From 66d4dd852f9d854c9d971b4ef8c5f83deda270e8 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Sun, 12 Jun 2022 14:19:35 +0930 Subject: [PATCH 01/21] added action.yml --- action.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 action.yml diff --git a/action.yml b/action.yml new file mode 100644 index 00000000..04a60dc9 --- /dev/null +++ b/action.yml @@ -0,0 +1,10 @@ +name: Check Markdown links + +on: push + +jobs: + markdown-link-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - uses: gaurav-nelson/github-action-markdown-link-check@v1 From 68f00cd4f895d307e099d1211d5a079e31425138 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Sun, 12 Jun 2022 14:29:53 +0930 Subject: [PATCH 02/21] created workflows folder and added action.yml to workflows --- action.yml => workflows/action.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename action.yml => workflows/action.yml (100%) diff --git a/action.yml b/workflows/action.yml similarity index 100% rename from action.yml rename to workflows/action.yml From 012357b6bd74acafa12934e8d4e5bfc36f5fbcc1 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Sun, 12 Jun 2022 14:33:00 +0930 Subject: [PATCH 03/21] moved workflows to .github --- {workflows => .github/workflows}/action.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {workflows => .github/workflows}/action.yml (100%) diff --git a/workflows/action.yml b/.github/workflows/action.yml similarity index 100% rename from workflows/action.yml rename to .github/workflows/action.yml From 139dbeb2bfe7ac382618651a280e9bb3552fc1a2 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Mon, 13 Jun 2022 12:47:17 +0930 Subject: [PATCH 04/21] fixed pull request checklist deadlink --- docs/faqs/contributor-faq.md | 3 +-- docs/faqs/developer-faq.md | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/faqs/contributor-faq.md b/docs/faqs/contributor-faq.md index 71e930ce..b189180d 100644 --- a/docs/faqs/contributor-faq.md +++ b/docs/faqs/contributor-faq.md @@ -30,7 +30,7 @@ Coding style (brackets, variable names, etc.) must conform to the conventions. * The class and all the members must be documented thoroughly. * Check your code with the tool `tools/checker.php`. Call `php tools/checker.php` for detailed instructions. -Please open a pull request and follow the [pull request guidelines](pull-request-checklist.md). +Please open a pull request and follow the [pull request guidelines](../additional-resources/pull-request-checklist.md). ## Troubleshooting @@ -247,4 +247,3 @@ To contribute to a bug fix: 3. Fix the bug and add a test. 4. Create a pull request for your branch. 5. After approval and merge make sure the issue is closed. - diff --git a/docs/faqs/developer-faq.md b/docs/faqs/developer-faq.md index 81b46548..a5427321 100644 --- a/docs/faqs/developer-faq.md +++ b/docs/faqs/developer-faq.md @@ -30,7 +30,7 @@ Coding style (brackets, variable names, etc.) must conform to the conventions. * The class and all the members should be properly documented. * Check your code with the tool `tools/checker.php`. Call `php tools/checker.php` for detailed instructions. -Please open a pull request and follow the [pull request guidelines](pull-request-checklist.md). +Please open a pull request and follow the [pull request guidelines](../additional-resources/pull-request-checklist.md). ### Can I use QT designer to create GUI widgets? From bfb621507bd8c0232c226ffc9cedb0ac644a1363 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Mon, 13 Jun 2022 20:11:16 +0930 Subject: [PATCH 05/21] set max-depth to 2 --- .github/workflows/action.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 04a60dc9..d8ed50f0 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -8,3 +8,5 @@ jobs: steps: - uses: actions/checkout@master - uses: gaurav-nelson/github-action-markdown-link-check@v1 + with: + max-depth: 2 From 082df95d125c2edfc7747af8a92c21e7cebe6c9d Mon Sep 17 00:00:00 2001 From: greengypsy Date: Mon, 13 Jun 2022 20:19:09 +0930 Subject: [PATCH 06/21] set max-depth to 7 and change link in toppas.md --- .github/workflows/action.yml | 2 +- docs/topp/toppas.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index d8ed50f0..e4adc2dc 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -9,4 +9,4 @@ jobs: - uses: actions/checkout@master - uses: gaurav-nelson/github-action-markdown-link-check@v1 with: - max-depth: 2 + max-depth: 7 diff --git a/docs/topp/toppas.md b/docs/topp/toppas.md index cd496144..1ff58c05 100644 --- a/docs/topp/toppas.md +++ b/docs/topp/toppas.md @@ -13,7 +13,7 @@ The following figure shows a simple example pipeline that has just been created ![TOPPAS simple example](../images/topp/TOPPAS_simple_example.png) -More information about TOPPAS can be found in the [TOPPAS tutorial](../tutorials/TOPP/TOPPAS-tutorial.md). +More information about TOPPAS can be found in the [TOPPAS tutorial](../tutorials/TOPPAS/TOPPAS-tutorial.md). **The command line parameters of this tool are**: From 5ab700538e6616749ac225d42d0edf3ac23b32cb Mon Sep 17 00:00:00 2001 From: greengypsy Date: Mon, 13 Jun 2022 20:40:50 +0930 Subject: [PATCH 07/21] edited action.yml and fixed links --- .github/workflows/action.yml | 8 ++++++-- docs/faqs/contributor-faq.md | 4 ++-- docs/faqs/developer-faq.md | 4 ++-- docs/guides/contributors-quickstart-guide.md | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index e4adc2dc..3fd2bb6a 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -1,6 +1,9 @@ name: Check Markdown links -on: push +on: [pull_request] + schedule: + # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07) + - cron: "0 9 * * *" jobs: markdown-link-check: @@ -9,4 +12,5 @@ jobs: - uses: actions/checkout@master - uses: gaurav-nelson/github-action-markdown-link-check@v1 with: - max-depth: 7 + max-depth: -1 + check-modified-files-only: 'yes' diff --git a/docs/faqs/contributor-faq.md b/docs/faqs/contributor-faq.md index b189180d..689ade57 100644 --- a/docs/faqs/contributor-faq.md +++ b/docs/faqs/contributor-faq.md @@ -11,7 +11,7 @@ The following section provides general information to new contributors. * Check out the development version of OpenMS (see OpenMS [releases and installers](downloads/releases.md)). * Build OpenMS according to the installation instructions. -* Read the [OpenMS Coding Conventions](https://github.com/OpenMS/OpenMS/wiki/Coding-conventions). +* Read the [OpenMS Coding Conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html). * Read the [OpenMS Tutorial](../tutorials/user-tutorial.md). * Create a GitHub account. * Subscribe to the [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) or [contact us](../contact-us.md). @@ -23,7 +23,7 @@ to `TOOLS` if they are stable enough, are fully tested, fully documented, and a ### I have written a class for OpenMS. What should I do? -Follow the [OpenMS coding conventions](). +Follow the [OpenMS coding conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html). Coding style (brackets, variable names, etc.) must conform to the conventions. diff --git a/docs/faqs/developer-faq.md b/docs/faqs/developer-faq.md index a5427321..af8b24fb 100644 --- a/docs/faqs/developer-faq.md +++ b/docs/faqs/developer-faq.md @@ -11,7 +11,7 @@ The following section provides general information to new contributors. * Check out the development version of OpenMS (see website). * Build OpenMS by following the [installation instructions]() or [from source](../installations/build-openms-from-source.md). -* Read the [OpenMS Coding Conventions]() +* Read the [OpenMS Coding Conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html) * Read the [OpenMS Tutorial](../tutorials/user-tutorial.md). * Create a GitHub account. * Subscribe to the [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) or [contact-us](../contact-us.md). @@ -23,7 +23,7 @@ to `TOOLS` if they are stable enough, are fully tested, fully documented, and a ### I have written a class for OpenMS. What should I do? -Follow the [OpenMS coding conventions](). +Follow the [OpenMS coding conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html). Coding style (brackets, variable names, etc.) must conform to the conventions. diff --git a/docs/guides/contributors-quickstart-guide.md b/docs/guides/contributors-quickstart-guide.md index 81dd3732..e36ce91a 100644 --- a/docs/guides/contributors-quickstart-guide.md +++ b/docs/guides/contributors-quickstart-guide.md @@ -40,10 +40,10 @@ To create a fork: ### Coding conventions -See the manual for coding style recommended by OpenMS: [Coding conventions](https://github.com/OpenMS/OpenMS/wiki/Coding-conventions). +See the manual for coding style recommended by OpenMS: [Coding conventions](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html). ```{seealso} -[C++ Guide](https://github.com/OpenMS/OpenMS/wiki/Cpp-Guide). +[C++ Guide](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/developer_faq.html). ``` OpenMS automatically tests for common coding convention violations using a modified version of `cpplint`. From f5f217caae489d0e191281d00f91b9c338420b66 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Tue, 14 Jun 2022 15:24:19 +0930 Subject: [PATCH 08/21] added a config.json file for action.yml --- .github/workflows/action.yml | 1 + .github/workflows/config.json | 7 +++++++ 2 files changed, 8 insertions(+) create mode 100644 .github/workflows/config.json diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 3fd2bb6a..0391f171 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -14,3 +14,4 @@ jobs: with: max-depth: -1 check-modified-files-only: 'yes' + config-file: 'config.json' diff --git a/.github/workflows/config.json b/.github/workflows/config.json new file mode 100644 index 00000000..71bd1a22 --- /dev/null +++ b/.github/workflows/config.json @@ -0,0 +1,7 @@ +{ + "ignorePatterns": [ + { + "pattern": "^http://docs.github" + } + ] +} From 85e81fdea1253a48713bce01ac537bd8bf4e21cf Mon Sep 17 00:00:00 2001 From: greengypsy Date: Tue, 14 Jun 2022 15:39:45 +0930 Subject: [PATCH 09/21] corrected action.yml --- .github/workflows/action.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 0391f171..c8880d2a 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -1,9 +1,10 @@ name: Check Markdown links -on: [pull_request] - schedule: - # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07) - - cron: "0 9 * * *" +on: + pull_request: + schedule: + # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07) + - cron: "0 9 * * *" jobs: markdown-link-check: From 26f81b2b269e4526a40b8c5522ea02bb353f9183 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 16:24:52 +0930 Subject: [PATCH 10/21] made discussed changes to action.yml file --- .github/workflows/action.yml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index c8880d2a..34ffe5ec 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -1,10 +1,18 @@ -name: Check Markdown links +name: Documentation URLs Check on: pull_request: + push: + branches: + - 'release-*' + - 'develop' + - 'staging' + - main + tags: + - 'v*' schedule: # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07) - - cron: "0 9 * * *" + - cron: "1 2 * * *" jobs: markdown-link-check: @@ -16,3 +24,4 @@ jobs: max-depth: -1 check-modified-files-only: 'yes' config-file: 'config.json' + file-extension: '.md', '.rst' From b198c348b53b006cb772daf14976e2b8ec16c447 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:06:07 +0930 Subject: [PATCH 11/21] added quotation marks to main branch --- .github/workflows/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 34ffe5ec..da149e9e 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -7,7 +7,7 @@ on: - 'release-*' - 'develop' - 'staging' - - main + - 'main' tags: - 'v*' schedule: From 2df21474f85d78554b225d17e9e79590faf19224 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:08:54 +0930 Subject: [PATCH 12/21] added current branch to check if script works --- .github/workflows/action.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index da149e9e..871a6f98 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -8,6 +8,7 @@ on: - 'develop' - 'staging' - 'main' + - 'add_broken_dead_links_check_v2' tags: - 'v*' schedule: From 517784521420d5edd3716dd130c28f747d8238b8 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:12:09 +0930 Subject: [PATCH 13/21] removed rst extension --- .github/workflows/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 871a6f98..b3e0b4b1 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -25,4 +25,4 @@ jobs: max-depth: -1 check-modified-files-only: 'yes' config-file: 'config.json' - file-extension: '.md', '.rst' + file-extension: '.md' From e91bf0ca289773863b6d1759cfdf10b893a45627 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:17:55 +0930 Subject: [PATCH 14/21] fixed indentation in action.yml --- .github/workflows/action.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index b3e0b4b1..cfacfc0a 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -2,18 +2,18 @@ name: Documentation URLs Check on: pull_request: - push: - branches: - - 'release-*' - - 'develop' - - 'staging' - - 'main' - - 'add_broken_dead_links_check_v2' - tags: - - 'v*' - schedule: - # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07) - - cron: "1 2 * * *" + push: + branches: + - 'release-*' + - 'develop' + - 'staging' + - 'main' + + tags: + - 'v*' + schedule: + # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07) + - cron: "1 2 * * *" jobs: markdown-link-check: From 78d1fc7e2f66646f59bc4113c9d3c0b9d17bcb72 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:23:29 +0930 Subject: [PATCH 15/21] added current branch --- .github/workflows/action.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index cfacfc0a..9e6a5c8e 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -8,7 +8,8 @@ on: - 'develop' - 'staging' - 'main' - + - 'documentation_urls_check' + tags: - 'v*' schedule: From 9422c2d0eb6450a89ca38de138f0c50378d533cb Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:36:40 +0930 Subject: [PATCH 16/21] added full file path to config.json --- .github/workflows/action.yml | 3 +-- .github/workflows/config.json | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 9e6a5c8e..08e7fe2a 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -8,7 +8,6 @@ on: - 'develop' - 'staging' - 'main' - - 'documentation_urls_check' tags: - 'v*' @@ -25,5 +24,5 @@ jobs: with: max-depth: -1 check-modified-files-only: 'yes' - config-file: 'config.json' + config-file: '.github/workflows/config.json' file-extension: '.md' diff --git a/.github/workflows/config.json b/.github/workflows/config.json index 71bd1a22..7aa15122 100644 --- a/.github/workflows/config.json +++ b/.github/workflows/config.json @@ -1,7 +1,7 @@ { "ignorePatterns": [ { - "pattern": "^http://docs.github" + "pattern": "^http://docs.github", "^pkgs.org" } ] } From 9c780dcc91ae1673a45e1c9d068b799833f8bf80 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:37:55 +0930 Subject: [PATCH 17/21] added current branch again --- .github/workflows/action.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 08e7fe2a..3c1f1141 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -8,6 +8,7 @@ on: - 'develop' - 'staging' - 'main' + - 'documentation_urls_check' tags: - 'v*' From de1a91b168582771dd2ff45e3dd9576bbfc852be Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:40:34 +0930 Subject: [PATCH 18/21] added base braanch as develop --- .github/workflows/action.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 3c1f1141..df3ff8c5 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -23,6 +23,7 @@ jobs: - uses: actions/checkout@master - uses: gaurav-nelson/github-action-markdown-link-check@v1 with: + base_branch: 'develop' max-depth: -1 check-modified-files-only: 'yes' config-file: '.github/workflows/config.json' From 7055e5aa70c0f5f7af12fbf1ea653ce0fb29c565 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:41:41 +0930 Subject: [PATCH 19/21] base-branch --- .github/workflows/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index df3ff8c5..3f1bdab2 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -23,7 +23,7 @@ jobs: - uses: actions/checkout@master - uses: gaurav-nelson/github-action-markdown-link-check@v1 with: - base_branch: 'develop' + base-branch: 'develop' max-depth: -1 check-modified-files-only: 'yes' config-file: '.github/workflows/config.json' From e034ab17465731dd59ee2baef3519a9d945816d6 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:43:07 +0930 Subject: [PATCH 20/21] set base-branch to staging --- .github/workflows/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 3f1bdab2..7894abd3 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -23,7 +23,7 @@ jobs: - uses: actions/checkout@master - uses: gaurav-nelson/github-action-markdown-link-check@v1 with: - base-branch: 'develop' + base-branch: 'staging' max-depth: -1 check-modified-files-only: 'yes' config-file: '.github/workflows/config.json' From e9c4a75b174e7f57c5a6472e728d9ed0844c2fc4 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 24 Jun 2022 19:44:57 +0930 Subject: [PATCH 21/21] remove current branch --- .github/workflows/action.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 7894abd3..600f1116 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -8,7 +8,6 @@ on: - 'develop' - 'staging' - 'main' - - 'documentation_urls_check' tags: - 'v*'