Can't install `toil[cwl]==9.1.2` because of `psutil` dep

[lnicola]

$ pip install --user toil[cwl]
Collecting toil[cwl]
  Using cached toil-9.1.2-py3-none-any.whl.metadata (8.7 kB)
Requirement already satisfied: dill<0.4,>=0.3.2 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (0.3.9)
Requirement already satisfied: requests<=2.32.5 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (2.31.0)
Requirement already satisfied: docker<8,>=6.1.0 in /usr/lib/python3.14/site-packages (from toil[cwl]) (7.1.0)
Requirement already satisfied: urllib3<3,>=1.26.0 in /usr/lib/python3.14/site-packages (from toil[cwl]) (2.5.0)
Requirement already satisfied: python-dateutil in /usr/lib/python3.14/site-packages (from toil[cwl]) (2.9.0.post0)
Collecting psutil<8,>=6.1.0 (from toil[cwl])
  Downloading psutil-7.1.3-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl.metadata (23 kB)
Requirement already satisfied: PyPubSub<5,>=4.0.3 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (4.0.7)
Requirement already satisfied: addict<2.5,>=2.2.1 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (2.4.0)
Requirement already satisfied: enlighten<2,>=1.5.2 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (1.14.1)
Requirement already satisfied: configargparse<2,>=1.7 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (1.7.1)
Requirement already satisfied: ruamel.yaml>=0.15 in /usr/lib/python3.14/site-packages (from toil[cwl]) (0.18.16)
Requirement already satisfied: pyyaml<7,>=6 in /usr/lib64/python3.14/site-packages (from toil[cwl]) (6.0.2)
Requirement already satisfied: typing-extensions<5,>=4.6.2 in /usr/lib/python3.14/site-packages (from toil[cwl]) (4.15.0)
Requirement already satisfied: coloredlogs<16,>=15 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (15.0.1)
Requirement already satisfied: prompt_toolkit<4,>=3.0 in /usr/lib/python3.14/site-packages (from toil[cwl]) (3.0.41)
INFO: pip is looking at multiple versions of toil[cwl] to determine which version is compatible with other requirements. This could take a while.
Collecting toil[cwl]
  Using cached toil-9.1.1-py3-none-any.whl.metadata (8.7 kB)
  Using cached toil-9.1.0-py3-none-any.whl.metadata (8.7 kB)
  Using cached toil-9.0.0-py3-none-any.whl.metadata (8.7 kB)
  Using cached toil-8.2.0-py3-none-any.whl.metadata (8.7 kB)
  Using cached toil-8.0.0-py3-none-any.whl.metadata (8.3 kB)
Collecting psutil<7,>=6.1.0 (from toil[cwl])
  Using cached psutil-6.1.1-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB)
Collecting toil[cwl]
  Using cached toil-7.0.0-py3-none-any.whl.metadata (8.0 kB)
Requirement already satisfied: psutil<6,>=3.0.1 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (5.9.8)
Requirement already satisfied: cwltool==3.1.20240508115724 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (3.1.20240508115724)
Requirement already satisfied: schema-salad<9,>=8.4.20230128170514 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (8.9.20251102115403)
Requirement already satisfied: galaxy-tool-util<25 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (24.2.4)
Requirement already satisfied: galaxy-util<25 in ./.local/lib/python3.14/site-packages (from toil[cwl]) (24.2.4)
Requirement already satisfied: ruamel.yaml.clib>=0.2.6 in /usr/lib64/python3.14/site-packages (from toil[cwl]) (0.2.12)
Requirement already satisfied: networkx!=2.8.1,<4 in /usr/lib/python3.14/site-packages (from toil[cwl]) (3.6)
Requirement already satisfied: CacheControl[filecache] in ./.local/lib/python3.14/site-packages (from toil[cwl]) (0.14.4)
Requirement already satisfied: setuptools in /usr/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (78.1.1)
Requirement already satisfied: rdflib<7.1.0,>=4.2.2 in ./.local/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (7.0.0)
Requirement already satisfied: shellescape<3.9,>=3.4.1 in ./.local/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (3.8.1)
Requirement already satisfied: prov==1.5.1 in ./.local/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (1.5.1)
Requirement already satisfied: mypy-extensions in /usr/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (1.1.0)
Requirement already satisfied: pydot>=1.4.1 in ./.local/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (4.0.1)
Requirement already satisfied: argcomplete in /usr/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (3.6.3)
Requirement already satisfied: pyparsing!=3.0.2 in /usr/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (3.1.2)
Requirement already satisfied: cwl-utils>=0.32 in ./.local/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (0.40)
Requirement already satisfied: spython>=0.3.0 in ./.local/lib/python3.14/site-packages (from cwltool==3.1.20240508115724->toil[cwl]) (0.3.14)
Requirement already satisfied: lxml in /usr/lib64/python3.14/site-packages (from prov==1.5.1->cwltool==3.1.20240508115724->toil[cwl]) (6.0.1)
Requirement already satisfied: six>=1.9.0 in /usr/lib/python3.14/site-packages (from prov==1.5.1->cwltool==3.1.20240508115724->toil[cwl]) (1.17.0)
Requirement already satisfied: humanfriendly>=9.1 in ./.local/lib/python3.14/site-packages (from coloredlogs<16,>=15->toil[cwl]) (10.0)
Requirement already satisfied: blessed>=1.17.7 in ./.local/lib/python3.14/site-packages (from enlighten<2,>=1.5.2->toil[cwl]) (1.25.0)
Requirement already satisfied: prefixed>=0.3.2 in ./.local/lib/python3.14/site-packages (from enlighten<2,>=1.5.2->toil[cwl]) (0.9.0)
Requirement already satisfied: conda-package-streaming in ./.local/lib/python3.14/site-packages (from galaxy-tool-util<25->toil[cwl]) (0.12.0)
Requirement already satisfied: MarkupSafe in /usr/lib64/python3.14/site-packages (from galaxy-tool-util<25->toil[cwl]) (3.0.2)
Requirement already satisfied: packaging in /usr/lib/python3.14/site-packages (from galaxy-tool-util<25->toil[cwl]) (25.0)
Requirement already satisfied: pydantic!=2.6.0,!=2.6.1,>=2 in ./.local/lib/python3.14/site-packages (from galaxy-tool-util<25->toil[cwl]) (2.12.5)
Requirement already satisfied: sortedcontainers in ./.local/lib/python3.14/site-packages (from galaxy-tool-util<25->toil[cwl]) (2.4.0)
Requirement already satisfied: bleach in /usr/lib/python3.14/site-packages (from galaxy-util<25->toil[cwl]) (6.2.0)
Requirement already satisfied: boltons in ./.local/lib/python3.14/site-packages (from galaxy-util<25->toil[cwl]) (25.0.0)
Requirement already satisfied: docutils!=0.17,!=0.17.1 in /usr/lib/python3.14/site-packages (from galaxy-util<25->toil[cwl]) (0.21.2)
Requirement already satisfied: Routes in ./.local/lib/python3.14/site-packages (from galaxy-util<25->toil[cwl]) (2.5.1)
Requirement already satisfied: zipstream-new in ./.local/lib/python3.14/site-packages (from galaxy-util<25->toil[cwl]) (1.1.8)
Requirement already satisfied: isodate<0.7.0,>=0.6.0 in ./.local/lib/python3.14/site-packages (from rdflib<7.1.0,>=4.2.2->cwltool==3.1.20240508115724->toil[cwl]) (0.6.1)
Requirement already satisfied: charset-normalizer<4,>=2 in /usr/lib/python3.14/site-packages (from requests<=2.32.5->toil[cwl]) (3.4.3)
Requirement already satisfied: idna<4,>=2.5 in /usr/lib/python3.14/site-packages (from requests<=2.32.5->toil[cwl]) (3.10)
Requirement already satisfied: certifi>=2017.4.17 in /usr/lib/python3.14/site-packages (from requests<=2.32.5->toil[cwl]) (2025.7.9)
Requirement already satisfied: mistune<3.2,>=3 in /usr/lib/python3.14/site-packages (from schema-salad<9,>=8.4.20230128170514->toil[cwl]) (3.1.3)
Requirement already satisfied: msgpack<2.0.0,>=0.5.2 in /usr/lib64/python3.14/site-packages (from CacheControl[filecache]->toil[cwl]) (1.1.0)
Requirement already satisfied: filelock>=3.8.0 in ./.local/lib/python3.14/site-packages (from CacheControl[filecache]; extra == "cwl"->toil[cwl]) (3.20.0)
Requirement already satisfied: wcwidth>=0.1.4 in /usr/lib/python3.14/site-packages (from blessed>=1.17.7->enlighten<2,>=1.5.2->toil[cwl]) (0.2.13)
Requirement already satisfied: cwl-upgrader>=1.2.3 in ./.local/lib/python3.14/site-packages (from cwl-utils>=0.32->cwltool==3.1.20240508115724->toil[cwl]) (1.2.12)
Requirement already satisfied: pillow in /usr/lib64/python3.14/site-packages (from galaxy-util[image_util]>=22.1->galaxy-tool-util<25->toil[cwl]) (11.3.0)
Requirement already satisfied: annotated-types>=0.6.0 in ./.local/lib/python3.14/site-packages (from pydantic!=2.6.0,!=2.6.1,>=2->galaxy-tool-util<25->toil[cwl]) (0.7.0)
Requirement already satisfied: pydantic-core==2.41.5 in ./.local/lib/python3.14/site-packages (from pydantic!=2.6.0,!=2.6.1,>=2->galaxy-tool-util<25->toil[cwl]) (2.41.5)
Requirement already satisfied: typing-inspection>=0.4.2 in ./.local/lib/python3.14/site-packages (from pydantic!=2.6.0,!=2.6.1,>=2->galaxy-tool-util<25->toil[cwl]) (0.4.2)
Requirement already satisfied: webencodings in /usr/lib/python3.14/site-packages (from bleach->galaxy-util<25->toil[cwl]) (0.5.1)
Requirement already satisfied: zstandard>=0.15 in /usr/lib64/python3.14/site-packages (from conda-package-streaming->galaxy-tool-util<25->toil[cwl]) (0.25.0)
Requirement already satisfied: repoze.lru>=0.3 in ./.local/lib/python3.14/site-packages (from Routes->galaxy-util<25->toil[cwl]) (0.7)
Using cached toil-7.0.0-py3-none-any.whl (945 kB)
Installing collected packages: toil
Successfully installed toil-7.0.0

The notable part being Collecting psutil<7,>=6.1.0 (from toil[cwl]).

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1794

[adamnovak]

I don't think using psutil 3.0.1 and Toil 7.0.0 on Python 3.14 is the right dependency solution here; it might just be that no versions of psutil will really work for you for some reason, but 3.0.1 is too old to know that.

Why can't your system use the current psutil 7.1.3 release, which satisfies the requirement in Toil 9.1.2? If you pip install psutil==7.1.3, what explanation do you get for why you can't have that version?

[adamnovak]

Worth noting is that Toil won't officially support Python 3.14 until #5412 is in and released.

[lnicola]

$ pip install --user psutil==7.1.3
Collecting psutil==7.1.3
  Using cached psutil-7.1.3-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl.metadata (23 kB)
Using cached psutil-7.1.3-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl (263 kB)
Installing collected packages: psutil
  Attempting uninstall: psutil
    Found existing installation: psutil 5.9.8
    Uninstalling psutil-5.9.8:
      Successfully uninstalled psutil-5.9.8
Successfully installed psutil-7.1.3

$ pip install --user toil[cwl]==9.1.2
Collecting toil==9.1.2 (from toil[cwl]==9.1.2)
  Using cached toil-9.1.2-py3-none-any.whl.metadata (8.7 kB)
Requirement already satisfied: dill<0.4,>=0.3.2 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (0.3.9)
Requirement already satisfied: requests<=2.32.5 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (2.31.0)
Requirement already satisfied: docker<8,>=6.1.0 in /usr/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (7.1.0)
Requirement already satisfied: urllib3<3,>=1.26.0 in /usr/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (2.5.0)
Requirement already satisfied: python-dateutil in /usr/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (2.9.0.post0)
Requirement already satisfied: psutil<8,>=6.1.0 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (7.1.3)
Requirement already satisfied: PyPubSub<5,>=4.0.3 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (4.0.7)
Requirement already satisfied: addict<2.5,>=2.2.1 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (2.4.0)
Requirement already satisfied: enlighten<2,>=1.5.2 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (1.14.1)
Requirement already satisfied: configargparse<2,>=1.7 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (1.7.1)
Requirement already satisfied: ruamel.yaml>=0.15 in /usr/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (0.18.16)
Requirement already satisfied: pyyaml<7,>=6 in /usr/lib64/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (6.0.2)
Requirement already satisfied: typing-extensions<5,>=4.6.2 in /usr/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (4.15.0)
Requirement already satisfied: coloredlogs<16,>=15 in ./.local/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (15.0.1)
Requirement already satisfied: prompt_toolkit<4,>=3.0 in /usr/lib/python3.14/site-packages (from toil==9.1.2->toil[cwl]==9.1.2) (3.0.41)
INFO: pip is looking at multiple versions of toil[cwl] to determine which version is compatible with other requirements. This could take a while.
ERROR: Ignored the following versions that require a different python version: 3.1.20240909164951 Requires-Python <3.14,>=3.8; 3.1.20241007082533 Requires-Python <3.14,>=3.8; 3.1.20241024121129 Requires-Python <3.14,>=3.9; 3.1.20241112140730 Requires-Python <3.14,>=3.9; 3.1.20241217163858 Requires-Python <3.14,>=3.9; 3.1.20250110105449 Requires-Python <3.14,>=3.9; 3.1.20250715140722 Requires-Python <3.14,>=3.9
ERROR: Could not find a version that satisfies the requirement cwltool==3.1.20250715140722; extra == "cwl" (from toil[cwl]) (from versions: 1.0, 1.0.20150317015350, 1.0.20150318010828, 1.0.20150318015654, 1.0.20150324011020, 1.0.20150324012706, 1.0.20150324172633, 1.0.20150324173916, 1.0.20150324194338, 1.0.20150324200038, 1.0.20150324203244, 1.0.20150324211351, 1.0.20150326005309, 1.0.20150326211508, 1.0.20150327211418, 1.0.20150331014533, 1.0.20150401014645, 1.0.20150403144650, 1.0.20150407211342, 1.0.20150409193818, 1.0.20150415152714, 1.0.20150429022405, 1.0.20150508023316, 1.0.20150512154247, 1.0.20150512164512, 1.0.20150522025529, 1.0.20150525010411, 1.0.20150527172438, 1.0.20150601172915, 1.0.20150601200103, 1.0.20150602212140, 1.0.20150605134212, 1.0.20150606210100, 1.0.20150609024148, 1.0.20150609205603, 1.0.20150610150530, 1.0.20150621213723, 1.0.20150621230545, 1.0.20150622134207, 1.0.20150622144406, 1.0.20150622183905, 1.0.20150623020304, 1.0.20150623031442, 1.0.20150624181807, 1.0.20150624201710, 1.0.20150626032845, 1.0.20150626035015, 1.0.20150626035417, 1.0.20150627015636, 1.0.20150706174116, 1.0.20150707043955, 1.0.20150708115452, 1.0.20150709135652, 1.0.20150711153503, 1.0.20150713135958, 1.0.20150713152138, 1.0.20150713185212, 1.0.20150714132635, 1.0.20150715173345, 1.0.20150720194125, 1.0.20150722144138, 1.0.20150723141036, 1.0.20150728161219, 1.0.20150808190318, 1.0.20150813132038, 1.0.20150814015745, 1.0.20150814191928, 1.0.20150910021332, 1.0.20150915034626, 1.0.20150916041152, 1.0.20150916124227, 1.0.20150918080732, 1.0.20150923183439, 1.0.20150925123259, 1.0.20150929170517, 1.0.20151007133346, 1.0.20151009020717, 1.0.20151012161407, 1.0.20151012173709, 1.0.20151013134821, 1.0.20151013135545, 1.0.20151013173827, 1.0.20151022085449, 1.0.20151026181844, 1.0.20151104062100, 1.0.20151110030107, 1.0.20151112194920, 1.0.20151120220905, 1.0.20151121025646, 1.0.20151121032923, 1.0.20151122025918, 1.0.20151124040259, 1.0.20151124220039, 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ERROR: No matching distribution found for cwltool==3.1.20250715140722; extra == "cwl"

[adamnovak]

OK, so it looks like it's not really psutil that's the problem, but rather Toil pinning a cwltool that doesn't support 3.14 yet?

I think the problem should be fixed by #5412.

[mr-c]

@lnicola Now that #5412 is merged you can install toil-cwl-runner from source under Python version 3.14 using make develop extras=[cwl]. Does that fix the issue for you?

(This also includes the newer cwltool version that was released after toil 9.1.2: 48c5f1f )