Merge pull request #3230 from eseiler/infra/rename_to_main

[INFRA] Rename master to main

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,10 +8,10 @@ labels: [bug]
 body:
 - type: checkboxes
   attributes:
-    label: Does this problem persist on the current master?
-    description: Update to the latest master branch of SeqAn and see if the issue persists.
+    label: Does this problem persist on the current main?
+    description: Update to the latest main branch of SeqAn and see if the issue persists.
     options:
-    - label: I have verified the issue on the current master
+    - label: I have verified the issue on the current main
       required: true
 - type: checkboxes
   attributes:
@@ -65,7 +65,7 @@ body:
       Links? References? Anything that will give us more context about the issue you are encountering!
 
       If you already know how to fix the issue, you can directly create a pull-request instead of an issue.
-      See the [contributor guide](https://docs.seqan.de/seqan/3-master-user/about_contributing.html) for more details.
+      See the [contributor guide](https://docs.seqan.de/seqan3/main_user/about_contributing.html) for more details.
 
       Tip: You can attach images or log files by clicking this area to highlight it and then dragging files in.
   validations:

.github/ISSUE_TEMPLATE/feature_request.md

@@ -16,6 +16,6 @@ One of the following will happen to feature requests:
   * We will "accept" it and someone will start working on it for the next release.
   * We will convert it to a card in our [long-term project planning](https://github.com/seqan/seqan3/projects), but
     close the issue for now as no-one can work on it immediately. You are welcome to contribute patches yourself,
-    see the [contributor guide](https://docs.seqan.de/seqan/3-master-user/about_contributing.html).
+    see the [contributor guide](https://docs.seqan.de/seqan3/main_user/about_contributing.html).
   * The feature request is invalid and will be closed.
 -->

.github/ISSUE_TEMPLATE/release-checklist.md

@@ -9,11 +9,11 @@ assignees: ''
 
 - [ ] Update copyright year.
 - [ ] Create at least one pre-release s.t. our package maintainers can try out a new release of our library. ([Instructions](#prerelease))
-- [ ] Check that the [directory structure](https://github.com/seqan/seqan3/blob/master/doc/setup/quickstart_cmake/index.md) is valid.
+- [ ] Check that the [directory structure](https://github.com/seqan/seqan3/blob/main/doc/setup/quickstart_cmake/index.md) is valid.
 - [ ] Check for critical performance regressions (see [here](https://github.com/seqan/seqan3/wiki/cmp_benchmarks:-Example-Usage)).
 - [ ] Check [Nightlies](https://cdash.seqan.de/index.php?project=SeqAn3) for critical build failures.
 - [ ] Check workarounds in `platform.hpp`. Are they still valid, or can they be limited to specific compiler versions?
-- [ ] Check the [Changelog.md](https://github.com/seqan/seqan3/blob/master/CHANGELOG.md) for completeness (including changed headers). ([Instructions](#changelog))
+- [ ] Check the [Changelog.md](https://github.com/seqan/seqan3/blob/main/CHANGELOG.md) for completeness (including changed headers). ([Instructions](#changelog))
 - [ ] Update the index from cppreference.com so that up-to-date documentation links are generated. ([Instructions](#cppreference))
 
 ---
@@ -127,7 +127,7 @@ Note: Do not use `git clone --recurse-submodules https://github.com/seqan/seqan3
 <a name="changelog"></a>
 <details><summary>Checking the changelog</summary><br>
 
-- List all supported compiler, also add to https://docs.seqan.de/seqan/3-master-user/about_api.html#autotoc_md35.
+- List all supported compiler, also add to https://docs.seqan.de/seqan3/main_user/about_api.html#autotoc_md35.
 - Check that all links are consistent, e.g., `[\#2540](https://github.com/seqan/seqan3/pull/2538)`:
   - Search `(\[\\#)(\d+)(\]\(.+?)(\d+)(\))` and replace `$1$2$3$2$5` (i.e., replace link issue-id by the displayed id).
 
@@ -164,8 +164,8 @@ You can find a comprehensive list of the changes in our [changelog](https://docs
 <a name="version-bump"></a>
 <details><summary>Bumping the version</summary><br>
 
-- Bump succeeding version number in the master branch: [include/seqan3/version.hpp](https://github.com/seqan/seqan3/blob/3.0.2/include/seqan3/version.hpp#L19-L24).
+- Bump succeeding version number in the main branch: [include/seqan3/version.hpp](https://github.com/seqan/seqan3/blob/3.0.2/include/seqan3/version.hpp#L19-L24).
 - The `SEQAN3_RELEASE_CANDIDATE` must be set to `1` as `0` indicates a stable release.
-- Bump the latest stable version number of the API-Stability test in master: [test/api_stability/CMakeLists.txt](https://github.com/seqan/seqan3/blob/3.0.3/test/api_stability/CMakeLists.txt#L10).
+- Bump the latest stable version number of the API-Stability test in main: [test/api_stability/CMakeLists.txt](https://github.com/seqan/seqan3/blob/3.0.3/test/api_stability/CMakeLists.txt#L10).
 
 </details>

.github/pull_request_template.md

@@ -1,5 +1,5 @@
 <!--
-Please see https://github.com/seqan/seqan3/blob/master/CONTRIBUTING.md for a general overview.
+Please see https://github.com/seqan/seqan3/blob/main/CONTRIBUTING.md for a general overview.
 
 Please allow edits from maintainers:
 https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/allowing-changes-to-a-pull-request-branch-created-from-a-fork#enabling-repository-maintainer-permissions-on-existing-pull-requests

.github/workflows/README.md

@@ -56,7 +56,7 @@ Checks if any new snippets are to be added to the Cookbook. Will push a new comm
 
 ## cron_api.yml
 
-Runs the [API-Stability](https://github.com/seqan/seqan3/blob/master/test/api_stability/README.md) test.
+Runs the [API-Stability](https://github.com/seqan/seqan3/blob/main/test/api_stability/README.md) test.
 
 In case of failure, creates an issue containing error logs.
 

.github/workflows/ci_cmake.yml

@@ -7,7 +7,7 @@ name: CMake
 on:
   push:
     branches:
-      - 'master'
+      - 'main'
   pull_request:
     types:
       - unlabeled

.github/workflows/ci_coverage.yml

@@ -7,7 +7,7 @@ name: Coverage
 on:
   push:
     branches:
-      - 'master'
+      - 'main'
   pull_request:
     types:
       - unlabeled

.github/workflows/ci_documentation.yml

@@ -7,7 +7,7 @@ name: Documentation
 on:
   push:
     branches:
-      - 'master'
+      - 'main'
   pull_request:
     types:
       - unlabeled

.github/workflows/ci_linux.yml

@@ -7,7 +7,7 @@ name: Unit Linux
 on:
   push:
     branches:
-      - 'master'
+      - 'main'
   pull_request:
     types:
       - unlabeled

.github/workflows/ci_macos.yml

@@ -7,7 +7,7 @@ name: Unit macOS
 on:
   push:
     branches:
-      - 'master'
+      - 'main'
   pull_request:
     types:
       - unlabeled

.github/workflows/ci_misc.yml

@@ -7,7 +7,7 @@ name: Linux
 on:
   push:
     branches:
-      - 'master'
+      - 'main'
   pull_request:
     types:
       - unlabeled

.github/workflows/deploy_documentation.yaml

@@ -7,7 +7,7 @@ name: Deploy documentation (https://docs.seqan.de/)
 on:
   push:
     branches:
-      - master
+      - 'main'
   # Enables a manual trigger, may run on any branch
   workflow_dispatch:
 

.github/workflows/license_check.yaml

@@ -7,7 +7,7 @@ on:
   push:
     branches:
       - 'main'
-      - 'master'
+      - 'main'
   pull_request:
   workflow_dispatch:
 

.github/workflows/update_cookbook.yml

@@ -7,7 +7,7 @@ name: Cookbook
 on:
   push:
     branches:
-      - 'master'
+      - 'main'
 
 env:
   TZ: Europe/Berlin

.travis.yml

@@ -9,7 +9,7 @@ language: cpp
 
 branches:
   only:
-  - master
+  - main
 
 git:
   depth: 1

CHANGELOG.md

@@ -11,13 +11,13 @@
 This changelog contains a top-level entry for each release with sections on new features, API changes and notable
 bug-fixes (not all bug-fixes will be listed).
 
-Get to know SeqAn3 with our [tutorials](https://docs.seqan.de/seqan/3-master-user/usergroup1.html).
+Get to know SeqAn3 with our [tutorials](https://docs.seqan.de/seqan3/main_user/usergroup1.html).
 
 Please see the release announcement: https://www.seqan.de/announcing-seqan3/
 
-See the porting guide for some help on porting: https://docs.seqan.de/seqan/3-master-user/howto_porting.html
+See the porting guide for some help on porting: https://docs.seqan.de/seqan3/main_user/howto_porting.html
 
-See the documentation on [API stability](https://docs.seqan.de/seqan/3-master-user/about_api.html) to learn about
+See the documentation on [API stability](https://docs.seqan.de/seqan3/main_user/about_api.html) to learn about
 when API changes are allowed.
 
 <!--
@@ -333,7 +333,7 @@ applicable, when it will be removed. We recommend upgrading version-by-version t
 You can either directly check the reported code or verify with our documentation how the new API should be used.
 
 For a complete list of behavioural changes in our public and internal API, you can consult our API stability
-regression test suite and patches at https://github.com/seqan/seqan3/tree/master/test/api_stability/3.0.2.
+regression test suite and patches at https://github.com/seqan/seqan3/tree/main/test/api_stability/3.0.2.
 
 #### Alignment
 

CONTRIBUTING.md

@@ -18,7 +18,7 @@ The overall workflow of contributing changes to this repository is:
   2. Wait for comments from the team and then collectively decide on the best way to solve the issue.
   3. Fork the repository and create a branch on your fork.
   4. Commit the solution to your local branch.
-  5. Create a pull-request to our master branch from your branch.
+  5. Create a pull-request to our main branch from your branch.
   6. Wait for reviews and resolve reviewer comments.
   7. Wait for the PR to be merged.
 
@@ -65,7 +65,7 @@ When you are done with committing changes to your branch and you have tested you
 We have continuous integration in place that should inform you of test failures. Please try to resolve any
 breakage that your pull request introduces.
 
-[Here is a guide for setting up unit tests locally.](https://docs.seqan.de/seqan/3-master-user/setup_tests.html)
+[Here is a guide for setting up unit tests locally.](https://docs.seqan.de/seqan3/main_user/setup_tests.html)
 
 If there are test failures that you don't understand, clearly indicate that you have seen the errors, but cannot resolve
 them – then the first reviewer will have a look at them. Otherwise the PR will be treated as still being

README.md

@@ -31,16 +31,16 @@
     The picture, or alternative text, should link to `[2]`.
 -->
 
-[1]: https://img.shields.io/github/actions/workflow/status/seqan/seqan3/ci_linux.yml?branch=master&style=flat&logo=github&label=SeqAn3%20CI "Open GitHub actions page"
-[2]: https://github.com/seqan/seqan3/actions?query=branch%3Amaster
-[3]: https://codecov.io/gh/seqan/seqan3/branch/master/graph/badge.svg?token=BH1FQiBBle "Open Codecov page"
+[1]: https://img.shields.io/github/actions/workflow/status/seqan/seqan3/ci_linux.yml?branch=main&style=flat&logo=github&label=SeqAn3%20CI "Open GitHub actions page"
+[2]: https://github.com/seqan/seqan3/actions?query=branch%3Amain
+[3]: https://codecov.io/gh/seqan/seqan3/branch/main/graph/badge.svg?token=BH1FQiBBle "Open Codecov page"
 [4]: https://codecov.io/gh/seqan/seqan3
 [5]: https://img.shields.io/badge/license-BSD-green.svg "Open Copyright page"
-[6]: https://docs.seqan.de/seqan/3-master-user/about_copyright.html
+[6]: https://docs.seqan.de/seqan3/main_user/about_copyright.html
 [7]: https://img.shields.io/github/release/seqan/seqan3.svg "Get the latest release"
 [8]: https://github.com/seqan/seqan3/releases/latest
 [9]: https://img.shields.io/badge/platform-linux%20%7C%20bsd%20%7C%20osx-informational.svg "Read more about our API"
-[10]: https://docs.seqan.de/seqan/3-master-user/about_api.html
+[10]: https://docs.seqan.de/seqan3/main_user/about_api.html
 [11]: https://img.shields.io/github/stars/seqan/seqan3.svg?style=social "See who starred us"
 [12]: https://github.com/seqan/seqan3/stargazers
 [13]: https://img.shields.io/twitter/follow/SeqAnLib.svg?label=follow&style=social "Follow us on Twitter"
@@ -57,7 +57,7 @@ for:
 
 By leveraging *Modern C++* it provides unprecedented ease-of-use without sacrificing performance.
 
-Please see the [online documentation](https://docs.seqan.de/seqan/3-master-user/) for more details.
+Please see the [online documentation](https://docs.seqan.de/seqan3/main_user/) for more details.
 
 ## Quick facts
 
@@ -83,7 +83,7 @@ Please see the [online documentation](https://docs.seqan.de/seqan/3-master-user/
 
 We recommend that you use CMake to build your project:
 
-  * [Setup-Tutorial](https://docs.seqan.de/seqan/3-master-user/setup.html)
+  * [Setup-Tutorial](https://docs.seqan.de/seqan3/main_user/setup.html)
   * Using CMake guarantees that all optional dependencies are automatically detected and activated.
 
 Quick-Setup without CMake:
@@ -107,6 +107,6 @@ g++-11 -O3 -DNDEBUG -Wall -Wextra                               \
 
 ## Sponsorships
 
-[![Vercel](https://raw.githubusercontent.com/seqan/seqan3/master/test/documentation/.vercel/powered-by-vercel.svg)](https://vercel.com/?utm_source=seqan&utm_campaign=oss)
+[![Vercel](https://raw.githubusercontent.com/seqan/seqan3/main/test/documentation/.vercel/powered-by-vercel.svg)](https://vercel.com/?utm_source=seqan&utm_campaign=oss)
 
 Vercel is kind enough to sponsor our documentation preview-builds within our pull requests. Check them out!

doc/howto/porting/index.md

@@ -46,7 +46,7 @@ SeqAn2 and SeqAn3 can coexist in the same application, however certain care shou
 
 ## Versions
 
-There are some incompatibilities between SeqAn-2.4 and SeqAn3, please update to the master-branch of SeqAn2 or
+There are some incompatibilities between SeqAn-2.4 and SeqAn3, please update to the main branch of SeqAn2 or
 use the 2.5 release (when available).
 
 ## Paths and Namespaces

doc/howto/write_a_view/index.md

@@ -14,7 +14,7 @@ This HowTo documents how to write a view using the standard library and some hel
 \note
 Some of the links from this HowTo only resolve in the developer documentation because
 they refer to entities from the seqan3::detail namespace.
-We recommend you open this tutorial from [the developer documentation](https://docs.seqan.de/seqan/3-master-dev/).
+We recommend you open this tutorial from [the developer documentation](https://docs.seqan.de/seqan3/main_dev/).
 
 # Motivation
 

doc/setup/quickstart_cmake/index.md

@@ -193,7 +193,7 @@ cmake_minimum_required (VERSION 3.14)
 
 project (my_app LANGUAGES CXX VERSION 1.0.0)
 
-set (seqan3_git_tag "#.#.#") # adapt as needed, e.g. "3.2.0" or "master"
+set (seqan3_git_tag "#.#.#") # adapt as needed, e.g. "3.2.0" or "main"
 
 message (STATUS "Fetching SeqAn3 ${seqan3_git_tag}:")
 

doc/tutorial/01_introduction/index.md

@@ -36,8 +36,8 @@ Most of them are compilable as-is, but some are only valid in their context,
 e.g. they depend on other code snippets given before/after the current one or
 other statements implied by the text. You can **copy'n'paste** freely from these examples,
 this implies no copyright-obligations (however distributing SeqAn or an application
-using it does, see [Copyright](https://docs.seqan.de/seqan/3-master-user/about_copyright.html) and
-[Citing](https://docs.seqan.de/seqan/3-master-user/about_citing.html)).
+using it does, see [Copyright](https://docs.seqan.de/seqan3/main_user/about_copyright.html) and
+[Citing](https://docs.seqan.de/seqan3/main_user/about_citing.html)).
 
 You may ask why we do not use std::cout or std::cerr for console output.
 Actually, for the given text it does not make a difference since seqan3::debug_stream prints to std::cerr as well.
@@ -61,19 +61,19 @@ so don't worry too much if your solution is different from ours.
 # API documentation
 
 While the tutorials provide you with a walkthrough of some of our modules, the
-[API documentation](https://docs.seqan.de/seqan/3-master-user/modules.html) will be the go-to reference when you start
+[API documentation](https://docs.seqan.de/seqan3/main_user/modules.html) will be the go-to reference when you start
 developing code with SeqAn.
 
 Some helpful tips when browsing our documentation:
 
 * You can search for seqan3 entities with the **search bar** in the top-right corner.
   E.g., start typing `debug_str` and the pop-up will suggest the `debug_stream` for you.
 * If you don't have a specific entity you are searching for, the **landing pages** of each module are always a good
-  start. E.g., the [Alphabet landing page](https://docs.seqan.de/seqan/3-master-user/group__alphabet.html) first lists
+  start. E.g., the [Alphabet landing page](https://docs.seqan.de/seqan3/main_user/group__alphabet.html) first lists
   all submodules (Adaptation, Aminoacid, ...) and general alphabet-related seqan3 entities, followed by a detailed
   description of our alphabet module. Searching for keywords on this page might point you in the right direction.
 * If you know you've seen some code snippet somewhere but don't remember where, have a look at our
-  [cookbook](https://docs.seqan.de/seqan/3-master-user/cookbook.html). It is not structured and huge, but works
+  [cookbook](https://docs.seqan.de/seqan3/main_user/cookbook.html). It is not structured and huge, but works
   well if you do a key word search with `Ctrl+F`.
 
 We recommend you to open the API documentation in separate browser tab s.t. you can easily switch back to the tutorial.
@@ -85,10 +85,10 @@ of SeqAn on [Github](https://github.com/seqan/seqan3/issues/new/choose) and ask
 
 Modules structure the SeqAn library into logical units. There are, for instance,
 
-* [`alphabet`](https://docs.seqan.de/seqan/3-master-user/group__alphabet.html): `seqan3::dna4` etc.
-* [`io`](http://docs.seqan.de/seqan/3-master-user/group__io.html): read/write FASTA, SAM, ...
-* [`alignment`](http://docs.seqan.de/seqan/3-master-user/group__alignment.html): compute pairwise alignments etc.
-* [`search`](http://docs.seqan.de/seqan/3-master-user/group__search.html): search via an FM-Index etc.
+* [`alphabet`](https://docs.seqan.de/seqan3/main_user/group__alphabet.html): `seqan3::dna4` etc.
+* [`io`](http://docs.seqan.de/seqan3/main_user/group__io.html): read/write FASTA, SAM, ...
+* [`alignment`](http://docs.seqan.de/seqan3/main_user/group__alignment.html): compute pairwise alignments etc.
+* [`search`](http://docs.seqan.de/seqan3/main_user/group__search.html): search via an FM-Index etc.
 
 and some more.
 
@@ -104,7 +104,7 @@ compile time measurably.
 \assignment{Assignment 2: Modules and API documentation}
 In your program of assignment 1, initialise a vector of `seqan3::dna4` instead of `int`.
 The vector shall store the DNA string `ACTG`.
-Check the [API documentation](http://docs.seqan.de/seqan/3-master-user/modules.html) for which header you need to include.
+Check the [API documentation](http://docs.seqan.de/seqan3/main_user/modules.html) for which header you need to include.
 Additionally, browse the documentation for `seqan3::dna4` on how to initialise a `seqan3::dna4` letter.
 \endassignment
 \solution

doc/tutorial/03_concepts/index.md

@@ -245,10 +245,10 @@ The class `seqan3::bitpacked_sequence<alphabet_type>` behaves just like `std::ve
 values are packed into a single byte/word to save space. Also analog to `std::vector`, not every `alphabet_type` can
 be used. To avoid misuse and weird error messages, the type is constrained.
 
-Have a look at the documentation of [`seqan3::bitpacked_sequence`](http://docs.seqan.de/seqan/3-master-user/classseqan3_1_1bitpacked__sequence.html).
+Have a look at the documentation of [`seqan3::bitpacked_sequence`](http://docs.seqan.de/seqan3/main_user/classseqan3_1_1bitpacked__sequence.html).
 It has one constrained template parameter.
 Do you understand the requirements imposed on `alphabet_type` when using the
-[`seqan3::bitpacked_sequence`](http://docs.seqan.de/seqan/3-master-user/classseqan3_1_1bitpacked__sequence.html)?
+[`seqan3::bitpacked_sequence`](http://docs.seqan.de/seqan3/main_user/classseqan3_1_1bitpacked__sequence.html)?
 
 \hint
 In order to use the `seqan3::bitpacked_sequence` the  `alphabet_type` must model the following:

include/seqan3/alphabet/all.hpp

@@ -153,7 +153,7 @@
  *
  * In SeqAn it is recommended you use the STL container classes like std::vector for storing sequence data,
  * but you can use other class templates if they satisfy the respective seqan3::container, e.g. `std::deque` or
- * <a href="https://github.com/facebook/folly/blob/master/folly/docs/FBVector.md" target="_blank">
+ * <a href="https://github.com/facebook/folly/blob/main/folly/docs/FBVector.md" target="_blank">
  * <tt>folly::fbvector</tt></a> or even <a href="https://doc.qt.io/qt-5/qvector.html" target="_blank">
  * <tt>Qt::QVector</tt></a>.
  *