diff --git a/.azure-pipelines.yml b/.azure-pipelines.yml index 01250378c..e82caddcb 100644 --- a/.azure-pipelines.yml +++ b/.azure-pipelines.yml @@ -1,13 +1,13 @@ trigger: branches: include: - - master + - main - release-* - refs/tags/* variables: isRefTag: $[startsWith(variables['Build.SourceBranch'], 'refs/tags')] - isMaster: $[eq(variables['Build.SourceBranch'], 'refs/heads/master')] + isMain: $[eq(variables['Build.SourceBranch'], 'refs/heads/main')] stages: - stage: CI @@ -78,7 +78,7 @@ stages: - template: ci/build-images.yml - stage: BuildNativeLibs - condition: or(eq(variables.isMaster, true), eq(variables.isRefTag, true)) + condition: or(eq(variables.isMain, true), eq(variables.isRefTag, true)) jobs: - job: Linux_OSX strategy: diff --git a/.github/workflows/quarto-render.yml b/.github/workflows/quarto-render.yml index 4e9eb23fb..9aa61eccf 100644 --- a/.github/workflows/quarto-render.yml +++ b/.github/workflows/quarto-render.yml @@ -25,7 +25,7 @@ jobs: - name: "Deploy to gh-pages" uses: peaceiris/actions-gh-pages@v3 # Change to the name of your repo's primary branch name: - if: github.ref == 'refs/heads/master' + if: github.ref == 'refs/heads/main' with: # This is GitHub Actions magic; no secrets for us to manage; and this works first-time # without any extra configs other than visiting Settings -> Pages in your GitHub repo. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b0345f248..e4d3ab3b2 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -7,7 +7,7 @@ Thanks for your interest in TileDB-VCF. The notes below give some pointers for f - operating system and version (windows, linux, macos, etc.) - TileDB and TileDB-VCF version (for example, the output of `conda list` or `git status`). - if possible, a minimal working example demonstrating the bug or issue (along with any data to re-create, when feasible) -- Please paste code blocks with triple backquotes (```) so that github will format it nicely. See [GitHub's guide on Markdown](https://guides.github.com/features/mastering-markdown) for more formatting tricks. +- Please paste code blocks with triple backquotes (```) so that github will format it nicely. See [GitHub's guide on Markdown](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax) for more formatting tricks. ## Contributing Code *By contributing code to TileDB-VCF, you are agreeing to release it under the [MIT License](https://github.com/TileDB-Inc/TileDB/tree/dev/LICENSE).* @@ -17,4 +17,4 @@ Thanks for your interest in TileDB-VCF. The notes below give some pointers for f - [Please follow these instructions to build from source](https://docs.tiledb.com/main/how-to/installation/building-from-source) - Make changes locally, then rebuild as appropriate for the level of changes (e.g.: `make` for `libtilebvcf` or `python setup.py develop` for `apis/python`). - Make sure to run `make check`, or `pytest` to verify changes against tests (add new tests where applicable). -- Please submit [pull requests](https://help.github.com/en/desktop/contributing-to-projects/creating-a-pull-request) against the default [`master` branch of TileDB-VCF](https://github.com/TileDB-Inc/TileDB-VCF/tree/master). +- Please submit [pull requests](https://help.github.com/en/desktop/contributing-to-projects/creating-a-pull-request) against the default [`main` branch of TileDB-VCF](https://github.com/TileDB-Inc/TileDB-VCF/tree/main). diff --git a/README.md b/README.md index 56f62c703..0385e4c6e 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ TileDB logo -[![Build Status](https://img.shields.io/azure-devops/build/tiledb-inc/836549eb-f74a-4986-a18f-7fbba6bbb5f0/8/master?label=Azure%20Pipelines&logo=azure-pipelines&style=flat-square)](https://dev.azure.com/TileDB-Inc/CI/_build/latest?definitionId=8&branchName=master) +[![Build Status](https://img.shields.io/azure-devops/build/tiledb-inc/836549eb-f74a-4986-a18f-7fbba6bbb5f0/8/master?label=Azure%20Pipelines&logo=azure-pipelines&style=flat-square)](https://dev.azure.com/TileDB-Inc/CI/_build/latest?definitionId=8&branchName=main) [![Docker-CLI](https://img.shields.io/static/v1?label=Docker&message=tiledbvcf-cli&color=099cec&logo=docker&style=flat-square)](https://hub.docker.com/repository/docker/tiledb/tiledbvcf-cli) [![Docker-Py](https://img.shields.io/static/v1?label=Docker&message=tiledbvcf-py&color=099cec&logo=docker&style=flat-square)](https://hub.docker.com/repository/docker/tiledb/tiledbvcf-py) @@ -112,11 +112,3 @@ https://github.com/TileDB-Inc/TileDB/blob/dev/CODE_OF_CONDUCT.md). [docshowto]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics/how-to [docsreference]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics/api-reference [blog]: https://tiledb.com/blog/population-genomics-is-a-data-management-problem - - -[install]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/installation/quick-install -[build]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/installation/building-from-source - -[use-cli]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/usage/cli -[use-py]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/usage/python -[use-spark]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/usage/spark diff --git a/ci/build-images.yml b/ci/build-images.yml index 095bc18af..ca2ec5fcf 100644 --- a/ci/build-images.yml +++ b/ci/build-images.yml @@ -19,7 +19,7 @@ steps: - task: Docker@2 displayName: Push Latest Tag - condition: eq(variables['build.sourceBranch'], 'refs/heads/master') + condition: eq(variables['build.sourceBranch'], 'refs/heads/main') inputs: command: push containerRegistry: 'dockerHub' diff --git a/docker/README.md b/docker/README.md index a3de7b666..c988f595e 100644 --- a/docker/README.md +++ b/docker/README.md @@ -138,13 +138,13 @@ Check out [TileDB-VCF's docs][vcf-docs] for installation instructions, detailed ## License -This project is licensed under the MIT License - see the [LICENSE.md](https://github.com/TileDB-Inc/TileDB-VCF/blob/master/LICENSE) file for details. +This project is licensed under the MIT License - see the [LICENSE.md](https://github.com/TileDB-Inc/TileDB-VCF/blob/main/LICENSE) file for details. [vcf-repo]: https://github.com/TileDB-Inc/TileDB-VCF [docker]: https://hub.docker.com/u/tiledb [tiledb]: https://github.com/TileDB-Inc/TileDB -[vcf-docs]: https://docs.tiledb.com/solutions/integrations/population-genomics -[cli-api]: https://docs.tiledb.com/solutions/integrations/population-genomics/api-reference/cli -[py-api]: https://docs.tiledb.com/solutions/integrations/population-genomics/api-reference/python +[vcf-docs]: https://tiledb-inc.github.io/TileDB-VCF/documentation/index.html +[cli-api]: https://tiledb-inc.github.io/TileDB-VCF/documentation/ingestion/cli.html +[py-api]: https://tiledb-inc.github.io/TileDB-VCF/documentation/ingestion/python.html [vcf-samples-20]: https://console.tiledb.com/arrays/details/TileDB-Inc/vcf-samples-20-data diff --git a/documentation/docker/README.md b/documentation/docker/README.md index a3de7b666..c988f595e 100644 --- a/documentation/docker/README.md +++ b/documentation/docker/README.md @@ -138,13 +138,13 @@ Check out [TileDB-VCF's docs][vcf-docs] for installation instructions, detailed ## License -This project is licensed under the MIT License - see the [LICENSE.md](https://github.com/TileDB-Inc/TileDB-VCF/blob/master/LICENSE) file for details. +This project is licensed under the MIT License - see the [LICENSE.md](https://github.com/TileDB-Inc/TileDB-VCF/blob/main/LICENSE) file for details. [vcf-repo]: https://github.com/TileDB-Inc/TileDB-VCF [docker]: https://hub.docker.com/u/tiledb [tiledb]: https://github.com/TileDB-Inc/TileDB -[vcf-docs]: https://docs.tiledb.com/solutions/integrations/population-genomics -[cli-api]: https://docs.tiledb.com/solutions/integrations/population-genomics/api-reference/cli -[py-api]: https://docs.tiledb.com/solutions/integrations/population-genomics/api-reference/python +[vcf-docs]: https://tiledb-inc.github.io/TileDB-VCF/documentation/index.html +[cli-api]: https://tiledb-inc.github.io/TileDB-VCF/documentation/ingestion/cli.html +[py-api]: https://tiledb-inc.github.io/TileDB-VCF/documentation/ingestion/python.html [vcf-samples-20]: https://console.tiledb.com/arrays/details/TileDB-Inc/vcf-samples-20-data diff --git a/documentation/index.md b/documentation/index.md index 56f62c703..0385e4c6e 100644 --- a/documentation/index.md +++ b/documentation/index.md @@ -1,6 +1,6 @@ TileDB logo -[![Build Status](https://img.shields.io/azure-devops/build/tiledb-inc/836549eb-f74a-4986-a18f-7fbba6bbb5f0/8/master?label=Azure%20Pipelines&logo=azure-pipelines&style=flat-square)](https://dev.azure.com/TileDB-Inc/CI/_build/latest?definitionId=8&branchName=master) +[![Build Status](https://img.shields.io/azure-devops/build/tiledb-inc/836549eb-f74a-4986-a18f-7fbba6bbb5f0/8/master?label=Azure%20Pipelines&logo=azure-pipelines&style=flat-square)](https://dev.azure.com/TileDB-Inc/CI/_build/latest?definitionId=8&branchName=main) [![Docker-CLI](https://img.shields.io/static/v1?label=Docker&message=tiledbvcf-cli&color=099cec&logo=docker&style=flat-square)](https://hub.docker.com/repository/docker/tiledb/tiledbvcf-cli) [![Docker-Py](https://img.shields.io/static/v1?label=Docker&message=tiledbvcf-py&color=099cec&logo=docker&style=flat-square)](https://hub.docker.com/repository/docker/tiledb/tiledbvcf-py) @@ -112,11 +112,3 @@ https://github.com/TileDB-Inc/TileDB/blob/dev/CODE_OF_CONDUCT.md). [docshowto]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics/how-to [docsreference]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics/api-reference [blog]: https://tiledb.com/blog/population-genomics-is-a-data-management-problem - - -[install]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/installation/quick-install -[build]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/installation/building-from-source - -[use-cli]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/usage/cli -[use-py]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/usage/python -[use-spark]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/usage/spark diff --git a/documentation/the-solution.md b/documentation/the-solution.md index e2fbf2425..559a1d1df 100644 --- a/documentation/the-solution.md +++ b/documentation/the-solution.md @@ -30,7 +30,7 @@ _But what about updates?_ That's the topic of the next section. ## Updates -TileDB-VCF is based on TileDB Embedded which supports [rapid updates](https://docs.tiledb.com/main/solutions/tiledb-embedded/internal-mechanics/writing) via [immutable fragments](https://docs.tiledb.com/main/basic-concepts/data-format#immutable-fragments). That means that every time a new batch of samples is added to the 3D array, the previous contents of the array are not modified at all. Each batch write operation is totally independent and _lock-free—_any number of threads or processes can write simultaneously without synchronization, while ensuring consistency. With TileDB-VCF, both update time and storage size scales linearly with the number of new samples, **solving the N+1 problem**. +TileDB-VCF is based on TileDB Embedded which supports [rapid updates](https://docs.tiledb.com/main/background/internal-mechanics/writing) via [immutable fragments](https://docs.tiledb.com/main/background/key-concepts-and-data-format#fragments-1). That means that every time a new batch of samples is added to the 3D array, the previous contents of the array are not modified at all. Each batch write operation is totally independent and _lock-free—_any number of threads or processes can write simultaneously without synchronization, while ensuring consistency. With TileDB-VCF, both update time and storage size scales linearly with the number of new samples, **solving the N+1 problem**. ## Easy and cost-efficient scaling