ci: fix doc

.github/workflows/ci.yml

@@ -6,6 +6,9 @@ on:
   pull_request:
     branches: [ devel ]
 
+permissions:
+  contents: write
+
 jobs:
 
   Test:
@@ -31,10 +34,31 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install package and dependencies on ${{ matrix.os }}
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev]
+
       - name: Run tests on ${{ matrix.os }}
         run: |
           python -m pip install --upgrade pip
           pip install -e .[dev]
           # stop the build if there are Python syntax errors or undefined names
           ruff check . --select=E9,F63,F7,F82
           pytest
+
+      - name: Buid Sphinx doc on ${{ matrix.os }}
+        if: runner.os == 'Linux' && ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }} && ${{ matrix.python-version == '3.12'}}
+        run: |
+          sudo apt-get update && sudo apt-get -y install make
+          pip install -e .[dev,docs]
+          make -C docs html
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        if: runner.os == 'Linux' && ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }} && ${{ matrix.python-version == '3.12'}}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html
+          force_orphan: true

.gitignore

@@ -12,6 +12,7 @@ __pycache__
 .coverage.*
 coverage.xml
 htmlcov/
+tiledb/
 
 # setup and build artifacts
 docs/_*
@@ -31,6 +32,7 @@ venv/
 .Trashes
 ehthumbs.db
 Thumbs.db
-
 tmp/
-_scratch/
+_scratch/
+.vscode
+example.py

docs/Makefile

@@ -4,8 +4,9 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = _build
+PAPER         = a4
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
@@ -15,11 +16,11 @@ endif
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(SOURCEDIR)
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
@@ -29,9 +30,7 @@ help:
 	@echo "  pickle     to make pickle files"
 	@echo "  json       to make JSON files"
 	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
 	@echo "  applehelp  to make an Apple Help Book"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
 	@echo "  epub       to make an epub"
 	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
 	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
@@ -82,15 +81,6 @@ htmlhelp:
 	@echo "Build finished; now you can run HTML Help Workshop with the" \
 	      ".hhp project file in $(BUILDDIR)/htmlhelp."
 
-qthelp:
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/cooler.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/cooler.qhc"
-
 applehelp:
 	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
 	@echo
@@ -99,15 +89,6 @@ applehelp:
 	      "~/Library/Documentation/Help or install it in your application" \
 	      "bundle."
 
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/cooler"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/cooler"
-	@echo "# devhelp"
-
 epub:
 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
 	@echo

docs/source/conf.py

@@ -31,15 +31,15 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.viewcode",
     "sphinx.ext.autosummary",
-    "sphinx.ext.napoleon", 
+    "sphinx.ext.napoleon",
     "recommonmark",
 ]
 
 numpydoc_show_class_members = False
 napoleon_use_rtype = False
 autodoc_typehints = "description"
 autodoc_class_signature = "separated"
-templates_path = ['_templates']
+templates_path = ["_templates"]
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 source_suffix = {
     ".rst": "restructuredtext",
@@ -52,8 +52,8 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'alabaster'
-html_static_path = ['_static']
+html_theme = "furo"
+html_static_path = ["_static"]
 htmlhelp_basename = "momicsdoc"
 
 # -- Options for manual page output ---------------------------------------

docs/source/index.rst

@@ -15,7 +15,7 @@ The `momics` package aims to facilitate:
 * Scalable: cloud-native, out-of-core operations on the data;
 * Export: data export.
 
-Follow cooler development on `GitHub <https://github.com/js2264/momics>`_.
+Follow `momics` development on `GitHub <https://github.com/js2264/momics>`_.
 
 Contents:
 

pyproject.toml

@@ -28,9 +28,11 @@ classifiers = [
 ]
 dependencies = [
     "tiledb",
+    "libtiledb-sql-py",
     "pyBigWig",
     "numpy", 
-    "pandas"
+    "pandas", 
+    "pyarrow>=1.0",
 ]
 
 [project.urls]

src/momics/__init__.py

@@ -10,7 +10,7 @@
 """
 
 from ._version import __format_version__, __version__
-from .api import Momics
+from .Momics import Momics
 
 __all__ = [
     "__version__",

src/momics/utils.py

@@ -0,0 +1,27 @@
+import os
+import shutil
+import pyBigWig
+import numpy as np
+
+
+def get_chr_lengths(bw):
+    with pyBigWig.open(bw) as bw:
+        {chrom: length for chrom, length in bw.chroms().items()}
+
+
+def _check_chr_lengths(bw_files):
+    reference_lengths = {}
+    with pyBigWig.open(list(bw_files.values())[0]) as bw:
+        reference_lengths = {chrom: length for chrom, length in bw.chroms().items()}
+
+    # Compare chromosome lengths with other files
+    for file in list(bw_files.values())[1:]:
+        with pyBigWig.open(file) as bw:
+            lengths = {chrom: length for chrom, length in bw.chroms().items()}
+            if lengths != reference_lengths:
+                raise Exception(
+                    "Provided .bw files do not have identical chromomosome lengths."
+                )
+
+    # return np.array(list(reference_lengths.values()), dtype=np.int64)
+    return reference_lengths

tests/test_main.py

@@ -5,14 +5,14 @@
 import pytest
 
 import momics
-from momics import api
 
 testdir = os.path.dirname(os.path.realpath(__file__))
 
+
 @pytest.mark.parametrize(
     "file_path",
     [(os.path.join(testdir, "data", "test.momics"))],
 )
 def test_api(file_path):
-    clr = momics.api.Momics(file_path)
-    print(clr)
+    mom = momics.Momics(file_path)
+    print(mom)