From b5004052a6142334916a33ecfdb39853f038fe6a Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 21 May 2024 13:45:27 +0000 Subject: [PATCH 1/3] Update template to v0.4.0 --- .cruft.json | 54 +++++++++++++++++++++++----------------------- .gitignore.rej | 9 ++++++++ docs/conf.py | 2 +- docs/conf.py.rej | 16 ++++++++++++++ pyproject.toml.rej | 28 ++++++++++++++++++++++++ 5 files changed, 81 insertions(+), 28 deletions(-) create mode 100644 .gitignore.rej create mode 100644 docs/conf.py.rej create mode 100644 pyproject.toml.rej diff --git a/.cruft.json b/.cruft.json index b3f28eeab..989cf33ca 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,29 +1,29 @@ { - "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "586b1652162ff7994b0070a034023d64289ae416", - "checkout": "v0.3.1", - "context": { - "cookiecutter": { - "project_name": "squidpy", - "package_name": "squidpy", - "project_description": "Spatial Single Cell Analysis in Python", - "author_full_name": "Giovanni Palla", - "author_email": "giovanni.palla@helmholtz-muenchen.de", - "github_user": "giovp", - "project_repo": "https://github.com/scverse/squidpy", - "license": "BSD 3-Clause License", - "_copy_without_render": [ - ".github/workflows/build.yaml", - ".github/workflows/test.yaml", - "docs/_templates/autosummary/**.rst" - ], - "_render_devdocs": false, - "_jinja2_env_vars": { - "lstrip_blocks": true, - "trim_blocks": true - }, - "_template": "https://github.com/scverse/cookiecutter-scverse" - } - }, - "directory": null + "template": "https://github.com/scverse/cookiecutter-scverse", + "commit": "87a407a65408d75a949c0b54b19fd287475a56f8", + "checkout": "v0.4.0", + "context": { + "cookiecutter": { + "project_name": "squidpy", + "package_name": "squidpy", + "project_description": "Spatial Single Cell Analysis in Python", + "author_full_name": "Giovanni Palla", + "author_email": "giovanni.palla@helmholtz-muenchen.de", + "github_user": "giovp", + "project_repo": "https://github.com/scverse/squidpy", + "license": "BSD 3-Clause License", + "_copy_without_render": [ + ".github/workflows/build.yaml", + ".github/workflows/test.yaml", + "docs/_templates/autosummary/**.rst" + ], + "_render_devdocs": false, + "_jinja2_env_vars": { + "lstrip_blocks": true, + "trim_blocks": true + }, + "_template": "https://github.com/scverse/cookiecutter-scverse" + } + }, + "directory": null } diff --git a/.gitignore.rej b/.gitignore.rej new file mode 100644 index 000000000..9d0a7e93c --- /dev/null +++ b/.gitignore.rej @@ -0,0 +1,9 @@ +diff a/.gitignore b/.gitignore (rejected hunks) +@@ -18,6 +18,7 @@ __pycache__/ + /.pytest_cache/ + /.cache/ + /data/ ++/node_modules/ + + # docs + /docs/generated/ diff --git a/docs/conf.py b/docs/conf.py index 661768eec..8275749e7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,5 @@ # Configuration file for the Sphinx documentation builder. -# + # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html diff --git a/docs/conf.py.rej b/docs/conf.py.rej new file mode 100644 index 000000000..d8d315e84 --- /dev/null +++ b/docs/conf.py.rej @@ -0,0 +1,16 @@ +diff a/docs/conf.py b/docs/conf.py (rejected hunks) +@@ -36,10 +36,10 @@ needs_sphinx = "4.0" + + html_context = { + "display_github": True, # Integrate GitHub +- "github_user": "giovp", # Username +- "github_repo": project_name, # Repo name +- "github_version": "main", # Version +- "conf_py_path": "/docs/", # Path in the checkout to the docs root ++ "github_user": "giovp", ++ "github_repo": "https://github.com/scverse/squidpy", ++ "github_version": "main", ++ "conf_py_path": "/docs/", + } + + # -- General configuration --------------------------------------------------- diff --git a/pyproject.toml.rej b/pyproject.toml.rej new file mode 100644 index 000000000..ca510772c --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,28 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -7,7 +7,7 @@ name = "squidpy" + version = "0.0.1" + description = "Spatial Single Cell Analysis in Python" + readme = "README.md" +-requires-python = ">=3.9" ++requires-python = ">=3.10" + license = {file = "LICENSE"} + authors = [ + {name = "Giovanni Palla"}, +@@ -33,7 +33,7 @@ doc = [ + "docutils>=0.8,!=0.18.*,!=0.19.*", + "sphinx>=4", + "sphinx-book-theme>=1.0.0", +- "myst-nb", ++ "myst-nb>=1.1.0", + "sphinxcontrib-bibtex>=1.0.0", + "sphinx-autodoc-typehints", + "sphinxext-opengraph", +@@ -98,7 +98,7 @@ ignore = [ + "D107", + # Errors from function calls in argument defaults. These are fine when the result is immutable. + "B008", +- # __magic__ methods are are often self-explanatory, allow missing docstrings ++ # __magic__ methods are often self-explanatory, allow missing docstrings + "D105", + # first line should end with a period [Bug: doesn't work with single-line docstrings] + "D400", From 59063f055d2d870bf3269db2362e3b018a7c25b3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 21 May 2024 13:46:53 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .cruft.json | 54 ++++++++++++++++++++++++------------------------ .gitignore.rej | 2 +- docs/conf.py.rej | 4 ++-- 3 files changed, 30 insertions(+), 30 deletions(-) diff --git a/.cruft.json b/.cruft.json index 989cf33ca..c47860bbc 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,29 +1,29 @@ { - "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "87a407a65408d75a949c0b54b19fd287475a56f8", - "checkout": "v0.4.0", - "context": { - "cookiecutter": { - "project_name": "squidpy", - "package_name": "squidpy", - "project_description": "Spatial Single Cell Analysis in Python", - "author_full_name": "Giovanni Palla", - "author_email": "giovanni.palla@helmholtz-muenchen.de", - "github_user": "giovp", - "project_repo": "https://github.com/scverse/squidpy", - "license": "BSD 3-Clause License", - "_copy_without_render": [ - ".github/workflows/build.yaml", - ".github/workflows/test.yaml", - "docs/_templates/autosummary/**.rst" - ], - "_render_devdocs": false, - "_jinja2_env_vars": { - "lstrip_blocks": true, - "trim_blocks": true - }, - "_template": "https://github.com/scverse/cookiecutter-scverse" - } - }, - "directory": null + "template": "https://github.com/scverse/cookiecutter-scverse", + "commit": "87a407a65408d75a949c0b54b19fd287475a56f8", + "checkout": "v0.4.0", + "context": { + "cookiecutter": { + "project_name": "squidpy", + "package_name": "squidpy", + "project_description": "Spatial Single Cell Analysis in Python", + "author_full_name": "Giovanni Palla", + "author_email": "giovanni.palla@helmholtz-muenchen.de", + "github_user": "giovp", + "project_repo": "https://github.com/scverse/squidpy", + "license": "BSD 3-Clause License", + "_copy_without_render": [ + ".github/workflows/build.yaml", + ".github/workflows/test.yaml", + "docs/_templates/autosummary/**.rst" + ], + "_render_devdocs": false, + "_jinja2_env_vars": { + "lstrip_blocks": true, + "trim_blocks": true + }, + "_template": "https://github.com/scverse/cookiecutter-scverse" + } + }, + "directory": null } diff --git a/.gitignore.rej b/.gitignore.rej index 9d0a7e93c..de758b8f5 100644 --- a/.gitignore.rej +++ b/.gitignore.rej @@ -4,6 +4,6 @@ diff a/.gitignore b/.gitignore (rejected hunks) /.cache/ /data/ +/node_modules/ - + # docs /docs/generated/ diff --git a/docs/conf.py.rej b/docs/conf.py.rej index d8d315e84..5b8038922 100644 --- a/docs/conf.py.rej +++ b/docs/conf.py.rej @@ -1,6 +1,6 @@ diff a/docs/conf.py b/docs/conf.py (rejected hunks) @@ -36,10 +36,10 @@ needs_sphinx = "4.0" - + html_context = { "display_github": True, # Integrate GitHub - "github_user": "giovp", # Username @@ -12,5 +12,5 @@ diff a/docs/conf.py b/docs/conf.py (rejected hunks) + "github_version": "main", + "conf_py_path": "/docs/", } - + # -- General configuration --------------------------------------------------- From 07384f4ff6e0e0fe9a3b188c68f5080535346e67 Mon Sep 17 00:00:00 2001 From: giovp Date: Mon, 27 May 2024 13:35:42 +0200 Subject: [PATCH 3/3] update --- .gitignore.rej | 9 --------- docs/conf.py.rej | 16 ---------------- pyproject.toml.rej | 28 ---------------------------- 3 files changed, 53 deletions(-) delete mode 100644 .gitignore.rej delete mode 100644 docs/conf.py.rej delete mode 100644 pyproject.toml.rej diff --git a/.gitignore.rej b/.gitignore.rej deleted file mode 100644 index de758b8f5..000000000 --- a/.gitignore.rej +++ /dev/null @@ -1,9 +0,0 @@ -diff a/.gitignore b/.gitignore (rejected hunks) -@@ -18,6 +18,7 @@ __pycache__/ - /.pytest_cache/ - /.cache/ - /data/ -+/node_modules/ - - # docs - /docs/generated/ diff --git a/docs/conf.py.rej b/docs/conf.py.rej deleted file mode 100644 index 5b8038922..000000000 --- a/docs/conf.py.rej +++ /dev/null @@ -1,16 +0,0 @@ -diff a/docs/conf.py b/docs/conf.py (rejected hunks) -@@ -36,10 +36,10 @@ needs_sphinx = "4.0" - - html_context = { - "display_github": True, # Integrate GitHub -- "github_user": "giovp", # Username -- "github_repo": project_name, # Repo name -- "github_version": "main", # Version -- "conf_py_path": "/docs/", # Path in the checkout to the docs root -+ "github_user": "giovp", -+ "github_repo": "https://github.com/scverse/squidpy", -+ "github_version": "main", -+ "conf_py_path": "/docs/", - } - - # -- General configuration --------------------------------------------------- diff --git a/pyproject.toml.rej b/pyproject.toml.rej deleted file mode 100644 index ca510772c..000000000 --- a/pyproject.toml.rej +++ /dev/null @@ -1,28 +0,0 @@ -diff a/pyproject.toml b/pyproject.toml (rejected hunks) -@@ -7,7 +7,7 @@ name = "squidpy" - version = "0.0.1" - description = "Spatial Single Cell Analysis in Python" - readme = "README.md" --requires-python = ">=3.9" -+requires-python = ">=3.10" - license = {file = "LICENSE"} - authors = [ - {name = "Giovanni Palla"}, -@@ -33,7 +33,7 @@ doc = [ - "docutils>=0.8,!=0.18.*,!=0.19.*", - "sphinx>=4", - "sphinx-book-theme>=1.0.0", -- "myst-nb", -+ "myst-nb>=1.1.0", - "sphinxcontrib-bibtex>=1.0.0", - "sphinx-autodoc-typehints", - "sphinxext-opengraph", -@@ -98,7 +98,7 @@ ignore = [ - "D107", - # Errors from function calls in argument defaults. These are fine when the result is immutable. - "B008", -- # __magic__ methods are are often self-explanatory, allow missing docstrings -+ # __magic__ methods are often self-explanatory, allow missing docstrings - "D105", - # first line should end with a period [Bug: doesn't work with single-line docstrings] - "D400",