Refactoring gc_derivatization

.github/workflows/anaconda.yaml

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+name: Anaconda Build
+
+on: ['push', 'pull_request', 'workflow_dispatch']
+
+jobs:
+  anaconda_build:
+    name: Anaconda Build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Create build environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: gc-meox-tms-build
+          auto-update-conda: true
+          environment-file: conda/environment-build.yaml
+          python-version: 3.8
+      - name: Show conda config
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          conda env list
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python
+          python --version
+      - name: Show environment variables
+        shell: bash -l {0}
+        run: |
+          env | sort
+      - name: Build the conda package
+        shell: bash -l {0}
+        run: |
+          export BUILDDIR=$RUNNER_TEMP/gc-meox-tms/_build
+          [ "$RUNNING_OS" = "Windows" ] && export BUILDDIR=$RUNNER_TEMP\\gc-meox-tms\\_build
+          conda config --set anaconda_upload no
+          conda build --numpy 1.18.1 --no-include-recipe \
+            --channel bioconda --channel conda-forge \
+            --croot ${BUILDDIR} \
+            ./conda
+      - name: Upload package artifact from build
+        uses: actions/upload-artifact@v2
+        with:
+          name: conda-package-artifact
+          path: ${{ runner.temp }}/gc-meox-tms/_build
+          retention-days: 1

.github/workflows/project_automation.yml

@@ -0,0 +1,11 @@
+name: Add issues to project
+
+on:
+  issues:
+    types:
+      - opened
+
+jobs:
+  call-workflow:
+    uses: recetox/galaxytools/.github/workflows/add_issue_to_project.yml@master
+    secrets: inherit

.github/workflows/publish_pypi.yaml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+        python -m build --sdist --wheel
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1.8
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/python-package-conda.yaml

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+name: Python Package using Conda
+
+on: ['push', 'pull_request', 'workflow_dispatch']
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Add conda to PATH
+        run: |
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install dependencies
+        run: |
+          conda update conda
+          conda env update --file conda/environment-dev.yaml --name base
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml

.github/workflows/python-package.yaml

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+name: Python Package
+
+on: ['push', 'pull_request', 'workflow_dispatch']
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10']
+
+    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
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
+      - uses: actions/upload-artifact@v3
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
+        with:
+          name: coverage-report
+          path: |
+            coverage.xml
+            xunit-result.xml
+
+  sonar-cloud:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Pull coverage report
+        uses: actions/download-artifact@v2
+        with:
+          name: coverage-report
+          path: ${{ github.workspace }}
+      - name: Adjust coverage source path
+        run: sed -i "s+$PWD/++g" coverage.xml
+      - name: SonarCloud Scan
+        if: env.SONAR_TOKEN != null
+        uses: sonarsource/sonarcloud-github-action@master
+        with:
+          args: >
+            -Dsonar.projectKey=RECETOX_gc-meox-tms
+            -Dsonar.organization=recetox
+            -Dsonar.host.url=https://sonarcloud.io
+            -Dsonar.python.version="3.10"
+            -Dsonar.sources=gc_meox_tms/
+            -Dsonar.tests=tests/
+            -Dsonar.python.coverage.reportPaths=coverage.xml
+            -Dsonar.python.xunit.reportPath=xunit-result.xml
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.0.1]
+
+### Added
+* documented functions with docstrings to make use of Python's built-in `help()` function [#23](https://github.com/RECETOX/gc-meox-tms/pull/23)
+* added developer documentation [#23](https://github.com/RECETOX/gc-meox-tms/pull/23)
+* added `Publish to PyPi` GitHub Actions workflow [#24](https://github.com/RECETOX/gc-meox-tms/pull/24)
+
+## [1.0.0]
+
+### Added
+* added **Anaconda build**, **Python Package with pip** (inc. **SonarCloud**), and **Python Package with Conda** GH Actions.
+* added test coverage for main and IO functionality
+* added conda dev environment and conda meta.yaml recipe
+* added CHANGELOG.md
+
+### Changed
+* changed package structure
+* divided main functionality, IO handling, and CLI into designated modules
+
+### Fixed
+* fixed not working examples in IPython notebook

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 RECETOX
+
+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.