Split tiledbsc and tiledbsoma into separate branches

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: TileDB-SingleCell Python CI
+name: TileDB-SOMA Python CI
 
 on:
   pull_request:
@@ -25,7 +25,7 @@ jobs:
             cxx: g++-11
 
     steps:
-    - name: Checkout TileDB-SingleCell
+    - name: Checkout TileDB-SOMA
       uses: actions/checkout@v2
 
     - name: Set up Python ${{ matrix.python-version }}
@@ -56,11 +56,22 @@ jobs:
         packages_dir: dist-wheel
         verbose: true
 
-    - name: Publish package to PyPI
-      if: matrix.os == 'ubuntu-22.04' && github.event_name == 'release' && !github.event.release.prerelease
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_TOKEN }}
-        packages_dir: dist-wheel
-        verbose: true
+# Later: when tiledbsoma is released
+#    - name: Publish package to PyPI
+#      if: matrix.os == 'ubuntu-22.04' && github.event_name == 'release' && !github.event.release.prerelease
+#      uses: pypa/gh-action-pypi-publish@master
+#      with:
+#        user: __token__
+#        password: ${{ secrets.PYPI_TOKEN }}
+#        packages_dir: dist-wheel
+#        verbose: true
+
+# Notes:
+# The above is fine for releases; notes here are for manual ops.
+# https://towardsdatascience.com/create-your-own-python-package-and-publish-it-into-pypi-9306a29bc116
+# TL;DR:
+# o cd apis/python
+# o python setup.py sdist
+# o python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+#   - Be sure to use username __token__ and password being the token you set up at test.pypi.org
+# o pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple tiledbsoma

.github/workflows/cpp-ci.yml

@@ -1,4 +1,4 @@
-name: TileDB-SingleCell C++ CI
+name: TileDB-SOMA C++ CI
 
 on:
   pull_request:
@@ -37,7 +37,7 @@ jobs:
       shell: bash
       if: ${{ runner.os != 'Windows' }}
 
-    - name: Checkout TileDB-SingleCell
+    - name: Checkout TileDB-SOMA
       uses: actions/checkout@v2
 
     - name: Set up Python ${{ matrix.python-version }}
@@ -59,7 +59,7 @@ jobs:
         mkdir -p test/soco
         ./apis/python/tools/ingestor --soco -o test/soco -n data/pbmc3k_processed.h5ad data/10x-pbmc-multiome-v1.0/subset_100_100.h5ad
 
-    - name: Run libtiledbsc tests
+    - name: Run libtiledbsoma tests
       shell: bash
       run: |
         source ./scripts/test

.gitignore

@@ -48,7 +48,7 @@ examples/cmake_project/build
 # Python distribution / packaging
 .eggs
 *.egg-info
-apis/python/src/tiledbsc/_version.py
+apis/python/src/tiledbsoma/_version.py
 
 /.quarto/
 

.readthedocs.yml

@@ -1,5 +1,5 @@
 # Note: builds at
-# https://readthedocs.com/projects/tiledb-inc-tiledb-singlecell/builds/
+# https://readthedocs.com/projects/tiledb-inc-tiledb-soma/builds/
 # (permissioned)
 
 # Don't build any extra formats
@@ -25,7 +25,7 @@ build:
   tools:
     python: "3.8"
   commands:
-    # `pip install -e .` or `python setup.py develop` will _not_ let python find the tiledbsc package
+    # `pip install -e .` or `python setup.py develop` will _not_ let python find the tiledbsoma package
     # within sphinx build
     #- apt-get install python3-sphinx
     - python -m pip install -r doc/requirements_doc.txt

CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# Contributing to TileDB-SingleCell
+# Contributing to TileDB-SOMA
 
-Thanks for your interest in TileDB-SingleCell. The notes below give some pointers for filing issues and bug reports, or contributing to the code.
+Thanks for your interest in TileDB-SOMA. The notes below give some pointers for filing issues and bug reports, or contributing to the code.
 
 ## Contribution Checklist
 - Reporting a bug? Please include the following information
   - operating system and version (windows, linux, macos, etc.)
-  - TileDB and TileDB-SingleCell version (for example, the output of `conda list` or `git status`).
+  - TileDB and TileDB-SOMA 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.
 
 ## Contributing Code
-*By contributing code to TileDB-SingleCell, you are agreeing to release it under the [MIT License](https://github.com/TileDB-Inc/TileDB/tree/dev/LICENSE).*
+*By contributing code to TileDB-SOMA, you are agreeing to release it under the [MIT License](https://github.com/TileDB-Inc/TileDB/tree/dev/LICENSE).*
 
 ### Contribution Workflow
 
-- [Please follow these instructions to build from source](https://docs.tiledb.com/developer/tiledbsc/installation)
+- [Please follow these instructions to build from source](https://docs.tiledb.com/developer/tiledbsoma/installation)
 - Make changes locally, then rebuild as appropriate for the level of changes (e.g.: `make` for `libtilebsc` 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 [`main` branch of TileDB-SC](https://github.com/TileDB-Inc/TileDB-SC/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-SOMA](https://github.com/TileDB-Inc/TileDB-SOMA/tree/master).

Doxyfile

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "TileDB-SingleCell"
+PROJECT_NAME           = "TileDB-SOMA"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -864,7 +864,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = libtiledbsc/include libtiledbsc/src
+INPUT                  = libtiledbsoma/include libtiledbsoma/src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

README.md

@@ -1,8 +1,8 @@
 <a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/dev/doc/source/_static/tiledb-logo_color_no_margin_@4x.png" alt="TileDB logo" width="400"></a>
 
-[![TileDB-SingleCell CI](https://github.com/single-cell-data/TileDB-SingleCell/actions/workflows/ci.yml/badge.svg)](https://github.com/single-cell-data/TileDB-SingleCell/actions/workflows/ci.yml)
+[![TileDB-SOMA CI](https://github.com/single-cell-data/TileDB-SOMA/actions/workflows/ci.yml/badge.svg)](https://github.com/single-cell-data/TileDB-SOMA/actions/workflows/ci.yml)
 
-# TileDB-SingleCell
+# TileDB-SOMA
 
 A C++ library with APIs in Python and R for efficient storage and retrieval of single-cell data using [TileDB Embedded][tiledb].
 

apis/python/README-dev.md

@@ -5,30 +5,10 @@
   * `flake8 . tools/[a-z]*`
   * `mypy .`
   * `python -m pytest tests`
-* And/or you can follow https://github.com/single-cell-data/TileDB-SingleCell/pull/193:
+* And/or you can follow https://github.com/single-cell-data/TileDB-SOMA/pull/193:
   * `pip install pre-commit && pre-commit install`
   * Then on every `git commit` all configured linters will be run locally on the changed files, and the commit will be blocked if there is any error.
 * PyPI:
-  * https://pypi.org/project/tiledbsc/
+  * https://pypi.org/project/tiledbsoma/
   * `tiledbinc` is an owner
-  * See https://github.com/single-cell-data/TileDB-SingleCell/pull/178 for setups that were done
-* Public-bucket status quo:
-  * `s3://tiledb-singlecell-data`
-
-```
-aws-login
-cd ~/tiledb-singlecell-data
-aws --profile prod-admin s3 sync . s3://tiledb-singlecell-data
-```
-
-  * `s3://tiledb-singlecell-docs`
-
-```
-aws-login
-cd ~/git/single-cell-data/TileDB-SingleCell/apis/python
-sh mkmd.sh
-cd ~/git/single-cell-data/TileDB-SingleCell
-quarto render
-aws --profile prod-admin s3 sync docs s3://tiledb-singlecell-docs/docs
-reload and double-check https://tiledb-singlecell-docs.s3.amazonaws.com/docs/overview.html
-```
+  * See https://github.com/single-cell-data/TileDB-SOMA/pull/178 for setups that were done