From 6114fcdc8cece5eda5b80075b4e17d793fd3453b Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 21 May 2024 13:44:30 +0000 Subject: [PATCH 1/6] Update template to v0.4.0 --- .cruft.json | 4 ++-- .github/workflows/test.yaml | 6 +++--- .gitignore.rej | 9 +++++++++ README.md | 2 +- docs/conf.py | 2 +- docs/conf.py.rej | 16 ++++++++++++++++ docs/contributing.md | 2 +- pyproject.toml | 2 +- pyproject.toml.rej | 19 +++++++++++++++++++ 9 files changed, 53 insertions(+), 9 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 559185338..ff8201b2b 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,7 +1,7 @@ { "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "586b1652162ff7994b0070a034023d64289ae416", - "checkout": "v0.3.1", + "commit": "87a407a65408d75a949c0b54b19fd287475a56f8", + "checkout": "v0.4.0", "context": { "cookiecutter": { "project_name": "scirpy", diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 0230ee0ac..73a7df140 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -24,11 +24,11 @@ jobs: matrix: include: - os: ubuntu-latest - python: "3.9" + python: "3.10" - os: ubuntu-latest - python: "3.11" + python: "3.12" - os: ubuntu-latest - python: "3.11" + python: "3.12" pip-flags: "--pre" name: PRE-RELEASE DEPENDENCIES 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/README.md b/README.md index 88de01ae9..542e0eeb0 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ Please refer to the [documentation][link-docs]. In particular, the ## Installation -You need to have Python 3.9 or newer installed on your system. If you don't have +You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge). There are several alternative options to install scirpy: diff --git a/docs/conf.py b/docs/conf.py index 196215c57..6298aa21f 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..e03f5bc8f --- /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": "grst", # 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": "grst", ++ "github_repo": "https://github.com/scverse/scirpy", ++ "github_version": "main", ++ "conf_py_path": "/docs/", + } + + # -- General configuration --------------------------------------------------- diff --git a/docs/contributing.md b/docs/contributing.md index a4db9310c..5da79870d 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -51,7 +51,7 @@ and [prettier][prettier-editors]. ## Writing tests ```{note} -Remember to first install the package with `pip install '-e[dev,test]'` +Remember to first install the package with `pip install -e '.[dev,test]'` ``` This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added diff --git a/pyproject.toml b/pyproject.toml index dc671ee7f..b3b0b8be4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -148,7 +148,7 @@ 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", diff --git a/pyproject.toml.rej b/pyproject.toml.rej new file mode 100644 index 000000000..41fbe04af --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,19 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -7,7 +7,7 @@ name = "scirpy" + version = "0.0.1" + description = "A very interesting piece of code" + readme = "README.md" +-requires-python = ">=3.9" ++requires-python = ">=3.10" + license = {file = "LICENSE"} + authors = [ + {name = "Gregor Sturm"}, +@@ -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", From eb2dfc045bebef7b00fff23cf79d92207c5007bd 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 13:45:44 +0000 Subject: [PATCH 2/6] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .gitignore.rej | 2 +- docs/conf.py.rej | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) 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 e03f5bc8f..ff9c99644 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": "grst", # 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 15e670e5f9b8b56bf0dd12bf5bf04bfba71c10b6 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Wed, 22 May 2024 09:05:27 +0200 Subject: [PATCH 3/6] Fix merge conflicts; keep tests for python 3.9 --- .github/workflows/test.yaml | 2 +- .gitignore | 1 + .gitignore.rej | 9 --------- docs/conf.py.rej | 16 ---------------- pyproject.toml | 2 +- pyproject.toml.rej | 19 ------------------- 6 files changed, 3 insertions(+), 46 deletions(-) delete mode 100644 .gitignore.rej delete mode 100644 docs/conf.py.rej delete mode 100644 pyproject.toml.rej diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 73a7df140..491b49f78 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -24,7 +24,7 @@ jobs: matrix: include: - os: ubuntu-latest - python: "3.10" + python: "3.9" - os: ubuntu-latest python: "3.12" - os: ubuntu-latest diff --git a/.gitignore b/.gitignore index bf4392768..8e61e8fc6 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ sinfo-requirements.txt notebooks tutorial .idea +/node_modules/ # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] 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 ff9c99644..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": "grst", # 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": "grst", -+ "github_repo": "https://github.com/scverse/scirpy", -+ "github_version": "main", -+ "conf_py_path": "/docs/", - } - - # -- General configuration --------------------------------------------------- diff --git a/pyproject.toml b/pyproject.toml index b3b0b8be4..43bc17b83 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,7 +52,7 @@ 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", # for tutorial diff --git a/pyproject.toml.rej b/pyproject.toml.rej deleted file mode 100644 index 41fbe04af..000000000 --- a/pyproject.toml.rej +++ /dev/null @@ -1,19 +0,0 @@ -diff a/pyproject.toml b/pyproject.toml (rejected hunks) -@@ -7,7 +7,7 @@ name = "scirpy" - version = "0.0.1" - description = "A very interesting piece of code" - readme = "README.md" --requires-python = ">=3.9" -+requires-python = ">=3.10" - license = {file = "LICENSE"} - authors = [ - {name = "Gregor Sturm"}, -@@ -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", From c2bd11a45aa536e22099c82d1e3f779674cf5618 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Wed, 22 May 2024 09:06:16 +0200 Subject: [PATCH 4/6] Fix README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 542e0eeb0..88de01ae9 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ Please refer to the [documentation][link-docs]. In particular, the ## Installation -You need to have Python 3.10 or newer installed on your system. If you don't have +You need to have Python 3.9 or newer installed on your system. If you don't have Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge). There are several alternative options to install scirpy: From a1680a959388398f0371af826d31ae0d6daabf2a Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 2 Jul 2024 08:09:14 +0200 Subject: [PATCH 5/6] Update test.yaml --- .github/workflows/test.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 491b49f78..b51780a80 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -52,9 +52,6 @@ jobs: python -m pip install --upgrade pip wheel - name: Install dependencies run: | - # Workaround issue with scikit-bio - # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813 - pip install git+https://github.com/grst/scikit-bio.git@main pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion]" - name: Test env: From a108ca07c1906af82a828d217d76556126a261d1 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 2 Jul 2024 08:21:55 +0200 Subject: [PATCH 6/6] Update test.yaml --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index b51780a80..b16d38e00 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -52,7 +52,7 @@ jobs: python -m pip install --upgrade pip wheel - name: Install dependencies run: | - pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion]" + pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion,diversity]" - name: Test env: MPLBACKEND: agg