Migrate CI dependency installation from pip to uv #338
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This reverts commit 2377b15.
AntObi
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enhancement
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WalkthroughThe pull request introduces modifications to the CI workflow and updates to the Changes
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
pyproject.toml (1)
95-109: Consider reorganising dependency groupsThe new optional group contains packages that overlap with existing groups like
crystal_space,featurisers, andvisualisation. Consider:
- Using the existing groups as building blocks for the optional group
- Defining the version constraints in a single location to avoid inconsistencies
Example reorganisation:
[project.optional-dependencies] # Base groups with version constraints crystal_space = [ "mp-api==0.42.2", "ElementEmbeddings==0.6.1", "umap-learn==0.5.3", "kaleido==0.2.1", "pydantic==2.9.2" ] # Combined groups optional = [ "crystal_space", "featurisers", "visualisation" ]
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.github/workflows/ci.yml(1 hunks)pyproject.toml(1 hunks)
🧰 Additional context used
🪛 yamllint (1.35.1)
.github/workflows/ci.yml
[error] 41-41: trailing spaces
(trailing-spaces)
🔇 Additional comments (1)
.github/workflows/ci.yml (1)
33-34: LGTM: Proper cache configuration
The cache configuration is correctly set up with pyproject.toml as the dependency path, which will improve CI performance by caching Python packages between runs.
.github/workflows/ci.yml
Outdated
| pip install uv | ||
| uv pip install -e ".[optional,dev]" --system | ||
|
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🛠️ Refactor suggestion
Consider pinning uv version and fix whitespace
Whilst the migration to UV is a good improvement for faster dependency installation, consider:
- Pin the UV version for reproducible builds
- Remove the trailing whitespace on line 41
Apply this diff:
- pip install uv
- uv pip install -e ".[optional,dev]" --system
-
+ pip install uv==0.1.5
+ uv pip install -e ".[optional,dev]" --system📝 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.
| pip install uv | |
| uv pip install -e ".[optional,dev]" --system | |
| pip install uv==0.1.5 | |
| uv pip install -e ".[optional,dev]" --system |
🧰 Tools
🪛 yamllint (1.35.1)
[error] 41-41: trailing spaces
(trailing-spaces)
| optional = [ | ||
| "pydantic>=2.9.2", | ||
| "mp-api>=0.42.2", | ||
| "pymatviz>=0.14", | ||
| "seaborn>=0.13.2", | ||
| "pymatgen>=2024.2.20", | ||
| "matminer>=0.9.2", | ||
| "umap-learn>=0.5.3", | ||
| "kaleido>=0.2.1", | ||
| "ase>=3.22.0", | ||
| "numpy", | ||
| "ElementEmbeddings>=0.4", | ||
| "dash>=2.18.2", | ||
|
|
||
| ] |
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💡 Codebase verification
Version constraints in optional dependencies require adjustment
The codebase analysis reveals:
pymatgenis extensively used across the project, particularly in core functionality like structure prediction and screeningElementEmbeddingsis not directly imported, only referenced in a comment for an adapted function
Recommendations:
- Align the optional
pymatgenversion (>=2024.2.20) closer to the strict version (==2024.11.13) to ensure consistent behaviour, suggest using>=2024.11.13 - Remove
ElementEmbeddingsfrom optional dependencies as it's not actively used in the codebase
🔗 Analysis chain
Review version inconsistencies between optional and strict groups
There are notable version differences between the optional and strict groups:
pymatgen: >=2024.2.20 vs ==2024.11.13ElementEmbeddings: >=0.4 vs ==0.6.1
These differences could lead to inconsistent behaviour between development and production environments.
Let's verify the compatibility of these versions:
Version differences between optional and strict dependencies need attention
The version history shows significant updates between the specified versions:
pymatgen: 20+ releases between 2024.2.20 and 2024.11.13ElementEmbeddings: 4 releases between 0.4 and 0.6.1
Let's verify if these packages are actively used in the codebase to assess the impact:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for breaking changes in the version differences
# Check pymatgen releases between 2024.2.20 and 2024.11.13
curl -s https://pypi.org/pypi/pymatgen/json | jq -r '.releases | keys[]' | grep -E "2024\.(2|3|4|5|6|7|8|9|10|11)\.[0-9]+" | sort -V
# Check ElementEmbeddings releases between 0.4 and 0.6.1
curl -s https://pypi.org/pypi/ElementEmbeddings/json | jq -r '.releases | keys[]' | grep -E "0\.[4-6]" | sort -V
Length of output: 494
Script:
#!/bin/bash
# Check usage of pymatgen and ElementEmbeddings in the codebase
echo "=== pymatgen usage ==="
rg "import.*pymatgen" -A 2
rg "from pymatgen" -A 2
echo -e "\n=== ElementEmbeddings usage ==="
rg "import.*ElementEmbeddings" -A 2
rg "from ElementEmbeddings" -A 2
Length of output: 5785
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #338 +/- ##
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Coverage 77.44% 77.44%
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Files 31 31
Lines 2589 2589
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Hits 2005 2005
Misses 584 584 ☔ View full report in Codecov by Sentry. |
Summary by CodeRabbit
New Features
Improvements