master-to-main

.azure-pipelines.yml

@@ -1,5 +1,5 @@
 trigger:
-- master
+- main
 - "*.*.x"
 
 variables:

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -14,7 +14,7 @@ body:
  required: true
  - label: I have confirmed this bug exists on the latest version of scanpy.
  required: true
- - label: (optional) I have confirmed this bug exists on the master branch of scanpy.
+ - label: (optional) I have confirmed this bug exists on the main branch of scanpy.
  required: false
 - type: markdown
  attributes:

.github/workflows/check-pr.yml

@@ -4,7 +4,6 @@ on:
  pull_request:
  branches:
  - main
- - master
  types:
  # milestone changes
  - milestoned

.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
  - id: check-merge-conflict
  - id: detect-private-key
  - id: no-commit-to-branch
- args: ["--branch=master", "--branch=main"]
+ args: ["--branch=main"]
 
 ci:
  autofix_prs: false

docs/dev/code.md

@@ -20,5 +20,5 @@ We ignore a couple of flake8 checks which are documented in the .flake8 file in
 To learn how to ignore checks per line please read
 [flake8 violations](https://flake8.pycqa.org/en/latest/user/violations.html).
 Additionally, we use Scanpy’s
-[EditorConfig](https://github.com/scverse/scanpy/blob/master/.editorconfig),
+[EditorConfig](https://github.com/scverse/scanpy/blob/main/.editorconfig),
 so using an editor/IDE with support for both is helpful.

docs/dev/getting-set-up.md

@@ -21,7 +21,7 @@ This is very straight forward if you're using [GitHub's CLI](https://cli.github.
 $ gh repo fork scverse/scanpy --clone --remote
 ```
 
-This will fork the repo to your github account, create a clone of the repo on your current machine, add our repository as a remote, and set the `master` development branch to track our repository.
+This will fork the repo to your github account, create a clone of the repo on your current machine, add our repository as a remote, and set the `main` development branch to track our repository.
 
 To do this manually, first make a fork of the repository by clicking the "fork" button on our main github package. Then, on your machine, run:
 
@@ -32,7 +32,7 @@ git clone https://github.com/{your-username}/scanpy.git
 cd scanpy
 # Add our repository as a remote
 git remote add upstream https://github.com/scverse/scanpy.git
-# git branch --set-upstream-to "upstream/master"
+# git branch --set-upstream-to "upstream/main"
 ```
 
 ### `pre-commit`
@@ -61,11 +61,11 @@ If you choose not to run the hooks on each commit, you can run them manually wit
 ### Creating a branch for your feature
 
 All development should occur in branches dedicated to the particular work being done.
-Additionally, unless you are a maintainer, all changes should be directed at the `master` branch.
+Additionally, unless you are a maintainer, all changes should be directed at the `main` branch.
 You can create a branch with:
 
 ```shell
-git checkout master # Starting from the master branch
+git checkout main  # Starting from the main branch
 git pull # Syncing with the repo
 git checkout -b {your-branch-name} # Making and changing to the new branch
 ```

docs/dev/release.md

@@ -67,4 +67,4 @@ If you want to replicate the process more exactly, make sure you are careful,
 and create a version tag before building (make sure you delete it after uploading to TestPyPI!).
 
 [hatch-build]: https://hatch.pypa.io/latest/config/build/
-[publish workflow]: https://github.com/scverse/scanpy/tree/master/.github/workflows/publish.yml
+[publish workflow]: https://github.com/scverse/scanpy/tree/main/.github/workflows/publish.yml

docs/dev/testing.md

@@ -21,7 +21,7 @@ It can take a while to run the whole test suite. There are a few ways to cut dow
 
 ## Writing tests
 
-You can refer to the [existing test suite](https://github.com/scverse/scanpy/tree/master/scanpy/tests) for examples.
+You can refer to the [existing test suite](https://github.com/scverse/scanpy/tree/main/scanpy/tests) for examples.
 If you haven't written tests before, Software Carpentry has an [in-depth guide](https://katyhuff.github.io/2016-07-11-scipy/testing/01-basics.html) on the topic.
 
 We highly recommend using [Test Driven Development](https://en.wikipedia.org/wiki/Test-driven_development) when contributing code.

docs/extensions/git_ref.py

@@ -32,7 +32,7 @@ def get() -> str | None:
  try:
  git_ref = git("rev-parse", "HEAD")
  except Exception:
- git_ref = "master"
+ git_ref = "main"
  return git_ref
 
 

scanpy/tools/_rank_genes_groups.py

@@ -582,7 +582,7 @@ def rank_genes_groups(
  Notes
  -----
  There are slight inconsistencies depending on whether sparse
- or dense data are passed. See `here <https://github.com/scverse/scanpy/blob/master/scanpy/tests/test_rank_genes_groups.py>`__.
+ or dense data are passed. See `here <https://github.com/scverse/scanpy/blob/main/scanpy/tests/test_rank_genes_groups.py>`__.
 
  Examples
  --------