cellarr-array 0.0.1__tar.gz

cellarr_array-0.0.1/.coveragerc

@@ -0,0 +1,28 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = cellarr_array
+# omit = bad_file.py
+
+[paths]
+source =
+    src/
+    */site-packages/
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:

cellarr_array-0.0.1/.github/workflows/publish-pypi.yml

@@ -0,0 +1,55 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Publish to PyPI
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      repository-projects: write
+      contents: write
+      pages: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build docs
+        run: |
+          tox -e docs
+
+      - run: touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      # This uses the trusted publisher workflow so no token is required.
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

cellarr_array-0.0.1/.github/workflows/run-tests.yml

@@ -0,0 +1,33 @@
+name: Run tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox

cellarr_array-0.0.1/.gitignore

@@ -0,0 +1,54 @@
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.DS_Store
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.coverage.*
+.tox
+junit*.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/api/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/
+.conda*/
+.python-version

cellarr_array-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.2
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell

cellarr_array-0.0.1/.readthedocs.yml

@@ -0,0 +1,27 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - {path: ., method: pip}

cellarr_array-0.0.1/AUTHORS.md

@@ -0,0 +1,3 @@
+# Contributors
+
+* Jayaram Kancherla [jayaram.kancherla@gmail.com](mailto:jayaram.kancherla@gmail.com)

cellarr_array-0.0.1/CHANGELOG.md

@@ -0,0 +1,13 @@
+# Changelog
+
+## Version 0.0.1
+
+Initial implementation of the sparse and dense arrays backed by TileDB. 
+
+- Supports reading of objects
+  - Directly slices the TileDB object is all arguments to subset are contiguous blocks. 
+  - Otherwise redirects them to `multi_index`, if one of the argument to subset is a slice, drops the last because of inclusive upper bounds in this method. 
+
+  This helps keeps slicing consistent across various operations and trying to be performant in the process.
+
+- Supports writing of various data objects into dense and sparse arrays. Expects all chunks to be aligned along the rows. 

cellarr_array-0.0.1/CONTRIBUTING.md

@@ -0,0 +1,371 @@
+```{todo} THIS IS SUPPOSED TO BE AN EXAMPLE. MODIFY IT ACCORDING TO YOUR NEEDS!
+
+   The document assumes you are using a source repository service that promotes a
+   contribution model similar to [GitHub's fork and pull request workflow].
+   While this is true for the majority of services (like GitHub, GitLab,
+   BitBucket), it might not be the case for private repositories (e.g., when
+   using Gerrit).
+
+   Also notice that the code examples might refer to GitHub URLs or the text
+   might use GitHub specific terminology (e.g., *Pull Request* instead of *Merge
+   Request*).
+
+   Please make sure to check the document having these assumptions in mind
+   and update things accordingly.
+```
+
+```{todo} Provide the correct links/replacements at the bottom of the document.
+```
+
+```{todo} You might want to have a look on [PyScaffold's contributor's guide],
+
+   especially if your project is open source. The text should be very similar to
+   this template, but there are a few extra contents that you might decide to
+   also include, like mentioning labels of your issue tracker or automated
+   releases.
+```
+
+# Contributing
+
+Welcome to `cellarr-array` contributor's guide.
+
+This document focuses on getting any potential contributor familiarized with
+the development processes, but [other kinds of contributions] are also appreciated.
+
+If you are new to using [git] or have never collaborated in a project previously,
+please have a look at [contribution-guide.org]. Other resources are also
+listed in the excellent [guide created by FreeCodeCamp] [^contrib1].
+
+Please notice, all users and contributors are expected to be **open,
+considerate, reasonable, and respectful**. When in doubt,
+[Python Software Foundation's Code of Conduct] is a good reference in terms of
+behavior guidelines.
+
+## Issue Reports
+
+If you experience bugs or general issues with `cellarr-array`, please have a look
+on the [issue tracker].
+If you don't see anything useful there, please feel free to fire an issue report.
+
+:::{tip}
+Please don't forget to include the closed issues in your search.
+Sometimes a solution was already reported, and the problem is considered
+**solved**.
+:::
+
+New issue reports should include information about your programming environment
+(e.g., operating system, Python version) and steps to reproduce the problem.
+Please try also to simplify the reproduction steps to a very minimal example
+that still illustrates the problem you are facing. By removing other factors,
+you help us to identify the root cause of the issue.
+
+## Documentation Improvements
+
+You can help improve `cellarr-array` docs by making them more readable and coherent, or
+by adding missing information and correcting mistakes.
+
+`cellarr-array` documentation uses [Sphinx] as its main documentation compiler.
+This means that the docs are kept in the same repository as the project code, and
+that any documentation update is done in the same way was a code contribution.
+
+```{todo} Don't forget to mention which markup language you are using.
+
+    e.g.,  [reStructuredText] or [CommonMark] with [MyST] extensions.
+```
+
+```{todo} If your project is hosted on GitHub, you can also mention the following tip:
+
+   :::{tip}
+      Please notice that the [GitHub web interface] provides a quick way of
+      propose changes in `cellarr-array`'s files. While this mechanism can
+      be tricky for normal code contributions, it works perfectly fine for
+      contributing to the docs, and can be quite handy.
+
+      If you are interested in trying this method out, please navigate to
+      the `docs` folder in the source [repository], find which file you
+      would like to propose changes and click in the little pencil icon at the
+      top, to open [GitHub's code editor]. Once you finish editing the file,
+      please write a message in the form at the bottom of the page describing
+      which changes have you made and what are the motivations behind them and
+      submit your proposal.
+   :::
+```
+
+When working on documentation changes in your local machine, you can
+compile them using [tox] :
+
+```
+tox -e docs
+```
+
+and use Python's built-in web server for a preview in your web browser
+(`http://localhost:8000`):
+
+```
+python3 -m http.server --directory 'docs/_build/html'
+```
+
+## Code Contributions
+
+```{todo} Please include a reference or explanation about the internals of the project.
+
+   An architecture description, design principles or at least a summary of the
+   main concepts will make it easy for potential contributors to get started
+   quickly.
+```
+
+### Submit an issue
+
+Before you work on any non-trivial code contribution it's best to first create
+a report in the [issue tracker] to start a discussion on the subject.
+This often provides additional considerations and avoids unnecessary work.
+
+### Create an environment
+
+Before you start coding, we recommend creating an isolated [virtual environment]
+to avoid any problems with your installed Python packages.
+This can easily be done via either [virtualenv]:
+
+```
+virtualenv <PATH TO VENV>
+source <PATH TO VENV>/bin/activate
+```
+
+or [Miniconda]:
+
+```
+conda create -n cellarr-array python=3 six virtualenv pytest pytest-cov
+conda activate cellarr-array
+```
+
+### Clone the repository
+
+1. Create an user account on GitHub if you do not already have one.
+
+2. Fork the project [repository]: click on the *Fork* button near the top of the
+   page. This creates a copy of the code under your account on GitHub.
+
+3. Clone this copy to your local disk:
+
+   ```
+   git clone git@github.com:YourLogin/cellarr-array.git
+   cd cellarr-array
+   ```
+
+4. You should run:
+
+   ```
+   pip install -U pip setuptools -e .
+   ```
+
+   to be able to import the package under development in the Python REPL.
+
+   ```{todo} if you are not using pre-commit, please remove the following item:
+   ```
+
+5. Install [pre-commit]:
+
+   ```
+   pip install pre-commit
+   pre-commit install
+   ```
+
+   `cellarr-array` comes with a lot of hooks configured to automatically help the
+   developer to check the code being written.
+
+### Implement your changes
+
+1. Create a branch to hold your changes:
+
+   ```
+   git checkout -b my-feature
+   ```
+
+   and start making changes. Never work on the main branch!
+
+2. Start your work on this branch. Don't forget to add [docstrings] to new
+   functions, modules and classes, especially if they are part of public APIs.
+
+3. Add yourself to the list of contributors in `AUTHORS.rst`.
+
+4. When you’re done editing, do:
+
+   ```
+   git add <MODIFIED FILES>
+   git commit
+   ```
+
+   to record your changes in [git].
+
+   ```{todo} if you are not using pre-commit, please remove the following item:
+   ```
+
+   Please make sure to see the validation messages from [pre-commit] and fix
+   any eventual issues.
+   This should automatically use [flake8]/[black] to check/fix the code style
+   in a way that is compatible with the project.
+
+   :::{important}
+   Don't forget to add unit tests and documentation in case your
+   contribution adds an additional feature and is not just a bugfix.
+
+   Moreover, writing a [descriptive commit message] is highly recommended.
+   In case of doubt, you can check the commit history with:
+
+   ```
+   git log --graph --decorate --pretty=oneline --abbrev-commit --all
+   ```
+
+   to look for recurring communication patterns.
+   :::
+
+5. Please check that your changes don't break any unit tests with:
+
+   ```
+   tox
+   ```
+
+   (after having installed [tox] with `pip install tox` or `pipx`).
+
+   You can also use [tox] to run several other pre-configured tasks in the
+   repository. Try `tox -av` to see a list of the available checks.
+
+### Submit your contribution
+
+1. If everything works fine, push your local branch to the remote server with:
+
+   ```
+   git push -u origin my-feature
+   ```
+
+2. Go to the web page of your fork and click "Create pull request"
+   to send your changes for review.
+
+   ```{todo} if you are using GitHub, you can uncomment the following paragraph
+
+      Find more detailed information in [creating a PR]. You might also want to open
+      the PR as a draft first and mark it as ready for review after the feedbacks
+      from the continuous integration (CI) system or any required fixes.
+
+   ```
+
+### Troubleshooting
+
+The following tips can be used when facing problems to build or test the
+package:
+
+1. Make sure to fetch all the tags from the upstream [repository].
+   The command `git describe --abbrev=0 --tags` should return the version you
+   are expecting. If you are trying to run CI scripts in a fork repository,
+   make sure to push all the tags.
+   You can also try to remove all the egg files or the complete egg folder, i.e.,
+   `.eggs`, as well as the `*.egg-info` folders in the `src` folder or
+   potentially in the root of your project.
+
+2. Sometimes [tox] misses out when new dependencies are added, especially to
+   `setup.cfg` and `docs/requirements.txt`. If you find any problems with
+   missing dependencies when running a command with [tox], try to recreate the
+   `tox` environment using the `-r` flag. For example, instead of:
+
+   ```
+   tox -e docs
+   ```
+
+   Try running:
+
+   ```
+   tox -r -e docs
+   ```
+
+3. Make sure to have a reliable [tox] installation that uses the correct
+   Python version (e.g., 3.7+). When in doubt you can run:
+
+   ```
+   tox --version
+   # OR
+   which tox
+   ```
+
+   If you have trouble and are seeing weird errors upon running [tox], you can
+   also try to create a dedicated [virtual environment] with a [tox] binary
+   freshly installed. For example:
+
+   ```
+   virtualenv .venv
+   source .venv/bin/activate
+   .venv/bin/pip install tox
+   .venv/bin/tox -e all
+   ```
+
+4. [Pytest can drop you] in an interactive session in the case an error occurs.
+   In order to do that you need to pass a `--pdb` option (for example by
+   running `tox -- -k <NAME OF THE FALLING TEST> --pdb`).
+   You can also setup breakpoints manually instead of using the `--pdb` option.
+
+## Maintainer tasks
+
+### Releases
+
+```{todo} This section assumes you are using PyPI to publicly release your package.
+
+   If instead you are using a different/private package index, please update
+   the instructions accordingly.
+```
+
+If you are part of the group of maintainers and have correct user permissions
+on [PyPI], the following steps can be used to release a new version for
+`cellarr-array`:
+
+1. Make sure all unit tests are successful.
+2. Tag the current commit on the main branch with a release tag, e.g., `v1.2.3`.
+3. Push the new tag to the upstream [repository],
+   e.g., `git push upstream v1.2.3`
+4. Clean up the `dist` and `build` folders with `tox -e clean`
+   (or `rm -rf dist build`)
+   to avoid confusion with old builds and Sphinx docs.
+5. Run `tox -e build` and check that the files in `dist` have
+   the correct version (no `.dirty` or [git] hash) according to the [git] tag.
+   Also check the sizes of the distributions, if they are too big (e.g., >
+   500KB), unwanted clutter may have been accidentally included.
+6. Run `tox -e publish -- --repository pypi` and check that everything was
+   uploaded to [PyPI] correctly.
+
+[^contrib1]: Even though, these resources focus on open source projects and
+    communities, the general ideas behind collaborating with other developers
+    to collectively create software are general and can be applied to all sorts
+    of environments, including private companies and proprietary code bases.
+
+
+[black]: https://pypi.org/project/black/
+[commonmark]: https://commonmark.org/
+[contribution-guide.org]: http://www.contribution-guide.org/
+[creating a pr]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request
+[descriptive commit message]: https://chris.beams.io/posts/git-commit
+[docstrings]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[first-contributions tutorial]: https://github.com/firstcontributions/first-contributions
+[flake8]: https://flake8.pycqa.org/en/stable/
+[git]: https://git-scm.com
+[github web interface]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository
+[github's code editor]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository
+[github's fork and pull request workflow]: https://guides.github.com/activities/forking/
+[guide created by freecodecamp]: https://github.com/freecodecamp/how-to-contribute-to-open-source
+[miniconda]: https://docs.conda.io/en/latest/miniconda.html
+[myst]: https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html
+[other kinds of contributions]: https://opensource.guide/how-to-contribute
+[pre-commit]: https://pre-commit.com/
+[pypi]: https://pypi.org/
+[pyscaffold's contributor's guide]: https://pyscaffold.org/en/stable/contributing.html
+[pytest can drop you]: https://docs.pytest.org/en/stable/usage.html#dropping-to-pdb-python-debugger-at-the-start-of-a-test
+[python software foundation's code of conduct]: https://www.python.org/psf/conduct/
+[restructuredtext]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[tox]: https://tox.readthedocs.io/en/stable/
+[virtual environment]: https://realpython.com/python-virtual-environments-a-primer/
+[virtualenv]: https://virtualenv.pypa.io/en/stable/
+
+
+```{todo} Please review and change the following definitions:
+```
+
+[repository]: https://github.com/<USERNAME>/cellarr-array
+[issue tracker]: https://github.com/<USERNAME>/cellarr-array/issues

cellarr_array-0.0.1/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2025 Jayaram Kancherla
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.