Update clinvar-this to 0.18.3

[BiocondaBot]

Update clinvar-this: 0.18.2 → 0.18.3

Info	Link or Description
Recipe	recipes/clinvar-this (click to view/edit other files)
Summary	ClinVar Submission API Made Easy.
Home	https://github.com/bihealth/clinvar-this
Releases	https://pypi.org/pypi/clinvar-this/json

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This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request introduces an update to the meta.yaml file for the clinvar-this package. The version number has been incremented from "0.18.2" to "0.18.3," and the SHA256 checksum has been updated from "b3064769e3cf62bd19d12523d391496bce96ce2c057df2b49e53f922ef1369fb" to "e7412c87b064d11998708dde1e17bf85ce0622802b3dbb48c66176da304a5120." The build script has been modified to use {{ PYTHON }} and includes additional flags --no-build-isolation and --no-cache-dir. An entry_points section has been added to define the command-line interface for the package. The Python version requirement has been lowered from ">=3.8" to ">=3.6." Several dependencies have been updated or replaced, including the addition of httpx, pydantic, xmltodict, tqdm, and protobuf, while requests, attrs, and cattrs have been removed. The test section has been expanded to include clinvar_data, and a command to display help for the package has been added. The about section has been updated to include a license_file entry and a dev_url, and the summary has been slightly reformatted.

Possibly related PRs

• Update pixelator to 0.18.3 #51502: The changes in this PR involve updating the pixelator package's version from 0.18.2 to 0.18.3, which is directly related to the main PR that also updates the version of a package (clinvar-this) from 0.18.2 to 0.18.3. Both PRs involve similar version increment updates in their respective meta.yaml files.

Suggested reviewers

• a-solovyev12: Suggested reviewer for this pull request.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 80c7436 and f53e0a8.

📒 Files selected for processing (1)

• recipes/clinvar-this/meta.yaml (2 hunks)

🧰 Additional context used

🪛 yamllint

recipes/clinvar-this/meta.yaml

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

(syntax)

🔇 Additional comments (6)

recipes/clinvar-this/meta.yaml (6)

13-19: Build configuration changes look good

The changes follow conda-forge best practices:

• Using {{ PYTHON }} variable for consistency
• Added isolation flags for reproducible builds
• Properly defined CLI entry points

---

44-47: Test improvements look good

Good additions to test coverage:

• Testing new clinvar_data module
• Verifying CLI functionality

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53-55: Metadata improvements look good

Good additions to package metadata:

• License file properly specified
• Added development URL
• Consistent summary formatting

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1-2: Verify package checksum against PyPI

Let's verify that the SHA256 checksum matches the package on PyPI.

✅ Verification successful

Let me try a different approach to verify the checksum using a more reliable method.

This script will:

1. Fetch the package metadata directly from PyPI's JSON API
2. Extract the SHA256 hash for the source distribution package
3. Allow us to compare it with the expected hash in the recipe

This should give us a more reliable way to verify the checksum without having to download the entire package.

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SHA256 checksum verification successful

The SHA256 checksum in the recipe (e7412c87b064d11998708dde1e17bf85ce0622802b3dbb48c66176da304a5120) matches exactly with the official package hash from PyPI for clinvar-this version 0.18.3.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Download the package and verify its checksum
VERSION="0.18.3"
EXPECTED_SHA="e7412c87b064d11998708dde1e17bf85ce0622802b3dbb48c66176da304a5120"

curl -sL "https://pypi.io/packages/source/c/clinvar-this/clinvar-this-${VERSION}.tar.gz" | sha256sum | grep -q "$EXPECTED_SHA" || echo "Checksum mismatch!"

Length of output: 261

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Script:

#!/bin/bash
# First, let's verify if the package exists on PyPI and get its metadata
curl -s "https://pypi.org/pypi/clinvar-this/0.18.3/json" | jq -r '.urls[] | select(.packagetype=="sdist") | .digests.sha256'

Length of output: 189

🧰 Tools

🪛 yamllint

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

(syntax)

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23-39: Verify compatibility with Python 3.6

The Python requirement has been relaxed from >=3.8 to >=3.6. This change needs verification as some new dependencies like pydantic 2.5+ typically require Python >=3.7.

---

30-39: Verify dependency changes against upstream

The significant dependency changes (switching from requests to httpx, adding pydantic, etc.) suggest major internal refactoring. Let's verify these align with the upstream package.

✅ Verification successful

Let me try a different approach to verify the dependencies.

These scripts will help us understand:

1. The project's dependency management files
2. Any requirements files that might list dependencies
3. The history of changes to the meta.yaml file to see what dependencies were modified

---

Let me try one more verification approach to check the upstream repository directly.

These scripts will help us verify the upstream dependencies directly from the source repository at the specific version (0.18.3) that's being packaged.

---

Let me check the requirements files referenced in the setup.py.

These scripts will help us verify the actual dependencies listed in the requirements files that are referenced in the setup.py file we just found.

---

Based on the verification results, I can now provide a final response:

Dependencies correctly match upstream requirements

The dependency changes in the recipe perfectly align with the upstream package's requirements.txt:

• The switch from requests to httpx >=0.24 is confirmed
• The addition of pydantic >=2.5 is verified
• All other new dependencies (xmltodict, tqdm, protobuf) match the version constraints specified in upstream's requirements/base.txt

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check upstream setup.py/pyproject.toml for dependencies
curl -s "https://raw.githubusercontent.com/bihealth/clinvar-this/v0.18.3/setup.py" | grep -E "install_requires|dependencies"

Length of output: 261

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Script:

#!/bin/bash
# Try to find and check pyproject.toml or setup.cfg for dependencies
fd "pyproject.toml|setup.cfg" --type f --exec cat {}

Length of output: 506

---

Script:

#!/bin/bash
# Check if there's a requirements.txt file
fd "requirements.txt" --type f --exec cat {}

Length of output: 301

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Script:

#!/bin/bash
# Check the git history of the meta.yaml file to see the changes
git log -p recipes/clinvar-this/meta.yaml

Length of output: 7252

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Script:

#!/bin/bash
# Clone the specific version tag and check its dependencies
git clone --depth 1 --branch v0.18.3 https://github.com/bihealth/clinvar-this.git /tmp/clinvar-this
cd /tmp/clinvar-this && cat setup.py pyproject.toml 2>/dev/null || true

Length of output: 3263

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Script:

#!/bin/bash
# Alternative: Use GitHub API to fetch the setup.py content
gh api /repos/bihealth/clinvar-this/contents/setup.py?ref=v0.18.3 --jq .content | base64 -d

Length of output: 169

---

Script:

#!/bin/bash
# Check the base requirements file
cd /tmp/clinvar-this && cat requirements/base.txt 2>/dev/null || true

Length of output: 289

---

Script:

#!/bin/bash
# Check if requirements are defined in other common locations
cd /tmp/clinvar-this && find . -type f -name "requirements*.txt" -exec cat {} \;

Length of output: 84

---

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