Stable and tested pre-release (#22)

* added example and parser * fixed stash error * API update * fixed test * API update * fixed parser * API update * functionality now in PlateManager class * Refactor import statements for PlateManager class * Refactor import statements for PlateManager class * Remove poetry.lock from version control * Refactor import statements for PlateManager class deleted unused * added and fixed unit tests * specified correct verion * added parser integration tests * Refactor Python version matrix in tests.yml * Add coverage badge workflow * Update dependency installation in coverage workflow * Update dependency installation in coverage workflow * Refactor coverage workflow and add coverage badge generation * Refactor coverage workflow and remove coverage badge generation * Refactor import statements to use lowercase package names * Rename MTPHandler to temp_handler * Refactor temp_handler package and remove unused modules * Refactor temp_handler package and remove unused modules lowercase naming * Delete MTPHandler directory * added docs and tests * Refactor temp_handler package and remove unused modules * Refactor test workflow to include nbval and nbval-lax options * Refactor README.md to update project overview and installation instructions * Deleted original files to prepare for case renaming * Refactor MTPHandler package and remove unused modules * Delete MTPHandler directory * bump 0.2.5 * resolved merge coflicts --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com>
FAIRChemistry · Sep 21, 2024 · 64f9a78 · 64f9a78
1 parent 6d27a7f
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diff --git a/.github/workflows/publish_pypi.yaml b/.github/workflows/publish_pypi.yaml
@@ -0,0 +1,117 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    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 pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/mtphandler  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/mtphandler
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -27,4 +27,4 @@ jobs:
 
       - name: Run tests with pytest
         run: |
-          poetry run pytest
+          poetry run pytest --nbval --nbval-lax
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 haeussma
+Copyright (c) 2023 Max Häussler
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
-# MTPHandler - _🚧 currently unstable 🚧_
+# MTPHandler
 
 [![Documentation](https://img.shields.io/badge/Documentation-Online-blue.svg)](https://fairchemistry.github.io/MTPHandler/)
 [![Tests](https://github.com/FAIRChemistry/MTPHandler/actions/workflows/tests.yml/badge.svg)](https://github.com/FAIRChemistry/MTPHandler/actions/workflows/tests.yml)
-[![PyPI version](https://badge.fury.io/py/MTPHandler.svg)](https://badge.fury.io/py/MTPHandler)
+[![PyPI version](https://badge.fury.io/py/mtphandler.svg)](https://badge.fury.io/py/mtphandler)
 
 
 ## ℹ️ Overview
 
-MTPHandler is a tool for managing and processing data from microtiter plates. It allows to directly read in the output files of various photometers, enabling low friction data processing. The tool facilitates a workflow for reading in raw data, assigning molecules with their respective concentration and and unit to wells. Furthermore, wells for creating a standard curve can be automatically detected and applied to different calibration models, which can be used to calculate the concentration of unknown samples. Finally, the plate data can be transformed into time-course concentration data in the EnzymeML format for subsequent analysis of the concentration data.
+`mtphandler` is a tool for managing and processing data from microtiter plates. It allows to directly read in the output files of various photometers, enabling low friction data processing. The tool facilitates a workflow for reading in raw data, assigning molecules with their respective concentration and and unit to wells. Furthermore, wells for creating a standard curve can be automatically detected and applied to different calibration models, which can be used to calculate the concentration of unknown samples. Finally, the plate data can be transformed into time-course concentration data in the EnzymeML format for subsequent analysis of the concentration data.
 
 ``` mermaid
 graph LR
@@ -65,13 +65,14 @@ The following table lists the currently supported plate readers output files:
 
 ## 📦 Installation
 
-Install `MTPHandler` via pip:
+Install `MTPHandler` from PyPI:
 
 ```bash
 pip install MTPHandler # 🚧 not released yet
 ```
 or from source:
-
 ```bash
 pip install git+https://github.com/FAIRChemistry/MTPHandler.git
 ```
+
+Please refer to the [documentation](https://fairchemistry.github.io/MTPHandler/) for more information on how to use the package.