Safety CI > msk-access/uncollapsed_bam

feature/use_static_bed_file_for_ABRA

1 year, 4 months ago

2e63782a

Update subworkflows

Server Error.

feature/use_static_bed_file_for_ABRA

1 year, 4 months ago

068064f2

Update to specific version of submodules subworkflows v1.2.7 commandlinetools v1.3.5

Server Error.

feature/use_static_bed_file_for_ABRA

1 year, 4 months ago

6822bc63

Update subworkflows

Server Error.

pyup-scheduled-update-2024-12-01

1 year, 5 months ago

eb438147

Update tox from 3.27.1 to 4.23.2

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-12-01

1 year, 5 months ago

6254ecea

Update toil from 5.10.0 to 7.0.0

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-12-01

1 year, 5 months ago

be3443e0

Update setuptools from 65.4.1 to 75.6.0

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-12-01

1 year, 5 months ago

e6b70a62

Update pytest from 7.2.0 to 8.3.4

setuptools 65.4.1 and pytest-runner 6.0.1 have known security vulnerabilities.

Package	Installed	Affected	Info
setuptools	65.4.1	<70.0.0	show Affected versions of Setuptools allow for remote code execution via its download functions. These functions, which are used to download packages from URLs provided by users or retrieved from package index servers, are susceptible to code injection. If these functions are exposed to user-controlled inputs, such as package URLs, they can execute arbitrary commands on the system.
setuptools	65.4.1	<65.5.1	show Setuptools 65.5.1 includes a fix for CVE-2022-40897: Python Packaging Authority (PyPA) setuptools before 65.5.1 allows remote attackers to cause a denial of service via HTML in a crafted package or custom PackageIndex page. There is a Regular Expression Denial of Service (ReDoS) in package_index.py.
setuptools	65.4.1	<78.1.1	show Affected versions of Setuptools are vulnerable to Path Traversal via PackageIndex.download(). The impact is Arbitrary File Overwrite: An attacker would be allowed to write files to arbitrary locations on the filesystem with the permissions of the process running the Python code, which could escalate to RCE depending on the context.
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

feature/use_static_bed_file_for_ABRA

1 year, 6 months ago

8e270032

Update uncollapsed_bam_generation.cwl

setuptools 65.4.1 and pytest-runner 6.0.1 have known security vulnerabilities.

Package	Installed	Affected	Info
setuptools	65.4.1	<70.0.0	show Affected versions of Setuptools allow for remote code execution via its download functions. These functions, which are used to download packages from URLs provided by users or retrieved from package index servers, are susceptible to code injection. If these functions are exposed to user-controlled inputs, such as package URLs, they can execute arbitrary commands on the system.
setuptools	65.4.1	<65.5.1	show Setuptools 65.5.1 includes a fix for CVE-2022-40897: Python Packaging Authority (PyPA) setuptools before 65.5.1 allows remote attackers to cause a denial of service via HTML in a crafted package or custom PackageIndex page. There is a Regular Expression Denial of Service (ReDoS) in package_index.py.
setuptools	65.4.1	<78.1.1	show Affected versions of Setuptools are vulnerable to Path Traversal via PackageIndex.download(). The impact is Arbitrary File Overwrite: An attacker would be allowed to write files to arbitrary locations on the filesystem with the permissions of the process running the Python code, which could escalate to RCE depending on the context.
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

feature/use_static_bed_file_for_ABRA

1 year, 6 months ago

776c359e

Update subworkflows

setuptools 65.4.1 and pytest-runner 6.0.1 have known security vulnerabilities.

Package	Installed	Affected	Info
setuptools	65.4.1	<70.0.0	show Affected versions of Setuptools allow for remote code execution via its download functions. These functions, which are used to download packages from URLs provided by users or retrieved from package index servers, are susceptible to code injection. If these functions are exposed to user-controlled inputs, such as package URLs, they can execute arbitrary commands on the system.
setuptools	65.4.1	<65.5.1	show Setuptools 65.5.1 includes a fix for CVE-2022-40897: Python Packaging Authority (PyPA) setuptools before 65.5.1 allows remote attackers to cause a denial of service via HTML in a crafted package or custom PackageIndex page. There is a Regular Expression Denial of Service (ReDoS) in package_index.py.
setuptools	65.4.1	<78.1.1	show Affected versions of Setuptools are vulnerable to Path Traversal via PackageIndex.download(). The impact is Arbitrary File Overwrite: An attacker would be allowed to write files to arbitrary locations on the filesystem with the permissions of the process running the Python code, which could escalate to RCE depending on the context.
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-11-01

1 year, 6 months ago

272e3843

Update toil from 5.10.0 to 7.0.0

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-11-01

1 year, 6 months ago

03dded2d

Update tox from 3.27.1 to 4.23.2

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-11-01

1 year, 6 months ago

59df782c

Update setuptools from 65.4.1 to 75.3.0

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-11-01

1 year, 6 months ago

4549038c

Update pytest from 7.2.0 to 8.3.3

setuptools 65.4.1 and pytest-runner 6.0.1 have known security vulnerabilities.

Package	Installed	Affected	Info
setuptools	65.4.1	<70.0.0	show Affected versions of Setuptools allow for remote code execution via its download functions. These functions, which are used to download packages from URLs provided by users or retrieved from package index servers, are susceptible to code injection. If these functions are exposed to user-controlled inputs, such as package URLs, they can execute arbitrary commands on the system.
setuptools	65.4.1	<65.5.1	show Setuptools 65.5.1 includes a fix for CVE-2022-40897: Python Packaging Authority (PyPA) setuptools before 65.5.1 allows remote attackers to cause a denial of service via HTML in a crafted package or custom PackageIndex page. There is a Regular Expression Denial of Service (ReDoS) in package_index.py.
setuptools	65.4.1	<78.1.1	show Affected versions of Setuptools are vulnerable to Path Traversal via PackageIndex.download(). The impact is Arbitrary File Overwrite: An attacker would be allowed to write files to arbitrary locations on the filesystem with the permissions of the process running the Python code, which could escalate to RCE depending on the context.
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-10-01

1 year, 7 months ago

a82ae767

Update tox from 3.27.1 to 4.21.0

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

pyup-scheduled-update-2024-10-01

1 year, 7 months ago

6fa15ee8

Update toil from 5.10.0 to 7.0.0

pytest-runner 6.0.1 has known security vulnerabilities.

Package	Installed	Affected	Info
pytest-runner	6.0.1	>0	show Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684. It is recommended that you: - Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option. - Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option. - Select a tool to bootstrap and then run tests such as tox. https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

Package

Installed

Affected

Info

pytest-runner

6.0.1

>0

show

Pytest-runner depends on deprecated features of setuptools and relies on features that break security mechanisms in pip. For example ‘setup_requires’ and ‘tests_require’ bypass pip --require-hashes. See also pypa/setuptools#1684.
It is recommended that you:
- Remove 'pytest-runner' from your setup_requires, preferably removing the setup_requires option.
- Remove 'pytest' and any other testing requirements from tests_require, preferably removing the tests_requires option.
- Select a tool to bootstrap and then run tests such as tox.
https://github.com/pytest-dev/pytest-runner/blob/289a77b179535d8137118e3b8591d9e727130d6d/README.rst

msk-access/uncollapsed_bam_generation