diff --git a/dist/scaccordion-0.2.1.6-py2.py3-none-any.whl b/dist/scaccordion-0.2.1.6-py2.py3-none-any.whl new file mode 100644 index 0000000..be4462a Binary files /dev/null and b/dist/scaccordion-0.2.1.6-py2.py3-none-any.whl differ diff --git a/dist/scaccordion-0.2.1.6-py3-none-any.whl b/dist/scaccordion-0.2.1.6-py3-none-any.whl new file mode 100644 index 0000000..848c492 Binary files /dev/null and b/dist/scaccordion-0.2.1.6-py3-none-any.whl differ diff --git a/dist/scaccordion-0.2.1.6.tar.gz b/dist/scaccordion-0.2.1.6.tar.gz new file mode 100644 index 0000000..c4f5458 Binary files /dev/null and b/dist/scaccordion-0.2.1.6.tar.gz differ diff --git a/docs/requirements.txt b/docs/requirements.txt index a948e96..04d6d91 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,14 @@ myst-parser nbsphinx -sphinx_rtd_theme -sphinx \ No newline at end of file +sphinxcontrib-bibtex +sphinx +plotly +sphinx-rtd-size +gprofiler-official +sankeyflow +nbformat +anndata +scanpy +sphinx-design +sphinx-book-theme +pygments \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py index e6b24ad..14fe5fc 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -15,6 +15,9 @@ version = '0.1.8.8' extensions = [ + 'sphinx_design', + "sphinx.ext.napoleon", + 'sphinxcontrib.bibtex', 'sphinx.ext.duration', 'sphinx.ext.doctest', 'sphinx.ext.autodoc', @@ -29,10 +32,54 @@ 'sphinx': ('https://www.sphinx-doc.org/en/master/', None), } intersphinx_disabled_domains = ['std'] - templates_path = ['_templates'] -html_theme = 'sphinx_rtd_theme' +# -- HTML output options +html_theme = 'sphinx_book_theme' +html_logo = "_static/logo.png" +# Specific parameters passed directly to the 'sphinx_book_theme'. +html_theme_options = { + "repository_url": "https://github.com/CostaLab/pyCrossTalkeR", + "use_repository_button": True, + "use_download_button": True, + "use_fullscreen_button": True, + "collapse_navbar": True, + "show_toc_level": 4, + "show_navbar_depth": 2, + "logo": { + "text": "pyCrossTalkeR", + } +} + + +sphinx_rtd_size_width = "85%" + + +# -- It hides the input/output prompt numbers (In [1]: / Out [1]:). +nbsphinx_prolog = """ +.. raw:: html + + +""" # -- Options for EPUB output -epub_show_urls = 'footnote' \ No newline at end of file +epub_show_urls = 'footnote' + +# -- Static files configuration +html_js_files = [ + "require.min.js", + "custom.js", +] + +html_static_path = ["_static"] +html_css_files = [ + "custom.css", +] \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index d36a72b..244c55a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,34 +1,31 @@ [tool.poetry] name = "scaccordion" -version = "0.2.1.5" +version = "0.2.1.6" description = "" authors = ["James Nagai "] readme = "README.md" + include = [ { path = "data/"}, ] - [tool.poetry.dependencies] -python = "^3.11" -setuptools = "82.0.1" -Cython = "^3.2.0" -scikit-learn = "^1.5.2" -matplotlib = "^3.9.1" +python = ">=3.11.14" +scikit-learn = ">1.5.2" +matplotlib = ">3.9.1" seaborn = "^0.13.2" -pot = "^0.9.4" -rpy2 = "^3.5.10" -pydiffmap = "^0.2.0.1" -networkx = "^3.3" -tqdm = "^4.66.5" -tables = "^3.9.1" -skimpy = "^0.0.14" -phate = "^1.0.11" -conorm = "^1.2.0" -scipy = "^1.6.0" -numpy="^2.0.0" -genieclust="^1.3.0" -kmedoids = "^0.5.3.1" +pot = ">0.9.4" +rpy2 = ">3.5.10" +pydiffmap = ">=0.2.0.1" +networkx = ">3.3" +tqdm = ">4.66.5" +tables = ">3.9.1" +skimpy = ">0.0.14" +phate = ">=2.0.0" +scipy = ">1.6.0" +numpy=">1.24" +genieclust=">1.1.5" +kmedoids = ">0.5.3.1" [build-system] requires = ["poetry-core"] diff --git a/scaccordion/__pycache__/__init__.cpython-310.pyc b/scaccordion/__pycache__/__init__.cpython-310.pyc index 6cc3bb9..0ced47f 100644 Binary files a/scaccordion/__pycache__/__init__.cpython-310.pyc and b/scaccordion/__pycache__/__init__.cpython-310.pyc differ diff --git a/scaccordion/__pycache__/__init__.cpython-312.pyc b/scaccordion/__pycache__/__init__.cpython-312.pyc index 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this is a string, then edge weights will be accessed via the edge attribute with this key (that is, the weight of the edge joining `u` to `v` will be ``G.edges[u, v][weight]``). 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