From c20c6f76b7bd9043bed204880481a4a002b9fb6e Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 10:39:19 -0500 Subject: [PATCH 1/8] read the docs --- .readthedocs.yaml | 13 +++++++++++++ docs/conf.py | 38 +++++++++++++++++++------------------- docs/index.rst | 2 +- docs/install.rst | 20 ++++++++++---------- 4 files changed, 43 insertions(+), 30 deletions(-) create mode 100644 .readthedocs.yaml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..db935c8 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: 2 + +build: + os: ubuntu-24.04 + tools: + python: "3.12" + +sphinx: + configuration: docs/conf.py + +python: + install: + - requirements: requirements.doc.txt diff --git a/docs/conf.py b/docs/conf.py index 086cd1b..c06c937 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -11,15 +11,13 @@ sys.path.insert(0, str(HERE.parent)) import scallops # noqa - -project = "scallops" +project = "SCALLOPS" copyright = "2026, Genentech" -author = "scallops team" +author = "SCALLOPS team" # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration extensions = [ - "myst_parser", # allow md files "nbsphinx", "sphinx.ext.autodoc", "sphinx.ext.autosummary", @@ -42,28 +40,30 @@ templates_path = ["_templates"] exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] -# intersphinx_mapping = dict( -# matplotlib=("https://matplotlib.org/stable/", None), -# numpy=("https://numpy.org/doc/stable/", None), -# pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), -# pytest=("https://docs.pytest.org/en/latest/", None), -# python=("https://docs.python.org/3", None), -# scipy=("https://docs.scipy.org/doc/scipy/", None), -# seaborn=("https://seaborn.pydata.org/", None), -# skimage=("https://scikit-image.org/docs/stable/api/", None), -# sklearn=("https://scikit-learn.org/dev/", None), -# xarray=("https://docs.xarray.dev/", None), -# ) +intersphinx_mapping = dict( + matplotlib=("https://matplotlib.org/stable/", None), + numpy=("https://numpy.org/doc/stable/", None), + pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), + pytest=("https://docs.pytest.org/en/latest/", None), + python=("https://docs.python.org/3", None), + scipy=("https://docs.scipy.org/doc/scipy/", None), + seaborn=("https://seaborn.pydata.org/", None), + skimage=("https://scikit-image.org/docs/stable/api/", None), + sklearn=("https://scikit-learn.org/dev/", None), + xarray=("https://docs.xarray.dev/", None), +) intersphinx_disabled_reftypes = ["*"] # -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output html_theme = "sphinx_rtd_theme" html_static_path = ["_static"] + + # Add custom CSS files -html_css_files = [ - "css/custom.css", -] +# html_css_files = [ +# "css/custom.css", +# ] def skip_private_members(app, what, name, obj, skip, options): diff --git a/docs/index.rst b/docs/index.rst index 8c11219..ae5e5fc 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -88,5 +88,5 @@ complex biological systems data. example_commands workflows example_notebooks - api faq + api diff --git a/docs/install.rst b/docs/install.rst index 27ef2e7..6220c25 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -2,7 +2,16 @@ Installation ************ -. + +PyPI Release +========================= +Install SCALLOPS using your favorite environment manager:: + + pip install scallops + + +Developer Instructions +======================== 1. Clone the repository:: @@ -30,12 +39,3 @@ Installation .. _Mamba: https://mamba.readthedocs.io/en/latest/installation.html .. _Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html - - - -Coming Soon: PyPI Release -========================= -We are planning to upload SCALLOPS to **PyPI** soon . Once available, you will -be able to install the package using:: - - pip install scallops From 18774c25198c95cae24d459810b60ab776482cb9 Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 11:15:46 -0500 Subject: [PATCH 2/8] updated --- requirements.doc.txt | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/requirements.doc.txt b/requirements.doc.txt index 06add2a..6c56034 100644 --- a/requirements.doc.txt +++ b/requirements.doc.txt @@ -1,7 +1,6 @@ -ipython==9.6.0 -myst_parser==4.0.1 -nbsphinx==0.9.7 +ipython==9.9.0 +nbsphinx==0.9.8 sphinx-copybutton==0.5.2 -sphinx==8.1.3 +sphinx==9.1.0 sphinx_argparse==0.5.2 -sphinx_rtd_theme==3.0.2 +sphinx_rtd_theme==3.1.0 From 4cf5d439e3dfd9648b071f8ee8e5088a1362e122 Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 11:20:37 -0500 Subject: [PATCH 3/8] install package --- .readthedocs.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index db935c8..8fb09a7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,10 +4,14 @@ build: os: ubuntu-24.04 tools: python: "3.12" - + jobs: + post_checkout: + - git fetch --unshallow || true sphinx: configuration: docs/conf.py python: install: - requirements: requirements.doc.txt + - method: pip + path: . From 4f40912ceecec6f65c04d244900183544b5a664f Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 11:28:24 -0500 Subject: [PATCH 4/8] install package --- docs/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index c06c937..18578f5 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -11,7 +11,7 @@ sys.path.insert(0, str(HERE.parent)) import scallops # noqa -project = "SCALLOPS" +project = "scallops" copyright = "2026, Genentech" author = "SCALLOPS team" @@ -33,7 +33,7 @@ suppress_warnings = [ "nbsphinx", ] -autodoc_default_options = {"members": True, "member-order": "bysource"} +autodoc_default_options = {"members": True} autodoc_typehints = "description" autosummary_generate = True todo_include_todos = False From b30d1b614cf023eba8cd6db04fb7cae610cce653 Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 11:35:39 -0500 Subject: [PATCH 5/8] install package --- .readthedocs.yaml | 7 ++++--- pyproject.toml | 5 ++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 8fb09a7..16f8b8f 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -12,6 +12,7 @@ sphinx: python: install: - - requirements: requirements.doc.txt - - method: pip - path: . + - method: pip + path: . + extra_requirements: + - doc diff --git a/pyproject.toml b/pyproject.toml index 9b84d19..763ab7c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -85,7 +85,7 @@ dask-ml = [ cellpose = [ "cellpose<4" ] -ufish= [ +ufish = [ "ufish" ] test = [ @@ -99,12 +99,11 @@ dev = [ ] doc = [ "ipython", - "myst_parser", "nbsphinx", "sphinx-copybutton", "sphinx", "sphinx_argparse", - "sphinx_rtd_theme" + "sphinx_rtd_theme", ] all = [ "napari", From 50ade251f7d4520c9ddfc72884501ad8d1948586 Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 12:04:44 -0500 Subject: [PATCH 6/8] install package --- .readthedocs.yaml | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 16f8b8f..6f9dd30 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,18 +1,17 @@ version: 2 +sphinx: + configuration: docs/conf.py +python: + install: + - requirements: requirements.docs.txt + build: os: ubuntu-24.04 tools: python: "3.12" jobs: + install: + - pip install -e ".[doc]" post_checkout: - git fetch --unshallow || true -sphinx: - configuration: docs/conf.py - -python: - install: - - method: pip - path: . - extra_requirements: - - doc From 59b044b0161d998a695a930de6f0d634b33c1aa7 Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 12:10:25 -0500 Subject: [PATCH 7/8] install package --- .readthedocs.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 6f9dd30..3858f57 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -15,3 +15,4 @@ build: - pip install -e ".[doc]" post_checkout: - git fetch --unshallow || true + - git lfs pull From e28ed9fc0277f437d8ead15673db467783ac7476 Mon Sep 17 00:00:00 2001 From: Joshua Gould Date: Thu, 22 Jan 2026 12:12:31 -0500 Subject: [PATCH 8/8] lfs --- .readthedocs.yaml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 3858f57..d8e859a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -15,4 +15,17 @@ build: - pip install -e ".[doc]" post_checkout: - git fetch --unshallow || true - - git lfs pull + # Download and uncompress the binary + # https://git-lfs.github.com/ + - wget https://github.com/git-lfs/git-lfs/releases/download/v3.1.4/git-lfs-linux-amd64-v3.1.4.tar.gz + - tar xvfz git-lfs-linux-amd64-v3.1.4.tar.gz git-lfs + # Modify LFS config paths to point where git-lfs binary was downloaded + - git config filter.lfs.process "`pwd`/git-lfs filter-process" + - git config filter.lfs.smudge "`pwd`/git-lfs smudge -- %f" + - git config filter.lfs.clean "`pwd`/git-lfs clean -- %f" + # Make LFS available in current repository + - ./git-lfs install + # Download content from remote + - ./git-lfs fetch + # Make local files to have the real content on them + - ./git-lfs checkout