Add readthedocs page for mapca

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Nilearn cache
+nilearn_cache

.readthedocs.yml

@@ -10,7 +10,7 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  version: 3.7
+  version: "3.11"
   install:
     - method: pip
       path: .

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api.rst

@@ -0,0 +1,12 @@
+API Reference
+=============
+
+.. automodule:: mapca.mapca
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: mapca.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/conf.py

@@ -0,0 +1,47 @@
+# Configuration file for the Sphinx documentation builder.
+import os
+import sys
+
+# Add project root to path
+sys.path.insert(0, os.path.abspath(".."))
+
+import mapca
+
+# -- Project information -----------------------------------------------------
+project = "mapca"
+copyright = "2020, mapca developers"
+author = "mapca developers"
+release = mapca.__version__
+
+# -- General configuration ---------------------------------------------------
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+
+# -- Intersphinx configuration -----------------------------------------------
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "nilearn": ("https://nilearn.github.io/stable/", None),
+    "nibabel": ("https://nipy.org/nibabel/", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+}
+
+# -- Autodoc configuration ---------------------------------------------------
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "show-inheritance": True,
+}

docs/index.rst

@@ -0,0 +1,23 @@
+mapca: Moving Average PCA
+=========================
+
+A Python implementation of the moving average principal components analysis
+methods from GIFT.
+
+``mapca`` estimates the dimensionality of fMRI data by accounting for spatial
+correlations through subsampling and applying information-theoretic criteria
+(AIC, KIC, MDL) to determine the optimal number of principal components.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   api
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installation.rst

@@ -0,0 +1,24 @@
+Installation
+============
+
+Requirements
+------------
+
+``mapca`` requires Python >= 3.5 and the following packages:
+
+- nibabel >= 2.5.1
+- nilearn
+- numpy >= 1.15
+- scikit-learn >= 0.22
+- scipy >= 1.3.3
+
+Install
+-------
+
+You can install ``mapca`` from PyPI::
+
+    pip install mapca
+
+Or install the latest development version from GitHub::
+
+    pip install git+https://github.com/ME-ICA/mapca.git

mapca/tests/conftest.py

@@ -1,5 +1,6 @@
 import os
-from urllib.request import urlretrieve
+
+import requests
 
 import pytest
 
@@ -28,7 +29,10 @@ def fetch_file(osf_id, path, filename):
     url = 'https://osf.io/{}/download'.format(osf_id)
     full_path = os.path.join(path, filename)
     if not os.path.isfile(full_path):
-        urlretrieve(url, full_path)
+        r = requests.get(url)
+        r.raise_for_status()
+        with open(full_path, "wb") as f:
+            f.write(r.content)
     return full_path