janpipek · janpipek · Sep 22, 2025 · Sep 22, 2025 · Sep 22, 2025 · Sep 22, 2025
diff --git a/.gitignore b/.gitignore
@@ -56,7 +56,7 @@ coverage.xml
 *.log
 
 # Sphinx documentation
-doc/_build/
+docs/_build/
 
 # PyBuilder
 target/

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,18 @@
+version: 2
+
+sphinx:
+   configuration: docs/conf.py
+
+build:
+   os: ubuntu-24.04
+   tools:
+      python: "3.13"
+   jobs:
+      pre_create_environment:
+         - asdf plugin add uv
+         - asdf install uv latest
+         - asdf global uv latest
+      create_environment:
+         - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+      install:
+         - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs
diff --git a/Justfile b/Justfile
@@ -41,3 +41,6 @@ publish: build
 
 examples:
     uv run --extra all python -m physt.examples
+
+docs:
+    uv run --extra all sphinx-build -b html docs/ docs/_build/html
diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ uv run --with "physt[terminal]>=0.8.3" -m physt.examples
 
 ## Command-line interface (experimental)
 
-You can run (and install) `physt` as a command-line application to quickly analyse 
+You can run (and install) `physt` as a command-line application to quickly analyse
 data files. This functionality is currently in development.
 
 ```shell
@@ -52,7 +52,7 @@ hist << 190                      # <--- add a forgotten value
 hist.plot()                      # <--- and plot it
 ```
 
-![Heights plot](doc/heights.png)
+![Heights plot](docs/heights.png)
 
 ## 2D example
 
@@ -65,7 +65,7 @@ iris_hist = h2(iris["sepal_length"], iris["sepal_width"], "pretty", bin_count=[1
 iris_hist.plot(show_zero=False, cmap="gray_r", show_values=True);
 ```
 
-![Iris 2D plot](doc/iris-2d.png)
+![Iris 2D plot](docs/iris-2d.png)
 
 ## 3D directional example
 
@@ -86,19 +86,18 @@ h = special_histograms.spherical(data)
 h.projection("theta", "phi").plot.globe_map(density=True, figsize=(7, 7), cmap="rainbow")
 ```
 
-![Directional 3D plot](doc/globe.png)
+![Directional 3D plot](docs/globe.png)
 
 See more in docstring's and notebooks:
 
-- Basic tutorial: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/tutorial.ipynb>
-- Binning: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/binning.ipynb>
-- 2D histograms: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/2d_histograms.ipynb>
-- Special histograms (polar, spherical, cylindrical - *beta*): <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/special_histograms.ipynb>
-- Adaptive histograms: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/adaptive_histogram.ipynb>
-- Use dask for large (not "big") data - *alpha*: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/dask.ipynb>
-- Geographical bins . *alpha*: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/geospatial.ipynb>
-- Plotting with vega backend: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/doc/vega-examples.ipynb>
-...and others, see the `doc` directory.
+- Basic tutorial: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/docs/tutorial.ipynb>
+- Binning: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/docs/binning.ipynb>
+- 2D histograms: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/docs/2d_histograms.ipynb>
+- Special histograms (polar, spherical, cylindrical - *beta*): <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/docs/special_histograms.ipynb>
+- Adaptive histograms: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/docs/adaptive_histogram.ipynb>
+- Use dask for large (not "big") data - *alpha*: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/docs/dask.ipynb>
+- Geographical bins . *alpha*: <http://nbviewer.jupyter.org/github/janpipek/physt/blob/dev/docs/geospatial.ipynb>
+...and others, see the `docs` directory.
 
 ## Installation
 

diff --git a/doc/2d_histograms.ipynb → docs/2d_histograms.ipynb b/doc/2d_histograms.ipynb → docs/2d_histograms.ipynb
diff --git a/doc/Makefile → docs/Makefile b/doc/Makefile → docs/Makefile
diff --git a/doc/_static/css/physt-custom.css → docs/_static/css/physt-custom.css b/doc/_static/css/physt-custom.css → docs/_static/css/physt-custom.css
diff --git a/doc/adaptive_histogram.ipynb → docs/adaptive_histogram.ipynb b/doc/adaptive_histogram.ipynb → docs/adaptive_histogram.ipynb
diff --git a/doc/ascii.ipynb → docs/ascii.ipynb b/doc/ascii.ipynb → docs/ascii.ipynb
diff --git a/doc/binning.ipynb → docs/binning.ipynb b/doc/binning.ipynb → docs/binning.ipynb
diff --git a/doc/collections.ipynb → docs/collections.ipynb b/doc/collections.ipynb → docs/collections.ipynb
diff --git a/doc/conf.py → docs/conf.py b/doc/conf.py → docs/conf.py
@@ -53,7 +53,7 @@
 
 # General information about the project.
 project = "Physt"
-copyright = "2016, Jan Pipek"
+copyright = "2016-2025, Jan Pipek"
 author = "Jan Pipek"
 
 import physt.binnings

diff --git a/doc/dask.ipynb → docs/dask.ipynb b/doc/dask.ipynb → docs/dask.ipynb
diff --git a/doc/geospatial.ipynb → docs/geospatial.ipynb b/doc/geospatial.ipynb → docs/geospatial.ipynb
diff --git a/doc/globe.png → docs/globe.png b/doc/globe.png → docs/globe.png
diff --git a/doc/heights.png → docs/heights.png b/doc/heights.png → docs/heights.png
diff --git a/doc/index.rst → docs/index.rst b/doc/index.rst → docs/index.rst
diff --git a/doc/interrupted-workflow.ipynb → docs/interrupted-workflow.ipynb b/doc/interrupted-workflow.ipynb → docs/interrupted-workflow.ipynb
diff --git a/doc/io.ipynb → docs/io.ipynb b/doc/io.ipynb → docs/io.ipynb
diff --git a/doc/iris-2d.png → docs/iris-2d.png b/doc/iris-2d.png → docs/iris-2d.png
diff --git a/doc/merge-bins.ipynb → docs/merge-bins.ipynb b/doc/merge-bins.ipynb → docs/merge-bins.ipynb
diff --git a/doc/modules.rst → docs/modules.rst b/doc/modules.rst → docs/modules.rst
diff --git a/doc/physt-logo.svg → docs/physt-logo.svg b/doc/physt-logo.svg → docs/physt-logo.svg
diff --git a/doc/physt-logo64.png → docs/physt-logo64.png b/doc/physt-logo64.png → docs/physt-logo64.png
diff --git a/doc/physt.compat.rst → docs/physt.compat.rst b/doc/physt.compat.rst → docs/physt.compat.rst
diff --git a/doc/physt.examples.rst → docs/physt.examples.rst b/doc/physt.examples.rst → docs/physt.examples.rst
diff --git a/doc/physt.io.rst → docs/physt.io.rst b/doc/physt.io.rst → docs/physt.io.rst
diff --git a/doc/physt.plotting.rst → docs/physt.plotting.rst b/doc/physt.plotting.rst → docs/physt.plotting.rst
diff --git a/doc/physt.rst → docs/physt.rst b/doc/physt.rst → docs/physt.rst
diff --git a/doc/plotly.ipynb → docs/plotly.ipynb b/doc/plotly.ipynb → docs/plotly.ipynb
diff --git a/doc/plotting.ipynb → docs/plotting.ipynb b/doc/plotting.ipynb → docs/plotting.ipynb
diff --git a/doc/special_histograms.ipynb → docs/special_histograms.ipynb b/doc/special_histograms.ipynb → docs/special_histograms.ipynb
diff --git a/doc/statistics_and_maths.ipynb → docs/statistics_and_maths.ipynb b/doc/statistics_and_maths.ipynb → docs/statistics_and_maths.ipynb
diff --git a/doc/tutorial.ipynb → docs/tutorial.ipynb b/doc/tutorial.ipynb → docs/tutorial.ipynb
diff --git a/doc/vega-examples.ipynb → docs/vega-examples.ipynb b/doc/vega-examples.ipynb → docs/vega-examples.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -26,11 +26,19 @@ dependencies = [
 ]
 
 [tool.uv]
-dev-dependencies = ["physt[all]"]
+dev-dependencies = [
+    "bumpver>=2025.1131",
+    "mypy>=1.18.2",
+    "nbsphinx>=0.9.7",
+    "physt[all]",
+    "pytest>=8.4.1",
+    "pytest-xdist>=3.8.0",
+    "sphinx>=7.4.7",
+    "sphinx-rtd-theme>=3.0.2",
+    "sphinxcontrib-apidoc>=0.6.0",
+]
 
 [project.optional-dependencies]
-dev = ["pytest", "mypy>=1.8", "types-setuptools", "bumpver", "pytest-xdist"]
-# doc = ["sphinx", "sphinx_rtd_theme", "sphixncontrib-apidoc", "nbsphinx"]
 astropy = ["astropy>=6.0"]
 dask = ["dask[array]>=2023.0"]
 pandas = ["pandas>=1.3"]
@@ -62,7 +70,7 @@ include = '\.pyi?$'
 # TODO: revisit
 ignore_missing_imports = true
 # plugins = ["numpy.typing.mypy_plugin"]
-exclude = ["doc"]
+exclude = ["docs"]
 
 [tool.isort]
 profile = "black"
@@ -76,7 +84,7 @@ where = ["src"]
 [tool.ruff]
 # Be a bit tolerant
 # line-length = 100
-extend-exclude = ["doc"]
+extend-exclude = ["docs"]
 target-version = "py39"
 
 [tool.ruff.per-file-ignores]