diff --git a/docs/_static/clock_table.txt b/docs/_static/clock_table.txt index 41c3080..0a827c2 100644 --- a/docs/_static/clock_table.txt +++ b/docs/_static/clock_table.txt @@ -35,6 +35,8 @@ +---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | leerpc | methylation | Homo sapiens | 2019 | None | None | https://doi.org/10.18632/aging.102049 | None | +---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| linblood | methylation | Homo sapiens | 2016 | None | None | https://doi.org/10.18632/aging.100908 | None | ++---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | mammalian1 | methylation | multi | 2023 | None | anti_logp2 | https://doi.org/10.1038/s43587-023-00462-6 | This is the DNAm age predictor from the paper in which there is no adjustment for species | +---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | mammalian2 | methylation | multi | 2023 | None | anti_log_log | https://doi.org/10.1038/s43587-023-00462-6 | This is the relative DNAm age predictor from the paper, with min=0 and max=1 | @@ -77,7 +79,9 @@ +---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | thompsonmultitissue | methylation | Mus musculus | 2018 | None | None | https://doi.org/10.18632/aging.101590 | None | +---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| zhangen | methylation | Homo sapiens | 2019 | None | None | https://doi.org/10.1186/s13073-019-0667-1 | None | +| zhangblup | methylation | Homo sapiens | 2017 | None | None | https://doi.org/10.1186/s13073-019-0667-1 | None | ++---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| zhangen | methylation | Homo sapiens | 2017 | None | None | https://doi.org/10.1186/s13073-019-0667-1 | None | +---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | zhangmortality | methylation | Homo sapiens | 2019 | None | None | https://doi.org/10.1038/ncomms14617 | None | +---------------------+-----------------+--------------+------+-------------------------------------------+-----------------------+----------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/docs/source/conf.py b/docs/source/conf.py index 269eef9..f5e1f22 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -13,7 +13,7 @@ project = 'pyaging' copyright = '2023, Lucas Paulo de Lima Camillo' author = 'Lucas Paulo de Lima Camillo' -release = '0.0.7' +release = '0.0.8' # 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predict_ages_with_model( """ # Create an AnnLoader - use_cuda = device == 'cuda' + use_cuda = device == "cuda" dataloader = AnnLoader(adata, batch_size=1024, use_cuda=use_cuda) # Use the AnnLoader for batched prediction @@ -821,11 +826,17 @@ def filter_missing_features( """ n_missing_features = sum(adata.var["percent_na"] == 1) if n_missing_features > 0: - logger.info(f"Removing {n_missing_features} missing features added", indent_level=indent_level+1) + logger.info( + f"Removing {n_missing_features} added features", + indent_level=indent_level + 1, + ) adata = adata[:, adata.var["percent_na"] < 1].copy() else: - logger.info("No missing features, so adata size did not change", indent_level=indent_level+1) - + logger.info( + "No missing features, so adata size did not change", + indent_level=indent_level + 1, + ) + return adata diff --git a/pyproject.toml b/pyproject.toml index 3f8f343..86c4a4b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "pyaging" -version = "0.0.7" +version = "0.0.8" description = "A Python-based compendium of GPU-optimized aging clocks." authors = ["Lucas Paulo de Lima Camillo "] license = "BSD"