scdataloader 1.0.6__tar.gz → 1.2.1__tar.gz

scdataloader-1.2.1/.cursorignore

@@ -0,0 +1,21 @@
+*.json
+*.csv
+*.txt
+*.md
+*.ipynb
+*.Rmd
+*.Rproj
+*.Rproj.user
+*.parquet
+*.ckpt
+*.h5ad
+site/
+*.lamindb
+*.lndb
+*.out
+*.html
+*.pdf
+*.npy
+*.npz
+*.whl
+*.gz

scdataloader-1.2.1/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug, help wanted
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

scdataloader-1.2.1/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement, question
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

scdataloader-1.2.1/.github/PULL_REQUEST_TEMPLATE.md

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+### Summary :memo:
+_Write an overview about it._
+
+### Details
+_Describe more what you did on changes._
+1. (...)
+2. (...)
+
+### Bugfixes :bug: (delete if dind't have any)
+-
+
+### Checks
+- [ ] Closed #798
+- [ ] Tested Changes
+- [ ] Stakeholder Approval

scdataloader-1.2.1/.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

scdataloader-1.2.1/.github/release_message.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+previous_tag=$(git tag --sort=-creatordate | sed -n 2p)
+git shortlog "${previous_tag}.." | sed 's/^./    &/'

scdataloader-1.2.1/.github/rename_project.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+while getopts a:n:u:d: flag
+do
+    case "${flag}" in
+        a) author=${OPTARG};;
+        n) name=${OPTARG};;
+        u) urlname=${OPTARG};;
+        d) description=${OPTARG};;
+    esac
+done
+
+echo "Author: $author";
+echo "Project Name: $name";
+echo "Project URL name: $urlname";
+echo "Description: $description";
+
+echo "Renaming project..."
+
+original_author="jkobject"
+original_name="scdataloader"
+original_urlname="scDataLoader"
+original_description="Awesome scdataloader created by jkobject"
+# for filename in $(find . -name "*.*") 
+for filename in $(git ls-files) 
+do
+    sed -i "s/$original_author/$author/g" $filename
+    sed -i "s/$original_name/$name/g" $filename
+    sed -i "s/$original_urlname/$urlname/g" $filename
+    sed -i "s/$original_description/$description/g" $filename
+    echo "Renamed $filename"
+done
+
+mv scdataloader $name
+
+# This command runs only once on GHA!
+rm -rf .github/template.yml

scdataloader-1.2.1/.github/workflows/main.yml

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+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  ci:
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.10"]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install project
+        run: make virtualenv
+        continue-on-error: false
+      - name: Run linter
+        run: make lint
+        continue-on-error: false
+      - name: Run tests
+        run: make test
+      - name: "Upload coverage to Codecov"
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

scdataloader-1.2.1/.github/workflows/release.yml

@@ -0,0 +1,48 @@
+name: Upload Python Package
+
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - "*" # Push events to matching v*, i.e. v1.0, v20.15.10
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  release:
+    name: Create Release
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # by default, it uses a depth of 1
+          # this fetches all history so that we can read each commit
+          fetch-depth: 0
+      - name: Generate Changelog
+        run: .github/release_message.sh > release_message.md
+      - name: Release
+        uses: softprops/action-gh-release@v1
+        with:
+          body_path: release_message.md
+
+  deploy:
+    needs: release
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.10"]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Build and publish
+        run: |
+          uv build && uv publish -u __token__ -p ${{ secrets.POETRY_TOKEN }}

scdataloader-1.2.1/.gitignore

@@ -0,0 +1,133 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# templates
+.github/templates/*
+.DS_Store

scdataloader-1.2.1/ABOUT_THIS_TEMPLATE.md

@@ -0,0 +1,70 @@
+## Structure
+
+Lets take a look at the structure of this template:
+
+```text
+├── Containerfile            # The file to build a container using buildah or docker
+├── CONTRIBUTING.md          # Onboarding instructions for new contributors
+├── docs                     # Documentation site (add more .md files here)
+│   └── index.md             # The index page for the docs site
+├── .github                  # Github metadata for repository
+│   ├── release_message.sh   # A script to generate a release message
+│   └── workflows            # The CI pipeline for Github Actions
+├── .gitignore               # A list of files to ignore when pushing to Github
+├── HISTORY.md               # Auto generated list of changes to the project
+├── LICENSE                  # The license for the project
+├── Makefile                 # A collection of utilities to manage the project
+├── MANIFEST.in              # A list of files to include in a package
+├── mkdocs.yml               # Configuration for documentation site
+├── scdataloader             # The main python package for the project
+│   ├── base.py              # The base module for the project
+│   ├── __init__.py          # This tells Python that this is a package
+│   ├── __main__.py          # The entry point for the project
+│   └── VERSION              # The version for the project is kept in a static file
+├── README.md                # The main readme for the project
+├── setup.py                 # The setup.py file for installing and packaging the project
+├── requirements.txt         # An empty file to hold the requirements for the project
+├── requirements-test.txt    # List of requirements for testing and devlopment
+├── setup.py                 # The setup.py file for installing and packaging the project
+└── tests                    # Unit tests for the project (add mote tests files here)
+    ├── conftest.py          # Configuration, hooks and fixtures for pytest
+    ├── __init__.py          # This tells Python that this is a test package
+    └── test_base.py         # The base test case for the project
+```
+
+### Why to include `tests`, `history` and `Containerfile` as part of the release?
+
+The `MANIFEST.in` file is used to include the files in the release, once the 
+project is released to PyPI all the files listed on MANIFEST.in will be included
+even if the files are static or not related to Python.
+
+Some build systems such as RPM, DEB, AUR for some Linux distributions, and also
+internal repackaging systems tends to run the tests before the packaging is performed.
+
+The Containerfile can be useful to provide a safer execution environment for 
+the project when running on a testing environment.
+
+I added those files to make it easier for packaging in different formats.
+
+## The Makefile
+
+All the utilities for the template and project are on the Makefile
+
+```bash
+❯ make
+Usage: make <target>
+
+Targets:
+help:             ## Show the help.
+install:          ## Install the project in dev mode.
+fmt:              ## Format code using black & isort.
+lint:             ## Run pep8, black, mypy linters.
+test: lint        ## Run tests and generate coverage report.
+watch:            ## Run tests on every change.
+clean:            ## Clean unused files.
+virtualenv:       ## Create a virtual environment.
+release:          ## Create a new tag for release.
+docs:             ## Build the documentation.
+switch-to-poetry: ## Switch to poetry package manager.
+init:             ## Initialize the project based on an application template.
+```

scdataloader-1.2.1/CONTRIBUTING.md

@@ -0,0 +1,113 @@
+# How to develop on this project
+
+scdataloader welcomes contributions from the community.
+
+**You need PYTHON3!**
+
+This instructions are for linux base systems. (Linux, MacOS, BSD, etc.)
+## Setting up your own fork of this repo.
+
+- On github interface click on `Fork` button.
+- Clone your fork of this repo. `git clone git@github.com:YOUR_GIT_USERNAME/scDataLoader.git`
+- Enter the directory `cd scDataLoader`
+- Add upstream repo `git remote add upstream https://github.com/jkobject/scDataLoader`
+
+## Setting up your own virtual environment
+
+Run `make virtualenv` to create a virtual environment.
+then activate it with `source .venv/bin/activate`.
+
+## Install the project in develop mode
+
+Run `make install` to install the project in develop mode.
+
+## Run the tests to ensure everything is working
+
+Run `make test` to run the tests.
+
+## Create a new branch to work on your contribution
+
+Run `git checkout -b my_contribution`
+
+## Make your changes
+
+Edit the files using your preferred editor. (we recommend VIM or VSCode)
+
+## Format the code
+
+Run `make fmt` to format the code.
+
+## Run the linter
+
+Run `make lint` to run the linter.
+
+## Test your changes
+
+Run `make test` to run the tests.
+
+Ensure code coverage report shows `100%` coverage, add tests to your PR.
+
+## Build the docs locally
+
+Run `make docs` to build the docs.
+
+Ensure your new changes are documented.
+
+## Commit your changes
+
+This project uses [conventional git commit messages](https://www.conventionalcommits.org/en/v1.0.0/).
+
+Example: `fix(package): update setup.py arguments 🎉` (emojis are fine too)
+
+## Push your changes to your fork
+
+Run `git push origin my_contribution`
+
+## Submit a pull request
+
+On github interface, click on `Pull Request` button.
+
+Wait CI to run and one of the developers will review your PR.
+## Makefile utilities
+
+This project comes with a `Makefile` that contains a number of useful utility.
+
+```bash 
+❯ make
+Usage: make <target>
+
+Targets:
+help:             ## Show the help.
+install:          ## Install the project in dev mode.
+fmt:              ## Format code using black & isort.
+lint:             ## Run pep8, black, mypy linters.
+test: lint        ## Run tests and generate coverage report.
+watch:            ## Run tests on every change.
+clean:            ## Clean unused files.
+virtualenv:       ## Create a virtual environment.
+release:          ## Create a new tag for release.
+docs:             ## Build the documentation.
+switch-to-poetry: ## Switch to poetry package manager.
+init:             ## Initialize the project based on an application template.
+```
+
+## Making a new release
+
+This project uses [semantic versioning](https://semver.org/) and tags releases with `X.Y.Z`
+Every time a new tag is created and pushed to the remote repo, github actions will
+automatically create a new release on github and trigger a release on PyPI.
+
+For this to work you need to setup a secret called `PIPY_API_TOKEN` on the project settings>secrets, 
+this token can be generated on [pypi.org](https://pypi.org/account/).
+
+To trigger a new release all you need to do is.
+
+1. If you have changes to add to the repo
+    * Make your changes following the steps described above.
+    * Commit your changes following the [conventional git commit messages](https://www.conventionalcommits.org/en/v1.0.0/).
+2. Run the tests to ensure everything is working.
+4. Run `make release` to create a new tag and push it to the remote repo.
+
+the `make release` will ask you the version number to create the tag, ex: type `0.1.1` when you are asked.
+
+> **CAUTION**:  The make release will change local changelog files and commit all the unstaged changes you have.

scdataloader-1.2.1/Containerfile

@@ -0,0 +1,5 @@
+FROM python:3.7-slim
+COPY . /app
+WORKDIR /app
+RUN pip install .
+CMD ["scdataloader"]