diff --git a/dependencies/python/ansible-lint.txt b/dependencies/python/ansible-lint.txt
index 128c2f5c332..388c539ae85 100644
--- a/dependencies/python/ansible-lint.txt
+++ b/dependencies/python/ansible-lint.txt
@@ -1,20 +1,31 @@
-ansible-core==2.12.3
-ansible-lint==5.4.0
-bracex==2.2.1
-cffi==1.15.0
-commonmark==0.9.1
-cryptography==36.0.1
-enrich==1.2.7
-Jinja2==3.0.3
-MarkupSafe==2.1.0
-packaging==21.3
-pycparser==2.21
-Pygments==2.11.2
-pyparsing==3.0.7
-PyYAML==6.0
-resolvelib==0.5.4
-rich==12.0.0
-ruamel.yaml==0.17.21
-ruamel.yaml.clib==0.2.6
-tenacity==8.0.1
-wcmatch==8.3
+ansible-compat==26.3.0
+ansible-core==2.20.5
+ansible-lint==26.4.0
+attrs==26.1.0
+black==26.5.0
+bracex==2.6
+cffi==2.0.0
+click==8.4.0
+cryptography==48.0.0
+distro==1.9.0
+filelock==3.29.0
+Jinja2==3.1.6
+jsonschema==4.26.0
+jsonschema-specifications==2025.9.1
+MarkupSafe==3.0.3
+mypy_extensions==1.1.0
+packaging==26.2
+pathspec==1.0.4
+platformdirs==4.9.6
+pycparser==3.0
+pytokens==0.4.1
+PyYAML==6.0.3
+referencing==0.37.0
+resolvelib==1.2.1
+rpds-py==0.30.0
+ruamel.yaml==0.19.1
+ruamel.yaml.clib==0.2.15
+subprocess-tee==0.4.2
+typing_extensions==4.15.0
+wcmatch==10.1
+yamllint==1.38.0
diff --git a/dependencies/python/black.txt b/dependencies/python/black.txt
index faa62eff05b..0d9ec1c3cfd 100644
--- a/dependencies/python/black.txt
+++ b/dependencies/python/black.txt
@@ -1,7 +1,7 @@
-black==22.1.0
-click==8.0.4
-mypy-extensions==0.4.3
-pathspec==0.9.0
-platformdirs==2.5.1
-tomli==2.0.1
-typing_extensions==4.1.1
+black==26.5.0
+click==8.4.0
+mypy_extensions==1.1.0
+packaging==26.2
+pathspec==1.1.1
+platformdirs==4.9.6
+pytokens==0.4.1
diff --git a/dependencies/python/cfn-lint.txt b/dependencies/python/cfn-lint.txt
index cbcdc2ce4c2..d500bf26613 100644
--- a/dependencies/python/cfn-lint.txt
+++ b/dependencies/python/cfn-lint.txt
@@ -1,21 +1,26 @@
-attrs==21.4.0
-aws-sam-translator==1.42.0
-boto3==1.21.18
-botocore==1.24.18
-cfn-lint==0.58.3
-jmespath==0.10.0
-jschema-to-python==1.2.3
-jsonpatch==1.32
-jsonpickle==2.1.0
-jsonpointer==2.2
-jsonschema==3.2.0
-junit-xml==1.9
-networkx==2.7.1
-pbr==5.8.1
-pyrsistent==0.18.1
-python-dateutil==2.8.2
-PyYAML==6.0
-s3transfer==0.5.2
-sarif-om==1.0.4
-six==1.16.0
-urllib3==1.26.8
+annotated-types==0.7.0
+attrs==26.1.0
+aws-sam-translator==1.109.0
+boto3==1.43.9
+botocore==1.43.9
+cfn-lint==1.51.0
+jmespath==1.1.0
+jsonpatch==1.33
+jsonpointer==3.1.1
+jsonschema==4.26.0
+jsonschema-specifications==2025.9.1
+mpmath==1.3.0
+networkx==3.6.1
+pydantic==2.12.5
+pydantic_core==2.41.5
+python-dateutil==2.9.0.post0
+PyYAML==6.0.3
+referencing==0.37.0
+regex==2026.5.9
+rpds-py==0.30.0
+s3transfer==0.17.0
+six==1.17.0
+sympy==1.14.0
+typing-inspection==0.4.2
+typing_extensions==4.15.0
+urllib3==2.7.0
diff --git a/dependencies/python/cpplint.txt b/dependencies/python/cpplint.txt
index f036ee5b2f6..6aabac21c30 100644
--- a/dependencies/python/cpplint.txt
+++ b/dependencies/python/cpplint.txt
@@ -1 +1 @@
-cpplint==1.6.0
+cpplint==2.0.2
diff --git a/dependencies/python/flake8.txt b/dependencies/python/flake8.txt
index 5e5ce6e5351..776c2696a50 100644
--- a/dependencies/python/flake8.txt
+++ b/dependencies/python/flake8.txt
@@ -1,4 +1,4 @@
-flake8==4.0.1
-mccabe==0.6.1
-pycodestyle==2.8.0
-pyflakes==2.4.0
+flake8==7.3.0
+mccabe==0.7.0
+pycodestyle==2.14.0
+pyflakes==3.4.0
diff --git a/dependencies/python/isort.txt b/dependencies/python/isort.txt
index 8eeb146b1ad..6dd8f57d4a4 100644
--- a/dependencies/python/isort.txt
+++ b/dependencies/python/isort.txt
@@ -1 +1 @@
-isort==5.10.1
+isort==8.0.1
diff --git a/dependencies/python/mypy.txt b/dependencies/python/mypy.txt
index 5ebae675996..d634a77a58d 100644
--- a/dependencies/python/mypy.txt
+++ b/dependencies/python/mypy.txt
@@ -1,4 +1,6 @@
-mypy==0.940
-mypy-extensions==0.4.3
-tomli==2.0.1
-typing_extensions==4.1.1
+ast_serialize==0.5.0
+librt==0.11.0
+mypy==2.1.0
+mypy_extensions==1.1.0
+pathspec==1.1.1
+typing_extensions==4.15.0
diff --git a/dependencies/python/pylint.txt b/dependencies/python/pylint.txt
index 84762636383..908b55fd124 100644
--- a/dependencies/python/pylint.txt
+++ b/dependencies/python/pylint.txt
@@ -1,9 +1,7 @@
-astroid==2.9.3
-isort==5.10.1
-lazy-object-proxy==1.7.1
-mccabe==0.6.1
-platformdirs==2.5.1
-pylint==2.12.2
-toml==0.10.2
-typing_extensions==4.1.1
-wrapt==1.13.3
+astroid==4.0.4
+dill==0.4.1
+isort==8.0.1
+mccabe==0.7.0
+platformdirs==4.9.6
+pylint==4.0.5
+tomlkit==0.15.0
diff --git a/dependencies/python/snakefmt.txt b/dependencies/python/snakefmt.txt
index bff3d4f4963..55812de21d7 100644
--- a/dependencies/python/snakefmt.txt
+++ b/dependencies/python/snakefmt.txt
@@ -1,11 +1,8 @@
-black==22.1.0
-click==8.0.4
-importlib-metadata==1.7.0
-mypy-extensions==0.4.3
-pathspec==0.9.0
-platformdirs==2.5.1
-snakefmt==0.6.0
-toml==0.10.2
-tomli==2.0.1
-typing_extensions==4.1.1
-zipp==3.7.0
+black==26.5.0
+click==8.4.0
+mypy_extensions==1.1.0
+packaging==26.2
+pathspec==1.1.1
+platformdirs==4.9.6
+pytokens==0.4.1
+snakefmt==1.1.0
diff --git a/dependencies/python/snakemake.txt b/dependencies/python/snakemake.txt
index a29bf5724e6..b71496825e6 100644
--- a/dependencies/python/snakemake.txt
+++ b/dependencies/python/snakemake.txt
@@ -1,38 +1,53 @@
-appdirs==1.4.4
-attrs==21.4.0
-certifi==2021.10.8
-charset-normalizer==2.0.12
-ConfigArgParse==1.5.3
-connection-pool==0.0.3
-datrie==0.8.2
-decorator==5.1.1
-docutils==0.18.1
-gitdb==4.0.9
-GitPython==3.1.27
-idna==3.3
-importlib-resources==5.4.0
-Jinja2==3.0.3
-jsonschema==4.4.0
-jupyter-core==4.9.2
-MarkupSafe==2.1.0
-nbformat==5.2.0
-plac==1.3.4
-psutil==5.9.0
-PuLP==2.6.0
-py==1.11.0
-pyrsistent==0.18.1
-PyYAML==6.0
-ratelimiter==1.2.0.post0
-requests==2.27.1
-retry==0.9.2
-smart-open==5.2.1
-smmap==5.0.0
-snakemake==7.2.1
-stopit==1.1.2
-tabulate==0.8.9
-toposort==1.7
-traitlets==5.1.1
-urllib3==1.26.8
-wrapt==1.14.0
-yte==1.2.0
-zipp==3.7.0
+annotated-types==0.7.0
+argparse-dataclass==2.0.0
+attrs==26.1.0
+certifi==2026.4.22
+charset-normalizer==3.4.7
+conda-inject==1.3.2
+ConfigArgParse==1.7.5
+connection_pool==0.0.3
+docutils==0.22.4
+dpath==2.2.0
+fastjsonschema==2.21.2
+gitdb==4.0.12
+GitPython==3.1.50
+greenlet==3.5.0
+humanfriendly==10.0
+idna==3.15
+immutables==0.21
+Jinja2==3.1.6
+jsonschema==4.26.0
+jsonschema-specifications==2025.9.1
+jupyter_core==5.9.1
+MarkupSafe==3.0.3
+nbformat==5.10.4
+packaging==25.0
+platformdirs==4.9.6
+psutil==7.2.2
+PuLP==3.3.1
+pydantic==2.13.4
+pydantic_core==2.46.4
+PyYAML==6.0.3
+referencing==0.37.0
+requests==2.34.2
+rpds-py==0.30.0
+smart_open==7.6.1
+smmap==5.0.3
+snakemake==9.21.0
+snakemake-interface-common==1.23.0
+snakemake-interface-executor-plugins==9.4.0
+snakemake-interface-logger-plugins==2.0.1
+snakemake-interface-report-plugins==1.3.0
+snakemake-interface-scheduler-plugins==2.0.2
+snakemake-interface-storage-plugins==4.4.1
+SQLAlchemy==2.0.49
+sqlmodel==0.0.37
+tabulate==0.10.0
+tenacity==9.1.4
+throttler==1.2.3
+traitlets==5.15.0
+typing-inspection==0.4.2
+typing_extensions==4.15.0
+urllib3==2.7.0
+wrapt==2.1.2
+yte==1.9.4
diff --git a/dependencies/python/sqlfluff.txt b/dependencies/python/sqlfluff.txt
index a4c5834a2e3..45b46e8e2cc 100644
--- a/dependencies/python/sqlfluff.txt
+++ b/dependencies/python/sqlfluff.txt
@@ -1,24 +1,15 @@
-appdirs==1.4.4
-attrs==21.4.0
-chardet==4.0.0
-click==8.0.4
-colorama==0.4.4
-diff-cover==6.4.4
-iniconfig==1.1.1
-Jinja2==3.0.3
-MarkupSafe==2.1.0
-packaging==21.3
-pathspec==0.9.0
-pluggy==1.0.0
-py==1.11.0
-Pygments==2.11.2
-pyparsing==3.0.7
-pytest==7.1.0
-PyYAML==6.0
-regex==2022.3.2
-sqlfluff==0.11.0
-tblib==1.7.0
-toml==0.10.2
-tomli==2.0.1
-tqdm==4.63.0
-typing_extensions==4.1.1
+chardet==7.4.3
+click==8.3.3
+colorama==0.4.6
+diff_cover==10.2.0
+Jinja2==3.1.6
+MarkupSafe==3.0.3
+pathspec==1.1.1
+platformdirs==4.9.6
+pluggy==1.6.0
+Pygments==2.20.0
+PyYAML==6.0.3
+regex==2026.5.9
+sqlfluff==4.2.1
+tblib==3.2.2
+tqdm==4.67.3
diff --git a/dependencies/python/yamllint.txt b/dependencies/python/yamllint.txt
index f2f126592ec..e54894f4a8d 100644
--- a/dependencies/python/yamllint.txt
+++ b/dependencies/python/yamllint.txt
@@ -1,3 +1,3 @@
-pathspec==0.9.0
-PyYAML==6.0
-yamllint==1.26.3
+pathspec==1.1.1
+PyYAML==6.0.3
+yamllint==1.38.0
diff --git a/dependencies/python/yq.txt b/dependencies/python/yq.txt
index f2620127353..372e94e2127 100644
--- a/dependencies/python/yq.txt
+++ b/dependencies/python/yq.txt
@@ -1,5 +1,5 @@
-argcomplete==2.0.0
-PyYAML==6.0
-toml==0.10.2
-xmltodict==0.12.0
-yq==2.14.0
+argcomplete==3.6.3
+PyYAML==6.0.3
+tomlkit==0.15.0
+xmltodict==1.0.4
+yq==3.4.3