Add Instanovo #51796
Add Instanovo #51796
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces an updated Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/instanovo/meta.yaml (1)
47-54: Consider adding functional tests.
While the current tests verify installation and dependencies, consider adding basic functional tests to ensure core functionality works. For example, test loading a model or processing a small example.
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📒 Files selected for processing (1)
- recipes/instanovo/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/instanovo/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/instanovo/meta.yaml (6)
12-18: LGTM! Build configuration follows best practices.
The build configuration correctly:
- Uses noarch: python for platform independence
- Includes run_exports to prevent ABI incompatibilities
- Uses appropriate pip installation flags
62-64: LGTM! Maintainer section is properly configured.
56-60: Verify license file existence.
Please ensure that LICENSE.md exists in the source distribution.
✅ Verification successful
License file verification successful
The LICENSE.md file exists in the source distribution at instanovo-1.0.0/LICENSE.md, confirming that the license file reference in meta.yaml is correct.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if LICENSE.md exists in the source distribution
VERSION="1.0.0"
PACKAGE="instanovo"
URL="https://pypi.io/packages/source/${PACKAGE:0:1}/$PACKAGE/$PACKAGE-$VERSION.tar.gz"
curl -sL "$URL" | tar tz | grep -i license
Length of output: 240
8-10: Verify source checksum.
The SHA256 checksum should be verified against the PyPI source package.
1-6: Verify package version compatibility.
The package is being introduced at version 1.0.0. Please ensure this matches the latest stable release on PyPI and the referenced GitHub repository.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
20-24: Consider broadening Python version support.
The current Python version constraint (>=3.10,<3.12) seems restrictive. If possible, consider testing with Python 3.9 to broaden compatibility.
recipes/instanovo/meta.yaml
Outdated
| run: | ||
| - click >=8.1.7 | ||
| - datasets >=3.0.1 | ||
| - hydra-core >=1.3.2 | ||
| - jaxtyping >=0.2.34 | ||
| - jiwer >=3.0.4 | ||
| - matchms >=0.27.0 | ||
| - neptune >=1.12.0 | ||
| - numpy >=1.26.4 | ||
| - omegaconf >=2.3.0 | ||
| - pandas >=2.2.3 | ||
| - polars >=1.9.0 | ||
| - pyopenms >=3.2.0 | ||
| - python-dotenv >=1.0.1 | ||
| - pytorch-lightning >=2.4.0 | ||
| - s3fs >=2024.6.1 | ||
| - scikit-learn >=1.5.2 | ||
| - spectrum_utils >=0.4.2 | ||
| - tensorboard >=2.18.0 | ||
| - pytorch >=2.4.1 | ||
| - tqdm >=4.66.5 |
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💡 Codebase verification
Based on the verification results, I can now provide a final response about the dependency availability concerns:
Several dependencies require attention in conda channels
Some required dependencies are not readily available in the standard conda channels:
pytorchpackage name might bepytorch-cpuorpytorch-gpuin conda-forgematchms,spectrum-utils, andpyopenmswere not found in conda-forge or bioconda- Other core dependencies like
numpy,pandas,scikit-learn,pytorch-lightning,jiwer, andjaxtypingare available in conda-forge
Please ensure these packages are available in the specified versions through conda channels or consider providing alternative installation methods in the documentation.
🔗 Analysis chain
Verify dependency availability in conda channels.
Please ensure all runtime dependencies are available in conda-forge or bioconda channels with the specified versions.
Since the sandbox environment doesn't have conda installed, I'll try to verify the package availability through a different approach by checking the conda-forge feedstock repositories which contain the package build recipes.
Let me check the bioconda channel for the missing packages, particularly for the bioinformatics-related ones like matchms, spectrum-utils, and pyopenms.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check availability of key dependencies
for pkg in pytorch-lightning pytorch numpy pandas scikit-learn; do
echo "Checking $pkg..."
conda search -c conda-forge $pkg
done
Length of output: 1322
Script:
#!/bin/bash
# Check existence of conda-forge feedstock repositories for the dependencies
for pkg in pytorch-lightning pytorch numpy pandas scikit-learn matchms spectrum-utils pyopenms jiwer jaxtyping; do
echo "Checking $pkg feedstock..."
gh repo view conda-forge/${pkg}-feedstock --json name,description,url 2>/dev/null || echo "Not found: $pkg"
done
Length of output: 3695
Script:
#!/bin/bash
# Check existence of bioconda packages
for pkg in matchms spectrum-utils pyopenms; do
echo "Checking $pkg in bioconda..."
gh repo view bioconda/bioconda-recipes --json name,description,url 2>/dev/null && \
rg -l "name:\s*$pkg\s*$" recipes/
done
# Also check for PyTorch which wasn't found in conda-forge
echo "Checking for pytorch package..."
rg -l "name:\s*pytorch\s*$" recipes/
Length of output: 1224
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/instanovo/meta.yaml (1)
48-56: Consider enhancing test coverage.
The current test configuration is good but could be improved by adding more comprehensive tests.
Consider adding these test commands:
commands:
- pip check
- python -c "import instanovo; print(instanovo.__version__)"
+ - python -c "from instanovo import models"
+ - python -c "from instanovo import data"📜 Review details
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📒 Files selected for processing (1)
- recipes/instanovo/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/instanovo/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/instanovo/meta.yaml (4)
1-7: LGTM: Package metadata is well-defined.
The package name and version are correctly specified using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-18: LGTM: Build configuration follows best practices.
The build configuration is well-structured:
- Uses noarch: python for architecture independence
- Correctly uses --no-deps for pip installation
- Includes run_exports for version pinning
57-67: LGTM: Package metadata is complete.
The about and extra sections provide all necessary information:
- License and license file are specified
- GitHub repository is linked
- DOI is included
- Maintainer is listed
8-11: Verify the source URL and checksum.
The source configuration looks correct, but let's verify the URL and checksum.
✅ Verification successful
Source URL and checksum are valid
The SHA256 checksum matches exactly with the one specified in the meta.yaml file, confirming the integrity of the package source configuration.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify PyPI package existence and checksum
curl -s "https://pypi.org/pypi/instanovo/1.0.0/json" | jq -r '.urls[] | select(.packagetype=="sdist") | .digests.sha256'
Length of output: 185
recipes/instanovo/meta.yaml
Outdated
| requirements: | ||
| host: | ||
| - python >=3.10,<3.12 | ||
| - setuptools >=69.1.1 | ||
| - pip | ||
| run: | ||
| - click >=8.1.7 | ||
| - datasets >=3.0.1 | ||
| - hydra-core >=1.3.2 | ||
| - jaxtyping >=0.2.34 | ||
| - jiwer >=3.0.4 | ||
| - matchms >=0.27.0 | ||
| - neptune >=1.12.0 | ||
| - numpy >=1.23,<1.27 | ||
| - omegaconf >=2.3.0 | ||
| - pandas >=2.2.3 | ||
| - polars >=1.9.0 | ||
| - pyopenms >=3.2.0 | ||
| - python-dotenv >=1.0.1 | ||
| - pytorch-lightning >=2.4.0 | ||
| - s3fs >=2024.6.1 | ||
| - scikit-learn >=1.5.2 | ||
| - spectrum_utils >=0.4.2 | ||
| - tensorboard >=2.18.0 | ||
| - pytorch >=2.4.1 | ||
| - tqdm >=4.66.5 | ||
| - eigen >=3.3.4 |
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Address dependency availability issues.
Based on previous review comments and analysis:
- Several dependencies are not available in conda channels:
matchmsspectrum_utilspyopenms
- Package name adjustments needed:
pytorchshould bepytorch-cpuorpytorch-gpuin conda-forge
- System dependency considerations:
eigenis typically a system-level dependency
Please make the following adjustments:
- Add these packages to conda-forge first or provide alternative installation methods
- Update pytorch package name according to conda-forge conventions
- Consider if eigen should be handled differently as a system dependency
Would you like assistance in creating conda-forge feedstock PRs for the missing packages?
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/instanovo/meta.yaml (1)
47-54: Consider adding more comprehensive tests.
While the current tests verify basic installation and importing, consider adding:
- Basic functionality tests
- Command-line interface tests if applicable
- Key feature verification tests
Would you like assistance in generating additional test commands?
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📒 Files selected for processing (1)
- recipes/instanovo/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/instanovo/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/instanovo/meta.yaml (4)
1-6: LGTM!
The package metadata section follows conda-forge best practices with proper templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM!
The source configuration correctly specifies the PyPI package source with proper checksum verification.
56-66: LGTM!
The package information section is complete with all required fields, proper license specification, and citation information.
16-17: Consider if run_exports is necessary for this package.
The run_exports section with max_pin="x.x" might be unnecessarily strict for a Python package. This is typically used for compiled libraries where ABI compatibility is important. For pure Python packages, this level of version pinning is usually not required and might make dependency resolution more difficult.
recipes/instanovo/meta.yaml
Outdated
| run: | ||
| - click >=8.1.7 | ||
| - datasets >=3.0.1 | ||
| - hydra-core >=1.3.2 | ||
| - jaxtyping >=0.2.34 | ||
| - jiwer >=3.0.4 | ||
| - matchms >=0.27.0 | ||
| - neptune >=1.12.0 | ||
| - numpy >=1.23,<1.27 | ||
| - omegaconf >=2.3.0 | ||
| - pandas >=2.2.3 | ||
| - polars >=1.9.0 | ||
| - pyopenms >=3.2.0 | ||
| - python-dotenv >=1.0.1 | ||
| - pytorch-lightning >=2.4.0 | ||
| - s3fs >=2024.6.1 | ||
| - scikit-learn >=1.5.2 | ||
| - spectrum_utils >=0.4.2 | ||
| - tensorboard >=2.18.0 | ||
| - pytorch-gpu >=2.4.1 | ||
| - tqdm >=4.66.5 |
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💡 Codebase verification
Package availability and PyTorch specification need attention
The verification confirms critical issues with the package requirements:
-
The following packages are not available in conda-forge:
matchmsspectrum_utilspyopenmspytorch-gpu(this specific name is not a valid conda-forge package)
-
For PyTorch:
- Neither
pytorch-gpunor the mainpytorchpackage exists as conda-forge feedstocks - Only
pytorch-cpuis found in conda-forge - The current specification
pytorch-gpu >=2.4.1will not work
- Neither
Recommendations:
- Use PyPI versions for
matchms,spectrum_utils, andpyopenmsby adding them topiprequirements - Replace
pytorch-gpuwith the correct package name from the channel where you intend to source it (likelypytorchfrom the pytorch channel)
🔗 Analysis chain
Address dependency availability and specification issues.
-
Several dependencies are not available in the conda channels:
matchmsspectrum_utilspyopenms
-
The
pytorch-gpuspecification might be too restrictive:- Some users might prefer CPU-only installations
- Consider using a metapackage or providing CPU/GPU variants
Consider these solutions:
- First ensure these packages are available in conda-forge:
- Submit feedstock PRs for missing packages
- Or use PyPI fallback for these specific packages
- For PyTorch, either:
- Use
pytorchas a metapackage - Or create CPU/GPU variants of this recipe
- Use
Let me verify the PyTorch package availability and naming conventions in conda-forge to provide a complete response.
Let me check for the main PyTorch package to complete the verification.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify package availability in conda-forge
for pkg in matchms spectrum_utils pyopenms; do
echo "Checking $pkg in conda-forge..."
gh repo view conda-forge/${pkg}-feedstock --json name,description,url 2>/dev/null || echo "Not found: $pkg"
done
Length of output: 771
Script:
#!/bin/bash
# Check pytorch packages in conda-forge
echo "Checking pytorch packages..."
gh search repos "pytorch-feedstock" --owner conda-forge --json name,description,url
# Check if pytorch-gpu exists as a separate package
echo -e "\nChecking pytorch-gpu specifically..."
gh repo view conda-forge/pytorch-gpu-feedstock --json name,description,url 2>/dev/null || echo "pytorch-gpu feedstock not found"
Length of output: 5521
Script:
#!/bin/bash
# Check main pytorch package
echo "Checking main pytorch package..."
gh repo view conda-forge/pytorch-feedstock --json name,description,url 2>/dev/null || echo "pytorch feedstock not found"
Length of output: 212
|
@hechth for reference |
|
@BioGeek I've updated matchms' dependencies to newer versions (py>3.10, numpy>2, numba>0.60). Currently I'm waiting for sparsestack to get updated on conda-forge, then I will make the next release for matchms with the newer dependencies and then will update the matchms bioconda package. Then you can base your package on matchms >=0.28.0 and I hope things should be fine. |
|
@hechth Thanks for the support! |
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Actionable comments posted: 1
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Review profile: CHILL
📒 Files selected for processing (1)
recipes/instanovo/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/instanovo/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/instanovo/meta.yaml (5)
1-7: LGTM: Package metadata is well-structured.
The package name and version are correctly defined using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-11: LGTM: Source configuration is properly defined.
The PyPI source URL and SHA256 checksum are correctly specified.
12-18: LGTM: Build configuration follows best practices.
The build section correctly specifies:
- Platform independence with
noarch: python - Proper pip installation command
run_exportsto prevent ABI breakage
47-55: LGTM: Test configuration is comprehensive.
The test section properly includes:
- Package import verification
- Dependency checks via pip
- Version verification
56-66: LGTM: Package information is complete.
The about and extra sections include all necessary metadata:
- Project homepage and summary
- License information
- Maintainer
- DOI identifier
recipes/instanovo/meta.yaml
Outdated
| requirements: | ||
| host: | ||
| - python >=3.10,<3.12 | ||
| - setuptools >=69.1.1 | ||
| - pip | ||
| run: | ||
| - click >=8.1.7 | ||
| - datasets >=3.0.1 | ||
| - hydra-core >=1.3.2 | ||
| - jaxtyping >=0.2.34 | ||
| - jiwer >=3.0.4 | ||
| - matchms >=0.28.1 | ||
| - neptune >=1.12.0 | ||
| - numpy >=2.0.0 | ||
| - omegaconf >=2.3.0 | ||
| - pandas >=2.2.3 | ||
| - polars >=1.9.0 | ||
| - pyopenms >=3.2.0 | ||
| - python-dotenv >=1.0.1 | ||
| - pytorch-lightning >=2.4.0 | ||
| - s3fs >=2024.6.1 | ||
| - scikit-learn >=1.5.2 | ||
| - spectrum_utils >=0.4.2 | ||
| - tensorboard >=2.18.0 | ||
| - pytorch-gpu >=2.4.1 | ||
| - tqdm >=4.66.5 | ||
|
|
There was a problem hiding this comment.
Critical: Several dependencies need attention.
Based on previous verification:
-
The following packages are not available in conda channels:
matchmsspectrum_utilspyopenms
-
pytorch-gpuis not a valid conda-forge package name. Consider:- Using
pytorchwith CUDA variants - Or specifying the correct channel for GPU support
- Using
Consider these solutions:
- First ensure these packages are available in conda-forge:
- Submit feedstock PRs for missing packages
- Or use PyPI fallback for these specific packages
- For PyTorch, either:
- Use
pytorchas the package name - Or specify the correct channel for GPU support
- Use
Would you like assistance in:
- Creating conda-forge feedstock PRs for the missing packages?
- Updating the PyTorch dependency specification?
|
@BioGeek seems like pyOpenMS is also on numpy < 2 - do you really need that library? |
|
xref #51992 |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/instanovo/meta.yaml (1)
48-56: Consider enhancing test coverage.While the basic import and version checks are good, consider adding functional tests to verify core features, especially for a scientific package.
Example additions:
test: imports: - instanovo commands: - pip check - python -c "import instanovo; print(instanovo.__version__)" + # Verify core functionality + - python -c "from instanovo import __version__; assert __version__ == '{{ version }}'" + - python -c "from instanovo.model import InstaNovo" requires: - pip
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📒 Files selected for processing (1)
recipes/instanovo/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/instanovo/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/instanovo/meta.yaml (3)
1-10: LGTM! Package metadata is well-defined.
The package metadata follows conda-forge conventions with proper Jinja2 templating and includes all required fields.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
57-67: LGTM! Package information is complete.
The about section includes all required fields with appropriate metadata, license information, and maintainer details.
20-47:
Critical: Address dependency availability and GPU requirements.
Several critical issues need attention:
-
Missing packages in conda channels:
matchmsspectrum_utilspyopenms
-
GPU dependencies:
pytorch-gpuis not a valid conda-forge package- Forcing GPU dependencies (
cudatoolkit) may not be suitable for all users
Suggested changes:
- Replace GPU-specific dependencies with more flexible options:
- - pytorch-gpu >=2.4.1
- - cudatoolkit
+ - pytorch >=2.4.1
+ - cudatoolkit # [cuda]- For the missing packages, either:
- Submit them to conda-forge first, or
- Add them as pip dependencies in the build script
Would you like assistance in:
- Creating conda-forge feedstock PRs for the missing packages?
- Implementing a more flexible GPU/CPU configuration?
| build: | ||
| noarch: python | ||
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage(name | lower, max_pin="x.x") }} | ||
|
|
There was a problem hiding this comment.
🛠️ Refactor suggestion
Remove unnecessary run_exports section.
The run_exports section is typically used for C/C++ libraries to ensure ABI compatibility. For a pure Python package (noarch: python), this section is unnecessary and could cause unintended version pinning issues.
Apply this diff to remove the section:
build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0
- run_exports:
- - {{ pin_subpackage(name | lower, max_pin="x.x") }}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| build: | |
| noarch: python | |
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | |
| number: 0 | |
| run_exports: | |
| - {{ pin_subpackage(name | lower, max_pin="x.x") }} | |
| build: | |
| noarch: python | |
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | |
| number: 0 |
|
@BioGeek seems like the problem is now somewhere with cuda - maybe @bgruening can confirm or has an idea of how to fix this? I did not wrap any packages using CUDA before. |
Add TODO comments dependencies of matchms have been updated Remove duplicate python lines, remove uper version bound Add upper python bound again unpin all packages re-add pinned packages, add eigen, add doi remove eigen, use pytorch-gpu Bump version of matchms to 0.28.0
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Actionable comments posted: 3
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Review profile: CHILL
📒 Files selected for processing (1)
recipes/instanovo/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/instanovo/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| - hydra-core >=1.3.2 | ||
| - jaxtyping >=0.2.34 | ||
| - jiwer >=3.0.4 | ||
| - matchms >=0.28.0 |
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Critical: Unavailable dependencies in conda channels
The following dependencies are not available in conda-forge or bioconda channels:
matchmspyopenmsspectrum_utils
These packages need to be added to conda-forge first. Until then, consider:
- Submitting feedstock PRs for these packages to conda-forge
- Or using PyPI fallback for these specific packages
Would you like assistance in creating conda-forge feedstock PRs for these packages?
Also applies to: 37-37, 42-42
| - scikit-learn >=1.5.2 | ||
| - spectrum_utils >=0.4.2 | ||
| - tensorboard >=2.18.0 | ||
| - pytorch >=2.4.1 |
There was a problem hiding this comment.
Update PyTorch and CUDA configuration
Current issues:
pytorchversion >=2.4.1 is not yet availablecudatoolkitshould have a version constraint- Consider making CUDA optional for CPU-only installations
Recommendations:
- Use a more conservative PyTorch version that's available in conda-forge
- Add version constraint for cudatoolkit
- Consider splitting into CPU/GPU variants
Apply this diff to update the configuration:
- - pytorch >=2.4.1
- - cudatoolkit
+ - pytorch >=2.0.0
+ - cudatoolkit >=11.8Also applies to: 46-46
| run_exports: | ||
| - {{ pin_subpackage(name | lower, max_pin="x.x") }} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Remove unnecessary run_exports section
The run_exports section is typically used for C/C++ libraries to ensure ABI compatibility. For a pure Python package (noarch: python), this section is unnecessary and could cause unintended version pinning issues.
Apply this diff to remove the section:
build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0
- run_exports:
- - {{ pin_subpackage(name | lower, max_pin="x.x") }}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| run_exports: | |
| - {{ pin_subpackage(name | lower, max_pin="x.x") }} | |
| build: | |
| noarch: python | |
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | |
| number: 0 |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/instanovo/meta.yaml (1)
31-42: Address dependency availability in conda channels.Several dependencies are not available in conda channels:
matchmsspectrum_utilspyopenmsOptions to resolve this:
- Submit these packages to conda-forge first (recommended)
- Use PyPI fallback for these specific packages
- Wait for the updated
matchmspackage (as mentioned byhechthin PR comments)Would you like assistance in:
- Creating conda-forge feedstock PRs for the missing packages?
- Setting up a staged deployment plan to coordinate with the
matchmsupdate?
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recipes/instanovo/meta.yaml(1 hunks)
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🪛 yamllint
recipes/instanovo/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/instanovo/meta.yaml (5)
1-10: LGTM! Package metadata is well-defined.
The package metadata section is correctly configured with proper templating and source verification.
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-18: Remove unnecessary run_exports section.
The run_exports section is typically used for C/C++ libraries to ensure ABI compatibility. For a pure Python package (noarch: python), this section is unnecessary.
48-56: LGTM! Test configuration is appropriate.
The test section includes necessary checks for package installation and importing.
57-67: LGTM! Package information is complete.
The about section contains all necessary metadata including license, homepage, and maintainer information.
44-46:
Update PyTorch and CUDA configuration.
Current issues:
- PyTorch version 2.4.1 is not yet available
- cudatoolkit should be optional and version-constrained
Recommendations:
- - pytorch >=2.4.1
- - cudatoolkit
+ - pytorch >=2.0.0
+ - cudatoolkit >=11.8 # Optional: Add selectors for GPU/CPU variantsConsider splitting into CPU/GPU variants to support both use cases.
Likely invalid or redundant comment.
| - jiwer >=3.0.4 | ||
| - matchms >=0.28.0 | ||
| - neptune >=1.12.0 | ||
| - numpy ==2.1.0rc1 |
There was a problem hiding this comment.
Update numpy version constraint.
Using a release candidate version (2.1.0rc1) in production is risky. Consider using a stable version:
- - numpy ==2.1.0rc1
+ - numpy >=2.0.0📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - numpy ==2.1.0rc1 | |
| - numpy >=2.0.0 |
Add instanovo, a package for de novo peptide sequencing
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