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

Update pepsirf to 1.7.0 #51138

Open
wants to merge 7 commits into
base: master
Choose a base branch
from
+34 −225
Open

Update pepsirf to 1.7.0 #51138

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
d73e10b
Update pepsirf to 1.7.0
BiocondaBot Oct 3, 2024
3b72676
add run_exports
mencian Oct 4, 2024
ee4a0bc
add -D_LIBCPP_DISABLE_AVAILABILITY
mencian Oct 4, 2024
1edfb44
try -std=c++17
mencian Oct 4, 2024
b36aa47
Merge branch 'master' into bump/pepsirf
mencian Nov 4, 2024
27c481c
Update build.sh
mencian Nov 12, 2024
29687c3
Merge branch 'master' into bump/pepsirf
mencian Nov 12, 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
27 changes: 21 additions & 6 deletions recipes/pepsirf/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,23 @@
#!/bin/bash
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make pepsirf

mkdir -p "${PREFIX}/bin/"
cp pepsirf "${PREFIX}/bin/"
mkdir -p "${PREFIX}/bin"

export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"

if [[ `uname` == "Darwin" ]]; then
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
else
export CONFIG_ARGS=""
fi

cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
"${CONFIG_ARGS}"
cmake --build build --target pepsirf -j "${CPU_COUNT}" -v

chmod 0755 build/pepsirf
mv build/pepsirf "${PREFIX}/bin"
104 changes: 0 additions & 104 deletions recipes/pepsirf/build_failure.linux-64.yaml
View file
Open in desktop

This file was deleted.

104 changes: 0 additions & 104 deletions recipes/pepsirf/build_failure.osx-64.yaml
View file
Open in desktop

This file was deleted.

24 changes: 13 additions & 11 deletions recipes/pepsirf/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
{% set version = "1.6.0" %}
{% set sha256 = "a31341508ff83c1695a5ae37d92d61191fa8016568222b5501a434eb73f72a55" %}
{% set version = "1.7.0" %}
{% set sha256 = "52eba4ab6d5b60d3256c200b48e4a05fb5167296a55bf8faac17e9204b7ad075" %}

package:
name: pepsirf
version: {{ version }}

source:
url: https://github.com/LadnerLab/PepSIRF/archive/refs/tags/1.6.0.zip
url: https://github.com/LadnerLab/PepSIRF/archive/refs/tags/1.7.0.zip
sha256: {{ sha256 }}

build:
number: 3
number: 0
run_exports:
- {{ pin_subpackage('pepsirf', max_pin="x") }}

requirements:
build:
- cmake
- make
- boost
- zlib
- {{ compiler('cxx') }}
host:
- zlib
- boost
- boost-cpp
run:
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

Incomplete Replacement of 'boost' Dependencies

The dependency has been updated from boost to boost-cpp in recipes/pepsirf/meta.yaml. However, multiple references to boost still exist throughout the codebase, indicating that the replacement is not fully implemented. This may lead to inconsistencies or build issues.

Files still referencing 'boost':

  • recipes/build-fail-blacklist
  • recipes/bioconductor-netboost/meta.yaml
  • recipes/bte/meta.yaml
  • recipes/cansam/meta.yaml
  • recipes/galaxy-ml/meta.yaml
  • recipes/metagraph/meta.yaml
  • recipes/reseq/meta.yaml
  • recipes/sankoff/meta.yaml
  • recipes/scelestial/meta.yaml
  • recipes/tagger/meta.yaml
  • recipes/vamos/meta.yaml
  • recipes/scelestial/meta.yaml
  • recipes/reviewer/meta.yaml
  • (and many others as identified in the search results)

Please ensure that all instances of boost are appropriately replaced with boost-cpp where necessary to maintain consistency and avoid potential issues.

🔗 Analysis chain

Verify the impact of changing 'boost' to 'boost-cpp'.

The dependency has been updated from 'boost' to 'boost-cpp' in both build and run requirements. This change is likely intentional to specify a more targeted dependency on Boost's C++ components. However, it's important to ensure that this change doesn't negatively impact the build process or runtime behavior.

To verify the impact of this change, you can run the following script:

Also applies to: 26-26

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if the package builds and tests successfully with the new boost-cpp dependency.

# Test: Attempt to build the package
conda build .

# Test: Run the package tests
conda build . --test

Length of output: 184

Script:

#!/bin/bash
# Description: Verify that 'boost' has been replaced with 'boost-cpp' throughout the codebase.

# Search for any remaining references to 'boost'
echo "Searching for remaining 'boost' references..."
rg 'boost\b' .

# Confirm that 'boost-cpp' is correctly referenced
echo "Searching for 'boost-cpp' references..."
rg 'boost-cpp' .

Length of output: 132494

- boost
- boost-cpp

test:
commands:
Expand All @@ -35,6 +35,8 @@ test:
- pepsirf subjoin -h

about:
home: https://github.com/LadnerLab/PepSIRF
license: GPL-3.0-Only
summary: Peptide-based Serological Immune Response Framework
home: https://github.com/LadnerLab/PepSIRF
license: GPL-3.0-only
license_family: GPL3
summary: "Peptide-based Serological Immune Response Framework."
dev_url: https://github.com/LadnerLab/PepSIRF
Loading