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Update latest main #2073

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48cea18
prepare for mypy 1.12
mr-c Oct 4, 2024
75e073c
remove usage of ancient shellescape backport of Stdlib's shlex (#2041)
a-detiste Oct 4, 2024
04fd426
setuptools is not a install requirement
mr-c Oct 4, 2024
0056ca5
gh-actions: fail-fast false
mr-c Oct 4, 2024
18b8fdf
Bump sphinx-rtd-theme from 2.0.0 to 3.0.0
dependabot[bot] Oct 7, 2024
6970186
Handle spurious `ReceiveScatterOutput` callbacks (#2051)
GlassOfWhiskey Oct 8, 2024
83000ae
prepare for future mypy release and enable --local-partial-types now
mr-c Oct 8, 2024
c6ad93a
Bump sphinx-rtd-theme from 3.0.0 to 3.0.1
dependabot[bot] Oct 10, 2024
82f37d5
Update black requirement from ~=24.8 to ~=24.10
dependabot[bot] Oct 8, 2024
1a2c939
Update lint-requirements.txt
mr-c Oct 8, 2024
83def6a
Update lint-requirements.txt
mr-c Oct 8, 2024
05af6c1
Drop Python 3.8
mr-c Oct 4, 2024
a956766
add more docs
mr-c Oct 4, 2024
606ec26
Bump mypy from 1.11.2 to 1.12.0
dependabot[bot] Oct 15, 2024
74a08ca
Update rdflib requirement from <7.1,>=4.2.2 to >=4.2.2,<7.2
dependabot[bot] Oct 17, 2024
e3e6bf9
Bump mypy from 1.12.0 to 1.12.1 (#2057)
dependabot[bot] Oct 22, 2024
8dee8e9
Bump mypy from 1.12.1 to 1.13.0 (#2058)
dependabot[bot] Oct 23, 2024
e3f6cf7
build binary wheels
mr-c Oct 23, 2024
6cfef62
binary wheels: only build on main and other optimizations
mr-c Oct 24, 2024
d810958
Update flake8-bugbear requirement from <24.9 to <24.11
dependabot[bot] Nov 1, 2024
9cda157
cpu_count can be None, so fallback to 1
mr-c Nov 2, 2024
ee30368
add note on docker platform issue (#2064)
Brilator Nov 8, 2024
0b64935
Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 …
dependabot[bot] Nov 11, 2024
048eb55
use max_cores in taskQueue instead of system cores (#2038)
kmavrommatis Nov 11, 2024
1557c8d
Use "run" with singularity/apptainer instead of "exec", when possible
sameeul Nov 10, 2024
c3c92eb
conformances testing: no longer skip tests for singularity/apptainer
mr-c Nov 12, 2024
e4d42b8
Bump codecov/codecov-action from 4 to 5
dependabot[bot] Nov 15, 2024
6c86caa
make-template: fix type error
mr-c Nov 27, 2024
7fa57dd
--no-warnings includes schema-salad; --validate should complain to st…
mr-c Dec 9, 2024
604fd12
Append "_latest" to image id if no tag is present (#2085)
sameeul Dec 11, 2024
d3c7bd5
Fix `cwltool:Loop` extension definition (#2081)
GlassOfWhiskey Dec 12, 2024
37d8539
Update flake8-bugbear requirement from <24.11 to <24.13 (#2086)
dependabot[bot] Dec 13, 2024
56e159f
Bump cibuildwheel from 2.21.3 to 2.22.0 (#2077)
dependabot[bot] Dec 13, 2024
cc6772e
Bump sphinx-rtd-theme from 3.0.1 to 3.0.2 (#2069)
dependabot[bot] Dec 13, 2024
6b8f06a
Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 (#2076)
dependabot[bot] Dec 13, 2024
f1d192d
argpase: colorize the --help output with rich-argparse
mr-c Nov 30, 2024
527884b
Proposal: Improved `ProvenanceProfile` definition (#2082)
fmigneault Dec 16, 2024
c6782ff
singularity: improve testing on version 4.x+
mr-c Dec 17, 2024
ae5fae4
README: Python supported versions list was outdated
mr-c Dec 20, 2024
6a61bed
docs: render the CLI groups too
mr-c Dec 20, 2024
f453cdc
Bump mypy from 1.13.0 to 1.14.0
dependabot[bot] Dec 23, 2024
baa668b
Bump mypy from 1.14.0 to 1.14.1
dependabot[bot] Dec 31, 2024
a67c898
Change caching pathmapper to respect the pathmapper factory
stxue1 Jan 9, 2025
459958b
Various cleanups to make the docs better.
mr-c Jan 22, 2025
f6aeeae
typo
mr-c Jan 22, 2025
dfa1dd0
Update black requirement from ==24.* to ==25.*
dependabot[bot] Jan 29, 2025
85976ec
black 2025 reformat
mr-c Jan 29, 2025
51516cf
Add missing cwl-runner refs
mr-c Jan 30, 2025
289b108
Bump mypy from 1.14.1 to 1.15.0
dependabot[bot] Feb 5, 2025
f741c0d
setup.py: modernize use of mypycify; switch to skiplist
mr-c Feb 5, 2025
393b698
cwlviewer: use importlib instead of __file__.
mr-c Feb 5, 2025
dc7fd2e
fix type errors discovered by mypyc
mr-c Feb 5, 2025
a1de5fa
more exception tracebacks, when in debug mode
mr-c Feb 5, 2025
a4d67ac
gh-actions: remove one last usage of the now-deprecated Ubuntu 20.04
mr-c Feb 11, 2025
38555fc
Update galaxy-util requirement from <24.2 to <24.3
dependabot[bot] Feb 13, 2025
1b56338
Update galaxy-tool-util requirement
dependabot[bot] Feb 13, 2025
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remove usage of ancient shellescape backport of Stdlib's shlex (#2041)
a-detiste authored Oct 4, 2024
commit 75e073cf7f54660cf5e0f5fec3b9054ce4da8dfa
4 changes: 2 additions & 2 deletions cwltool/command_line_tool.py
Original file line number Diff line number Diff line change
@@ -7,6 +7,7 @@
import logging
import os
import re
import shlex
import shutil
import threading
import urllib
@@ -31,7 +32,6 @@
cast,
)

import shellescape
from mypy_extensions import mypyc_attr
from ruamel.yaml.comments import CommentedMap, CommentedSeq
from schema_salad.avro.schema import Schema
@@ -1164,7 +1164,7 @@ def register_reader(f: CWLObjectType) -> None:
for b in builder.bindings:
arg = builder.generate_arg(b)
if b.get("shellQuote", True):
arg = [shellescape.quote(a) for a in aslist(arg)]
arg = [shlex.quote(a) for a in aslist(arg)]
cmd.extend(aslist(arg))
j.command_line = ["/bin/sh", "-c", " ".join(cmd)]
else:
4 changes: 2 additions & 2 deletions cwltool/job.py
Original file line number Diff line number Diff line change
@@ -5,6 +5,7 @@
import math
import os
import re
import shlex
import shutil
import signal
import stat
@@ -35,7 +36,6 @@
)

import psutil
import shellescape
from prov.model import PROV
from schema_salad.sourceline import SourceLine
from schema_salad.utils import json_dump, json_dumps
@@ -271,7 +271,7 @@ def _execute(
self.outdir,
" \\\n ".join(
[
shellescape.quote(str(arg)) if shouldquote(str(arg)) else str(arg)
shlex.quote(str(arg)) if shouldquote(str(arg)) else str(arg)
for arg in (runtime + self.command_line)
]
),
5 changes: 0 additions & 5 deletions mypy-stubs/shellescape/__init__.pyi

This file was deleted.

5 changes: 0 additions & 5 deletions mypy-stubs/shellescape/main.pyi

This file was deleted.

1 change: 0 additions & 1 deletion requirements.txt
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
requests>=2.6.1
ruamel.yaml>=0.16.0,<0.19
rdflib>=4.2.2,<7.1
shellescape>=3.4.1,<3.9
schema-salad>=8.7,<9
prov==1.5.1
mypy-extensions
1 change: 0 additions & 1 deletion setup.py
Original file line number Diff line number Diff line change
@@ -126,7 +126,6 @@
# https://github.com/ionrock/cachecontrol/issues/137
"ruamel.yaml >= 0.16, < 0.19",
"rdflib >= 4.2.2, < 7.1.0",
"shellescape >= 3.4.1, < 3.9",
"schema-salad >= 8.7, < 9",
"prov == 1.5.1",
"mypy-extensions",