chore: sync project template

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/DHARPA-Project/kiara_plugin.develop.git",
-  "commit": "e2d43d57283f53eaf5144915075567eff38d738a",
+  "commit": "96e37df1692a56068082857a41318dc7d17f1643",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/build-darwin.yaml

@@ -11,15 +11,15 @@ jobs:
     runs-on: macos-11
     strategy:
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.8", "3.9", "3.10", "3.11"]
     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]
+        run: pip install -U .[dev_testing]
       - name: display installed kiara and module package versions
         run: pip list | grep kiara
       - name: Test with pytest

.github/workflows/build-linux.yaml

@@ -18,56 +18,54 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.8", "3.9", "3.10", "3.11"]
     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]
+        run: pip install -U .[dev_testing]
       - name: display installed kiara and module package versions
         run: pip list | grep kiara
-      - name: Test with pytest
-        run: make test
+      - name: test with pytest
+        run: pytest --cov-report=xml --cov=kiara_plugin.topic_modelling tests
+      - name: Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel: true
+          flag-name: run ${{ join(matrix.*, ' - ') }}
+          format: cobertura
+          file: coverage.xml
 
-# 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
+  coverage:
+    name: test coverage
+    runs-on: ubuntu-latest
+    needs:
+      - test-linux
+    steps:
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel-finished: true
 
-# 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
+  mypy-linux:
+    name: mypy check on linux
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python_version: ["3.8", "3.9", "3.10", "3.11"]
+    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 .[dev_testing]
+      - name: Test with mypy
+        run: make mypy
 
   linting-linux:
     runs-on: ubuntu-latest
@@ -96,8 +94,8 @@ jobs:
     runs-on: ubuntu-latest
     needs:
       - test-linux
-#      - mypy-linux
-#      - linting-linux
+      - mypy-linux
+      - linting-linux
     steps:
       - name: Set up Python 3.11
         uses: actions/setup-python@v4
@@ -138,8 +136,8 @@ jobs:
     runs-on: ubuntu-latest
     needs:
       - test-linux
-      # - mypy-linux   # uncomment if this step is enabled
-      # - linting-linux   # uncomment if this step is enabled
+      - mypy-linux
+      - linting-linux
     steps:
       - name: "Set up Python 3.11"
         uses: actions/setup-python@v4

.github/workflows/build-windows.yaml

@@ -8,14 +8,14 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.8", "3.9", "3.10", "3.11"]
     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]
+        run: pip install -U .[dev_testing]
       - name: Test with pytest
         run: make test

README.md

@@ -32,75 +32,57 @@ TODO
 If you only want to work on the modules, and not the core *Kiara* codebase, follow the instructions below. Otherwise, please
 check the notes on how to setup a *Kiara* development environment under (TODO).
 
-#### Linux & Mac OS X (using make)
+#### Using `pixi` (recommended)
 
-For *NIX-like operating system, setting up a development environment is relatively easy:
+The recommended way to setup a development environment is to use [pixi](https://github.com/prefix-dev/pixi). Check out [their install instructions](https://github.com/prefix-dev/pixi#installation).
 
-```console
-git clone https://github.com/DHARPA-Project/kiara_plugin.topic_modelling.git
-cd kiara_plugin.topic_modelling
-python3 -m venv .venv
-source .venv/bin/activate
-make init
-```
+Once you have `pixi` installed, you need to initialize the environment once:
 
-#### Windows (or manual pip install)
+```
+pixi run install-dev-env
+```
 
-It's impossible to lay out all the ways Python can be installed on a machine, and virtual- (or conda-)envs can be created, so I'll assume you know how to do this.
-One simple way is to install the [Anaconda (individual edition)](https://docs.anaconda.com/anaconda/install/index.html), then use the Anaconda navigator to create a new environment, install the 'git' package in it (if your system does not already have it), and use the 'Open Terminal' option of that environment to start up a terminal that has that virtual-/conda-environment activated.
+You also need to do this whenever a depdendency of this plugin is updated (for example the core `kiara` package).
 
-Once that is done, `cd` into a directory where you want this project folder to live, and do:
+Once that is done, you can enter the environment with:
 
-```console
-# make sure your virtual env is activated!!!
-git clone https://github.com/DHARPA-Project/kiara_plugin.topic_modelling.git
-cd kiara_plugin.topic_modelling
-pip install --extra-index-url https://pypi.fury.io/dharpa/ -U -e .[all_dev]
+```
+pixi shell
 ```
 
-#### Try it out
-
-After this is done, you should be able to run the included example module via:
+This will start a sub-shell with the virtual environment activated, and all dependencies of the plugin package installed. To confirm it works, you can run any `kiara` command:
 
-```console
-kiara run topic_modelling_example text_1="xxx" text_2="yyy"
+```
+kiara --version
+# or
+kiara operation list
+# or
 ...
 ...
 ```
 
-### Re-activate the development environment
-
-The 'prepare' step from above only has to be done once. After that, to re-enable your virtual environment,
-you'll need to navigate to the directory again (wherever that is, in your case), and run the ``source`` command from before again:
+Once you are finished with your development session, you can exit the sub-shell as you would normally do in such cases:
 
-```console
-cd path/to/kiara_plugin.topic_modelling
-source .venv/bin/activate  # if it isn't activated already, for example by the Anaconda navigator
-kiara --help  # or whatever, point is, kiara should be available for you now,
+```
+exit
 ```
 
-### ``make`` targets (Linux & Mac OS X)
+Alternatively, you can also run the `kiara` executable directly, it is located in `.pixi/env/bin/kiara`. So either adapt your `PATH` variable, or do something like:
 
-- ``init``: init development project (install project & dev dependencies into virtualenv, as well as pre-commit git hook)
-- ``update-dependencies``: update development dependencies (mainly the core ``kiara`` package from git)
-- ``flake``: run *flake8* tests
-- ``mypy``: run mypy tests
-- ``test``: run unit tests
-- ``docs``: create static documentation pages (under ``build/site``)
-- ``serve-docs``: serve documentation pages (incl. auto-reload) for getting direct feedback when working on documentation
-- ``clean``: clean build directories
+```
+.pixi/env/bin/kiara operation list
+```
 
-For details (and other, minor targets), check the ``Makefile``.
+In most cases it's recommended to use a pixi shell though.
 
 
-### Running tests
+### Using pre-defined development-related tasks
 
-``` console
-> make test
-# or
-> make coverage
-```
+The included `pixi.toml` file includes some useful tasks that help with development:
 
+- `pixi run pre-commit-check`: runs a set of checks against all files
+- `pixi run tests`: runs the unit tests
+- `pixi run mypy`: run mypy checks
 
 ## Copyright & license
 

pixi.toml

@@ -3,15 +3,18 @@ name = "kiara-plugin-topic_modelling"
 version = "0.1.0"
 description = "A Kiara plugin toho create a Topic Modelling workflow."
 authors = ["Mariella De Crouy Chanel <mariella.decrouychanel@uni.lu>"]
-channels = ["conda-forge", "dharpa"]
+channels = ["dharpa", "conda-forge"]
 platforms = ["linux-64", "win-64", "osx-64", "osx-arm64"]
 
 [tasks]
-install-dev-env = "pip install -e '.[dev_utils]'"
+install-dev-env = "pip install --upgrade -e '.[dev_utils]'"
 pre-commit-check = ".pixi/env/bin/pre-commit run --all-files"
+tests = "py.test"
+mypy = "mypy  --namespace-packages --explicit-package-base src/kiara_plugin/topic_modelling"
 kiara = ".pixi/env/bin/kiara"
 show-versions = ".pixi/env/bin/kiara --version"
 delete-context = ".pixi/env/bin/kiara context delete"
+install-dev-dependency = ".pixi/env/bin/pip install -e"
 
 [dependencies]
 python = "3.11.*"

pyproject.toml

@@ -47,7 +47,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12"
 ]
 dependencies = [
-    "kiara>=0.5.6,<0.6.0",
+    "kiara>=0.5.9,<0.6.0",
     "kiara_plugin.core_types>=0.5.0,<0.6.0",
     "kiara-plugin.tabular>=0.5.1,<0.6.0",
 ]
@@ -240,5 +240,9 @@ plugins = [
 
 # mypy per-module options:
 [[tool.mypy.overrides]]
-module = ["placholder.dummy.*"]
+module = [
+    "appdirs.*",
+    "pyarrow.*",
+    "ruamel.*"
+]
 ignore_missing_imports = true