diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml deleted file mode 100644 index 2849ba7..0000000 --- a/.github/workflows/python-publish.yml +++ /dev/null @@ -1,84 +0,0 @@ -# This workflow will upload a Python Package using Twine when a release is created -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries - -# This workflow uses actions that are not certified by GitHub. -# They are provided by a third-party and are governed by -# separate terms of service, privacy policy, and support -# documentation. - -name: Upload Python Package - -on: - push: - tags: - - 'v*' - -permissions: - contents: read - -jobs: - deploy: - - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: '3.x' - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install build twine sphinx sphinx_rtd_theme - - name: Generate documentation with Sphinx - run: | - sphinx-apidoc -o docs src/waltlabtools - sphinx-build -b html docs docs/_build - - name: Build package - run: python -m build - - name: Build wheels - run: python -m build --wheel - - name: Check built distributions - run: twine check dist/* - - name: Upload to PyPI - if: startsWith(github.ref, 'refs/tags/') - env: - TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} - TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} - run: twine upload dist/* - # - name: Upload to Anaconda - # if: startsWith(github.ref, 'refs/tags/') - # env: - # ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }} - # run: | - # anaconda login --username tylerdougan --password $ANACONDA_API_TOKEN - # anaconda upload dist/*.whl - - release: - needs: deploy - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Create GitHub Release - uses: actions/create-release@v1 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - with: - tag_name: ${{ github.ref }} - release_name: Release ${{ github.ref }} - draft: false - prerelease: false - body: | - Release notes for version ${{ github.ref }} - - - name: Upload release assets - uses: actions/upload-release-asset@v1 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - with: - upload_url: ${{ steps.create_release.outputs.upload_url }} - asset_path: dist/ - asset_name: $(basename $dist/*) - asset_content_type: application/zip diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml deleted file mode 100644 index 4b91006..0000000 --- a/.github/workflows/release.yml +++ /dev/null @@ -1,84 +0,0 @@ -name: Build, Test, and Release - -on: - push: - tags: - - 'v*' - - -jobs: - build: - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest, windows-latest, macos-latest] - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - python -m pip install build twine sphinx cibuildwheel sphinx_rtd_theme - # pip install -r requirements.txt - - - - name: Generate documentation with Sphinx - run: | - sphinx-apidoc -o docs src/waltlabtools - sphinx-build -b html docs docs/_build - - - name: Build wheels - run: cibuildwheel --output-dir dist - - - name: Check built distributions - run: twine check dist/* - - - name: Upload to PyPI - if: startsWith(github.ref, 'refs/tags/') - env: - TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} - TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} - run: twine upload dist/* - - # - name: Upload to Anaconda - # if: startsWith(github.ref, 'refs/tags/') - # env: - # ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }} - # run: | - # anaconda login --username tylerdougan --password $ANACONDA_API_TOKEN - # anaconda upload dist/*.whl - - release: - needs: build - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Create GitHub Release - uses: actions/create-release@v1 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - with: - tag_name: ${{ github.ref }} - release_name: Release ${{ github.ref }} - draft: false - prerelease: false - body: | - Release notes for version ${{ github.ref }} - - - name: Upload release assets - uses: actions/upload-release-asset@v1 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - with: - upload_url: ${{ steps.create_release.outputs.upload_url }} - asset_path: dist/ - asset_name: $(basename $dist/*) - asset_content_type: application/zip diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml deleted file mode 100644 index b7d022a..0000000 --- a/conda/conda_build_config.yaml +++ /dev/null @@ -1,6 +0,0 @@ -python: - - 3.6 - - 3.7 - - 3.8 - - 3.9 - - 3.10 \ No newline at end of file diff --git a/conda/meta.yaml b/conda/meta.yaml deleted file mode 100644 index 2a6ae79..0000000 --- a/conda/meta.yaml +++ /dev/null @@ -1,48 +0,0 @@ -{% set name = "waltlabtools" %} -{% set version = "0.5.5" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - -build: - noarch: python - number: 0 - string: py{{ environ.get("PY_VER") }}_{{ environ.get("GIT_DESCRIBE_NUMBER", 0) }} - script: {{ PYTHON }} -m pip install . -vv - -requirements: - build: - - python {{ python }} - - matplotlib>=3.3 - - numpy>=1.16 - - pandas>=0.25 - - scipy>=1.3 - - scikit-learn>=0.21 - - jax>=0.2 - - numba>=0.48 - - setuptools - host: - - python {{ python }} - - pip - run: - - python {{ python }} - - numpy >=1.16 - - scipy >=1.3 - - matplotlib-base >3.3 - - pandas >=0.25 - -about: - home: https://github.com/tylerdougan/waltlabtools - summary: A collection of tools for biomedical research assay analysis in Python. - license: GPL-3.0 - license_family: GPL3 - license_file: LICENSE - doc_url: https://waltlabtools.readthedocs.io - -extra: - recipe-maintainers: - - tylerdougan diff --git a/src/waltlabtools.egg-info/PKG-INFO b/src/waltlabtools.egg-info/PKG-INFO deleted file mode 100644 index 58cc306..0000000 --- a/src/waltlabtools.egg-info/PKG-INFO +++ /dev/null @@ -1,133 +0,0 @@ -Metadata-Version: 2.1 -Name: waltlabtools -Version: 1.0.0b1 -Summary: A collection of tools for biomedical research assay analysis in Python. -Home-page: https://github.com/tylerdougan/waltlabtools -Download-URL: https://pypi.org/project/waltlabtools/#files -Author: Tyler Dougan -Author-email: tyler_dougan@hst.harvard.edu -License: GNU General Public License v3 (GPLv3) -Project-URL: Bug Tracker, https://github.com/tylerdougan/waltlabtools/issues -Project-URL: Documentation, https://waltlabtools.readthedocs.io/README.html -Project-URL: Conda, https://anaconda.org/tylerdougan/waltlabtools -Keywords: python,numpy,modeling,curve-fitting,diagnostics,biomedical-data-science,calibration-curve,assay,elisa,concentrations,mosaic -Classifier: Programming Language :: Python :: 3 -Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) -Classifier: Operating System :: OS Independent -Requires-Python: >=3.6 -Description-Content-Type: text/x-rst -License-File: LICENSE -Requires-Dist: matplotlib>=3.3 -Requires-Dist: numpy>=1.16 -Requires-Dist: pandas>=0.25 -Requires-Dist: scipy>=1.3 -Requires-Dist: scikit-learn>=0.21 - -waltlabtools -============ - -.. image:: https://img.shields.io/conda/vn/tylerdougan/waltlabtools?label=Anaconda - :target: https://anaconda.org/tylerdougan/waltlabtools - :alt: Conda -.. image:: https://img.shields.io/pypi/v/waltlabtools?label=PyPI - :target: https://pypi.org/project/waltlabtools - :alt: PyPI -.. image:: https://img.shields.io/readthedocs/waltlabtools?label=Documentation - :target: https://waltlabtools.readthedocs.io/en/latest/ - :alt: Documentation -.. image:: https://img.shields.io/github/repo-size/tylerdougan/waltlabtools?label=GitHub - :target: https://github.com/tylerdougan/waltlabtools - :alt: GitHub - - -A collection of tools for biomedical research assay analysis in Python. - -Key Features ------------- - -- Analysis for assays such as - `digital ELISA `__, - including single-molecule array (Simoa) assays -- Read instrument-generated files and calculate calibration curves, - concentrations, limits of detection, and more -- Free and open-source software under the - `GNU General Public License v3 `__ - -Getting Started ---------------- - -Installation -^^^^^^^^^^^^ - -You can install waltlabtools using -`Anaconda `__ (recommended) or -`PyPI `__. If you're not comfortable -with the command line, begin by installing -`Anaconda Navigator `__. Then follow -`these instructions `__ -to add the channel ``tylerdougan``, and install waltlabtools from this channel. - -Alternatively, install waltlabtools from the command line with -``conda install -c tylerdougan waltlabtools`` (recommended; requires you to -first install Anaconda or -`Miniconda `__) or -``pip install waltlabtools`` (requires -`pip `__, which should come -with Python). - - -Dependencies -^^^^^^^^^^^^ - -- waltlabtools requires - - - `numpy `__ ≥ 1.10 - - - `scipy `__ ≥ 1.3 - -- If installing with pip or conda, numpy and scipy will be installed - automatically - -- Specific modules have additional requirements: - - - `waltlabtools.read `__ - (for importing data from Quanterix instruments) requires - - - `pandas `__ ≥ 0.25 - -- waltlabtools also plays well with - - - `JAX `__ - for accelerated numerical computing – waltlabtools will use jax.numpy - instead of numpy if jax is loaded - - - `JupyterLab `__ - for interactively writing code - - - `pandas `__ - for data import/export and organization - - - `matplotlib `__ for plotting - - - `scikit-learn `__ for data analysis - -All of these packages can all be installed using -`conda `__ -or `pip `__. - - -Usage -^^^^^ - -.. code-block:: python - - import waltlabtools as wlt # waltlabtools main functionality - ------ - - -Development of waltlabtools is led by the -`Walt Lab `__ for Advanced Diagnostics -at `Brigham and Women's Hospital `__, -`Harvard Medical School `__, and the -`Wyss Institute for Biologically Inspired Engineering `__. diff --git a/src/waltlabtools.egg-info/SOURCES.txt b/src/waltlabtools.egg-info/SOURCES.txt deleted file mode 100644 index c64330f..0000000 --- a/src/waltlabtools.egg-info/SOURCES.txt +++ /dev/null @@ -1,19 +0,0 @@ -LICENSE -README.rst -pyproject.toml -setup.cfg -setup.py -src/waltlabtools/__init__.py -src/waltlabtools/_backend.py -src/waltlabtools/_plot.py -src/waltlabtools/cal_curve.py -src/waltlabtools/core.py -src/waltlabtools/dropna.py -src/waltlabtools/model.py -src/waltlabtools/mosaic.py -src/waltlabtools/read.py -src/waltlabtools.egg-info/PKG-INFO -src/waltlabtools.egg-info/SOURCES.txt -src/waltlabtools.egg-info/dependency_links.txt -src/waltlabtools.egg-info/requires.txt -src/waltlabtools.egg-info/top_level.txt \ No newline at end of file diff --git a/src/waltlabtools.egg-info/dependency_links.txt b/src/waltlabtools.egg-info/dependency_links.txt deleted file mode 100644 index 8b13789..0000000 --- a/src/waltlabtools.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/src/waltlabtools.egg-info/requires.txt b/src/waltlabtools.egg-info/requires.txt deleted file mode 100644 index cd7db22..0000000 --- a/src/waltlabtools.egg-info/requires.txt +++ /dev/null @@ -1,5 +0,0 @@ -matplotlib>=3.3 -numpy>=1.16 -pandas>=0.25 -scipy>=1.3 -scikit-learn>=0.21 diff --git a/src/waltlabtools.egg-info/top_level.txt b/src/waltlabtools.egg-info/top_level.txt deleted file mode 100644 index 0ca9a47..0000000 --- a/src/waltlabtools.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -waltlabtools