diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index bacd71d..c3ab81a 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -30,12 +30,12 @@ jobs: pixi-version: v0.63.1 - name: Build documentation with Sphinx - run: pixi run sphinx-build -b html source build/html + run: pixi run -e sphinx-doc sphinx-html - name: Upload artifact uses: actions/upload-pages-artifact@v3 with: - path: "build/html" + path: "build_docs" deploy: needs: build diff --git a/.gitignore b/.gitignore index 59cbae3..cea89ed 100644 --- a/.gitignore +++ b/.gitignore @@ -78,7 +78,7 @@ instance/ .scrapy # Sphinx documentation -docs/ +build_docs/ # PyBuilder .pybuilder/ diff --git a/README.md b/README.md index 870ced2..c7c55f7 100644 --- a/README.md +++ b/README.md @@ -93,19 +93,27 @@ pixi shell # use development dependencies like jupyter notebooks/ipython jupyterlab ``` -#### Tests + +### Tests ```bash # Run tests pixi run test ``` -#### Linting +### Linting ```bash # Linting pixi run lint pixi run format ``` +### Documentation +```bash +# Build Sphinx documentation +pixi run -e sphinx-doc sphinx-html +# Output will be in build/html/index.html +``` + ## License MIT License diff --git a/doc/css/code_select.css b/doc/css/code_select.css deleted file mode 100644 index a9e26cb..0000000 --- a/doc/css/code_select.css +++ /dev/null @@ -1,5 +0,0 @@ -.language-pycon .gp, -.language-pycon .go { - /* Generic.Prompt, Generic.Output */ - user-select: none; -} \ No newline at end of file diff --git a/doc/doc_src/configuration.md b/doc/doc_src/configuration.md deleted file mode 100644 index cafae11..0000000 --- a/doc/doc_src/configuration.md +++ /dev/null @@ -1,12 +0,0 @@ -# Configuration Example - -pkoffee has no configuration files, but if it had one it could be included as examples like so: - -!!! note - - This is not a real configuration! - - -``` yaml title="example_script.yml" ---8<-- "doc/doc_src/example_config/example_config.yml" -``` \ No newline at end of file diff --git a/doc/doc_src/example_config/example_config.yml b/doc/doc_src/example_config/example_config.yml deleted file mode 100644 index 87ad0f2..0000000 --- a/doc/doc_src/example_config/example_config.yml +++ /dev/null @@ -1 +0,0 @@ -not_a_real_config: true \ No newline at end of file diff --git a/doc/doc_src/example_data/coffee_productivity.csv b/doc/doc_src/example_data/coffee_productivity.csv deleted file mode 100644 index 6229fbb..0000000 --- a/doc/doc_src/example_data/coffee_productivity.csv +++ /dev/null @@ -1,100 +0,0 @@ -cups,productivity -9,0.4243156703924034 -8,0.589516058691207 -9,0.3976154915592352 -10,0.25612534784434804 -10,0.2551499691190779 -10,0.2544811374916391 -5,1.9606664492718828 -2,2.6495260408721273 -2,1.7358154455318033 -9,0.38159701625932085 -4,1.4962433969766564 -2,2.761635684137699 -1,5.0 -7,1.0154395686122686 -5,1.6953449967664196 -11,0.15880507132783364 -2,2.2079383673934396 -1,1.8494438258455546 -7,0.9688597718869353 -3,2.37069690108341 -12,0.09839495778556077 -2,0.6253093378580398 -1,1.117601389817493 -1,0.274029309512801 -11,0.16248227375788973 -0,0.09090909090909091 -7,0.8723310144846369 -8,0.6500838715972812 -6,1.2893456799807168 -9,0.41277018784708097 -12,0.09832353384648478 -10,0.25039020382702754 -2,2.108777104925814 -12,0.0970887442200735 -2,1.4294950727908968 -12,0.09819173100707018 -9,0.40899410914994916 -3,1.6143279875636596 -11,0.15945591178409524 -6,1.520198027764937 -5,1.9355871019392192 -1,2.021127230571263 -8,0.640381127245083 -11,0.16465477892657993 -12,0.09872963451272254 -11,0.15987211674973087 -12,0.1002360748287057 -9,0.4358164821774892 -8,0.6107513082132634 -11,0.16086228838178415 -11,0.16423507211710472 -9,0.41845174483000785 -11,0.15239585215116394 -8,0.6441612852681292 -4,1.5692492971570744 -12,0.0966132368359234 -10,0.26589952737616296 -7,0.8062930713108734 -6,1.3366744687040273 -2,1.5632733446450995 -8,0.6615765967723954 -5,1.37720124745427 -6,1.2620181260655685 -0,0.0 -5,1.570009960017413 -6,1.318725999988861 -0,1.1428571428571428 -1,1.3450500551604032 -3,1.3443815506484893 -11,0.15966374303082048 -1,0.0 -10,0.2579356110795984 -7,0.9182923141720066 -4,2.7098545976892603 -3,2.1653645317858032 -3,3.112711514442092 -5,2.0690916141406386 -4,2.1142830754230886 -4,2.414915054225256 -8,0.589516058691207 -11,0.1554496960953931 -0,0.0 -6,1.2229452385163726 -10,0.2595203679370181 -1,0.5021872749579849 -8,0.6582511455408541 -2,0.7960273328302898 -9,0.39567319781791194 -8,0.6334244011650595 -2,1.1371819040432711 -10,0.2694554477732479 -10,0.2516612200901089 -3,2.2648555184202337 -4,2.1654854909450068 -6,1.2847634855879484 -9,0.42073790720011234 -10,0.253540742437403 -5,1.5414643243807329 -1,3.0531926811076455 diff --git a/doc/doc_src/example_script.md b/doc/doc_src/example_script.md deleted file mode 100644 index 2d3ac80..0000000 --- a/doc/doc_src/example_script.md +++ /dev/null @@ -1,5 +0,0 @@ -# Example Script - -``` py title="example_script.py" ---8<-- "doc/doc_src/snippets/example_script.py" -``` diff --git a/doc/doc_src/index.md b/doc/doc_src/index.md deleted file mode 100644 index 4ab0748..0000000 --- a/doc/doc_src/index.md +++ /dev/null @@ -1 +0,0 @@ ---8<-- "README.md" \ No newline at end of file diff --git a/doc/doc_src/installation.md b/doc/doc_src/installation.md deleted file mode 100644 index 6e3e14f..0000000 --- a/doc/doc_src/installation.md +++ /dev/null @@ -1,23 +0,0 @@ -# Installation - -Follow these steps to install the project and its dependencies: - -1. **Clone the repository**: - -```shell -git clone git@github.com:s3-school/pkoffee-solution.git pkoffee && cd pkoffee -``` - -2. **Create a workspace envorinment with pixi** -`pkoffee` manages its dependencies with [`pixi`](https://pixi.sh/latest/). It provides tasks to run tests or run the dummy executable: - -```shell -# install the development environment containing all dependencies, test and documentation tools -pixi install -# Run the tests, make coverage reports -pixi run test -# build the documentation -pixi run doc -# call the pkoffee in the default environment of the workspace -pixi run pkoffee -``` diff --git a/doc/doc_src/license.md b/doc/doc_src/license.md deleted file mode 100644 index fb9520e..0000000 --- a/doc/doc_src/license.md +++ /dev/null @@ -1,3 +0,0 @@ -``` md title="LICENSE" ---8<-- "LICENSE" -``` \ No newline at end of file diff --git a/doc/doc_src/snippets/example_notebook.ipynb b/doc/doc_src/snippets/example_notebook.ipynb deleted file mode 100644 index 83271da..0000000 --- a/doc/doc_src/snippets/example_notebook.ipynb +++ /dev/null @@ -1,73 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from importlib.metadata import version\n", - "\n", - "print(\"pkoffee version: \", version(\"pkoffee\")) # noqa: T201 explicit print" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from pathlib import Path\n", - "\n", - "from pkoffee.data import load_csv\n", - "\n", - "data = load_csv(Path(\"../example_data/coffee_productivity.csv\"))\n", - "data.head()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from pkoffee.productivity_analysis import fit_all_models, format_model_rankings\n", - "\n", - "models = fit_all_models(data)\n", - "print(format_model_rankings(models)) # noqa: T201" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from pkoffee.visualization import plot_models\n", - "\n", - "plot_models(data, models)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "default", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.13.10" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/doc/doc_src/snippets/example_script.py b/doc/doc_src/snippets/example_script.py deleted file mode 100644 index d4b5f89..0000000 --- a/doc/doc_src/snippets/example_script.py +++ /dev/null @@ -1,60 +0,0 @@ -"""Script demonstrating how to use the PKoffee package to analyze coffee productivity data.""" # noqa: INP001 example script - -import logging -from pathlib import Path - -from pkoffee.data import load_csv -from pkoffee.fit_model import Model -from pkoffee.productivity_analysis import fit_all_models, format_model_rankings -from pkoffee.visualization import FigureParameters, Show, plot_models - - -def main() -> None: - """Run example analysis.""" - logger = logging.getLogger(__name__) - logging.basicConfig(level=logging.INFO) - # Path to your data file - data_file = Path("../example_data/coffee_productivity.csv") - - # Load data - logger.info("Loading data...") - data = load_csv(data_file) - logger.info("Loaded %s data points", len(data)) - logger.info("Cups range: %s to %s", data["cups"].min(), data["cups"].max()) - logger.info( - "Productivity range: %s to %s", f"{data['productivity'].min():.2f}", f"{data['productivity'].max():.2f}" - ) - - # Fit models - logger.info("Fitting models...") - models = fit_all_models(data) - logger.info("Successfully fitted %s models", len([m for m in models if m.r_squared > 0])) - - # sort the models per best fit - Model.sort(models) - - # logger.info rankings - logger.info(format_model_rankings(models)) - - # Create visualization - logger.info("Creating visualization...") - output_path = Path("analysis_results.png") - plot_models( - data, - models, - output_path=output_path, - fig_params=FigureParameters(y_limits=(-0.2, 8.0)), - show=Show.NO, # deactivate showing the figure to run in CI - ) - - logger.info("✓ Analysis complete! Results saved to: %s", output_path) - - # Access best model - best_model = models[0] - logger.info("Best model: %s", best_model.name) - logger.info("R² score: %s", f"{best_model.r_squared:.4f}") - logger.info("Parameters: %s", best_model.params) - - -if __name__ == "__main__": - main() diff --git a/doc/doc_src/usage.md b/doc/doc_src/usage.md deleted file mode 100644 index 91ed708..0000000 --- a/doc/doc_src/usage.md +++ /dev/null @@ -1,6 +0,0 @@ -# Usage -`pkoffee` is the example project for the s3 school. It implements a dummy script: - -``` -pixi run pkoffee -``` \ No newline at end of file diff --git a/doc/images/documentation_logo.svg b/doc/images/documentation_logo.svg deleted file mode 100644 index 16fe0f5..0000000 --- a/doc/images/documentation_logo.svg +++ /dev/null @@ -1 +0,0 @@ -documentation: maindocumentationmain \ No newline at end of file diff --git a/doc/images/logo.svg b/doc/images/logo.svg deleted file mode 100644 index 2aecdef..0000000 --- a/doc/images/logo.svg +++ /dev/null @@ -1,91 +0,0 @@ - - - - - - - - - - - - image/svg+xml - - - - - - - s3draft - - diff --git a/doc/mkdocs.yml b/doc/mkdocs.yml deleted file mode 100644 index b1d7083..0000000 --- a/doc/mkdocs.yml +++ /dev/null @@ -1,72 +0,0 @@ -site_name: pkoffee -site_url: https://github.com/s3-school/pkoffee-solution/pages.html -site_dir: 'public/' - -docs_dir: "doc_src" -use_directory_urls: False - -extra_css: # to prevent selection of surounding stuff in doctests display -- css/code_select.css - -nav: -- Home: index.md -- User Guide: - - Installation: installation.md - - Configuration: configuration.md - - Usage: usage.md -- Examples and notebooks: - - Example Notebook: snippets/example_notebook.md # generated by the "example" task in pixi manifest - - Example Script: example_script.md -- API Reference: reference # default of api-autonav -- License: license.md - -theme: - name: material # material theme from mkdocs-material - palette: - scheme: slate # default dark mode - logo: doc/images/logo.png - features: - - navigation.indexes # https://github.com/tlambert03/mkdocs-api-autonav?tab=readme-ov-file#mkdocs-material-suggestions - -# material display information about repository -repo_url: https://github.com/s3-school/pkoffee-solution - -plugins: -- search -- autorefs -- mkdocstrings: - enabled: !ENV [ENABLE_MKDOCSTRINGS, true] - default_handler: python - handlers: - python: - paths: ["../src"] # paths to search for modules - options: # see https://mkdocstrings.github.io/python/usage/ - show_source: true # default value is also true - show_inheritance_diagram: true - inherited_members: true - docstring_style: numpy - line_length: 118 - summary: true - signature_crossrefs: true - separate_signature: true - inventories: - - https://docs.python.org/3/objects.inv - - https://numpy.org/doc/stable/objects.inv - - https://pandas.pydata.org/docs/objects.inv # version specific: https://pandas.pydata.org/pandas-docs/version/2.0/objects.inv - - https://seaborn.pydata.org/objects.inv - - https://matplotlib.org/stable/objects.inv # version specific: https://matplotlib.org/3.5.0/objects.inv -- api-autonav: - modules: ['../src/pkoffee'] - -markdown_extensions: -- admonition -- pymdownx.details -- pymdownx.highlight: - anchor_linenums: true - line_spans: __span - pygments_lang_class: true -- pymdownx.inlinehilite -- pymdownx.superfences -- pymdownx.snippets: # include files not in docs folder - base_path: [.] - check_paths: true diff --git a/doc/analysis.ipynb b/docs/analysis.ipynb similarity index 98% rename from doc/analysis.ipynb rename to docs/analysis.ipynb index 9d54345..fc10ad7 100644 --- a/doc/analysis.ipynb +++ b/docs/analysis.ipynb @@ -5,7 +5,7 @@ "id": "c2b07c61", "metadata": {}, "source": [ - "# PKoffee Analysis\n", + "# PKoffee Analysis example\n", "\n", "Welcome to the **PKoffee** project analysis notebook! ☕️\n", "\n", @@ -39,7 +39,7 @@ "id": "51afb4da", "metadata": {}, "source": [ - "# 1. Load the data\n", + "## 1. Load the data\n", "\n", "The experimental data are in file `../analysis/coffee_productivity.csv`" ] diff --git a/source/conf.py b/docs/conf.py similarity index 88% rename from source/conf.py rename to docs/conf.py index c95d360..40a26a2 100644 --- a/source/conf.py +++ b/docs/conf.py @@ -24,6 +24,8 @@ "sphinx.ext.autodoc", "sphinx.ext.viewcode", "sphinx.ext.napoleon", + "myst_parser", + "nbsphinx", ] autodoc_default_options = { @@ -41,3 +43,7 @@ html_theme = "sphinx_rtd_theme" html_static_path = ["_static"] + +# nbsphinx configuration - execute notebooks during documentation build +nbsphinx_execute = "always" +nbsphinx_kernel_name = "python3" diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..a62eb1d --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,11 @@ +.. include:: ../README.md + :parser: myst_parser.sphinx_ + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + readme + analysis + modules \ No newline at end of file diff --git a/source/modules.rst b/docs/modules.rst similarity index 100% rename from source/modules.rst rename to docs/modules.rst diff --git a/source/pkoffee.rst b/docs/pkoffee.rst similarity index 72% rename from source/pkoffee.rst rename to docs/pkoffee.rst index 7bf750a..872be22 100644 --- a/source/pkoffee.rst +++ b/docs/pkoffee.rst @@ -2,55 +2,52 @@ pkoffee ======= .. automodule:: pkoffee - :members: - :undoc-members: - :show-inheritance: - -.. toctree:: - :maxdepth: 2 + :no-index: - pkoffee.cli - pkoffee.data - pkoffee.fit_model - pkoffee.fit_model_io - pkoffee.log - pkoffee.metrics - pkoffee.parametric_function - pkoffee.productivity_analysis - pkoffee.visualization +Submodules +---------- .. automodule:: pkoffee.cli :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.data :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.fit_model :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.fit_model_io :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.log :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.metrics :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.parametric_function :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.productivity_analysis :members: :undoc-members: + :show-inheritance: .. automodule:: pkoffee.visualization :members: :undoc-members: + :show-inheritance: diff --git a/docs/readme.rst b/docs/readme.rst new file mode 100644 index 0000000..afa40d1 --- /dev/null +++ b/docs/readme.rst @@ -0,0 +1,5 @@ +Welcome to PKoffee +================== + +.. include:: ../README.md + :parser: myst_parser.sphinx_ diff --git a/pixi.lock b/pixi.lock index 4e89b7b..7b72596 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,6 +1,6 @@ version: 6 environments: - 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conda: https://prefix.dev/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda diff --git a/pixi.toml b/pixi.toml index 32910d1..c39a0d7 100644 --- a/pixi.toml +++ b/pixi.toml @@ -11,10 +11,6 @@ python = ["3.12.*", "3.13.*", "3.14.*"] [dependencies] pkoffee = { path = "." } -ty = ">=0.0.12,<0.0.13" -ruff = ">=0.14.12,<0.15" -sphinx = ">=9.1.0,<10" -nbsphinx = ">=0.9.8,<0.10" [package] name = "pkoffee" @@ -89,27 +85,29 @@ depends-on = [{"task" = "run_on_snippets", "args" = ["*.ipynb", "jupyter nbconve [feature.dev.dependencies] jupyterlab = ">=4.4.3,<5" ruff = ">=0.14,<0.15" +ty = ">=0.0.12,<0.0.13" [feature.dev.tasks] format = "ruff format" lint = "ruff check" type-check = "ty check src" -[feature.doc.dependencies] -mkdocstrings-python = ">=2.0.0,<3" -mkdocs-material = ">=9.6.14,<10" # material brings mkdocs, markdown and pymdown-extension +[feature.sphinx-doc.dependencies] +sphinx = ">=9.1.0,<10" +nbsphinx = ">=0.9.8,<0.10" +myst-parser = ">=5.0.0" +jupyter = ">=1.0.0,<2" +ipykernel = ">=6.0.0,<7" + +[feature.sphinx-doc.pypi-dependencies] +sphinx-rtd-theme = ">=3.1.0, <4" -[feature.doc.pypi-dependencies] -mkdocs-api-autonav = ">=0.4.0, <0.5" # automatically generate documentation for full package +[feature.sphinx-doc.tasks] +sphinx-html = { cmd = "sphinx-build -b html docs build_docs", cwd = "." } +sphinx-clean = "rm -rf build_docs" -# Doc task requires to run example task before (to convert the notebooks to markdown and execute scripts to verify their validity -# however the doc task doesn't depend on the example task, because in CI they typically run in different jobs -[feature.doc.tasks.doc] -args = [{"arg" = "docDir", default="htmldoc"}] -cmd = [ - "cp", "-r", "doc/images", "doc/doc_src/doc/images", "&&", # copy the images included in readme (included in doc) in doc source folder because mkdocs can not include files outside of src folder - "mkdocs", "build", "--strict", "--clean", "-f", "doc/mkdocs.yml", "-d", "../{{ docDir }}" -] +[tasks] +build-package = "python -m build" [environments] prod = { features = ["py313"], solve-group = "prod" } @@ -117,6 +115,7 @@ test = { features = ["test", "py313"], solve-group = "prod" } # use default for the dev environment so tasks are resolved in this environment (avoids having to specify env) # no need to include doc: pixi will figure the environment to use from the task if it is unique default = { features = ["dev", "test", "py313"], solve-group = "prod" } +build = { solve-group = "prod" } # python 3.14 environments for testing prod314 = { features = ["py314"], solve-group = "prod314" } @@ -127,7 +126,8 @@ prod312 = { features = ["py312"], solve-group = "prod312" } testpy312 = {features = ["test", "py312"] } # Doc environment only contains documentation tools, not the package dependencies -doc = { features = ["doc"], no-default-feature = true } +sphinx-doc = { features = ["sphinx-doc", "py313"], solve-group = "prod" } [pypi-dependencies] -sphinx-rtd-theme = ">=3.1.0, <4" +build = ">=1.4.0, <2" +twine = ">=6.2.0, <7" diff --git a/source/index.rst b/source/index.rst deleted file mode 100644 index 9213bf4..0000000 --- a/source/index.rst +++ /dev/null @@ -1,19 +0,0 @@ -pkoffee documentation -===================== - -Coffee Productivity Analysis Package - -A comprehensive toolkit for analyzing the relationship between coffee consumption -and productivity through statistical modeling and visualization. - - -.. toctree:: - :maxdepth: 2 - :caption: API Reference: - - modules - -.. automodule:: pkoffee - :members: - :undoc-members: - :show-inheritance: \ No newline at end of file