Move to main branch and fix broken links (#527)

.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:

.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.

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).

README.md

@@ -1,6 +1,6 @@
 <a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/dev/doc/source/_static/[email protected]" alt="TileDB logo" width="400"></a>
 
-[![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

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'

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.
 
 <!-- links -->
 [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

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.
 
 <!-- links -->
 [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

documentation/index.md

@@ -1,6 +1,6 @@
 <a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/dev/doc/source/_static/[email protected]" alt="TileDB logo" width="400"></a>
 
-[![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

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