From 363098b237f8c1813a1985b72124c82dcb6e5647 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Tue, 30 Jan 2024 14:56:32 +0100 Subject: [PATCH] [INFRA] Rename master to main --- .github/ISSUE_TEMPLATE/bug_report.yml | 8 ++++---- .github/ISSUE_TEMPLATE/feature_request.md | 2 +- .github/ISSUE_TEMPLATE/release-checklist.md | 10 +++++----- .github/pull_request_template.md | 2 +- .github/workflows/README.md | 2 +- .github/workflows/ci_cmake.yml | 2 +- .github/workflows/ci_coverage.yml | 2 +- .github/workflows/ci_documentation.yml | 2 +- .github/workflows/ci_linux.yml | 2 +- .github/workflows/ci_macos.yml | 2 +- .github/workflows/ci_misc.yml | 2 +- .github/workflows/deploy_documentation.yaml | 2 +- .github/workflows/license_check.yaml | 2 +- .github/workflows/update_cookbook.yml | 2 +- .travis.yml | 2 +- CHANGELOG.md | 8 ++++---- CONTRIBUTING.md | 4 ++-- README.md | 16 +++++++-------- doc/howto/porting/index.md | 2 +- doc/howto/write_a_view/index.md | 2 +- doc/setup/quickstart_cmake/index.md | 2 +- doc/tutorial/01_introduction/index.md | 20 +++++++++---------- doc/tutorial/03_concepts/index.md | 4 ++-- include/seqan3/alphabet/all.hpp | 2 +- .../argument_parser/argument_parser.hpp | 2 +- include/seqan3/core/platform.hpp | 2 +- test/scripts/check_include_order.pl | 4 ++-- test/scripts/create_all_hpp.sh | 9 +++------ 28 files changed, 59 insertions(+), 62 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 997b0c5c88..8f4404694f 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.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: diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index 33132b4223..0a14e96922 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.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. --> diff --git a/.github/ISSUE_TEMPLATE/release-checklist.md b/.github/ISSUE_TEMPLATE/release-checklist.md index 3c8fef488f..34ea187bfb 100644 --- a/.github/ISSUE_TEMPLATE/release-checklist.md +++ b/.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
Checking the changelog
-- 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
Bumping the version
-- 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).
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index f16fbe0218..07e2c09acd 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,5 +1,5 @@ -[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! diff --git a/doc/howto/porting/index.md b/doc/howto/porting/index.md index 1b93a1694a..eb307e6541 100644 --- a/doc/howto/porting/index.md +++ b/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 diff --git a/doc/howto/write_a_view/index.md b/doc/howto/write_a_view/index.md index 70cd7b1944..2d15c62090 100644 --- a/doc/howto/write_a_view/index.md +++ b/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 diff --git a/doc/setup/quickstart_cmake/index.md b/doc/setup/quickstart_cmake/index.md index 9ef60e9d72..284ac8b2cc 100644 --- a/doc/setup/quickstart_cmake/index.md +++ b/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}:") diff --git a/doc/tutorial/01_introduction/index.md b/doc/tutorial/01_introduction/index.md index a6420c288d..503d08ec9b 100644 --- a/doc/tutorial/01_introduction/index.md +++ b/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. @@ -61,7 +61,7 @@ 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: @@ -69,11 +69,11 @@ 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 diff --git a/doc/tutorial/03_concepts/index.md b/doc/tutorial/03_concepts/index.md index f6a6a7d1d9..09e0352c8b 100644 --- a/doc/tutorial/03_concepts/index.md +++ b/doc/tutorial/03_concepts/index.md @@ -245,10 +245,10 @@ The class `seqan3::bitpacked_sequence` 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: diff --git a/include/seqan3/alphabet/all.hpp b/include/seqan3/alphabet/all.hpp index 5ef06e2d8a..13b875301a 100644 --- a/include/seqan3/alphabet/all.hpp +++ b/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 - * + * * folly::fbvector or even * Qt::QVector. * diff --git a/include/seqan3/argument_parser/argument_parser.hpp b/include/seqan3/argument_parser/argument_parser.hpp index 8c29b2d281..5626208a21 100644 --- a/include/seqan3/argument_parser/argument_parser.hpp +++ b/include/seqan3/argument_parser/argument_parser.hpp @@ -166,7 +166,7 @@ class argument_parser * The application name must only contain alpha-numeric characters, `_` or `-`, * i.e. the following regex must evaluate to true: `"^[a-zA-Z0-9_-]+$"`. * - * See the [argument parser tutorial](https://docs.seqan.de/seqan/3-master-dev/tutorial_argument_parser.html) + * See the [argument parser tutorial](https://docs.seqan.de/seqan3/main_dev/tutorial_argument_parser.html) * for more information about the version check functionality. */ argument_parser(std::string const app_name, diff --git a/include/seqan3/core/platform.hpp b/include/seqan3/core/platform.hpp index f92ab6a680..aec8b8aad8 100644 --- a/include/seqan3/core/platform.hpp +++ b/include/seqan3/core/platform.hpp @@ -277,7 +277,7 @@ static_assert(sdsl::sdsl_version_major == 3, "Only version 3 of the SDSL is supp #if defined(_GLIBCXX_USE_CXX11_ABI) && _GLIBCXX_USE_CXX11_ABI == 0 # ifndef SEQAN3_DISABLE_LEGACY_STD_DIAGNOSTIC # pragma message \ - "We do not actively support compiler that have -D_GLIBCXX_USE_CXX11_ABI=0 set, and it might be that SeqAn does not compile due to this. It is known that all compiler of CentOS 7 / RHEL 7 set this flag by default (and that it cannot be overridden!). Note that these versions of the OSes are community-supported (see https://docs.seqan.de/seqan/3-master-user/about_api.html#platform_stability for more details). You can disable this warning by setting -DSEQAN3_DISABLE_LEGACY_STD_DIAGNOSTIC." + "We do not actively support compiler that have -D_GLIBCXX_USE_CXX11_ABI=0 set, and it might be that SeqAn does not compile due to this. It is known that all compiler of CentOS 7 / RHEL 7 set this flag by default (and that it cannot be overridden!). Note that these versions of the OSes are community-supported (see https://docs.seqan.de/seqan3/main_user/about_api.html#platform_stability for more details). You can disable this warning by setting -DSEQAN3_DISABLE_LEGACY_STD_DIAGNOSTIC." # endif // SEQAN3_DISABLE_LEGACY_STD_DIAGNOSTIC #endif // _GLIBCXX_USE_CXX11_ABI == 0 diff --git a/test/scripts/check_include_order.pl b/test/scripts/check_include_order.pl index 3cff7b52fa..c7d5810b7e 100755 --- a/test/scripts/check_include_order.pl +++ b/test/scripts/check_include_order.pl @@ -7,8 +7,8 @@ # Usage check_include_order.pl [] [] .... # Will output the names of the files that have incorrect include order. # -# Usage example: `check_include_order.pl $(git diff --name-only HEAD origin/master)` -# Checks all files that have been touch since last master for any incorrect include ordering +# Usage example: `check_include_order.pl $(git diff --name-only HEAD origin/main)` +# Checks all files that have been touch since last main for any incorrect include ordering # # Usage example: `check_include_order.pl $(find include -type f) # Checks all files of seqan3 for incorrect include ordering diff --git a/test/scripts/create_all_hpp.sh b/test/scripts/create_all_hpp.sh index 990309f879..0857109c4e 100755 --- a/test/scripts/create_all_hpp.sh +++ b/test/scripts/create_all_hpp.sh @@ -22,12 +22,9 @@ print_header() { CURRENT_YEAR=$1 cat << EOF -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-${CURRENT_YEAR}, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-${CURRENT_YEAR}, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-${CURRENT_YEAR} Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-${CURRENT_YEAR} Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause EOF }