v1.0.0a0

README.md

@@ -123,7 +123,7 @@ Below we will show the basic BismarkPlot workflow.
 ### Single sample
 
 ```python
-import src.bismarkplot.Genome
+import src.bsxplorer.Genome
 import bismarkplot
 
 # Firstly, we need to read the regions annotation (e.g. reference genome .gff)
@@ -282,7 +282,7 @@ Output for _Brachypodium distachyon_:
 
 ```python
 # For analyzing samples with different reference genomes, we need to initialize several genomes instances
-import src.bismarkplot.Genome
+import src.bsxplorer.Genome
 
 genome_filenames = ["arabidopsis.gff", "brachypodium.gff", "cucumis.gff", "mus.gff"]
 reports_filenames = ["arabidopsis.txt", "brachypodium.txt", "cucumis.txt", "mus.txt"]
@@ -319,7 +319,7 @@ Output:
 Other genomic regions from .gff can be analyzed too with ```.exon``` or ```.near_tss/.near_tes``` option for ```bismarkplot.Genome```
 
 ```python
-import src.bismarkplot.Genome
+import src.bsxplorer.Genome
 
 exons = [
     src.bismarkplot.genome.Genome.from_gff(file).exon(min_length=100) for file in genome_filenames
@@ -363,7 +363,7 @@ TSS output:
 BismarkPlot allows user to visualize chromosome methylation levels across full genome
 
 ```python
-import src.bismarkplot.ChrLevels
+import src.bsxplorer.ChrLevels
 import bismarkplot
 
 chr = src.bismarkplot.levels.ChrLevels.from_bismark(

docs/conf.py

@@ -1,10 +1,10 @@
 import os
 import sys
 
-project = 'BismarkPlot'
+project = 'BSXplorer'
 copyright = '2023, shitohana'
 author = 'shitohana'
-release = '1.0.0'
+release = '1.0.0a0'
 sys.path.insert(0, os.path.abspath('../src'))
 sys.path.append(os.path.abspath('.'))
 
@@ -28,7 +28,7 @@
 autosummary_generate = True
 autodoc_member_order = 'bysource'
 add_module_names = False
-html_short_title = 'BismarkPlot Documentation'
+html_short_title = 'BSXplorer Documentation'
 
 
 html_theme = 'sphinx_rtd_theme'

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bsxplorer"
-version = "1.0.0"
+version = "1.0.0a0"
 authors = [
   { name="shitohana", email="[email protected]" },
 ]
@@ -40,17 +40,17 @@ classifiers = [
 # dynamic = ["version", "description"]
 
 [project.urls]
-Homepage = "https://github.com/shitohana/BismarkPlot"
-Documentation = "https://shitohana.github.io/BismarkPlot/"
-"Bug Tracker" = "https://github.com/shitohana/BismarkPlot/issues"
+Homepage = "https://github.com/shitohana/BSXplorer"
+Documentation = "https://shitohana.github.io/BSXplorer/"
+"Bug Tracker" = "https://github.com/shitohana/BSXplorer/issues"
 
 [tool.hatch.build]
 exclude = ["/venv", "/dist", "/test", "/docs"]
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/bismarkplot"]
+packages = ["src/bsxplorer"]
 
 [project.scripts]
-bsxplorer-metagene = "bismarkplot.templates.cons_MetageneReport:main"
-bsxplorer-category = "bismarkplot.templates.cons_CategoryReport:main"
-bsxplorer-chr = "bismarkplot.templates.cons_ChrLevelsReport:main"
+bsxplorer-metagene = "bsxplorer.templates.cons_MetageneReport:main"
+bsxplorer-category = "bsxplorer.templates.cons_CategoryReport:main"
+bsxplorer-chr = "bsxplorer.templates.cons_ChrLevelsReport:main"

src/bismarkplot/ArrowReaders.py → src/bsxplorer/ArrowReaders.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from pathlib import Path
-from abc import ABC, abstractmethod
 
 import pyarrow as pa
 import pyarrow.csv as pcsv

src/bismarkplot/Base.py → src/bsxplorer/Base.py

@@ -9,11 +9,11 @@
 import polars as pl
 import pyarrow as pa
 from pyreadr import write_rds
+from matplotlib.axes import Axes
+import plotly.graph_objects as go
 
 from .ArrowReaders import CsvReader, ParquetReader, BismarkOptions
 from .utils import remove_extension, prepare_labels, MetageneSchema, ReportBar
-from matplotlib.axes import Axes
-import plotly.graph_objects as go
 
 
 class MetageneBase:

src/bismarkplot/Binom.py → src/bsxplorer/Binom.py

@@ -161,7 +161,7 @@ def region_pvalue(
         --------
         If there no preprocessed file:
 
-        >>> import bismarkplot as bp
+        >>> import bsxplorer as bp
         >>> report_path = "/path/to/report.txt"
         >>> genome_path = "/path/to/genome.gff"
         >>> c_binom = bp.BinomialData.preprocess(report_path, report_type="bismark")

src/bismarkplot/ChrLevels.py → src/bsxplorer/ChrLevels.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import os
-from multiprocessing import cpu_count
 
 import numpy as np
 import polars as pl
@@ -16,7 +15,7 @@
 from abc import ABC, abstractmethod
 import warnings
 
-from .utils import approx_batch_num, interval, decompress, ReportBar
+from .utils import interval, decompress, ReportBar
 from .ArrowReaders import CsvReader, BismarkOptions, ParquetReader
 
 

src/bismarkplot/Clusters.py → src/bsxplorer/Clusters.py

@@ -12,9 +12,6 @@
 import polars as pl
 from dynamicTreeCut import cutreeHybrid
 from dynamicTreeCut.dynamicTreeCut import get_heights
-from matplotlib import pyplot as plt, colormaps
-from matplotlib.figure import Figure
-from pyreadr import write_rds
 from fastcluster import linkage
 from scipy.cluster.hierarchy import leaves_list, optimal_leaf_ordering
 from scipy.spatial.distance import pdist
@@ -24,7 +21,6 @@
 
 from .Base import MetageneBase, MetageneFilesBase
 from abc import ABC, abstractmethod
-from .utils import prepare_labels, hm_flank_lines
 
 
 class _ClusterBase(ABC):

src/bismarkplot/GenomeClass.py → src/bsxplorer/GenomeClass.py

@@ -2,6 +2,7 @@
 
 import polars as pl
 from pathlib import Path
+
 from .utils import MetageneSchema
 
 

src/bismarkplot/MetageneClasses.py → src/bsxplorer/MetageneClasses.py

@@ -13,14 +13,13 @@
 import seaborn as sns
 
 from .Plots import LinePlot, LinePlotFiles, HeatMap, HeatMapFiles
-from .ArrowReaders import CsvReader, BismarkOptions, ParquetReader
 from .SeqMapper import Mapper, Sequence
 from .Base import (
     MetageneBase, MetageneFilesBase,
     BismarkReportReader, ParquetReportReader, BinomReportReader
 )
 from .Clusters import ClusterSingle, ClusterMany
-from .utils import MetageneSchema, ReportBar
+from .utils import MetageneSchema
 from .GenomeClass import Genome
 
 pl.enable_string_cache(True)

src/bismarkplot/Plots.py → src/bsxplorer/Plots.py

@@ -2,7 +2,6 @@
 
 import itertools
 import re
-from dataclasses import dataclass
 
 import numpy as np
 import polars as pl
@@ -13,7 +12,6 @@
 from plotly import graph_objects as go, express as px
 from pyreadr import write_rds
 from scipy.signal import savgol_filter
-# todo add to dependencies sklearn
 from sklearn.decomposition import PCA as PCA_sklearn
 
 from .Base import PlotBase, MetageneFilesBase

src/bismarkplot/SeqMapper.py → src/bsxplorer/SeqMapper.py

@@ -3,7 +3,6 @@
 import gc
 import gzip
 import io
-import multiprocessing
 import os
 import shutil
 import tempfile

src/bismarkplot/__init__.py → src/bsxplorer/__init__.py

@@ -1,7 +1,7 @@
 from .MetageneClasses import Metagene, MetageneFiles
-from .Plots import LinePlot, LinePlotFiles, HeatMap, HeatMapFiles
+from .Plots import LinePlot, LinePlotFiles, HeatMap, HeatMapFiles, PCA
 from .Binom import BinomialData, RegionStat
 from .GenomeClass import Genome
 from .ChrLevels import ChrLevels
 
-__version__ = '1.0.0'
+__version__ = '1.0.0a0'