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Update pyproject.toml to resolve pip install issue #657

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Update pyproject.toml to resolve pip install issue #657

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Update _m3gnet.py
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Merge pull request #1 from zz11ss11zz/zz11ss11zz-patch-1
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1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ where = ["src"]
"describers/data/*.json",
"describers/data/megnet_models/*",
"describers/data/m3gnet_models/matbench_mp_e_form/0/m3gnet/*",
"apps/pes/params/*.json",
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Tip

Codebase Verification

Update required: Incorrect path specified in pyproject.toml

The path "apps/pes/params/.json" specified in pyproject.toml doesn't match the actual location of the JSON files in the repository. The correct path appears to be "src/maml/apps/pes/params/.json". Please update the pyproject.toml file with the correct path to ensure that the necessary JSON files are included in the package distribution.

  • Update line 70 in pyproject.toml to: 
    "src/maml/apps/pes/params/*.json",

On a positive note, no sensitive information was detected in any of the JSON files found in the repository.

Analysis chain

LGTM! This change resolves the reported installation issue.

The addition of "apps/pes/params/*.json" to the package-data section ensures that the necessary JSON files are included in the package distribution when installing with pip install. This should resolve the FileNotFoundError that was occurring.

Please verify that the JSON files in the apps/pes/params directory do not contain any sensitive information that should not be distributed with the package.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify JSON files in apps/pes/params do not contain sensitive information.

# Test: Search for common sensitive information patterns in the JSON files.
# Expect: No matches found.
rg --type json -i -e 'password|secret|token|key|credentials' apps/pes/params

Length of output: 134

Script:

#!/bin/bash
# Description: Locate JSON files and check for sensitive information

# Step 1: Find all JSON files in the repository
echo "Searching for JSON files:"
fd -e json

# Step 2: If JSON files are found, search for sensitive information patterns
echo -e "\nChecking JSON files for sensitive information:"
fd -e json -x rg -i -e 'password|secret|token|key|credentials' {}

# Step 3: Check if the specific directory mentioned in pyproject.toml exists
echo -e "\nChecking for the existence of apps/pes/params directory:"
fd -t d "apps/pes/params"

Length of output: 4518

]

[tool.black]
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2 changes: 1 addition & 1 deletion src/maml/describers/_m3gnet.py
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Expand Up @@ -134,6 +134,6 @@ def transform_one(self, structure: Structure | Molecule):
g = self.describer_model.graph_layers[i](g)
atom_fea[f"gc_{i + 1}"] = g[Index.ATOMS]
atom_fea_dict = {k: v for k, v in atom_fea.items() if k in self.output_layers}
if isinstance(self.return_type, dict):
if self.return_type is dict:
return atom_fea_dict
return pd.DataFrame(np.concatenate(list(atom_fea_dict.values()), axis=1))
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