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Enforce openjdk 21, part 4/4 (Purple, Sage, Sigs, Virusinterpreter) #52274

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merged 4 commits into from
Nov 25, 2024
Merged

Enforce openjdk 21, part 4/4 (Purple, Sage, Sigs, Virusinterpreter) #52274

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2013a3c
Enforce openjdk<=21 for hmftools-purple
luan-n-nguyen Nov 21, 2024
bda48df
Enforce openjdk<=21 for hmftools-sage
luan-n-nguyen Nov 21, 2024
cb47814
Enforce openjdk<=21 for hmftools-sigs
luan-n-nguyen Nov 21, 2024
f23ae2d
Enforce openjdk<=21 for hmftools-virus-interpreter
luan-n-nguyen Nov 21, 2024
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4 changes: 2 additions & 2 deletions recipes/hmftools-purple/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,14 @@ source:

build:
noarch: generic
number: 2
number: 3
run_exports:
- {{ pin_subpackage('hmftools-purple', max_pin="x") }}

requirements:
run:
- zlib
- openjdk >=8
- openjdk >=8,<=21
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💡 Codebase verification

OpenJDK version constraints are inconsistent across hmftools packages

The verification reveals inconsistencies in OpenJDK version constraints across hmftools packages:

  • Only 4 packages specify the upper bound <=21: purple, redux, sage (>=9), and virus-interpreter
  • All other packages (19) only specify the lower bound >=8
  • One package (sage) has a different minimum version requirement >=9

These inconsistencies should be addressed to maintain uniformity across the hmftools suite.

🔗 Analysis chain

Verify OpenJDK version constraint consistency

The OpenJDK version constraint >=8,<=21 aligns with the PR objectives. Let's verify this constraint is consistent across related packages.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check OpenJDK version constraints across hmftools packages
# Expected: All hmftools packages should use the same OpenJDK version constraint

echo "Checking OpenJDK constraints in hmftools packages:"
fd 'meta.yaml$' recipes/hmftools- --exec grep -H 'openjdk' {}

Length of output: 279

Script:

#!/bin/bash
# Let's try a different approach to find hmftools packages
echo "Finding hmftools packages:"
fd 'meta.yaml$' | grep 'hmftools'

echo -e "\nChecking OpenJDK constraints in these packages:"
fd 'meta.yaml$' | grep 'hmftools' | xargs grep -H 'openjdk'

Length of output: 2266

- xorg-libxtst
- circos >=0.69.6
- perl-gd >=2.76 # Fixes missing GD perl module error (even though circos does install GD)
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4 changes: 2 additions & 2 deletions recipes/hmftools-sage/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,14 @@ source:

build:
noarch: generic
number: 3
number: 4
run_exports:
- {{ pin_subpackage('hmftools-sage', max_pin="x") }}

requirements:
run:
- zlib
- openjdk >=9
- openjdk >=9,<=21
- bioconductor-variantannotation
- bioconductor-genomicranges
- r-dplyr
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4 changes: 2 additions & 2 deletions recipes/hmftools-sigs/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,14 @@ source:

build:
noarch: generic
number: 0
number: 1
run_exports:
- {{ pin_subpackage('hmftools-sigs', max_pin='x') }}

requirements:
run:
- zlib
- openjdk >=8
- openjdk >=8,<=21

test:
commands:
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4 changes: 2 additions & 2 deletions recipes/hmftools-virus-interpreter/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,13 @@ source:

build:
noarch: generic
number: 0
number: 1
run_exports:
- {{ pin_subpackage("hmftools-virus-interpreter", max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
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💡 Codebase verification

OpenJDK constraints are inconsistent across hmftools packages

The verification reveals inconsistencies in OpenJDK version constraints across hmftools packages:

  • Most packages specify only a lower bound >=8
  • A few packages (virus-interpreter, sage, redux, purple, sigs) include an upper bound <=21
  • One package (sage) has a different lower bound >=9
  • One package (break-point-inspector) has no version constraint

The current change to virus-interpreter (>=8,<=21) is not consistent with the majority of hmftools packages, which only specify a lower bound.

🔗 Analysis chain

Verify consistency of OpenJDK constraints across hmftools packages.

While the constraint change aligns with the PR objective to enforce OpenJDK 21, let's verify this is consistent across all hmftools packages.

Consider if the upper bound of <=21 might be too restrictive for future updates. A more flexible approach might be to use >=8,<22 to allow for point releases of OpenJDK 21, while still preventing upgrades to future major versions without explicit testing.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check OpenJDK constraints across hmftools packages
# Expected: All hmftools packages should have the same OpenJDK constraint

echo "Checking OpenJDK constraints in hmftools packages:"
fd -t f "meta.yaml" recipes/hmftools- -x grep -H "openjdk" {}

Length of output: 277

Script:

#!/bin/bash
# Let's try a different approach using ripgrep to find hmftools recipes
# and check their OpenJDK constraints
echo "Searching for hmftools meta.yaml files and their OpenJDK constraints:"
rg -l "hmftools" --type yaml | grep "meta.yaml" | xargs grep -H "openjdk"

Length of output: 1492


test:
commands:
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