Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Enforce openjdk <=21 for all non-deprecated hmftools #52260

Closed
wants to merge 2 commits into from
Closed

Enforce openjdk <=21 for all non-deprecated hmftools #52260

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3962467
Enforce openjdk<=21 for all non-deprecated hmftools
luan-n-nguyen Nov 20, 2024
3caa474
Fix typo in Lilac openjdk version definition
luan-n-nguyen Nov 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions recipes/hmftools-amber/meta.yaml
View file
Open in desktop
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-amber", max_pin="x.x") }}

requirements:
run:
- zlib
- openjdk >=8
- openjdk >=8,<=21
- bioconductor-copynumber
- r-dplyr

Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-bam-tools/meta.yaml
View file
Open in desktop
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-bam-tools", max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

OpenJDK version constraints are inconsistent across hmftools packages

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

  • Most packages use >=8,<=21: amber, bam-tools, chord, cobalt, cuppa, esvee, isofox, lilac, linx, neo, orange, pave, peach, purple, redux, sigs, virus-interpreter
  • Some packages only specify >=8: gripss, mark-dups, protect, rose, sv-prep
  • One package requires >=9,<=21: sage
  • One related package has no version constraint: break-point-inspector
🔗 Analysis chain

Verify OpenJDK version constraint across hmftools packages.

The OpenJDK version constraint change aligns with the PR objectives. Let's verify consistency across other hmftools packages.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify OpenJDK constraints are consistent across hmftools packages
# Expected: All non-deprecated hmftools should use openjdk >=8,<=21

# Search for all hmftools meta.yaml files and check their openjdk constraints
fd meta.yaml recipes/hmftools- --exec grep -H "openjdk" {} \;

Length of output: 169

Script:

#!/bin/bash
# Let's try a different approach using ripgrep to find all hmftools recipes
# and their OpenJDK requirements
rg -l "hmftools" recipes --glob "meta.yaml" | xargs rg "openjdk" -l

Length of output: 884

Script:

#!/bin/bash
# Get the actual constraints for better analysis
rg -l "hmftools" recipes --glob "meta.yaml" | xargs rg "openjdk" -B1 -A1

Length of output: 3608


test:
commands:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-chord/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@ source:

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

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
- r-base
- r-randomforest

Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-cobalt/meta.yaml
View file
Open in desktop
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-cobalt", max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

OpenJDK version constraints are inconsistent across hmftools packages

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

  • Most packages have the upper bound <=21 as intended
  • However, several packages still use only the lower bound >=8:
    • hmftools-rose
    • hmftools-protect
    • hmftools-mark-dups
    • hmftools-gripss
    • hmftools-sv-prep
  • One package has a different lower bound:
    • hmftools-sage: >=9,<=21

These inconsistencies should be addressed to maintain uniform version constraints across all hmftools packages.

🔗 Analysis chain

LGTM: OpenJDK version constraint aligns with project requirements

The addition of <=21 upper bound is appropriate as it:

  • Prevents potential compatibility issues with future Java versions
  • Aligns with the PR objective to enforce OpenJDK <=21
  • Follows Bioconda guidelines for dependency pinning

Let's verify this change is consistent across other hmftools packages:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify OpenJDK constraints in other hmftools packages
# Expected: All non-deprecated hmftools should have the same OpenJDK constraint

# Search for OpenJDK requirements in hmftools recipes
echo "Checking OpenJDK constraints in hmftools recipes:"
fd "meta.yaml$" recipes/hmftools- --exec grep -H "openjdk" {}

Length of output: 277

Script:

#!/bin/bash
# Let's try a different approach using ripgrep to find hmftools recipes
echo "Checking OpenJDK constraints in hmftools recipes:"
rg "openjdk" recipes/hmftools-.*?/meta.yaml

Length of output: 225

Script:

#!/bin/bash
# First, let's find all hmftools recipes
echo "Finding hmftools recipes:"
fd "meta.yaml$" recipes | grep "hmftools-"

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

Length of output: 2345

- bioconductor-copynumber
- r-dplyr

Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-cuppa/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ source:

build:
noarch: generic
number: 1
number: 2
run_exports:
- {{ pin_subpackage("hmftools-cuppa", max_pin="x.x") }}

Expand All @@ -22,7 +22,7 @@ requirements:
- r-base >=4.2,<4.3.0a0
- unzip
run:
- openjdk >=8
- openjdk >=8,<=21
- python ==3.11
- numpy >=1.24
- pandas ==2.0.*
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-esvee/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@ source:

build:
noarch: generic
number: 5
number: 6
run_exports:
- {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
- sambamba ==0.6.8

test:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-isofox/meta.yaml
View file
Open in desktop
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-isofox', max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

OpenJDK constraints are inconsistent across hmftools packages

Several hmftools packages have different OpenJDK version constraints:

  • sage requires >=9,<=21
  • sv-prep, rose, protect, mark-dups, and gripss only specify >=8 without an upper bound
  • All other packages use the target constraint >=8,<=21

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

🔗 Analysis chain

Verify OpenJDK constraint consistency across hmftools packages.

The OpenJDK constraint update to >=8,<=21 aligns with the PR objectives. Let's verify this constraint is consistently applied across all non-deprecated hmftools packages.

Let me try a different search pattern to locate the hmftools recipes correctly.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify OpenJDK constraint consistency across hmftools packages
# Expected: All non-deprecated hmftools should use the same OpenJDK constraint

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

# Identify any inconsistencies in constraints
echo -e "\nChecking for inconsistent constraints:"
fd "meta.yaml$" recipes/hmftools- --exec grep -H "openjdk" {} | grep -v ">=8,<=21" || echo "No inconsistencies found"

Length of output: 619

Script:

#!/bin/bash
# Description: Verify OpenJDK constraint consistency across hmftools packages
# First, let's find all hmftools recipes correctly
echo "Finding all hmftools recipes:"
fd "meta.yaml$" | grep "hmftools-"

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

echo -e "\nChecking for inconsistent constraints:"
fd "meta.yaml$" | grep "hmftools-" | xargs grep -H "openjdk" | grep -v ">=8,<=21" || echo "No inconsistencies found"

Length of output: 2834


test:
commands:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-lilac/meta.yaml
View file
Open in desktop
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-lilac', max_pin="x") }}

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

test:
commands:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-linx/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@ source:

build:
noarch: generic
number: 1
number: 2
run_exports:
- {{ pin_subpackage('hmftools-linx', max_pin="x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

OpenJDK version constraints are inconsistent across hmftools packages

Several hmftools packages have different OpenJDK version constraints:

  • hmftools-sage: requires >=9,<=21
  • hmftools-sv-prep, hmftools-rose, hmftools-mark-dups, hmftools-gripss, hmftools-protect: only specify >=8 without upper bound
  • All other packages use >=8,<=21

These inconsistencies should be addressed to maintain uniform version constraints across the hmftools suite.

🔗 Analysis chain

Verify OpenJDK version constraint across hmftools packages.

The addition of <=21 aligns with the PR objectives to enforce OpenJDK version limits. Let's verify this change is consistent across other hmftools packages.

Let me try a different approach to search for the hmftools recipes.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify OpenJDK constraints in other hmftools recipes
# Expected: All non-deprecated hmftools should have the same OpenJDK constraint

# Search for all hmftools recipes and their OpenJDK requirements
echo "Checking OpenJDK constraints in hmftools recipes:"
fd --type f "meta.yaml" recipes/hmftools- --exec grep -H "openjdk" {}

# Check if any recipes have different version constraints
echo -e "\nChecking for inconsistent OpenJDK constraints:"
fd --type f "meta.yaml" recipes/hmftools- --exec grep -H "openjdk" {} | grep -v ">=8,<=21" || echo "All constraints are consistent"

Length of output: 659

Script:

#!/bin/bash
# Description: Verify OpenJDK constraints in other hmftools recipes
# Using a more reliable pattern to find hmftools recipes

# Search for all hmftools recipes and their OpenJDK requirements
echo "Checking OpenJDK constraints in hmftools recipes:"
fd "meta.yaml" | grep "hmftools-" | xargs grep -H "openjdk"

# Check if any recipes have different version constraints
echo -e "\nChecking for inconsistent OpenJDK constraints:"
fd "meta.yaml" | grep "hmftools-" | xargs grep -H "openjdk" | grep -v ">=8,<=21" || echo "All constraints are consistent"

Length of output: 1953

- xorg-libxtst
- r-tidyr
- r-dplyr
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-neo/meta.yaml
View file
Open in desktop
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-neo", max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

Inconsistent OpenJDK constraints found across hmftools packages

Several hmftools packages have different OpenJDK version constraints that need to be aligned:

  • hmftools-sage: requires >=9,<=21
  • hmftools-sv-prep: requires only >=8
  • hmftools-rose: requires only >=8
  • hmftools-protect: requires only >=8
  • hmftools-mark-dups: requires only >=8
  • hmftools-gripss: requires only >=8

All other packages correctly use >=8,<=21.

🔗 Analysis chain

LGTM: OpenJDK constraint aligns with project requirements

The OpenJDK version constraint >=8,<=21 is appropriate as it:

  • Maintains backward compatibility with Java 8
  • Prevents potential issues with future Java versions
  • Aligns with the PR objective to enforce OpenJDK ≤21

Let's verify this change is consistent across other hmftools packages:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify OpenJDK constraints in other hmftools packages
# Expected: All non-deprecated hmftools should have the same constraint

# Search for openjdk requirements in hmftools recipes
echo "Checking OpenJDK constraints in hmftools recipes:"
rg "openjdk.*[><=]" recipes/hmftools-*/meta.yaml

# Check if any hmftools recipes are missing the constraint
echo -e "\nChecking for hmftools recipes without the new constraint:"
rg -L "openjdk.*>=8,<=21" recipes/hmftools-*/meta.yaml

Length of output: 4103


test:
commands:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-orange/meta.yaml
View file
Open in desktop
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-orange', max_pin="x") }}

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

test:
commands:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-pave/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,14 @@ source:

build:
noarch: generic
number: 1
number: 2
run_exports:
- {{ pin_subpackage('hmftools-pave', max_pin="x.x") }}

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

test:
commands:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-peach/meta.yaml
View file
Open in desktop
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-peach", max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

OpenJDK constraint needs to be updated in several hmftools packages

The verification revealed inconsistent OpenJDK version constraints across hmftools packages. The following packages need to be updated to use >=8,<=21:

  • recipes/hmftools-gripss/meta.yaml: currently has >=8
  • recipes/hmftools-mark-dups/meta.yaml: currently has >=8
  • recipes/hmftools-protect/meta.yaml: currently has >=8
  • recipes/hmftools-rose/meta.yaml: currently has >=8
  • recipes/hmftools-sv-prep/meta.yaml: currently has >=8
  • recipes/hmftools-sage/meta.yaml: has a different constraint >=9,<=21
🔗 Analysis chain

Verify consistent OpenJDK constraints across hmftools

The OpenJDK version constraint looks good and aligns with the PR objectives. Let's verify this constraint is consistently applied across all non-deprecated hmftools packages.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check OpenJDK version constraints across all hmftools recipes
# Expected: All non-deprecated hmftools should use >=8,<=21

# Search for all hmftools meta.yaml files and their openjdk constraints
echo "Checking OpenJDK constraints in hmftools recipes:"
fd "meta.yaml$" recipes/hmftools- --exec grep -H "openjdk" {}

# Look for any inconsistent constraints
echo -e "\nChecking for inconsistent constraints:"
fd "meta.yaml$" recipes/hmftools- --exec grep -L "openjdk >=8,<=21" {}

Length of output: 550

Script:

#!/bin/bash
# Let's try a different approach using ripgrep to find hmftools recipes
echo "Searching for hmftools recipes and their OpenJDK constraints:"
rg -p "openjdk" "recipes/hmftools.*meta.yaml"

echo -e "\nListing all hmftools meta.yaml files to check coverage:"
rg --files "recipes" | grep "hmftools.*meta.yaml"

Length of output: 1204

Script:

#!/bin/bash
# Now that we have the correct paths, let's check the OpenJDK constraints
echo "Checking OpenJDK constraints in all hmftools recipes:"
for file in recipes/hmftools-*/meta.yaml; do
    echo "=== $file ==="
    grep -A1 "requirements:" "$file" | grep "openjdk"
done

Length of output: 4943

Script:

#!/bin/bash
# Let's try a different approach with more context lines and direct file content inspection
echo "Checking OpenJDK constraints in all hmftools recipes:"
for file in recipes/hmftools-*/meta.yaml; do
    echo "=== $file ==="
    grep -B2 -A2 "openjdk" "$file" || echo "No openjdk requirement found"
done

Length of output: 6022


test:
commands:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-purple/meta.yaml
View file
Open in desktop
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
- xorg-libxtst
- circos >=0.69.6
- perl-gd >=2.76 # Fixes missing GD perl module error (even though circos does install GD)
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-sage/meta.yaml
View file
Open in desktop
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
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

OpenJDK version constraint inconsistency detected

The OpenJDK version constraint >=9,<=21 in hmftools-sage differs from most other hmftools packages which use >=8,<=21. Additionally, some packages (gripss, mark-dups, protect, rose, sv-prep) only specify >=8 without an upper bound.

  • hmftools-sage/meta.yaml: Currently uses >=9,<=21
  • Most other hmftools packages: Use >=8,<=21
  • Several packages need upper bound: gripss, mark-dups, protect, rose, sv-prep
🔗 Analysis chain

Verify OpenJDK version constraint consistency

While the OpenJDK version constraint change aligns with the PR objectives, let's verify:

  1. Consistency of the constraint across other hmftools packages
  2. Compatibility of the package with Java 21 features

Let me try with the correct path pattern.

Let me try one more time with the correct path pattern.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check OpenJDK constraints across hmftools packages
# Expected: All non-deprecated hmftools should have consistent constraints

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

# Check if any hmftools packages specify different Java version requirements in their documentation
echo -e "\nChecking for Java version requirements in package documentation:"
fd "meta.yaml$" recipes/hmftools- --exec grep -H "java" {} || true

Length of output: 597

Script:

#!/bin/bash
# Description: Check OpenJDK constraints across hmftools packages
# Expected: All non-deprecated hmftools should have consistent constraints

# Check OpenJDK constraints in all hmftools meta.yaml files
echo "Checking OpenJDK constraints in hmftools packages:"
fd "meta.yaml$" --glob "recipes/hmftools-*" --exec grep -H "openjdk" {}

# Check if any hmftools packages specify different Java version requirements in their documentation
echo -e "\nChecking for Java version requirements in package documentation:"
fd "meta.yaml$" --glob "recipes/hmftools-*" --exec grep -H "java" {} || true

Length of output: 619

Script:

#!/bin/bash
# Description: Check OpenJDK constraints across hmftools packages
# Expected: All non-deprecated hmftools should have consistent constraints

# Check OpenJDK constraints in all hmftools meta.yaml files
echo "Checking OpenJDK constraints in hmftools packages:"
find recipes -type f -name "meta.yaml" -path "*/hmftools-*" -exec grep -H "openjdk" {} \;

# Check if any hmftools packages specify different Java version requirements in their documentation
echo -e "\nChecking for Java version requirements in package documentation:"
find recipes -type f -name "meta.yaml" -path "*/hmftools-*" -exec grep -H "java" {} \;

Length of output: 1719

- bioconductor-variantannotation
- bioconductor-genomicranges
- r-dplyr
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-sigs/meta.yaml
View file
Open in desktop
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:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-virus-interpreter/meta.yaml
View file
Open in desktop
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
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

OpenJDK constraint inconsistency found in several hmftools packages

Several hmftools packages are missing the upper bound constraint <=21:

  • recipes/hmftools-sv-prep/meta.yaml: openjdk >=8
  • recipes/hmftools-rose/meta.yaml: openjdk >=8
  • recipes/hmftools-protect/meta.yaml: openjdk >=8
  • recipes/hmftools-gripss/meta.yaml: openjdk >=8

Additionally, hmftools-sage has a different lower bound:

  • recipes/hmftools-sage/meta.yaml: openjdk >=9,<=21

Consider updating these packages to maintain consistency with the >=8,<=21 constraint.

🔗 Analysis chain

LGTM: OpenJDK constraint aligns with project requirements.

The addition of the upper bound <=21 for OpenJDK is appropriate and matches the PR objectives. Let's verify this constraint is consistently applied across other hmftools packages.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify OpenJDK constraint consistency across hmftools packages
# Expected: All non-deprecated hmftools should use "openjdk >=8,<=21"

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

Length of output: 286

Script:

#!/bin/bash
# Let's try a different approach to find hmftools recipes
echo "Searching for hmftools meta.yaml files..."
fd -t f '^meta.yaml$' recipes | grep 'hmftools-' | xargs grep -H 'openjdk'

Length of output: 1450


test:
commands:
Expand Down
Loading