Update to Python 3.12.x (#5736) #5951

dsotirho-ucsc · 2024-02-10T01:59:25Z

Connected issues: #5736

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Shorthand for review comments

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codecov · 2024-02-13T17:39:52Z

Codecov Report

Attention: Patch coverage is 82.35294% with 3 lines in your changes missing coverage. Please review.

Project coverage is 85.34%. Comparing base (24aaa42) to head (967df55).

Files with missing lines	Patch %	Lines
...llatlas/data/metadata/helpers/schema_validation.py	85.71%	2 Missing ⚠️
test/integration_test.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5951      +/-   ##
===========================================
- Coverage    85.35%   85.34%   -0.01%     
===========================================
  Files          155      155              
  Lines        20779    20789      +10     
===========================================
+ Hits         17735    17743       +8     
- Misses        3044     3046       +2

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

coveralls · 2024-02-13T17:39:57Z

coverage: 85.366% (-0.002%) from 85.368%
when pulling 967df55 on issues/dsotirho-ucsc/5736-update-python-to-3-12
into 24aaa42 on develop.

dsotirho-ucsc · 2024-10-08T22:42:46Z

IT failure due to combination of FIPS mode & the new bookworm-based Python image can be replicated with these commands:

$ sudo /usr/bin/docker run -it --rm --network gitlab-runner-net --env DOCKER_HOST=tcp://gitlab-dind:2375 --dns 172.21.0.2 --dns 169.254.169.253 122796619775.dkr.ecr.us-east-1.amazonaws.com/docker.io/library/docker:27.2.1 \
docker run -it --volume /var/run/docker.sock:/var/run/docker.sock docker.gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/runner:latest \
docker run -it docker.io/library/python:3.12.6-slim-bookworm \
bash

# apt-get update && apt-get upgrade -y && apt-get -y install build-essential curl unzip

# install -m 0755 -d /etc/apt/keyrings

# curl -fsSL https://download.docker.com/linux/debian/gpg -o /etc/apt/keyrings/docker.asc

# echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/debian "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | tee /etc/apt/sources.list.d/docker.list

# apt-get update

Terminal log:

$ ssh gitlab.hcadev

[ec2-user@ip-172-21-0-99 ~]$ sudo /usr/bin/docker run -it --rm --network gitlab-runner-net --env DOCKER_HOST=tcp://gitlab-dind:2375 --dns 172.21.0.2 --dns 169.254.169.253 122796619775.dkr.ecr.us-east-1.amazonaws.com/docker.io/library/docker:27.2.1 \
> docker run -it --volume /var/run/docker.sock:/var/run/docker.sock docker.gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/runner:latest \
> docker run -it docker.io/library/python:3.12.6-slim-bookworm \
> bash

root@02a62aa013df:/# apt-get update && apt-get upgrade -y && apt-get -y install build-essential curl unzip
Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB]
Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB]
Get:3 http://deb.debian.org/debian-security bookworm-security InRelease [48.0 kB]
Get:4 http://deb.debian.org/debian bookworm/main amd64 Packages [8787 kB]
Get:5 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [2468 B]
Get:6 http://deb.debian.org/debian-security bookworm-security/main amd64 Packages [188 kB]
Fetched 9232 kB in 2s (4113 kB/s)
Reading package lists... Done
Reading package lists... Done
...

root@02a62aa013df:/# install -m 0755 -d /etc/apt/keyrings

root@02a62aa013df:/# curl -fsSL https://download.docker.com/linux/debian/gpg -o /etc/apt/keyrings/docker.asc

root@02a62aa013df:/# echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/debian "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | tee /etc/apt/sources.list.d/docker.list
deb [arch=amd64 signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/debian bookworm stable

root@02a62aa013df:/# apt-get update
Hit:1 http://deb.debian.org/debian bookworm InRelease
Hit:2 http://deb.debian.org/debian bookworm-updates InRelease
Hit:3 http://deb.debian.org/debian-security bookworm-security InRelease
Get:4 https://download.docker.com/linux/debian bookworm InRelease [43.3 kB]
Get:5 https://download.docker.com/linux/debian bookworm/stable amd64 Packages [31.3 kB]
Fetched 74.6 kB in 1s (64.9 kB/s)
fatal error in libgcrypt, file ../../src/misc.c, line 92, function _gcry_fatal_error: requested algo not in md context

Fatal error: requested algo not in md context
Aborted

dsotirho-ucsc · 2024-10-30T19:49:25Z

Successful test mounting to /proc/sys/crypto/fips_enabled (run on gitlab dev):

sudo /usr/bin/docker run \
-it \
--rm \
--network gitlab-runner-net \
--env DOCKER_HOST=tcp://gitlab-dind:2375 \
--dns 172.21.0.2 \
--dns 169.254.169.253 \
122796619775.dkr.ecr.us-east-1.amazonaws.com/docker.io/library/docker:27.3.1 \
docker run \
-it \
--volume /var/run/docker.sock:/var/run/docker.sock \
docker.gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/runner:latest \
docker run \
-it \
--volume /var/run/docker.sock:/var/run/docker.sock \
--env DOCKER_BUILDKIT=1 docker.gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/runner:latest \
bash -c 'echo 0 > /root/zero; \
printf "FROM docker.io/library/python:3.12.6-slim-bookworm\n\
RUN --mount=type=bind,source=zero,target=/proc/sys/crypto/fips_enabled cat /proc/sys/crypto/fips_enabled\n\
RUN cat /proc/sys/crypto/fips_enabled\n" > /root/Dockerfile; \
docker build --no-cache --progress=plain /root'

Output:

...
#6 [stage-0 2/3] RUN --mount=type=bind,source=zero,target=/proc/sys/crypto/fips_enabled cat /proc/sys/crypto/fips_enabled
#6 0.523 0
#6 DONE 0.7s
...

hannes-ucsc · 2024-10-31T00:07:30Z

Simplified version below.

removed DOCKER_BUILDKIT=1 since that is the default anyways
converted the bash -c to just bash with a heredoc
converted the printf for the Dockerfile to a heredoc
removed the intermediate docker run of the runner image (I don't think it reflects reality)
~~removed the second RUN instruction (the one without the mount) from the Dockerfile~~

sudo /usr/bin/docker run \
    --interactive \
    --rm \
    --network gitlab-runner-net \
    --env DOCKER_HOST=tcp://gitlab-dind:2375 \
    --dns 172.21.0.2 \
    --dns 169.254.169.253 \
    122796619775.dkr.ecr.us-east-1.amazonaws.com/docker.io/library/docker:27.3.1 \
    docker run \
        --interactive \
        --rm \
        --volume /var/run/docker.sock:/var/run/docker.sock \
        docker.gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/runner:latest \
        bash <<EOF1
            echo 0 > zero
            docker build --no-cache --progress=plain -f - . <<EOF2
                FROM docker.io/library/python:3.12.6-slim-bookworm
                RUN cat /proc/sys/crypto/fips_enabled
                RUN --mount=type=bind,source=zero,target=/proc/sys/crypto/fips_enabled cat /proc/sys/crypto/fips_enabled
EOF2
EOF1

hannes-ucsc · 2024-10-31T17:13:55Z

Here's a simplified version of the reproduction as a paste-able one-liner for GitLab dev:

sudo /usr/bin/docker run \
    --interactive \
    --rm \
    --network gitlab-runner-net \
    --env DOCKER_HOST=tcp://gitlab-dind:2375 \
    --dns 172.21.0.2 \
    --dns 169.254.169.253 \
    122796619775.dkr.ecr.us-east-1.amazonaws.com/docker.io/library/docker:27.3.1 \
        docker run \
            --interactive \
            --rm \
            --volume /var/run/docker.sock:/var/run/docker.sock \
            docker.gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/runner:latest \
                docker run \
                    --interactive \
                    docker.io/library/python:3.12.6-slim-bookworm \
                    bash <<'EOF'
                        set -ex
                        apt-get update && apt-get -y install curl
                        install -m 0755 -d /etc/apt/keyrings
                        curl -fsSL https://download.docker.com/linux/debian/gpg -o /etc/apt/keyrings/docker.asc
                        echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/debian "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | tee /etc/apt/sources.list.d/docker.list
                        apt-get update
EOF

This ends in

+ apt-get update
Hit:1 http://deb.debian.org/debian bookworm InRelease
Hit:2 http://deb.debian.org/debian bookworm-updates InRelease
Hit:3 http://deb.debian.org/debian-security bookworm-security InRelease
Get:4 https://download.docker.com/linux/debian bookworm InRelease [43.3 kB]
Get:5 https://download.docker.com/linux/debian bookworm/stable amd64 Packages [31.3 kB]
Fetched 74.6 kB in 1s (87.5 kB/s)
Reading package lists...fatal error in libgcrypt, file ../../src/misc.c, line 92, function _gcry_fatal_error: requested algo not in md context

Fatal error: requested algo not in md context
bash: line 6:   274 Aborted                 apt-get update

The reason is that the InRelease file from Docker's package repository contains MD5 hashes of the files in the release. It also includes a SHA1 and SHA256 hash for each file. The file is signed so when apt-get tries to verify the signature, it must accumulate all the hashes, including the MD5s into the overall digest, using libgcrypt20 for that. Debian bookworm updated libgcrypt20. The previous version had an exception for MD5, in FIPS mode. The new version does not. A bug report was filed against Debian.

Most InRelease files from upstream don't contain MD5 hashes anymore and that's why the first apt-get update in the above reproduction succeeds.

hannes-ucsc · 2024-10-31T17:43:45Z

As to why the RUN --mount work-around fails with Docker Desktop on macOS: The host's /proc FS is mounted in all containers. This is the case even with our DinD setup on the EC2 instance with Amazon Linux, since all containers ultimately share the kernel, and therefore the /proc filesystem, with the host, even containers managed by the DinD daemon rather than the hosts Docker daemon.

With Docker Desktop with macOS the host is not the physical machine but a VM running a minimal Linux distro (LinuxKit). This distro and kernel don't provide /proc/sys/crypto and faking it is not easy. Even if we got it to work, runc would then refuse the mount. It only allows certain bind mounts in /proc, like /proc/sys/net. I am unsure as to why the DinD runc on the instance allows it but the workaround proves that it does.

The key observation is that we don't need the RUN --mount workaround when building the Dockerfile on macOS. The problem is not reproducible there because /proc/sys/crypto is completely absent and libgcrypt therefore doesn't attempt to enforce any FIPS restrictions.

We can

Index: Dockerfile
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/Dockerfile b/Dockerfile
--- a/Dockerfile	(revision 70f573de7639abf1180a0d78b575ea7b71a7a64a)
+++ b/Dockerfile	(date 1730396147875)
@@ -46,7 +46,8 @@
 RUN install -m 0755 -d /etc/apt/keyrings
 COPY --chmod=0644 bin/keys/docker-apt-keyring.pgp /etc/apt/keyrings/docker.gpg
 ARG azul_docker_version
-RUN --mount=type=bind,source=fips_enabled,target=/proc/sys/crypto/fips_enabled \
+ARG azul_proc_sys_crypto=/tmp
+RUN --mount=type=bind,source=fips_enabled,target=${azul_proc_sys_crypto}/fips_enabled \
     set -o pipefail \
     && ( \
       echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" \

and then override azul_proc_sys_crypto on the EC2 instance to actually point to /proc/sys/crypto.

Alternatively, we could disable FIPS mode on the instance.

Independently, we should ask Docker to remove the MD5 hashes from their InRelease file for bookworm. Either workaround (RUN --mount … target=${azul_proc_sys_crypto}/fips_enabled … or the FIPS mode disablement) could be reverted when they do.

Assignee to try the first workaround on tempdev. I verified it on my local Mac already.

Resolves error with libgcrypt on bookworm: Fatal error in libgcrypt, requested algo not in md context

hannes-ucsc · 2024-11-01T04:56:18Z

Independently, we should ask Docker to remove the MD5 hashes from their InRelease file for bookworm.

docker/docker-ce-packaging#1096

I also created #6675 so that we can add a FIXME referring to it in this PR.

Fulfills transitive requirement of distutils, which Python 3.12 removed from the standard library

For Python 3.12 support

Resolves error during `make requirements`: × Building wheel for jq (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [1390 lines of output] running bdist_wheel running build running build_ext ... jq.c:12124:55: error: no member named 'ob_digit' in 'struct _longobject' const digit* digits = ((PyLongObject*)x)->ob_digit; ~~~~~~~~~~~~~~~~~~ ^ jq.c:13608:47: error: no member named 'ob_digit' in 'struct _longobject' const digit* digits = ((PyLongObject*)b)->ob_digit; ~~~~~~~~~~~~~~~~~~ ^ 41 warnings and 7 errors generated. error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for jq

Resolves errors originating from flake8 failing to parse f-strings under Python 3.12 E122 continuation line missing indentation or outdented E131 continuation line unaligned for hanging indent E202 whitespace before ')' E202 whitespace before ']' E202 whitespace before '}' E203 whitespace before ':' E221 multiple spaces before operator E222 multiple spaces after operator E225 missing whitespace around operator E231 missing whitespace after ',' E231 missing whitespace after ':' E231 missing whitespace after ';' E271 multiple spaces after keyword E272 multiple spaces before keyword E702 multiple statements on one line (semicolon) E713 test for membership should be 'not in' W604 backticks are deprecated, use 'repr()'

Resolves error during `make requirements_update`: 19.11 Building wheels for collected packages: fastavro 19.11 Building wheel for fastavro (pyproject.toml): started 36.96 Building wheel for fastavro (pyproject.toml): finished with status 'error' 36.97 error: subprocess-exited-with-error 36.97 36.97 × Building wheel for fastavro (pyproject.toml) did not run successfully. 36.97 │ exit code: 1 36.97 ╰─> [73 lines of output] 36.97 <string>:31: SyntaxWarning: invalid escape sequence '\(' 36.97 running bdist_wheel 36.97 running build … 36.97 gcc: internal compiler error: Illegal instruction signal terminated program as 36.97 Please submit a full bug report, 36.97 with preprocessed source if appropriate. 36.97 See <file:///usr/share/doc/gcc-10/README.Bugs> for instructions. 36.97 error: command '/usr/bin/gcc' failed with exit code 4 36.97 [end of output]

Resolves error during test: ERROR: test_openapi (integration_test.OpenAPIIntegrationTest.test_openapi) (component='service') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/daniel/repo/azul1/test/integration_test.py", line 1856, in test_openapi validate_spec(spec) File "/Users/daniel/repo/azul1/.venv/lib/python3.12/site-packages/openapi_spec_validator/shortcuts.py", line 17, in validate_spec return validator.validate(spec, spec_url=spec_url) ... AttributeError: '_io.BufferedReader' object has no attribute 'decode'

Resolves DeprecationWarning during schema validation: Traceback (most recent call last): File "/Users/daniel/.pyenv/versions/3.12.6/lib/python3.12/unittest/suite.py", line 306, in _tearDownPreviousClass tearDownClass() AssertionError: ["{message : DeprecationWarning('Automatically retrieving remote references can be a security vulnerability and is discouraged by the JSON Schema specifications. Relying on this behavior is deprecated and will shortly become an error. If you are sure you want to remotely retrieve your reference and that it is safe to do so, you can find instructions for doing so via referencing.Registry in the referencing documentation (https://referencing.readthedocs.org).'), category : 'DeprecationWarning', filename : '/Users/daniel/repo/azul1/.venv/lib/python3.12/site-packages/jsonschema/exceptions.py', lineno : 475, line : None}", ...]

Resolves finding during `make pep8`: F842 local variable 'cs' is annotated but never used

Resolves finding during `make pep8` E122 continuation line missing indentation or outdented

Resolves error during test: AttributeError: 'not_called' is not a valid assertion. Use a spec for the mock if 'not_called' is meant to be an attribute.

github-actions bot added the orange [process] Done by the Azul team label Feb 10, 2024

dsotirho-ucsc added reqs [process] PR includes commit requiring ``make requirements`` upgrade [process] PR includes commit requiring manual upgrade labels Feb 10, 2024

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Update to Python 3.12.x #5736

Open

dsotirho-ucsc dismissed nadove-ucsc’s stale review via 310fbe5 October 14, 2024 17:03

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dsotirho-ucsc added 2 commits October 31, 2024 13:20

Update to Python 3.12.x (#5736)

605f8aa

Disable FIPS mode in Docker container during apt-get update

416ac79

Resolves error with libgcrypt on bookworm: Fatal error in libgcrypt, requested algo not in md context

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5736-update-python-to-3-12 branch from 70f573d to 0e71eec Compare October 31, 2024 20:45

hannes-ucsc mentioned this pull request Nov 1, 2024

Docker build with Bookworm base image fails on GL #6675

Open

dsotirho-ucsc added 14 commits November 4, 2024 08:57

Add FIXME (#6675)

3deaab5

Make requirements_update download binaries, not source packages

4fe0979

[R] Add setuptools as a requirement

82815b1

Fulfills transitive requirement of distutils, which Python 3.12 removed from the standard library

[R] Update azul-chalice to 1.31.2+13

b119314

For Python 3.12 support

Remove unassigned type-hinted variable

01067f2

Resolves finding during `make pep8`: F842 local variable 'cs' is annotated but never used

Reformat ternary operation

e8c5f2e

Resolves finding during `make pep8` E122 continuation line missing indentation or outdented

Fix broken assert of Mock object's not_called property

991429b

Resolves error during test: AttributeError: 'not_called' is not a valid assertion. Use a spec for the mock if 'not_called' is meant to be an attribute.

Ignore DeprecationWarning from datetime, add FIXME (#5953)

84e1066

[R] Ran make requirements_update

967df55

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Update to Python 3.12.x (#5736) #5951

Update to Python 3.12.x (#5736) #5951

dsotirho-ucsc commented Feb 10, 2024 •

edited by achave11-ucsc

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codecov bot commented Feb 13, 2024 •

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hannes-ucsc commented Nov 1, 2024

Update to Python 3.12.x (#5736) #5951

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Update to Python 3.12.x (#5736) #5951

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dsotirho-ucsc commented Feb 10, 2024 • edited by achave11-ucsc Loading

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dsotirho-ucsc commented Feb 10, 2024 •

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