docs branch update (#12)

* v1.3.2.post1 * v1.3.2.post2 * v1.3.2.post3 * console scripts and major upd * cons_ChrLevelsReport.py added improvements to cons_MetageneReport.py added dendrogram and PCA plot moving to new chr reader * PCA mine. move to sklearn * major changes. commit before merge * test commit * test commit (#10) * v1.0.0a0 * v1.0.0a0 * docs test * docs test * v1.0.0a0 * v1.0.0a1 * test * v1.0.0a1 * v1.0.0a2 * v1.0.0a2 project folders change * v1.0.0a3 * v1.0.0a3 * First rc merge (#11) * v1.0.0a3 * another try to fix * another try to fix * bugs with console * 1.0.0a5 * fixed .lit in > 0.20 polars.__version__ * minor improvements added CGmap new console script realisation * import fix * heatmap fix readme added * heatmap fix readme added * Update README.md * fix with html path
shitohana · Feb 15, 2024 · 9d4db9f · 9d4db9f
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diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
@@ -2,7 +2,9 @@ name: Publish to PyPI and TestPyPI
 
 on:
   push:
-    branches: [master]
+    branches:
+      - master
+      - test
 
 jobs:
   build-n-publish:
@@ -20,18 +22,18 @@ jobs:
         pip install
         build
         --user
-    - name: Build a binary wheel and a source tarball
+    - name: Build a binary wheel and a bsxplorer tarball
       run: >-
         python -m
         build
-#    - name: Publish distribution 📦 to Test PyPI
-#      if: startsWith(github.ref, 'refs/tags')
-#      uses: pypa/gh-action-pypi-publish@release/v1
-#      with:
-#        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-#        repository-url: https://test.pypi.org/legacy/
-    - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.ref, 'refs/tags')
+    - name: Publish to Test PyPI
+      if: github.ref == 'refs/heads/test'
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository-url: https://test.pypi.org/legacy/
+    - name: Publish to PyPI
+      if: github.ref == 'refs/heads/master'
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/README.md b/README.md
diff --git a/docs/_binom.rst b/docs/_binom.rst
@@ -3,7 +3,7 @@ Binomial
 
 Methods for calculating P-value for cytosine residues or genomic regions.
 
-.. currentmodule:: bismarkplot
+.. currentmodule:: bsxplorer
 
 .. autosummary::
     :nosignatures:

diff --git a/docs/_genome.rst b/docs/_genome.rst
@@ -3,7 +3,7 @@ Genome
 
 Genome class
 
-.. currentmodule:: bismarkplot
+.. currentmodule:: bsxplorer
 
 .. class:: Genome
 

diff --git a/docs/_metagene.rst b/docs/_metagene.rst
@@ -3,7 +3,7 @@ Metagene
 
 Metagene calculation and plotting related methods.
 
-.. currentmodule:: bismarkplot
+.. currentmodule:: bsxplorer
 
 .. autosummary::
     :nosignatures:

diff --git a/docs/_plots.rst b/docs/_plots.rst
@@ -3,7 +3,7 @@ Plots
 
 Reference for plotting classes.
 
-.. currentmodule:: bismarkplot
+.. currentmodule:: bsxplorer
 
 .. autosummary::
     :nosignatures:

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,14 +1,15 @@
 import os
 import sys
 
-project = 'BismarkPlot'
+project = 'BSXplorer'
 copyright = '2023, shitohana'
 author = 'shitohana'
-release = '1.4.1'
+release = '1.0.0rc4'
 sys.path.insert(0, os.path.abspath('../src'))
+sys.path.insert(0, os.path.abspath('..'))
 sys.path.append(os.path.abspath('.'))
 
-import bismarkplot
+import bsxplorer
 
 extensions = [
     # TODO add myst_parser to dependencies
@@ -28,7 +29,7 @@
 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'

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,4 +1,4 @@
-Welcome to BismarkPlot's documentation!
+Welcome to BSXplorer's documentation!
 =======================================
 This page gives an overview of all public objects, functions and methods.
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,23 +1,22 @@
-contourpy==1.0.7
-cycler==0.11.0
-fonttools==4.39.3
-kiwisolver==1.4.4
-packaging==23.1
-matplotlib>=3.7.1
-numpy>=1.24.2
-pandas>=2.0.0
-polars>=0.17.5
-scipy>=1.10.1
-Pillow==9.5.0
-pyparsing==3.0.9
-python-dateutil==2.8.2
-pytz==2023.3
-six==1.16.0
-typing-extensions==4.5.0
-tzdata==2023.3
+biopython>=1.81
+dynamicTreeCut>=0.1.1
+fastcluster>=1.2.6
+Jinja2>=3.1.2
+matplotlib>=3.8.0
+numba>=0.58.1
+numpy>=1.26.3
+pandas>=2.2.0
+plotly>=5.18.0
+polars>=0.20.7
+progress>=1.6
+pyarrow>=13.0.0
+pyreadr>=0.4.9
+scikit-learn>=1.4.0
+scipy>=1.12.0
+seaborn>=0.13.2
 sphinx_autodoc_typehints==1.23.0
 sphinx_book_theme==1.0.1
 myst-parser==2.0.0
 sphinx-rtd-theme==2.0.0
-progress==1.6
+myst-parser==2.0.0
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -3,26 +3,30 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [project]
-name = "bismarkplot"
-version = "1.4.1"
+name = "bsxplorer"
+version = "1.0.0rc4"
 authors = [
   { name="shitohana", email="kyudytskiy@gmail.com" },
 ]
 keywords = ['bismark', 'methylation', 'plot', 'bs-seq']
 license = {file = "LICENSE.txt"}
 dependencies = [
-    "matplotlib>=3.7.1",
-    "numpy>=1.24.2",
-    "pandas>=2.0.0",
-    "polars>=0.19.9",
-    "scipy>=1.10.1",
-    "pyarrow>=13.0.0",
-    "pyreadr>=0.4.9",
+    "biopython>=1.81",
     "dynamicTreeCut>=0.1.1",
+    "fastcluster>=1.2.6",
+    "Jinja2>=3.1.2",
+    "matplotlib>=3.8.0",
+    "numba>=0.58.1",
+    "numpy>=1.26.3",
+    "pandas>=2.2.0",
     "plotly>=5.18.0",
-    "numba==0.58.1",
-    "biopython==1.81",
-    "progress==1.6"
+    "polars>=0.20.7",
+    "progress>=1.6",
+    "pyarrow>=13.0.0",
+    "pyreadr>=0.4.9",
+    "scikit-learn>=1.4.0",
+    "scipy>=1.12.0",
+    "seaborn>=0.13.2"
 
 ]
 description = "Analytical framework for BS-seq data comparison and visualization"
@@ -36,13 +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/bsxplorer"]
+
 [project.scripts]
-bismarkplot-metagene = "bismarkplot.console_metagene:main"
-bismarkplot-chrs = "bismarkplot.console_chrs:main"
+bsxplorer-metagene = "bsxplorer.cons_master:metagene"
+bsxplorer-category = "bsxplorer.cons_master:category"
+bsxplorer-chr = "bsxplorer.cons_master:chr_levels"
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,16 @@
+biopython>=1.81
+dynamicTreeCut>=0.1.1
+fastcluster>=1.2.6
+Jinja2>=3.1.2
+matplotlib>=3.8.0
+numba>=0.58.1
+numpy>=1.26.3
+pandas>=2.2.0
+plotly>=5.18.0
+polars>=0.20.7
+progress>=1.6
+pyarrow>=13.0.0
+pyreadr>=0.4.9
+scikit-learn>=1.4.0
+scipy>=1.12.0
+seaborn>=0.13.2
diff --git a/src/bismarkplot/ArrowReaders.py b/src/bismarkplot/ArrowReaders.py