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[services, hailtop] Restore "shift supported python versions from 3.10-13 to 3.12-14" - #15663
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| if version_info < (3, 11): | ||
| raise EnvironmentError(f'Hail requires Python 3.11 or later, found {version_info.major}.{version_info.minor}') |
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Version check inconsistency: The runtime check allows Python 3.11+, but setup.py and setup-hailtop.py require Python 3.12+, and docker.py also enforces 3.12+. This creates an inconsistent state where Python 3.11 users could install Hail (passing the runtime check) but fail at build/docker image creation time. Should be:
if version_info < (3, 12):
raise EnvironmentError(f'Hail requires Python 3.12 or later, found {version_info.major}.{version_info.minor}')This aligns with the PR description stating "3.11 will NOT continue to be supported" and matches the python_requires=">=3.12" in both setup files.
Suggested change
| if version_info < (3, 11): | |
| raise EnvironmentError(f'Hail requires Python 3.11 or later, found {version_info.major}.{version_info.minor}') | |
| if version_info < (3, 12): | |
| raise EnvironmentError(f'Hail requires Python 3.12 or later, found {version_info.major}.{version_info.minor}') | |
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Splendid, excellent, first-rate.
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…0-13 to 3.12-14" (hail-is#15663) Reverts hail-is#15660; restores the changes in hail-is#15603. Should be ready to merge again after the dataproc update (hail-is#15662) --- ## Change Description Updates the default python version to 3.12 and shifts the list of supported versions to 3.12, 3.13, 3.14 to realign with the numpy's supported versions. Update: 3.11 will NOT continue to be supported. EMR has been shown to work ok with 3.12 and numpy support has already expired on 3.11. ## Security Assessment Delete all except the correct answer: - This change potentially impacts the Hail Batch instance as deployed by Broad Institute in GCP ### Impact Rating - This change has a low security impact ### Impact Description Python version updates in services and client libraries. ### Appsec Review - [ ] Required: The impact has been assessed and approved by appsec
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…0-13 to 3.12-14" (hail-is#15663) Reverts hail-is#15660; restores the changes in hail-is#15603. Should be ready to merge again after the dataproc update (hail-is#15662) --- ## Change Description Updates the default python version to 3.12 and shifts the list of supported versions to 3.12, 3.13, 3.14 to realign with the numpy's supported versions. Update: 3.11 will NOT continue to be supported. EMR has been shown to work ok with 3.12 and numpy support has already expired on 3.11. ## Security Assessment Delete all except the correct answer: - This change potentially impacts the Hail Batch instance as deployed by Broad Institute in GCP ### Impact Rating - This change has a low security impact ### Impact Description Python version updates in services and client libraries. ### Appsec Review - [ ] Required: The impact has been assessed and approved by appsec
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…0-13 to 3.12-14" (hail-is#15663) Reverts hail-is#15660; restores the changes in hail-is#15603. Should be ready to merge again after the dataproc update (hail-is#15662) --- ## Change Description Updates the default python version to 3.12 and shifts the list of supported versions to 3.12, 3.13, 3.14 to realign with the numpy's supported versions. Update: 3.11 will NOT continue to be supported. EMR has been shown to work ok with 3.12 and numpy support has already expired on 3.11. ## Security Assessment Delete all except the correct answer: - This change potentially impacts the Hail Batch instance as deployed by Broad Institute in GCP ### Impact Rating - This change has a low security impact ### Impact Description Python version updates in services and client libraries. ### Appsec Review - [ ] Required: The impact has been assessed and approved by appsec
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…0-13 to 3.12-14" (hail-is#15663) Reverts hail-is#15660; restores the changes in hail-is#15603. Should be ready to merge again after the dataproc update (hail-is#15662) --- ## Change Description Updates the default python version to 3.12 and shifts the list of supported versions to 3.12, 3.13, 3.14 to realign with the numpy's supported versions. Update: 3.11 will NOT continue to be supported. EMR has been shown to work ok with 3.12 and numpy support has already expired on 3.11. ## Security Assessment Delete all except the correct answer: - This change potentially impacts the Hail Batch instance as deployed by Broad Institute in GCP ### Impact Rating - This change has a low security impact ### Impact Description Python version updates in services and client libraries. ### Appsec Review - [ ] Required: The impact has been assessed and approved by appsec
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Collects the inputs for the gnomad-qc-deps images the v5 info HT runs (generate_variant_qc_annotations.py --generate-ac-info-ht) use, beside the script they serve, named for what they build rather than for the directory they sit in: - info_ht.Dockerfile + info_ht_cloudbuild.yaml, carried over from kl/split_info_ht_workflow so they are not stranded on a feature branch. - info_ht_hail_dev.Dockerfile, recovered: this built the currently-running :20260710-hail882835b-py312 image but only ever existed in /tmp, which macOS has since wiped. Its instructions are byte-identical to the published image's build history. - info_ht_hail_dev_venv.pins, the pins for that image's /opt/venv-312, verified byte-identical to the copy baked into the image layer. Named .pins, not requirements*.txt, so GitHub's dependency graph does not read image-exact pins as a manifest for the repo. These reproduce the overlay, not the whole stack. :20260710 was built with hail==0.2.137, so info_ht.Dockerfile as committed produces the equivalent of :20260826 rather than that tag; the header records this. It makes no difference to what runs, since the base's 3.11 venv is shadowed on PATH. The overlay exists because the dev Hail build requires Python >= 3.12 (hail-is/hail#15663 shifted supported versions from 3.10-3.13 to 3.12-3.14) and the base image's /opt/venv is 3.11, so it adds a 3.12 venv at /opt/venv-312 and puts it first on PATH. The build is main at 882835b, 84 commits past the 0.2.139 release; 882835b itself is only a CI commit, so the header points at the range rather than claiming a specific fix. The wheel is the one input the repo cannot regenerate, and the Hail bucket that published it expires around 2026-11-14, so it is mirrored to gs://gnomad-resources/hail-dev-wheels/0.2.139-882835b33794/. Both Dockerfiles now assert the Hail version and interpreter at build time, so a base/pin mismatch fails the build instead of a run. info_ht_cloudbuild .yaml has no default _TAG, so a forgotten --substitutions fails rather than pushing over a shared tag. Keeping cloudbuild config out of the repo root also avoids a collision: the v4/sample_qc README documents `gcloud builds submit --config cloudbuild.yaml` with a TAG_NAME substitution, which would otherwise pick up this file. Assisted-by: ClaudeCode:claude-opus-5
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Collects the inputs for the gnomad-qc-deps images the v5 info HT runs (generate_variant_qc_annotations.py --generate-ac-info-ht) use, beside the script they serve, named for what they build rather than for the directory they sit in: - info_ht.Dockerfile + info_ht_cloudbuild.yaml, carried over from kl/split_info_ht_workflow so they are not stranded on a feature branch. - info_ht_hail_dev.Dockerfile, recovered: this built the currently-running :20260710-hail882835b-py312 image but only ever existed in /tmp, which macOS has since wiped. Its instructions are byte-identical to the published image's build history. - info_ht_hail_dev_venv.pins, the pins for that image's /opt/venv-312, verified byte-identical to the copy baked into the image layer. Named .pins, not requirements*.txt, so GitHub's dependency graph does not read image-exact pins as a manifest for the repo. These reproduce the overlay, not the whole stack. :20260710 was built with hail==0.2.137, so info_ht.Dockerfile as committed produces the equivalent of :20260826 rather than that tag; the header records this. It makes no difference to what runs, since the base's 3.11 venv is shadowed on PATH. The overlay exists because the dev Hail build requires Python >= 3.12 (hail-is/hail#15663 shifted supported versions from 3.10-3.13 to 3.12-3.14) and the base image's /opt/venv is 3.11, so it adds a 3.12 venv at /opt/venv-312 and puts it first on PATH. The build is main at 882835b, 84 commits past the 0.2.139 release; 882835b itself is only a CI commit, so the header points at the range rather than claiming a specific fix. The wheel is the one input the repo cannot regenerate, and the Hail bucket that published it expires around 2026-11-14, so it is mirrored to gs://gnomad-resources/hail-dev-wheels/0.2.139-882835b33794/. Both Dockerfiles now assert the Hail version and interpreter at build time, so a base/pin mismatch fails the build instead of a run. info_ht_cloudbuild .yaml has no default _TAG, so a forgotten --substitutions fails rather than pushing over a shared tag. Keeping cloudbuild config out of the repo root also avoids a collision: the v4/sample_qc README documents `gcloud builds submit --config cloudbuild.yaml` with a TAG_NAME substitution, which would otherwise pick up this file. Assisted-by: ClaudeCode:claude-opus-5
klaricch
added a commit
to broadinstitute/gnomad_qc
that referenced
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Oct 29, 2026
Collects the inputs for the gnomad-qc-deps images the v5 info HT runs (generate_variant_qc_annotations.py --generate-ac-info-ht) use, beside the script they serve, named for what they build rather than for the directory they sit in: - info_ht.Dockerfile + info_ht_cloudbuild.yaml, carried over from kl/split_info_ht_workflow so they are not stranded on a feature branch. - info_ht_hail_dev.Dockerfile, recovered: this built the currently-running :20260710-hail882835b-py312 image but only ever existed in /tmp, which macOS has since wiped. Its instructions are byte-identical to the published image's build history. - info_ht_hail_dev_venv.pins, the pins for that image's /opt/venv-312, verified byte-identical to the copy baked into the image layer. Named .pins, not requirements*.txt, so GitHub's dependency graph does not read image-exact pins as a manifest for the repo. These reproduce the overlay, not the whole stack. :20260710 was built with hail==0.2.137, so info_ht.Dockerfile as committed produces the equivalent of :20260826 rather than that tag; the header records this. It makes no difference to what runs, since the base's 3.11 venv is shadowed on PATH. The overlay exists because the dev Hail build requires Python >= 3.12 (hail-is/hail#15663 shifted supported versions from 3.10-3.13 to 3.12-3.14) and the base image's /opt/venv is 3.11, so it adds a 3.12 venv at /opt/venv-312 and puts it first on PATH. The build is main at 882835b, 84 commits past the 0.2.139 release; 882835b itself is only a CI commit, so the header points at the range rather than claiming a specific fix. The wheel is the one input the repo cannot regenerate, and the Hail bucket that published it expires around 2026-11-14, so it is mirrored to gs://gnomad-resources/hail-dev-wheels/0.2.139-882835b33794/. Both Dockerfiles now assert the Hail version and interpreter at build time, so a base/pin mismatch fails the build instead of a run. info_ht_cloudbuild .yaml has no default _TAG, so a forgotten --substitutions fails rather than pushing over a shared tag. Keeping cloudbuild config out of the repo root also avoids a collision: the v4/sample_qc README documents `gcloud builds submit --config cloudbuild.yaml` with a TAG_NAME substitution, which would otherwise pick up this file. Assisted-by: ClaudeCode:claude-opus-5
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Reverts #15660; restores the changes in #15603. Should be ready to merge again after the dataproc update (#15662)
Change Description
Updates the default python version to 3.12 and shifts the list of supported versions to 3.12, 3.13, 3.14 to realign with the numpy's supported versions.
Update: 3.11 will NOT continue to be supported. EMR has been shown to work ok with 3.12 and numpy support has already expired on 3.11.
Security Assessment
Delete all except the correct answer:
Impact Rating
Impact Description
Python version updates in services and client libraries.
Appsec Review