Can add a new dev dependency - Key "dev-dependencies" already exists

[cda2024]

Steps to reproduce

I got a project with some dev-dependencies

[tool.pdm.dev-dependencies]
test = [
    "pytest", "pytest-cov"
]

Actual behavior

When I try to add a new one with
pdm add -dG certs altgraph
I get:

No module named 'pyshacl'
INFO: Adding group certs to lockfile
Adding packages to certs dev-dependencies: altgraph
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\users\uuu\.local\bin\pdm.exe\__main__.py", line 7, in <module>
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\pdm\core.py", line 346, in main
    return core.main(args or sys.argv[1:])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\pdm\core.py", line 264, in main
    raise cast(Exception, err).with_traceback(traceback) from None
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\pdm\core.py", line 259, in main
    self.handle(project, options)
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\pdm\core.py", line 195, in handle
    command.handle(project, options)
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\pdm\cli\commands\add.py", line 71, in handle
    self.do_add(
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\pdm\cli\commands\add.py", line 149, in do_add
    all_dependencies = project.all_dependencies
                       ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\pdm\project\core.py", line 365, in all_dependencies
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\tomlkit\container.py", line 624, in __getitem__
    item = self.item(key)
           ^^^^^^^^^^^^^^
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\tomlkit\container.py", line 472, in item
    return OutOfOrderTableProxy(self, idx)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\tomlkit\container.py", line 811, in __init__
    self._internal_container._validate_out_of_order_table()
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\tomlkit\container.py", line 154, in _validate_out_of_order_table
    self._validate_out_of_order_table(k)
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\tomlkit\container.py", line 158, in _validate_out_of_order_table
    OutOfOrderTableProxy(self, self._map[key])
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\tomlkit\container.py", line 806, in __init__
    self._internal_container.append(k, v, validate=False)
  File "C:\Users\uuu\AppData\Local\pipx\pipx\venvs\pdm\Lib\site-packages\tomlkit\container.py", line 265, in append
    raise KeyAlreadyPresent(key)
tomlkit.exceptions.KeyAlreadyPresent: Key "dev-dependencies" already exists.

Expected behavior

New dependency was added

[tool.pdm.dev-dependencies]
test = [
    "pytest", "pytest-cov"
]
certs = [
    "altgraph"
]

Environment Information

Both 2.17.1 and 2.17.3 will fail

# Paste the output of `pdm info && pdm info --env` below:

No module named 'pyshacl'
INFO: Inside an active virtualenv C:\Dev\XXX\.venv, reusing it.
Set env var PDM_IGNORE_ACTIVE_VENV to ignore it.
PDM version:
  2.17.3
Python Interpreter:
  C:\Dev\XXX\.venv\Scripts\python.exe (3.11)
Project Root:
  C:/Dev/XXX
Local Packages:


No module named 'pyshacl'
INFO: Inside an active virtualenv C:\Dev\XXX\.venv, reusing it.
Set env var PDM_IGNORE_ACTIVE_VENV to ignore it.
{
  "implementation_name": "cpython",
  "implementation_version": "3.11.7",
  "os_name": "nt",
  "platform_machine": "AMD64",
  "platform_release": "10",
  "platform_system": "Windows",
  "platform_version": "10.0.19045",
  "python_full_version": "3.11.7",
  "platform_python_implementation": "CPython",
  "python_version": "3.11",
  "sys_platform": "win32"
}

[cda2024]

Btw.
pdm import -dG certs --format requirements altgraph.req -v
will work.
Content of altgraph.req
altgraph

certs = ["altgraph"] was added to [tool.pdm.dev-dependencies]

[frostming]

This may be related to the structure of the TOML file. Can you show your pyproject.toml?

[cda2024]

Of courese, here it is:

[project]
name = "myproject"
requires-python = ">=3.11"
author = "unknown"
author_email = "unknown@xxx"
maintainers = [
    { name = "me", email = "me@xxx.de" },
]
description = "my desc"
readme = "README.md"
dependencies = [
    "pandas",
    "pandas-stubs",
    "types-openpyxl",
    "openpyxl",
    "xlsxwriter",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: Implementation :: CPython",
    "Programming Language :: Python :: Implementation :: PyPy",
]
dynamic = ["version"]
authors = [
    { name = "me", email = "me@xxx.de" },
]
keywords = [
    "a",
    "b",
]

[project.license]
text = "the bank"

[tool.pdm.dev-dependencies]
test = [
    "pytest", "pytest-cov"
]
pyflakes = [
    "pyflakes",
]
bandit = [
    "bandit",
]
black = [
    "black",
]
yamllint = [
    "yamllint",
]
pyroma = [
    "pyroma",
]
mypy = [
    "mypy",
    "pandas-stubs"
]
dodgy = [
    "dodgy",
]
flake8 = [
    "flake8",
]
jake = [
    "jake>=3.0.10",
]
pylama = [
    "pylama"
]

[project.urls]
gitlab = "https://gitlab.xxx.int/proj"

[tool.setuptools.package-data]
esgco2 = [
    "data/*",
]

[tool.pyprojectx]
main = [
    "pdm",
]

[tool.pyprojectx.venv]
dir = "@PROJECT_DIR/.venv"

[tool.pdm]
distribution = true

[build-system]
requires = [
    "pdm-backend",
]
build-backend = "pdm.backend"

[tool.pdm.version]
source = "file"
path = "./__version__.py"

[frostming]

It was fixed by tomlkit 0.13.2, you can upgrade it by:

pdm self add --pip-args=-U tomlkit