phytop #52176
phytop #52176
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (3)
recipes/phytop/meta.yaml (3)
17-17: Remove commented build stringThe commented build string
#string: pyhdfd78af_0appears to be unnecessary and should be removed.- #string: pyhdfd78af_0
146-154: Consider adding version constraints for runtime dependenciesWhile the runtime dependencies list looks appropriate, consider adding version constraints for critical dependencies to ensure compatibility. This is especially important for libraries like numpy and scipy that may have breaking changes between versions.
run: - python >=3.8 - - biopython - - matplotlib + - biopython >=1.81 + - matplotlib >=3.7 - networkx - lazy-property - ete3 - - numpy - - scipy + - numpy >=1.24 + - scipy >=1.10
155-155: Remove trailing whitespaceRemove trailing whitespace from line 155 for consistency.
🧰 Tools
🪛 yamllint
[error] 155-155: trailing spaces
(trailing-spaces)
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📒 Files selected for processing (2)
recipes/phytop/build.sh(1 hunks)recipes/phytop/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/phytop/build.sh
🧰 Additional context used
🪛 yamllint
recipes/phytop/meta.yaml
[error] 155-155: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/phytop/meta.yaml (1)
15-17: Verify the entry point's module path
Please verify that src.plot:main is the correct module path for the entry point. The module should exist in the package's source code.
#!/bin/bash
# Check if the entry point module exists in the source code
echo "Checking for src/plot.py..."
fd -e py "plot.py$" | grep -l "def main"
recipes/phytop/meta.yaml
Outdated
| - lazy-property=0.0.1=pyh9f0ad1d_0 | ||
| - lcms2=2.12=hddcbb42_0 | ||
| - ld_impl_linux-64=2.40=h41732ed_0 | ||
| - lerc=3.0=h9c3ff4c_0 | ||
| - libblas=3.9.0=17_linux64_openblas | ||
| - libbrotlicommon=1.0.9=h166bdaf_8 | ||
| - libbrotlidec=1.0.9=h166bdaf_8 | ||
| - libbrotlienc=1.0.9=h166bdaf_8 | ||
| - libcblas=3.9.0=17_linux64_openblas | ||
| - libclang=11.1.0=default_ha53f305_1 | ||
| - libdeflate=1.10=h7f98852_0 | ||
| - libedit=3.1.20191231=he28a2e2_2 | ||
| - libevent=2.1.10=h9b69904_4 | ||
| - libexpat=2.5.0=hcb278e6_1 | ||
| - libffi=3.3=h58526e2_2 | ||
| - libgcc-ng=13.1.0=he5830b7_0 | ||
| - libgfortran-ng=13.1.0=h69a702a_0 | ||
| - libgfortran5=13.1.0=h15d22d2_0 | ||
| - libglib=2.68.4=h3e27bee_0 | ||
| - libgomp=13.1.0=he5830b7_0 | ||
| - libiconv=1.17=h166bdaf_0 | ||
| - liblapack=3.9.0=17_linux64_openblas | ||
| - libllvm11=11.1.0=he0ac6c6_5 | ||
| - libogg=1.3.4=h7f98852_1 | ||
| - libopenblas=0.3.23=pthreads_h80387f5_0 | ||
| - libopus=1.3.1=h7f98852_1 | ||
| - libpng=1.6.39=h753d276_0 | ||
| - libpq=13.8=hd77ab85_0 | ||
| - libsqlite=3.42.0=h2797004_0 | ||
| - libstdcxx-ng=13.1.0=hfd8a6a1_0 | ||
| - libtiff=4.3.0=h0fcbabc_4 | ||
| - libuuid=2.38.1=h0b41bf4_0 | ||
| - libvorbis=1.3.7=h9c3ff4c_0 | ||
| - libwebp-base=1.3.0=h0b41bf4_0 | ||
| - libxcb=1.15=h0b41bf4_0 | ||
| - libxkbcommon=1.0.3=he3ba5ed_0 | ||
| - libxml2=2.9.10=h72842e0_4 | ||
| - libxslt=1.1.33=h15afd5d_2 | ||
| - libzlib=1.2.13=h166bdaf_4 | ||
| - lxml=4.8.0=py38h0a891b7_3 | ||
| - matplotlib=3.7.1=py38h578d9bd_0 | ||
| - matplotlib-base=3.7.1=py38hd6c3c57_0 | ||
| - munkres=1.1.4=pyh9f0ad1d_0 | ||
| - mysql-common=8.0.32=h14678bc_0 | ||
| - mysql-libs=8.0.32=h54cf53e_0 | ||
| - ncurses=6.4=hcb278e6_0 | ||
| - networkx=3.1=pyhd8ed1ab_0 | ||
| - nspr=4.35=h27087fc_0 | ||
| - nss=3.89=he45b914_0 | ||
| - numpy=1.24.3=py38h59b608b_0 | ||
| - olefile=0.46=pyh9f0ad1d_1 | ||
| - openjpeg=2.5.0=h7d73246_0 | ||
| - openssl=1.1.1u=hd590300_0 | ||
| - packaging=23.1=pyhd8ed1ab_0 | ||
| - pcre=8.45=h9c3ff4c_0 | ||
| - pillow=8.4.0=py38h8e6f84c_0 | ||
| - pip=23.1.2=pyhd8ed1ab_0 | ||
| - platformdirs=3.5.3=pyhd8ed1ab_0 | ||
| - pooch=1.7.0=pyha770c72_3 | ||
| - pthread-stubs=0.4=h36c2ea0_1001 | ||
| - pyparsing=3.0.9=pyhd8ed1ab_0 | ||
| - pyqt=5.12.3=py38h578d9bd_8 | ||
| - pyqt-impl=5.12.3=py38h0ffb2e6_8 | ||
| - pyqt5-sip=4.19.18=py38h709712a_8 | ||
| - pyqtchart=5.12=py38h7400c14_8 | ||
| - pyqtwebengine=5.12.1=py38h7400c14_8 | ||
| - pysocks=1.7.1=py38h578d9bd_5 | ||
| - python=3.8.8=hffdb5ce_0_cpython | ||
| - python-dateutil=2.8.2=pyhd8ed1ab_0 | ||
| - python_abi=3.8=3_cp38 | ||
| - qt=5.12.9=hda022c4_4 | ||
| - readline=8.2=h8228510_1 | ||
| - requests=2.31.0=pyhd8ed1ab_0 | ||
| - scipy=1.10.1=py38h59b608b_3 | ||
| - setuptools=67.7.2=pyhd8ed1ab_0 | ||
| - six=1.16.0=pyh6c4a22f_0 | ||
| - sqlite=3.42.0=h2c6b66d_0 | ||
| - tk=8.6.12=h27826a3_0 | ||
| - tornado=6.3.2=py38h01eb140_0 | ||
| - typing-extensions=4.6.3=hd8ed1ab_0 | ||
| - typing_extensions=4.6.3=pyha770c72_0 | ||
| - unicodedata2=15.0.0=py38h0a891b7_0 | ||
| - urllib3=2.0.3=pyhd8ed1ab_0 | ||
| - wheel=0.40.0=pyhd8ed1ab_0 | ||
| - xorg-kbproto=1.0.7=h7f98852_1002 | ||
| - xorg-libice=1.1.1=hd590300_0 | ||
| - xorg-libsm=1.2.4=h7391055_0 | ||
| - xorg-libx11=1.8.5=h8ee46fc_0 | ||
| - xorg-libxau=1.0.11=hd590300_0 | ||
| - xorg-libxdmcp=1.1.3=h7f98852_0 | ||
| - xorg-libxext=1.3.4=h0b41bf4_2 | ||
| - xorg-libxrender=0.9.10=h7f98852_1003 | ||
| - xorg-renderproto=0.11.1=h7f98852_1002 | ||
| - xorg-xextproto=7.3.0=h0b41bf4_1003 | ||
| - xorg-xproto=7.0.31=h7f98852_1007 | ||
| - xz=5.2.6=h166bdaf_0 | ||
| - zipp=3.15.0=pyhd8ed1ab_0 | ||
| - zlib=1.2.13=h166bdaf_4 | ||
| - zstd=1.5.2=h3eb15da_6 | ||
| - setuptools |
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🛠️ Refactor suggestion
Simplify build requirements
The build requirements section is overly specific and includes many unnecessary dependencies. For a Python package that uses setuptools, you typically only need:
pythonsetuptools- Any build-time dependencies required by setup.py
Consider simplifying to:
build:
- - biopython=1.81=py38h1de0b5d_0
- - ca-certificates=2023.5.7=hbcca054_0
[... remove all other specific versions ...]
+ - python
+ - setuptoolsAlso, remove the duplicate setuptools entry at line 145.
Committable suggestion skipped: line range outside the PR's diff.
recipes/phytop/meta.yaml
Outdated
| about: | ||
| home: https://github.com/zhangrengang/phytop/ | ||
| description: "Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL" |
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🛠️ Refactor suggestion
Add missing metadata fields
The about section should include additional metadata fields such as:
license: The software licenselicense_file: Path to the license filedoc_url: URL to documentationdev_url: URL to development repository
about:
home: https://github.com/zhangrengang/phytop/
description: "Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL"
+ license: # Add appropriate license
+ license_file: # Add path to license file
+ doc_url: # Add documentation URL if available
+ dev_url: # Add development repository URLCommittable suggestion skipped: line range outside the PR's diff.
| source: | ||
| url: https://github.com/shang-hongyun/phytop/archive/refs/tags/{{ version }}.tar.gz | ||
| sha256: {{ sha256 }} |
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💡 Codebase verification
Source repository URL needs to be updated
The source URL should point to zhangrengang/phytop instead of shang-hongyun/phytop. This is evident because:
- The homepage URL points to
zhangrengang/phytop - The package description indicates it's a tool for visualizing phylogenetic signals, which matches with the description in
zhangrengang/phytop - The
shang-hongyunrepository appears to be a fork or mirror that might not be maintained
🔗 Analysis chain
Verify the correct source repository
The source URL points to shang-hongyun/phytop while the homepage URL points to zhangrengang/phytop. Please verify if this is a fork or if one of these URLs needs to be updated.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if both repositories exist and their relationship
for repo in "shang-hongyun/phytop" "zhangrengang/phytop"; do
echo "Checking $repo..."
gh repo view $repo --json name,isArchived,isFork,parent 2>/dev/null
done
Length of output: 201
Script:
#!/bin/bash
# Let's try a different approach to verify the repositories
# First, let's check the meta.yaml file to get all URLs
cat recipes/phytop/meta.yaml
# Then let's check if we can find any references to either username in the codebase
echo -e "\nSearching for repository references:"
rg -i "shang-hongyun|zhangrengang" recipes/phytop/
Length of output: 5400
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