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Update mehari to 0.30.1 #51208

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Update mehari to 0.30.1 #51208

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330856f
Update mehari to 0.29.0
BiocondaBot Oct 7, 2024
5ba3ceb
fix: add libprotobuf to build dependencies
tedil Oct 7, 2024
455e79a
chore: use rocksdb libs from conda
tedil Oct 8, 2024
aae89e0
fix whitespace issue
tedil Oct 8, 2024
5263786
skip aarch64 build for now, since there is no corresponding conda pac…
tedil Oct 8, 2024
263fa11
Merge branch 'master' into bump/mehari
tedil Oct 8, 2024
92d1ae8
Update mehari to 0.29.1
BiocondaBot Oct 8, 2024
c6b2d6f
Update mehari to 0.29.5
BiocondaBot Oct 8, 2024
793875e
Merge branch 'master' into bump/mehari
tedil Oct 10, 2024
e84c20d
Update mehari to 0.29.6
BiocondaBot Oct 16, 2024
7efaf4e
Merge branch 'master' into bump/mehari
mencian Oct 28, 2024
97565b0
require rocksdb 8.10.2
tedil Nov 12, 2024
ca9ed87
forgot a space
tedil Nov 12, 2024
5218352
Merge branch 'master' into bump/mehari
tedil Nov 12, 2024
a0bc7e3
add rocksdb to run requirements
tedil Nov 12, 2024
c96889c
Merge branch 'bump/mehari' of github.com:bioconda/bioconda-recipes in…
tedil Nov 12, 2024
8db1eee
Update mehari to 0.30.0
BiocondaBot Nov 20, 2024
374e1ef
Update mehari to 0.30.1
BiocondaBot Nov 21, 2024
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2 changes: 2 additions & 0 deletions recipes/mehari/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,7 @@

# Make sure bindgen passes on our compiler flags.
export BINDGEN_EXTRA_CLANG_ARGS="${CPPFLAGS} ${CFLAGS} ${LDFLAGS}"
export ROCKSDB_LIB_DIR="/usr/lib/"
export SNAPPY_LIB_DIR="/usr/lib/"

cargo install --no-track --locked --root "${PREFIX}" --path .
14 changes: 9 additions & 5 deletions recipes/mehari/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{% set version = "0.28.1" %}
{% set sha256 = "b1bb238782036c05795b74fbb7e97ff998e234fd89f4501234b052d3f2a0d683" %}
{% set version = "0.29.1" %}
{% set sha256 = "467d1f219f02c8b23e253fb02bbe0bb2339fa0007c1707671aeb694040481961" %}
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💡 Codebase verification

Version update verified

The version in meta.yaml has been correctly updated to 0.29.1, matching the latest GitHub release. However, the PR objectives mention updating to 0.29.0. Please update the PR objectives to reflect the accurate version 0.29.1.

🔗 Analysis chain

Verify the version update

The version has been updated to 0.29.1, which is different from the 0.29.0 mentioned in the PR objectives. Please confirm if this is the intended version update.

The SHA256 checksum has been updated accordingly, which is correct when updating the package version.

To verify the correct version:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the latest release version of mehari
# Expected result: The latest release version should match the version in meta.yaml

# Fetch the latest release version from GitHub
LATEST_VERSION=$(gh release list --repo varfish-org/mehari --limit 1 | awk '{print $1}' | sed 's/^v//')

# Compare with the version in meta.yaml
YAML_VERSION=$(awk '/^{% set version = / {print $4}' recipes/mehari/meta.yaml | tr -d '"')

echo "Latest GitHub release: $LATEST_VERSION"
echo "Version in meta.yaml: $YAML_VERSION"

if [ "$LATEST_VERSION" = "$YAML_VERSION" ]; then
    echo "Versions match."
else
    echo "Version mismatch detected."
fi

Length of output: 420

Script:

#!/bin/bash
# Description: Correctly extract the version from meta.yaml and verify it against the latest GitHub release
# Expected result: The latest release version should match the version in meta.yaml

# Fetch the latest release version from GitHub
LATEST_VERSION=$(gh release list --repo varfish-org/mehari --limit 1 | awk '{print $1}' | sed 's/^v//')

# Extract the version from meta.yaml using grep and sed
YAML_VERSION=$(grep '^{% set version =' recipes/mehari/meta.yaml | sed -E 's/.*"([^"]+)".*/\1/')

echo "Latest GitHub release: $LATEST_VERSION"
echo "Version in meta.yaml: $YAML_VERSION"

if [ "$LATEST_VERSION" = "$YAML_VERSION" ]; then
    echo "Versions match."
else
    echo "Version mismatch detected."
fi

Length of output: 424

🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)


package:
name: mehari
Expand All @@ -25,6 +25,9 @@ requirements:
- cmake
- make
- pkg-config
- libprotobuf
- rocksdb
- snappy
host:
- clangdev
- openssl
Expand All @@ -45,6 +48,7 @@ about:
summary: VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust.
dev_url: https://github.com/varfish-org/mehari

extra:
additional-platforms:
- linux-aarch64
## Currently, there is no rocksdb package available from conda for linux-aarch64, skip for now.
#extra:
# additional-platforms:
# - linux-aarch64