.py`, there is no `pyproject.toml` present, should it be still set to true?

> - disabled = pythonOlder "3.7"; + disabled = pythonOlder "3.8"; You can also just remove this line entirely. It is not that useful.

I couldn't find explanation of the behaviour of `pythonOlder` either through google or `grep`ing through `nixpkgs`. Therefore wasn't sure if it is `<=` or `<`. Just to understand it: Is it not useful because current oldest python version available on nixpkgs is 3.9? (except `python2`).

> - disabled = pythonOlder "3.7"; + disabled = pythonOlder "3.8"; src = fetchFromGitHub { owner = "papis"; repo = pname; ```suggestion repo = "papis"; ```

Again to understand: is there a reason to avoid using `pname` variable there? Others have been fixed, thanks a lot for the feedback!

GaetanLepage · 2024-11-16T16:13:07Z

As far as I understand from arxiv repo, they use setup.py, there is no pyproject.toml present, should it be still set to true?

Yes, it should work nonetheless. (Although quite counter intuitive).

I couldn't find explanation of the behaviour of pythonOlder either through google or greping through nixpkgs. Therefore wasn't sure if it is <= or <.

pythonOlder litterally means "if older", so <. "3.11" is not older than "3.11", itself.

Just to learn it fully: is there a reason to avoid using pname variable there?

Yes, it could lead to a broken build if the name of the package is changed. It does not occur often, but this is considered as best practice.

Also, it is better to reply to the change requests directly in their individual message thread.

octvs · 2024-11-16T16:35:52Z

> As far as I understand from arxiv repo, they use `setup.py`, there is no `pyproject.toml` present, should it be still set to true? Yes, it should work nonetheless. (Although quite counter intuitive).

Now it fails to build with ```sh $ nix build .#python3Packages.arxiv warning: Git tree '/home/oct/git/nixpkgs' is dirty error: builder for '/nix/store/wam7hlzgi1mcbfmzycbdns3sjzah4l3j-python3.12-arxiv-2.1.0.drv' failed with exit code 1; last 25 log lines: writing requirements to arxiv.egg-info/requires.txt writing top-level names to arxiv.egg-info/top_level.txt reading manifest file 'arxiv.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'arxiv.egg-info/SOURCES.txt' Copying arxiv.egg-info to build/bdist.linux-x86_64/wheel/./arxiv-2.1.0-py3.12.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/arxiv-2.1.0.dist-info/WHEEL creating '/build/source/dist/.tmp-51_34jd5/arxiv-2.1.0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'arxiv/__init__.py' adding 'arxiv/arxiv.py' adding 'arxiv-2.1.0.dist-info/LICENSE.txt' adding 'arxiv-2.1.0.dist-info/METADATA' adding 'arxiv-2.1.0.dist-info/WHEEL' adding 'arxiv-2.1.0.dist-info/top_level.txt' adding 'arxiv-2.1.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built arxiv-2.1.0-py3-none-any.whl Finished creating a wheel... Finished executing pypaBuildPhase Running phase: pythonRuntimeDepsCheckHook Executing pythonRuntimeDepsCheck Checking runtime dependencies for arxiv-2.1.0-py3-none-any.whl - feedparser==6.0.10 not satisfied by version 6.0.11 - requests==2.31.0 not satisfied by version 2.32.3 For full logs, run 'nix log /nix/store/wam7hlzgi1mcbfmzycbdns3sjzah4l3j-python3.12-arxiv-2.1.0.drv'. ``` Somehow the `~=` clauses on `requirements.txt` of arxiv [1] does get understood as `==` which fails the build. It builds fine without `pyproject=true`. Beyond the build failure, can one find the reasoning [here][2] maybe?

> I couldn't find explanation of the behaviour of `pythonOlder` either through google or `grep`ing through `nixpkgs`. Therefore wasn't sure if it is `<=` or `<`. `pythonOlder` litterally means "if older", so `<`. "3.11" is not older than "3.11", itself.

Thanks, should it rather be removed still?

> Just to learn it fully: is there a reason to avoid using `pname` variable there? Yes, it could lead to a broken build if the name of the package is changed. It does not occur often, but this is considered as best practice.

That makes sense, thanks for the explanation. Let me know if I should do the same for the `meta.changelog`, which also refers back to `meta.homepage`. _Although I can't imagine a similar scenario for this case._ [1]: https://github.com/lukasschwab/arxiv.py/blob/a1180d0ec6851be4e8aaa5e11a1e5212724f1e8e/requirements.txt [2]: #253154

pkgs/development/python-modules/arxiv/default.nix

GaetanLepage

LGTM

GaetanLepage · 2024-11-22T08:00:49Z

`nixpkgs-review` result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 354823

`x86_64-linux`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

`aarch64-linux`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

`x86_64-darwin`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

`aarch64-darwin`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

pkgs/development/python-modules/arxiv/default.nix

octvs · 2024-11-23T18:04:53Z

Please leave a comment on why disable these tests.

Just done, thanks for the input.

GaetanLepage · 2024-11-23T21:47:18Z

Just done, thanks for the input.

@octvs I had force-pushed some (mostly cosmetic) changes to your branch. In your last-push you got rid of those changes.
Do you mind if I add them back ?

octvs · 2024-11-24T13:42:31Z

@octvs I had force-pushed some (mostly cosmetic) changes to your branch.

I've received an e-mail about that force-push, but I couldn't manage my way around GitHub well enough to see any changes.

In your last-push you got rid of those changes.

Yeah I also force-pushed for @natsukium's feedback, without the knowledge of your changes, so they got lost. Sorry. As far as GitHub UI lets me see those changes [1], I will try to recover them. ```diff diff --git a/pkgs/development/python-modules/arxiv/default.nix b/pkgs/development/python-modules/arxiv/default.nix index 462090a9fd51..87628f6d2cb6 100644 --- a/pkgs/development/python-modules/arxiv/default.nix +++ b/pkgs/development/python-modules/arxiv/default.nix @@ -2,11 +2,17 @@ lib, buildPythonPackage, fetchFromGitHub, + + # build-system + setuptools, + + # dependencies feedparser, + requests, + + # tests mock, pytestCheckHook, - requests, - setuptools, }: buildPythonPackage rec { pname = "arxiv"; ``` I haven't encountered these comments on inputs before, but if it is required/requested I will add them. ```diff diff --git a/pkgs/development/python-modules/papis/default.nix b/pkgs/development/python-modules/papis/default.nix index 135ad8498cd3..ed4045e381cf 100644 --- a/pkgs/development/python-modules/papis/default.nix +++ b/pkgs/development/python-modules/papis/default.nix @@ -1,6 +1,5 @@ { lib, - stdenv, arxiv, beautifulsoup4, bibtexparser, @@ -9,7 +8,6 @@ click, colorama, configparser, - docutils, dominate, fetchFromGitHub, filetype, @@ -28,11 +26,14 @@ pythonOlder, pyyaml, requests, - sphinx, - sphinx-click, stevedore, typing-extensions, whoosh, + + # tests + docutils, + sphinx, + sphinx-click, }: buildPythonPackage rec { pname = "papis"; ``` `stdenv` is needed on L103 [2]. Either your local repo is outdated or GitHub is messing with the information. So the resulting patch looks like this ```diff diff --git a/pkgs/development/python-modules/arxiv/default.nix b/pkgs/development/python-modules/arxiv/default.nix index 462090a9fd51..87628f6d2cb6 100644 --- a/pkgs/development/python-modules/arxiv/default.nix +++ b/pkgs/development/python-modules/arxiv/default.nix @@ -2,11 +2,17 @@ lib, buildPythonPackage, fetchFromGitHub, + + # build-system + setuptools, + + # dependencies feedparser, + requests, + + # tests mock, pytestCheckHook, - requests, - setuptools, }: buildPythonPackage rec { pname = "arxiv"; diff --git a/pkgs/development/python-modules/papis/default.nix b/pkgs/development/python-modules/papis/default.nix index 135ad8498cd3..145920bf28c8 100644 --- a/pkgs/development/python-modules/papis/default.nix +++ b/pkgs/development/python-modules/papis/default.nix @@ -9,7 +9,6 @@ click, colorama, configparser, - docutils, dominate, fetchFromGitHub, filetype, @@ -28,11 +27,14 @@ pythonOlder, pyyaml, requests, - sphinx, - sphinx-click, stevedore, typing-extensions, whoosh, + + # tests + docutils, + sphinx, + sphinx-click, }: buildPythonPackage rec { pname = "papis"; @@ -85,8 +87,11 @@ buildPythonPackage rec { ''; nativeCheckInputs = [ - pytestCheckHook + docutils git + pytestCheckHook + sphinx + sphinx-click ]; preCheck = '' ``` Let me know if you want me to push them. [1]: https://github.com/NixOS/nixpkgs/compare/fa2e3e50733ff191cb1ef0cd4773e652a3be9973..6f5cdeb728689ff87fbe7cbaaf271bda1d0b4e9a?diff=unified&w= [2]: https://github.com/NixOS/nixpkgs/blob/11faa20dff7862100b92d8bb6eabdc9aef18b21d/pkgs/development/python-modules/papis/default.nix#L103

GaetanLepage · 2024-11-24T14:58:45Z

Let me know if you want me to push them.

Ok no worry, I have just done it.

By the way, the code snippets in your messages don't show correctly:

GaetanLepage · 2024-11-24T15:05:30Z

`nixpkgs-review` result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 354823

`x86_64-linux`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

`aarch64-linux`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

`x86_64-darwin`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

`aarch64-darwin`

✅ 8 packages built:

papis (python312Packages.papis)
papis.dist (python312Packages.papis.dist)
python311Packages.arxiv
python311Packages.arxiv.dist
python311Packages.papis
python311Packages.papis.dist
python312Packages.arxiv
python312Packages.arxiv.dist

pkgs/development/python-modules/papis/default.nix

GaetanLepage · 2024-11-24T23:11:22Z

Hmm, looks like I am not able to force-push anymore... (permission denied)

choreutes · 2025-01-20T21:45:30Z

Hey everyone, sorry for zombie bumping this, but I figured this might be the most appropriate place to ask: I just pulled the upgrade from unstable via an overlay (I'm on 24.11 stable otherwise) and afterwards papis started telling me that it is missing whoosh. And indeed I can see that the dependency on whoosh disappeared with the upgrade. I guess I can easily fix papis on my end by switching to the plain python cache. But I'm still curious if the removal was by design and if so what the reason was.

Apart from that, thanks for bringing the upgrade to nixpkgs, I really appreciate it!

octvs · 2025-01-27T17:49:40Z

Hi there,

papis started telling me that it is missing whoosh. And indeed I can see that the dependency on whoosh disappeared with the upgrade.

The relevant changes were added by @GaetanLepage on [1] [2], which found its way into [3]. Maybe he could elaborate? [1]: bbca6d9 [2]: #354823 (comment) [3]: bfec9ac

GaetanLepage · 2025-01-27T18:43:47Z

Yes, I removed whoosh in an effort to replicate the dependencies mentioned upstream: papis/papis@v0.13...v0.14#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R64-R83
As whoosh was not mentioned and the package was still building fine without it, I didn't see any problem.

It seems that whoosh is more like an optional dependencies.
https://github.com/papis/papis/blob/d396c7445dd23c5e452400efe80b37cb0baa5068/doc/source/database_structure.rst#the-database

I see no issue with adding it back.
Can you make a PR @octvs or @choreutes ?

choreutes · 2025-01-28T08:50:20Z

It seems that whoosh is more like an optional dependencies. https://github.com/papis/papis/blob/d396c7445dd23c5e452400efe80b37cb0baa5068/doc/source/database_structure.rst#the-database

Yes, whoosh is mentioned in the pyproject file as an optional dependency. It doesn't sound like an optional feature in the documentation, though, at least to me. That's why I was confused.

I see no issue with adding it back. Can you make a PR @octvs or @choreutes ?

Maybe I can have a look at it on the weekend or so. Now that I'm looking at the optional dependencies I also see the jinja2 formatter there which offers some cool features. Maybe optional deps would be nice here, too, in case people really want to override?

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x86_64-darwin

aarch64-darwin

octvs commented Nov 23, 2024 via email

GaetanLepage commented Nov 23, 2024

octvs commented Nov 24, 2024 via email

GaetanLepage commented Nov 24, 2024

GaetanLepage commented Nov 24, 2024

nixpkgs-review result

x86_64-linux

aarch64-linux

x86_64-darwin

aarch64-darwin

GaetanLepage commented Nov 24, 2024

choreutes commented Jan 20, 2025

octvs commented Jan 27, 2025 via email

GaetanLepage commented Jan 27, 2025

choreutes commented Jan 28, 2025

octvs commented Nov 9, 2024 •

edited

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steeleduncan commented Nov 13, 2024 •

edited

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octvs commented Nov 15, 2024 •

edited

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octvs commented Nov 16, 2024 via email •

edited

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`nixpkgs-review` result

`x86_64-linux`

`aarch64-linux`

`x86_64-darwin`

`aarch64-darwin`

`nixpkgs-review` result

`x86_64-linux`

`aarch64-linux`

`x86_64-darwin`

`aarch64-darwin`