From 57539d3af82c62dca39662de1c41001516d05586 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 3 Jul 2024 12:01:03 +0200
Subject: [PATCH] =?UTF-8?q?=E2=AC=86=EF=B8=8F=20Bump=20jax=20from=200.4.29?=
 =?UTF-8?q?=20to=200.4.30=20(#615)?=
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* :arrow_up: Bump jax from 0.4.29 to 0.4.30

Bumps [jax](https://github.com/google/jax) from 0.4.29 to 0.4.30.
- [Release notes](https://github.com/google/jax/releases)
- [Changelog](https://github.com/google/jax/blob/main/CHANGELOG.md)
- [Commits](https://github.com/google/jax/compare/jax-v0.4.29...jax-v0.4.30)

---
updated-dependencies:
- dependency-name: jax
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* fix some warnings

* bump python version

* downgrade numpy

* fix copy setup test

* why even bother

* oops

* roll back rtol -> tol to support older scipy

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Dion Häfner <dion.haefner@simulation.science>
---
 pyproject.toml              | 2 +-
 requirements.txt            | 2 +-
 requirements_jax.txt        | 2 +-
 test/cli_test.py            | 9 +++++----
 veros/cli/veros_resubmit.py | 3 +--
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3b1c0683..530511aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.black]
 line-length = 120
-target-version = ['py37', 'py38', 'py39', 'py310']
+target-version = ['py38', 'py39', 'py310', 'py311', 'py312']
 
 
 [tool.pytest.ini_options]
diff --git a/requirements.txt b/requirements.txt
index c111750c..c01187fd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 click==8.1.7
 entrypoints==0.4
 requests==2.32.3
-numpy==2.0.0
+numpy==1.26.4
 scipy==1.13.1
 h5netcdf==1.3.0
 h5py==3.11.0
diff --git a/requirements_jax.txt b/requirements_jax.txt
index 521e60b2..5341870a 100644
--- a/requirements_jax.txt
+++ b/requirements_jax.txt
@@ -1 +1 @@
-jax==0.4.29
+jax==0.4.30
diff --git a/test/cli_test.py b/test/cli_test.py
index 61ec8e67..3688a3f0 100644
--- a/test/cli_test.py
+++ b/test/cli_test.py
@@ -2,7 +2,6 @@
 import sys
 import filecmp
 import fnmatch
-import pkg_resources
 import subprocess
 from textwrap import dedent
 
@@ -28,12 +27,14 @@ def runner():
 
 @pytest.mark.parametrize("setup", SETUPS)
 def test_veros_copy_setup(setup, runner, tmpdir):
-    result = runner.invoke(veros.cli.veros_copy_setup.cli, [setup, "--to", os.path.join(tmpdir, setup)])
+    import veros
+
+    outpath = os.path.join(tmpdir, setup)
+    result = runner.invoke(veros.cli.veros_copy_setup.cli, [setup, "--to", outpath])
     assert result.exit_code == 0, setup
     assert not result.output
 
-    outpath = os.path.join(tmpdir, setup)
-    srcpath = pkg_resources.resource_filename("veros", f"setups/{setup}")
+    srcpath = os.path.join(os.path.dirname(veros.__file__), "setups", setup)
     ignore = [
         f
         for f in os.listdir(srcpath)
diff --git a/veros/cli/veros_resubmit.py b/veros/cli/veros_resubmit.py
index 5ea0b1b9..a5e99155 100644
--- a/veros/cli/veros_resubmit.py
+++ b/veros/cli/veros_resubmit.py
@@ -3,7 +3,6 @@
 import functools
 import subprocess
 import shlex
-import pipes
 import sys
 import os
 import time
@@ -36,7 +35,7 @@ def write_next_n(n, filename):
 
 
 def unparse(args):
-    return " ".join(map(pipes.quote, args))
+    return shlex.join(args)
 
 
 def call_veros(cmd, name, n, runlen):