chore: cleanup

Author: makkus

.gitlab-ci.yml

@@ -3,46 +3,54 @@ default_language_version:
 
 repos:
 
+# cleans out all jupyter notebook result cells for git commit
+- repo: https://github.com/srstevenson/nb-clean
+  rev: 4.0.1
+  hooks:
+    - id: nb-clean
+
+# makes sure the commit message adheres to the commitlint standard
 - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-  rev: 'v9.20.0'
+  rev: 'v9.22.0'
   hooks:
     - id: commitlint
       stages: [commit-msg]
       additional_dependencies: ['@commitlint/config-conventional']
 
+# runs the mypy type checker
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v1.13.0'  # Use the sha / tag you want to point at
+  rev: 'v1.16.0'  # Use the sha / tag you want to point at
   hooks:
   - id: mypy
-    files: "^src/kiara"
+    files: "^src/"
     pass_filenames: true
-    args: ["--config-file", "pyproject.toml"]
-    additional_dependencies: [pydantic>=2.0.0, pydantic_settings, rich>=10.0.0, ruamel.yaml, anyio>=3.0.0, pyzmq>=22.0.3, bidict, sqlalchemy-stubs, types-python-slugify, types-setuptools, types-python-dateutil, dag_cbor>=0.3.0, multiformats>=0.2.0, textual, regex, types-pytz, types-orjson, dag_cbor>=0.3.2]
+    args: ["--config-file", "pyproject.toml", "--ignore-missing-imports"]
+    additional_dependencies: [pydantic>=2.0.0, rich>=10.0.0, ruamel.yaml, anyio>=3.0.0, pyzmq>=22.0.3, bidict, sqlalchemy-stubs, types-python-slugify, types-setuptools, types-python-dateutil, dag_cbor, multiformats, textual, regex, types-pytz, types-orjson]
 
+# runs the ruff linter and formater
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.3
+  rev: v0.11.13
   hooks:
-    - id: ruff
+    - id: ruff-check
       args: [ --fix ]
-    # Run the formatter.
     - id: ruff-format
 
+# misc tasks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0  # Use the ref you want to point at
+  rev: 'v5.0.0'
   hooks:
   - id: trailing-whitespace
-    exclude: '(setup.cfg|src/kiara/utils/cli/__init__.py)'
   - id: check-added-large-files
   - id: check-ast
   - id: check-json
   - id: check-merge-conflict
   - id: check-xml
   - id: check-yaml
-    exclude: '(tests/\*|ci/conda/kiara/meta.yaml)'
+    exclude: 'tests/\*'
   - id: debug-statements
   - id: end-of-file-fixer
-    exclude: '(.*.json|.*.j2)'
+    exclude: '.*.json'
   - id: requirements-txt-fixer
   - id: fix-encoding-pragma
   - id: mixed-line-ending

.kiara_complete.zsh

@@ -4,22 +4,14 @@
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
-docs: ## build documentation
-	mkdocs build
-
-serve-docs: ## serve and watch documentation
-	mkdocs serve --dirtyreload -a 0.0.0.0:8000
 
 clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
 
-clean-doc: ## remove doc artifacts
-	rm -fr build/site
-
 clean-build: ## remove build artifacts
 	rm -fr build/
 	rm -fr dist/
 	rm -fr .eggs/
-	find . -name '*.egg' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -rf {} +
 
 clean-pyc: ## remove Python file artifacts
 	find . -name '*.pyc' -exec rm -f {} +
@@ -34,32 +26,37 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 	rm -fr .mypy_cache
 
-init: clean ## initialize a development environment (to be run in virtualenv)
-	git init
-	git checkout -b develop || true
-	pip install -U pip
-	pip install --extra-index-url https://pypi.fury.io/dharpa/ --extra-index-url https://gitlab.com/api/v4/projects/25344049/packages/pypi/simple -U -e '.[all_dev]'
-	pre-commit install
-	pre-commit install --hook-type commit-msg
-	setup-cfg-fmt setup.cfg || true
-	git add "*" ".*"
-	pre-commit run --all-files || true
-	git add "*" ".*"
-
 mypy: ## run mypy
-	uv run mypy src/kiara
+	uv run mypy --namespace-packages --explicit-package-base src/
+
+lint:
+	uv run ruff check --fix src/
+
+format:
+	uv run ruff format src/
 
 test: ## run tests quickly with the default Python
 	uv run pytest tests
 
+docs:
+	uv run mkdocs build
+
+docs-serve:
+	uv run mkdocs serve
+
+check: lint mypy test ## run dev-related checks
+
+pre-commit: ## run pre-commit on all files
+	uv run pre-commit run --all-files
+
 coverage: ## check code coverage quickly with the default Python
 	coverage run -m pytest tests
 	coverage report -m
 	coverage html
 	xdg-open htmlcov/index.html
 
 render-api:
-	kiara render --source-type base_api --target-type kiara_api item kiara_api template_file=src/kiara/interfaces/python_api/kiara_api.py target_file=src/kiara/interfaces/python_api/kiara_api.py
+	uv run kiara render --source-type base_api --target-type kiara_api item kiara_api template_file=src/kiara/interfaces/python_api/kiara_api.py target_file=src/kiara/interfaces/python_api/kiara_api.py
 
 pre-commit: ## run pre-commit on all files
 	uv run pre-commit run --all-files

.pre-commit-config.yaml

@@ -24,57 +24,54 @@ created metadata. Most of this is not yet implemented.
 
 ### Requirements
 
-- Python (version >=3.6 -- some make targets only work for Python >=3.7, but *kiara* itself should work on 3.6)
-- pip, virtualenv
+- uv ( https://docs.astral.sh/uv/ )
 - git
-- make
-- [direnv](https://direnv.net/) (optional)
+- make (on Linux / Mac OS X -- optional)
 
 
-### Prepare development environment
+### Check out the source code & enter the project directory
 
 ```console
 git clone https://github.com/DHARPA-Project/kiara.git
 cd kiara
-python3 -m venv .venv
-source .venv/bin/activate
-make init
 ```
 
-If you use [direnv](https://direnv.net/), you can alternatively do:
+### Prepare development environment
 
-``` console
-git clone https://github.com/DHARPA-Project/kiara.git
-cd kiara
-cp .envrc.disabled .envrc
-direnv allow
-make init
-```
+The recommended way to setup a development environment is to use [uv](https://docs.astral.sh/uv/). Check out [their install instructions](https://docs.astral.sh/uv/getting-started/installation/).
 
-*Note*: you might want to adjust the Python version in ``.envrc`` (should not be necessary in most cases though)
+Once you have `uv` installed, you can either run `kiara` using the `uv run` command:
 
-### ``make`` targets
+```
+uv run kiara module list
+```
+
+or, activate the virtual environment and run `kiara` directly:
 
-- ``init``: init development project (install project & dev dependencies into virtualenv, as well as pre-commit git hook)
-- ``update-modules``: update default kiara modules 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
+```
+uv sync  # to make sure the virtualenv exists (and is up to date)
+source .venv/bin/activate
+kiara module list
+```
 
-For details (and other, minor targets), check the ``Makefile``.
+### Running pre-defined development-related tasks
 
+The included `Makefile` file includes some useful tasks that help with development. This requires `uv` and the `make` tool to be
+installed, which should be the case for Linux & Mac OS X systems.
 
-### Running tests
+- `make test`: runs the unit tests
+- `make mypy`: run mypy checks
+- `make lint`: run the `ruff` linter on the source code
+- `make format`: run the `ruff` formatter on the source code (similar to `black`)
+- `make docs`: build the documentation  (into `build` folder)
+- `make docs-serve`: serve the documentation (on port 8000)
 
-``` console
-> make test
-# or
-> make coverage
-```
+Alternatively, if you don't have the `make` command available, you can use `uv` directly to run those tasks:
 
+- `uv run pytest tests`
+- `uv run mypy src/`
+- `uv run ruff check --fix src/`
+- `uv run ruff format src/`
 
 ## Copyright & license
 

Makefile

@@ -75,6 +75,7 @@ dependencies = [
     "tzlocal>=2.1,<6.0",
     "zstandard>=0.22.0",
     "airium>=0.2.7",
+    "netext>=0.3.1",
 ]
 dynamic = ["version"]
 
@@ -441,6 +442,7 @@ module = [
     "jupytext",
     "lz4.*",
     "mmh3",
+    "netext.*",
     "pickle5",
     "pip.*",
     "pp",

README.md

@@ -54,6 +54,7 @@
     USE_CLICK_SHORT_HELP,
     highlighter,
 )
+from rich_click.rich_help_formatter import RichHelpFormatter
 from rich_click.rich_help_rendering import (
     _get_option_help,
     _make_command_help,
@@ -303,12 +304,13 @@ class MetavarHighlighter(RegexHighlighter):
                 ]
 
             metavar_highlighter = MetavarHighlighter()
+            formatter = RichHelpFormatter()
             rows = [
                 required,
                 highlighter(highlighter(",".join(opt_long_strs))),
                 highlighter(highlighter(",".join(opt_short_strs))),
                 metavar_highlighter(metavar),
-                _get_option_help(param, ctx),  # type: ignore
+                _get_option_help(param, ctx, formatter),  # type: ignore
             ]
 
             # Remove metavar if specified in config

onboarding.folder_to_table.json

@@ -25,6 +25,17 @@
 
 def print_ascii_graph(
     graph: nx.Graph, restart_interpreter_if_asciinet_installed: bool = False
+):
+    from netext import ConsoleGraph, EdgeSegmentDrawingMode
+
+    nx.set_edge_attributes(
+        graph, EdgeSegmentDrawingMode.ASCII, "$edge-segment-drawing-mode"
+    )
+    terminal_print(ConsoleGraph(graph))
+
+
+def print_ascii_graph_old(
+    graph: nx.Graph, restart_interpreter_if_asciinet_installed: bool = False
 ):
     try:
         from asciinet import graph_to_ascii  # type: ignore