Feature/v1.5.3 (#91)

* unbreak latex test: * fixed import bug in raw_dataset.py
FoxoTech · Jul 28, 2021 · 04f1ac1 · 04f1ac1
1 parent 3216fee
commit 04f1ac1
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Showing 6 changed files with 14 additions and 32 deletions.
diff --git a/conf.py b/conf.py
@@ -24,9 +24,9 @@
 author = 'FOXO Technologies, inc.'
 
 # The short X.Y version
-version = '1.4'
+version = '1.5'
 # The full version, including alpha/beta/rc tags
-release = '1.4.2'
+release = '1.5.2'
 
 
 # -- General configuration ---------------------------------------------------
@@ -126,7 +126,7 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_engine = 'xelatex'
+#latex_engine = 'xelatex'
 #latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #

diff --git a/methylprep/cli.py b/methylprep/cli.py
@@ -384,7 +384,7 @@ def cli_download(cmd_args):
         required=False,
         action='store_true',
         default=False,
-        help='If passed, will only create dictionaries and not process any samples',
+        help="Download IDAT files and meta data but don't process them further with run_pipeline.",
         )
 
     parser.add_argument(

diff --git a/methylprep/download/process_data.py b/methylprep/download/process_data.py
@@ -110,34 +110,17 @@ def process_series(id, path, seen_platforms, batch_size, **kwargs):
             data_dir = f"{path}/{platform}"
             LOGGER.info(f"Processing {id} -- {platform} samples")
             LOGGER.info(kwargs)
-            run_pipeline(data_dir, betas=True, batch_size=batch_size,
+            run_pipeline(data_dir,
+                betas=True,
+                save_control=True,
+                poobah=True,
+                export_poobah=True,
+                quality_mask=True,
+                batch_size=batch_size,
                 make_sample_sheet=kwargs.get('make_sample_sheet',False),
                 meta_data_frame=kwargs.get('meta_data_frame',False)
                 ) #make_sample_sheet handled within miniml.py logic
 
-            ''' # v1.3.x auto-consolidates, so no need for this function to run.
-            dfs = []
-            betas_list = list(Path(data_dir).glob('beta_values_*.pkl'))
-
-            #for i in range(1,len(betas_list) + 1):
-                #df = pd.read_pickle(f"beta_values_{i}.pkl")
-            for beta in betas_list:
-                df = pd.read_pickle(beta)
-                dfs.append(df)
-            if len(dfs) > 1:
-                LOGGER.info(f"Concatenating {len(betas_list)} beta_value files.")
-                joined_df = pd.concat(dfs, axis=1)
-            elif len(dfs) == 1:
-                joined_df = dfs[0]
-            else:
-                return
-
-            joined_df.to_pickle(Path(path,platform,f"{id}_beta_values.pkl"))
-            for beta in betas_list:
-                os.remove(beta)
-            LOGGER.info(f"Consolidated {id} {platform} samples; saved to {id}_beta_values.pkl")
-            '''
-
 
 def run_series_list(list_file, path, dict_only=False, batch_size=BATCH_SIZE, **kwargs):
     """Downloads the IDATs and metadata for a list of series, creating metadata dictionaries and dataframes of sample beta_values

diff --git a/methylprep/models/__init__.py b/methylprep/models/__init__.py
@@ -15,5 +15,4 @@
     'SigSet',
     'RawMetaDataset',
     'get_array_type',
-    'Sesame',
 ]
diff --git a/methylprep/models/raw_dataset.py b/methylprep/models/raw_dataset.py
@@ -3,17 +3,17 @@
 import pandas as pd
 # App
 from ..models import (
-    FG_PROBE_SUBSETS,
     ArrayType,
     Channel,
     ProbeType,
 )
+from ..models.probes import FG_PROBE_SUBSETS
 from ..files import IdatDataset
 from ..utils import inner_join_data
 from ..utils.progress_bar import * # checks environment and imports tqdm appropriately.
 from collections import Counter
 
-__all__ = ['RawDataset', 'MethylationDataset', 'get_raw_datasets', 'get_raw_meta_datasets', 'get_array_type']
+__all__ = ['RawDataset', 'MethylationDataset', 'get_raw_datasets', 'get_array_type']
 
 
 LOGGER = logging.getLogger(__name__)

diff --git a/methylprep/version.py b/methylprep/version.py
@@ -2,4 +2,4 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module module
-__version__ = '1.5.2'
+__version__ = '1.5.3'