initial commit

.cruft.json

@@ -0,0 +1,18 @@
+{
+  "template": "https://github.com/DHARPA-Project/kiara_plugin.develop.git",
+  "commit": "e2d43d57283f53eaf5144915075567eff38d738a",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "full_name": "Mariella De Crouy Chanel",
+      "email": "mariella.decrouychanel@uni.lu",
+      "project_name": "topic_modelling",
+      "project_slug": "topic_modelling",
+      "project_short_description": "A Kiara plugin toho create a Topic Modelling workflow.",
+      "github_user": "DHARPA-Project",
+      "anaconda_user": "dharpa",
+      "_template": "https://github.com/DHARPA-Project/kiara_plugin.develop.git"
+    }
+  },
+  "directory": null
+}

.envrc.disabled

@@ -0,0 +1,3 @@
+layout python3
+# or, uncomment for specific 'base'-version of python, e.g.:
+# layout python "$HOME/.asdf/installs/python/3.9.2/bin/python"

.git_archival.txt

@@ -0,0 +1 @@
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+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]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/suggest-a-module.md

@@ -0,0 +1,20 @@
+---
+name: Suggest a module
+about: Suggest a new module for kiara
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Module description**
+A description of the module, this will be copied into the actual module later on, so make sure you explain the module purpose with kiara users in mind. Use a short one-sentence overview as the first paragraph, then use as many paragraphs as you need to explain the module purpose and what it does.
+
+**Inputs**
+List all the inputs this module would need, along with their types, a short description, and whether they are required or should have default values. It can be assumed that a graph will always be an input, so you can skip that.
+
+**Outupts**
+List all the outputs this module would produce, along with their types and a short description of what they are.
+
+**Example code**
+If you have example code how to do what you are proposing to do, copy and paste it here.

.github/workflows/build-darwin.yaml

@@ -0,0 +1,26 @@
+name: "darwin tests for 'kiara_plugin.topic_modelling'"
+# This workflow is triggered on pushes to the repository.
+on: [push]
+env:
+  DEVELOPER_DIR: /Applications/Xcode_12.4.app/Contents/Developer
+  MACOSX_DEPLOYMENT_TARGET: 10.15
+
+jobs:
+  test-darwin:
+    name: pytest on darwin
+    runs-on: macos-11
+    strategy:
+      matrix:
+        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - name: "Set up Python ${{ matrix.python_version }}"
+        uses: actions/setup-python@v4
+        with:
+          python-version: "${{ matrix.python_version }}"
+      - uses: actions/checkout@v3
+      - name: install kiara_plugin.topic_modelling
+        run: pip install -U --extra-index-url https://pypi.fury.io/dharpa/ .[all,dev_testing]
+      - name: display installed kiara and module package versions
+        run: pip list | grep kiara
+      - name: Test with pytest
+        run: make test

.github/workflows/build-linux.yaml

@@ -0,0 +1,190 @@
+name: "linux tests and documentation builds for 'kiara_plugin.topic_modelling'"
+# This workflow is triggered on pushes to the repository.
+on: [push]
+
+jobs:
+
+#  commitlint:
+#    name: lint commit message
+#    runs-on: ubuntu-latest
+#    steps:
+#      - uses: actions/checkout@v2
+#        with:
+#          fetch-depth: 0
+#      - uses: wagoid/commitlint-github-action@v4
+
+  test-linux:
+    name: pytest on linux
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - name: "Set up Python ${{ matrix.python_version }}"
+        uses: actions/setup-python@v4
+        with:
+          python-version: "${{ matrix.python_version }}"
+      - uses: actions/checkout@v3
+      - name: install kiara_plugin.topic_modelling
+        run: pip install -U .[all,dev_testing]
+      - name: display installed kiara and module package versions
+        run: pip list | grep kiara
+      - name: Test with pytest
+        run: make test
+
+# Uncomment this if you have coveralls.io setup with this repo
+#  coverage:
+#    name: create and publish test coverage
+#    runs-on: ubuntu-latest
+#    steps:
+#      - name: "Set up Python 3.9"
+#        uses: actions/setup-python@v4
+#        with:
+#          python-version: "3.9"
+#      - uses: actions/checkout@v3
+#      - name: install kiara
+#        run: pip install -U .[all,dev_testing]
+#      - name: display installed kiara and module package versions
+#        run: pip list | grep kiara
+#      - name: Run coverage
+#        run: coverage run -m pytest tests
+#      - name: coveralls
+#        uses: coverallsapp/github-action@v2
+
+# Uncomment this if you want to run mypy
+#  mypy-linux:
+#    name: mypy check on linux
+#    runs-on: ubuntu-latest
+#    strategy:
+#      matrix:
+#        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+#    steps:
+#      - name: "Set up Python ${{ matrix.python_version }}"
+#        uses: actions/setup-python@v4
+#        with:
+#          python-version: "${{ matrix.python_version }}"
+#      - uses: actions/checkout@v3
+#      - name: install kiara_plugin.topic_modelling
+#        run: pip install -U .[all,dev_testing]
+#      - name: Test with mypy
+#        run: make mypy
+
+  linting-linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: pip cache
+        id: pip-cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.*') }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U ruff
+      # Include `--format=github` to enable automatic inline annotations.
+      - name: Run Ruff
+        run: ruff --output-format=github src/
+
+  build_python_package:
+    name: build python package
+    runs-on: ubuntu-latest
+    needs:
+      - test-linux
+#      - mypy-linux
+#      - linting-linux
+    steps:
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: install pip
+        run: pip install -U pip setuptools setuptools_scm build
+      - name: create packages
+        run: python -m build
+      - name: upload artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: build-dists
+          path: dist/
+
+  release_python_package:
+    name: publish python package to pypi
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    needs:
+      - build_python_package
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - name: Retrieve build distributions
+        uses: actions/download-artifact@v3
+        with:
+          name: build-dists
+          path: dist/
+      - name: publish to PyPI  # make sure you have pypi trusted publishing configured for this repo
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  build_and_release_conda_package:
+    name: conda package build (and upload if release)
+    runs-on: ubuntu-latest
+    needs:
+      - test-linux
+      # - mypy-linux   # uncomment if this step is enabled
+      # - linting-linux   # uncomment if this step is enabled
+    steps:
+      - name: "Set up Python 3.11"
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: pip cache
+        id: pip-cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.*') }}
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: install kiara
+        run: pip install kiara
+      - name: install required plugin packages
+        run: pip install git+https://github.com/DHARPA-Project/kiara_plugin.develop.git@develop
+      - name: build conda package
+        if: ${{ ( github.ref == 'refs/heads/develop') }}
+        run: kiara conda build-package --patch-data ci/conda/conda-pkg-patch.yaml .
+      - name: extract tag name
+        run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
+      - name: build & publish conda package
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        run: kiara conda build-package --publish --user dharpa --token ${{ secrets.ANACONDA_PUSH_TOKEN }} --patch-data ci/conda/conda-pkg-patch.yaml .
+
+  merge_tag_to_main:
+    name: merge current tag to main branch
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    needs:
+      - release_python_package
+      - build_and_release_conda_package
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - run: git config --global user.email "markus@frkl.io"
+    - run: git config --global user.name "Markus Binsteiner"
+    - name: extract tag name
+      run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
+    - name: checkout main branch
+      run: git checkout main
+    - name: merge tag
+      run: git merge "${RELEASE_VERSION}"
+    - name: push updated main branch
+      run: git push https://${{ secrets.GITHUB_TOKEN }}@github.com/DHARPA-Project/kiara_plugin.topic_modelling.git

.github/workflows/build-windows.yaml

@@ -0,0 +1,21 @@
+name: "windows tests for 'kiara_plugin.topic_modelling'"
+# This workflow is triggered on pushes to the repository.
+on: [push]
+
+jobs:
+  test-windows:
+    name: pytest on windows
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - name: "Set up Python ${{ matrix.python_version }}"
+        uses: actions/setup-python@v4
+        with:
+          python-version: "${{ matrix.python_version }}"
+      - uses: actions/checkout@v3
+      - name: install kiara_plugin.topic_modelling
+        run: pip install -U --extra-index-url https://pypi.fury.io/dharpa/ .[all,dev_testing]
+      - name: Test with pytest
+        run: make test

.gitignore

@@ -0,0 +1,67 @@
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+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/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/
+pip-wheel-metadata/
+.python-version
+src/kiara_plugin/topic_modelling/version.txt
+.direnv
+public
+site
+.dephell_report
+.mypy_cache
+.env
+docs/api-documentation.md
+.frkl
+.envrc
+build.sh
+onefile.spec
+*_complete.zsh.zwc
+ci/conda/**/build
+ci/conda/kiara_plugin.topic_modelling/meta.yaml
+.pixi
+pixi.lock
+dev.py