From 4a001d1e5f15e3750108f1a80a080dbcc2bf40ef Mon Sep 17 00:00:00 2001 From: snajder Date: Mon, 16 May 2022 13:17:50 +0200 Subject: [PATCH] Some cleaning up --- README.md | 1 - deploy_anaconda.sh | 27 --------------------------- meta.yaml | 4 ---- pycoMeth/Meth_Comp.py | 5 ++--- pycoMeth/Meth_Seg.py | 11 ++--------- pycoMeth/loader.py | 2 +- versipy_templates/README.md | 1 - versipy_templates/meta.yaml | 4 ---- 8 files changed, 5 insertions(+), 50 deletions(-) delete mode 100644 deploy_anaconda.sh diff --git a/README.md b/README.md index fb4947f..167968d 100644 --- 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 deleted file mode 100644 index 98a69d6..0000000 --- a/deploy_anaconda.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!bash -# -*- coding: utf-8 -*- - -set -e - -echo "Set up conda package manager" -wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh --quiet -bash miniconda.sh -b -p $HOME/miniconda -export PATH="$HOME/miniconda/bin:$PATH" -hash -r -conda config --set always_yes yes --set changeps1 no --set anaconda_upload no -conda update -q conda - -echo "Install packages needed for package build and upload" -conda install -q python=3.7 conda-build anaconda-client ripgrep conda-verify - -echo "compile package from setup.py" -python setup.py sdist - -echo "Build noarch package..." -conda build meta.yaml --python 3.7 --numpy 1.1 --output-folder conda_build -c bioconda -c conda-forge -c plotly -c snajder-r - -echo "Deploying to Anaconda.org..." -anaconda -v -t $1 upload conda_build/**/*.tar.bz2 - -echo "Successfully deployed to Anaconda.org." -exit 0 diff --git a/meta.yaml b/meta.yaml index 7623f2b..57408ad 100644 --- 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 index 0c2bb9d..c970301 100644 --- 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 index b004d31..6e1a780 100644 --- 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 index edaa5eb..222cc34 100644 --- 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 index 9e3adf6..83f8325 100644 --- 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 index 2a9f279..e2eb753 100644 --- 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