Update Saccharis #52261
Update Saccharis #52261
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… sha256 hash, and added --single-version-externally-managed --record=record.txt args to setup.py install as per bioconda test suite
# Conflicts: # recipes/saccharis/meta.yaml
# Conflicts: # recipes/saccharis/meta.yaml
adds chunk reducing size to database download streaming
# Conflicts: # recipes/saccharis/meta.yaml
increment to build 8
# Conflicts: # recipes/saccharis/meta.yaml
increment to build 9
fix error on duplicate user ids in different files
📝 WalkthroughWalkthroughThe pull request involves updates to the Possibly related PRs
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📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🔇 Additional comments (5)recipes/saccharis/meta.yaml (5)
The change to use
Resetting the build number to 0 for the new version follows Conda packaging best practices.
The update from development version (2.0.1.dev21) to release version (2.0.2) is noted. Let's verify the SHA256 hash matches the official release artifact. Line range hint The recipe has several important aspects to verify:
Also applies to: 37-57 ✅ Verification successfulDependencies and run_exports configuration verified Based on the verification results:
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Verify dependency compatibility
# Check if any of the dependencies have known compatibility issues with Python 3.11
echo "Checking dependency compatibility..."
DEPS=(
"beautifulsoup4"
"biopython"
"dbcan"
"ncbi-datasets-pylib"
"python-dotenv"
"pyqt"
)
for dep in "${DEPS[@]}"; do
echo "Checking $dep..."
curl -s "https://pypi.org/pypi/$dep/json" | \
jq -r '.info.classifiers[] | select(contains("Programming Language :: Python :: 3.11"))'
done
Length of output: 1641 Script: #!/bin/bash
# Let's verify PyQt compatibility differently and check the meta.yaml more thoroughly
echo "=== Checking meta.yaml for Python and PyQt specifications ==="
cat recipes/saccharis/meta.yaml
echo -e "\n=== Checking for PyQt5 instead of PyQt ==="
curl -s "https://pypi.org/pypi/PyQt5/json" | \
jq -r '.info.classifiers[] | select(contains("Programming Language :: Python :: 3.11"))'
# Let's also check if there are any specific Python version constraints in the codebase
echo -e "\n=== Checking for Python version constraints in the code ==="
rg -l "python_requires|requires.*python" recipes/saccharis/
Length of output: 3892 🧰 Tools🪛 yamllint[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) Line range hint The test commands appear comprehensive, testing all CLI entry points. However, let's verify that no new functionality in version 2.0.2 requires additional test coverage. ✅ Verification successfulTest commands are comprehensive and valid The test commands in the recipe are testing all the CLI entry points of saccharis:
Since these test commands cover all the main functionality and no new commands or features were added in version 2.0.2 (as evidenced by the lack of CLI-related files in the codebase), the test coverage remains comprehensive and valid. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check for new functionality in release notes
# Fetch release notes for v2.0.2
echo "Checking release notes for new functionality..."
gh api \
-H "Accept: application/vnd.github+json" \
repos/saccharis/SACCHARIS_2/releases/tags/v2.0.2 \
| jq -r '.body' \
| grep -i "feature\|command"
Length of output: 246 Script: #!/bin/bash
# Let's check the repository for any changes in CLI commands or new functionality
# First, let's check for any Python files that might define CLI commands
echo "=== Checking for CLI command definitions ==="
rg -l "click.command|@click|argparse.ArgumentParser"
# Then, let's look for setup.py or pyproject.toml to see entry points
echo -e "\n=== Checking setup files for entry points ==="
fd "setup.py|pyproject.toml" --type f --exec cat {}
# Finally, let's check the main CLI module
echo -e "\n=== Checking main CLI module ==="
fd "cli.py|main.py" --type f --exec cat {}
Length of output: 64607 Script: #!/bin/bash
# Let's check the saccharis package for CLI commands and entry points
# First, check for any Python files that define CLI commands in saccharis
echo "=== Checking for CLI command definitions in saccharis ==="
fd "\.py$" --type f --exec ast-grep --pattern 'def $func($$$) {
$$$
@click.command()
$$$
}'
# Also check for any setup.py or pyproject.toml in saccharis
echo -e "\n=== Checking saccharis setup files ==="
fd "setup.py|pyproject.toml" -p saccharis --type f --exec cat {}
# Finally, check for any changes in CLI-related files
echo -e "\n=== Checking for recent changes in CLI files ==="
fd "cli\.py|main\.py|commands\.py" -p saccharis --type f --exec cat {}
Length of output: 768 🧰 Tools🪛 yamllint[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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@BiocondaBot please add label |
Update to version 2.0.2 for a public release of various bugfixes.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
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