dotools_py.utility.create_report

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dotools_py.utility.create_report#

dotools_py.utility.create_report(log_file)[source]#

Create a report file.

This function takes a log_file that should have been set at the beginning of the session with dotools_py.settings.set.set_kernel_logger and add information regarding the session such as the machine characteristics and the version of the packages.

Parameters:
log_file str | Path

Path to the log file

Return type:

None

Returns:

Returns None. The log file is updated with session information.

Examples

>>> import dotools_py as do
>>> do.settings.set_kernel_logger('./History.log', overwrite=True)
>>> adata = do.dt.example_10x_processed()
>>> adata
>>> do.utility.create_report("./History.log")
>>> print(open("History.log").read())
[CODE 2026-01-22 13:59:28.904757]
>>> adata = do.dt.example_10x_processed()
[CODE 2026-01-22 13:59:29.617186]
>>> adata
[OUTPUT 2026-01-22 13:59:29.619246]
AnnData object with n_obs × n_vars = 700 × 1851
    obs: 'batch', 'condition', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'n_genes', 'n_counts', 'doublet_class', 'doublet_score', 'leiden', 'cell_type', 'autoAnnot', 'celltypist_conf_score', 'annotation', 'annotation_recluster'
    var: 'mean', 'std', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches', 'highly_variable_intersection'
    uns: 'annotation_colors', 'annotation_recluster_colors', 'batch_colors', 'hvg', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'pca', 'umap'
    obsm: 'X_CCA', 'X_pca', 'X_umap'
    varm: 'PCs'
    layers: 'counts', 'logcounts'
    obsp: 'connectivities', 'distances'
==================== Session Information ====================
OS:macOS-26.2-arm64-arm-64bit
Machine: arm64
Processor: arm
CPU cores (physical): 10
CPU cores (logical): 10
Total RAM (GB): 16.0
Python version: 3.11.13
-----
anndata     0.11.4
dotools_py  0.0.1
pandas      2.3.2
platform    1.0.8
-----
Cython                      3.1.4
IPython                     9.5.0
PIL                         11.3.0
adjustText                  1.3.0
altair                      6.0.0
argparse                    1.1
arrow                       1.3.0
attr                        25.3.0
attrs                       25.3.0
beartype                    0.22.8
charset_normalizer          3.4.3
cloudpickle                 3.1.1
comm                        0.2.3
coverage                    7.11.0
csv                         1.0
ctypes                      1.1.0
cycler                      0.12.1
cython                      3.1.4
dask                        2024.11.2
dateutil                    2.9.0.post0
decimal                     1.70
decorator                   5.2.1
defusedxml                  0.7.1
deprecated                  1.2.18
executing                   2.2.1
h5py                        3.14.0
idna                        3.10
igraph                      0.11.9
ipaddress                   1.0
ipywidgets                  8.1.7
jedi                        0.19.2
jinja2                      3.1.6
joblib                      1.5.2
json                        2.0.9
jsonpointer                 3.0.0
jsonschema                  4.25.1
kiwisolver                  1.4.9
lark                        1.2.2
leidenalg                   0.10.2
llvmlite                    0.45.0
logging                     0.5.1.2
markupsafe                  3.0.2
marshal                     4
matplotlib                  3.10.6
msgpack                     1.1.2
narwhals                    2.5.0
natsort                     8.4.0
numba                       0.62.0
numcodecs                   0.15.1
numpy                       2.3.3
packaging                   25.0
parso                       0.8.5
patsy                       1.0.1
polars                      1.33.1
prompt_toolkit              3.0.52
psutil                      7.1.0
pure_eval                   0.2.3
pyarrow                     21.0.0
pydot                       4.0.1
pygments                    2.19.2
pyparsing                   3.2.4
pytz                        2025.2
re                          2.2.1
rfc3339_validator           0.1.4
rfc3986_validator           0.1.1
scanpy                      1.11.4
scipy                       1.15.3
seaborn                     0.13.2
session_info                v1.0.1
six                         1.17.0
sklearn                     1.7.2
socketserver                0.4
sparse                      0.17.0
sqlite3                     2.6.0
stack_data                  0.6.3
statsmodels                 0.14.5
stdlib_list                 0.11.1
sys                         3.11.13 (main, Jun  5 2025, 08:21:08) [Clang 14.0.6 ]
tarfile                     0.9.0
texttable                   1.7.0
threadpoolctl               3.6.0
tlz                         1.0.0
toolz                       1.0.0
torch                       2.8.0
tqdm                        4.67.1
traitlets                   5.14.3
wcwidth                     0.2.13
wrapt                       1.17.3
yaml                        6.0.2
zarr                        2.18.7
zlib                        1.0
-----
Python 3.11.13 (main, Jun  5 2025, 08:21:08) [Clang 14.0.6 ]
macOS-26.2-arm64-arm-64bit
10 logical CPU cores, arm
-----
Session information updated at 2026-01-22 13:59
=============================================================
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