Some cleaning up

PMBio · May 16, 2022 · 4a001d1 · 4a001d1
1 parent d9f780f
commit 4a001d1
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Showing 8 changed files with 5 additions and 50 deletions.
diff --git a/README.md b/README.md
@@ -3,7 +3,6 @@
 [![GitHub license](https://img.shields.io/github/license/a-slide/pycoMeth.svg)](https://github.com/a-slide/pycoMeth/blob/master/LICENSE)
 [![Language](https://img.shields.io/badge/Language-Python3.7+-yellow.svg)](https://www.python.org/)
 [![DOI](https://img.shields.io/badge/DOI-10.1101%2F2022.02.16.480699-red)](https://www.biorxiv.org/content/10.1101/2022.02.16.480699v1)
-[![Build Status](https://travis-ci.com/a-slide/pycoMeth.svg?branch=master)](https://travis-ci.com/a-slide/pycoMeth)
 
 [![PyPI version](https://badge.fury.io/py/pycoMeth.svg)](https://badge.fury.io/py/pycoMeth)
 [![PyPI downloads](https://pepy.tech/badge/pycoMeth)](https://pepy.tech/project/pycoMeth)

diff --git a/deploy_anaconda.sh b/deploy_anaconda.sh
diff --git a/meta.yaml b/meta.yaml
@@ -37,14 +37,10 @@ test:
   imports:
     - pycoMeth.FileParser
     - pycoMeth.CoordGen
-    - pycoMeth.CpG_Aggregate
-    - pycoMeth.Interval_Aggregate
     - pycoMeth.Meth_Comp
     - pycoMeth.Comp_Report
     - pycoMeth.CGI_Finder
   commands:
-    - pycoMeth CpG_Aggregate --help
-    - pycoMeth Interval_Aggregate --help
     - pycoMeth Meth_Comp --help
     - pycoMeth Comp_Report --help
     - pycoMeth CGI_Finder --help

diff --git a/pycoMeth/Meth_Comp.py b/pycoMeth/Meth_Comp.py
@@ -4,19 +4,18 @@
 # Standard library imports
 import itertools
 import random
-from typing import IO, List, Generator, Dict, Any
+from typing import IO, List, Dict, Any
 from math import sqrt
 import fileinput
 
 # Third party imports
-import scipy.sparse
 from tqdm import tqdm
 import numpy as np
 import pandas as pd
 from scipy.stats import kruskal, mannwhitneyu, wilcoxon, fisher_exact, chi2_contingency
 from statsmodels.stats.multitest import multipletests
 from multiprocessing import Pool
-from meth5.meth5 import MetH5File
+from meth5 import MetH5File
 
 # Local imports
 from pycoMeth.common import *

diff --git a/pycoMeth/Meth_Seg.py b/pycoMeth/Meth_Seg.py
@@ -1,21 +1,14 @@
-import time
 from pathlib import Path
-from typing import IO, Iterable, List, Optional
+from typing import IO, List
 from multiprocessing import Queue, Process
-import argparse
 import logging
 
 import tqdm
-import pandas as pd
 import numpy as np
-from meth5.meth5 import MetH5File
+from meth5 import MetH5File
 from meth5.sparse_matrix import SparseMethylationMatrixContainer
 
-from pycoMeth.meth_seg.emissions import BernoulliPosterior
-from pycoMeth.meth_seg.hmm import SegmentationHMM
-from pycoMeth.meth_seg.postprocessing import cleanup_segmentation
 from pycoMeth.meth_seg.segments_csv_io import SegmentsWriterBED, SegmentsWriterBedGraph
-from pycoMeth.meth_seg.math import llr_to_p
 from pycoMeth.meth_seg.segment import segment
 
 

diff --git a/pycoMeth/loader.py b/pycoMeth/loader.py
@@ -1,4 +1,4 @@
-from meth5.meth5 import MetH5File
+from meth5 import MetH5File
 
 from typing import List, Tuple, Dict
 from pycoMeth.CoordGen import Coord

diff --git a/versipy_templates/README.md b/versipy_templates/README.md
@@ -3,7 +3,6 @@
 [![GitHub license](https://img.shields.io/github/license/a-slide/pycoMeth.svg)](https://github.com/a-slide/pycoMeth/blob/master/LICENSE)
 [![Language](https://img.shields.io/badge/Language-Python3.7+-yellow.svg)](https://www.python.org/)
 [![DOI](https://img.shields.io/badge/DOI-10.1101%2F2022.02.16.480699-red)](https://www.biorxiv.org/content/10.1101/2022.02.16.480699v1)
-[![Build Status](https://travis-ci.com/a-slide/pycoMeth.svg?branch=master)](https://travis-ci.com/a-slide/pycoMeth)
 
 [![PyPI version](https://badge.fury.io/py/pycoMeth.svg)](https://badge.fury.io/py/pycoMeth)
 [![PyPI downloads](https://pepy.tech/badge/pycoMeth)](https://pepy.tech/project/pycoMeth)

diff --git a/versipy_templates/meta.yaml b/versipy_templates/meta.yaml
@@ -28,14 +28,10 @@ test:
   imports:
     - pycoMeth.FileParser
     - pycoMeth.CoordGen
-    - pycoMeth.CpG_Aggregate
-    - pycoMeth.Interval_Aggregate
     - pycoMeth.Meth_Comp
     - pycoMeth.Comp_Report
     - pycoMeth.CGI_Finder
   commands:
-    - pycoMeth CpG_Aggregate --help
-    - pycoMeth Interval_Aggregate --help
     - pycoMeth Meth_Comp --help
     - pycoMeth Comp_Report --help
     - pycoMeth CGI_Finder --help