swap ca cb channels #93
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universvm
reviewed
Dec 19, 2023
src/aposteriori/data_prep/cli.py
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| type=click.Choice(["CNO", "CNOCB", "CNOCBCA", "CNOCBCAQ", "CNOCBCAP"]), | ||
| type=click.Choice(["CNO", "CNOCB", "CNOCACB", "CNOCACBQ", "CNOCACBP"]), |
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For backwards compatibility, can we add both?
type=click.Choice(["CNO", "CNOCB", "CNOCACB", "CNOCACBQ", "CNOCACBP", "CNOCBCA", "CNOCBCAQ", "CNOCBCAP" ]),
universvm
reviewed
Dec 19, 2023
src/aposteriori/data_prep/cli.py
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| elif atom_encoder == "CNOCACB": | ||
| codec = Codec.CNOCACB() | ||
| elif atom_encoder == "CNOCACBQ": | ||
| codec = Codec.CNOCACBQ() | ||
| elif atom_encoder == "CNOCACBP": | ||
| codec = Codec.CNOCACBP() |
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Same here maybe let's add both
universvm
requested changes
Dec 19, 2023
src/aposteriori/data_prep/cli.py
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| "CNOCBCA", | ||
| "CNOCBCAQ", | ||
| "CNOCBCAP", | ||
| ], f"Expected encoder to be CNO, CNOCB, CNOCBCA, CNOCBCAQ, CNOCBCAP, but got {atom_encoder}" | ||
| "CNOCACB", | ||
| "CNOCACBQ", | ||
| "CNOCACBP", | ||
| ], f"Expected encoder to be CNO, CNOCB, CNOCACB, CNOCACBQ, CNOCACBP, but got {atom_encoder}" |
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again here.
I would say let's raise a warning if you are using the old encoders saying they are deprecated and will be removed in future versions.
universvm
reviewed
Dec 20, 2023
src/aposteriori/data_prep/cli.py
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| codec = Codec.CNO() | ||
| elif atom_encoder == "CNOCB": | ||
| codec = Codec.CNOCB() | ||
| elif atom_encoder == "CNOCBCA": | ||
| codec = Codec.CNOCBCA() | ||
| elif atom_encoder == "CNOCBCAQ": | ||
| codec = Codec.CNOCBCAQ() | ||
| elif atom_encoder == "CNOCBCAP": | ||
| codec = Codec.CNOCBCAP() | ||
| elif atom_encoder == "CNOCACB" or atom_encoder == "CNOCBCA": | ||
| codec = Codec.CNOCACB() | ||
| if atom_encoder == "CNOCBCA": | ||
| warnings.warn("CNOCBCA encoding is deprecated and will be removed in future versions, atoms will be encoded as CNOCACB") | ||
| elif atom_encoder == "CNOCACBQ" or atom_encoder == "CNOCBCAQ": | ||
| codec = Codec.CNOCACBQ() | ||
| if atom_encoder == "CNOCBCAQ": | ||
| warnings.warn("CNOCBCAQ encoding is deprecated and will be removed in future versions, atoms will be encoded as CNOCACBQ") | ||
| elif atom_encoder == "CNOCACBP" or atom_encoder == "CNOCBCAP": | ||
| codec = Codec.CNOCACBP() | ||
| if atom_encoder == "CNOCBCAP": | ||
| warnings.warn("CNOCBCAP encoding is deprecated and will be removed in future versions, atoms will be encoded as CNOCACBP") | ||
| else: | ||
| assert atom_encoder in [ | ||
| "CNO", | ||
| "CNOCB", | ||
| "CNOCACB", | ||
| "CNOCACBQ", | ||
| "CNOCACBP", | ||
| "CNOCBCA", | ||
| "CNOCBCAQ", | ||
| "CNOCBCAP", | ||
| ], f"Expected encoder to be CNO, CNOCB, CNOCBCA, CNOCBCAQ, CNOCBCAP, but got {atom_encoder}" |
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How about we clean up this section to
# Mapping of current atom encoders to their corresponding Codec classes
current_codec_mapping = {
"CNO": Codec.CNO,
"CNOCB": Codec.CNOCB,
"CNOCACB": Codec.CNOCACB,
"CNOCACBQ": Codec.CNOCACBQ,
"CNOCACBP": Codec.CNOCACBP
}
# List of deprecated encodings and their replacements
deprecated_encodings = {
"CNOCBCA": "CNOCACB",
"CNOCBCAQ": "CNOCACBQ",
"CNOCBCAP": "CNOCACBP"
}
# Create Codec based on atom_encoder
if atom_encoder in current_codec_mapping:
codec = current_codec_mapping[atom_encoder]()
elif atom_encoder in deprecated_encodings:
replacement = deprecated_encodings[atom_encoder]
codec = current_codec_mapping[replacement]()
warnings.warn(f"{atom_encoder} encoding is deprecated and will be removed in future versions, "
f"atoms will be encoded as {replacement}")
else:
raise ValueError(f"Unknown atom_encoder: {atom_encoder}")
|
I made the changes except for the else condition because Click.choice for the -ae already handles this when an atom encoder is not valid. |
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Change the position of CA CB channels for readability and consistency