Merge pull request #923 from scilus/fixDoc

Fix Documentation - readthedoc v2

docs/.readthedocs.yaml → .readthedocs.yaml

@@ -8,15 +8,18 @@ version: 2
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-22.04
+  apt_packages:
+    - libblas-dev
+    - liblapack-dev
   tools:
-    python: "3.11"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: source/conf.py
+  configuration: docs/source/conf.py
 
 # We recommend specifying your dependencies to enable reproducible builds:
 # https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
-   - requirements: requirements.txt
+   - requirements: docs/requirements.txt

docs/Makefile

@@ -1,10 +1,9 @@
 # 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
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build
 
@@ -17,4 +16,4 @@ help:
 # 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) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/requirements.txt

@@ -1,23 +1,44 @@
-dipy>=1.1
-fury==0.2.*
-future==0.17.*
-h5py==2.9.*
-matplotlib==2.2.*
-nibabel==3.0.*
-nilearn==0.6.*
-numpy==1.21.*
-Pillow==10.2.0
-pybids==0.10.*
-pyparsing==2.2.*
-python-dateutil==2.7.*
-pytz==2018.4.*
-scikit-learn==0.22.*
-scipy==1.4.*
-setuptools==46.1.*
-six==1.15.*
-vtk==8.1.*
-trimeshpy==0.0.*
-coloredlogs==10.0.*
-statsmodels==0.11.*
+bids-validator==1.11.*
 bctpy==0.5.*
-mock==4.0.*
+bz2file==0.98.*
+coloredlogs==15.0.*
+cvxpy==1.4.*
+cycler==0.11.*
+Cython==0.29.*, !=0.29.29
+dipy==1.8.*
+deepdiff==6.3.0
+docopt==0.6.*
+formulaic==0.3.*
+fury==0.9.*
+future==0.18.*
+GitPython==3.1.*
+joblib==1.2.*
+kiwisolver==1.4.*
+matplotlib==3.6.*
+mock==5.1.*
+nibabel==5.2.*
+nilearn==0.9.*
+numpy==1.23.*
+openpyxl==3.0.*
+packaging == 23.2.*
+Pillow==10.2.*
+pybids==0.16.*
+pyparsing==3.0.*
+PySocks==1.7.*
+pytest==7.2.*
+pytest-console-scripts==1.3.*
+pytest-cov==4.1.0
+pytest-html==4.1.1
+pytest-mock==3.10.*
+python-dateutil==2.8.*
+pytz==2022.6.*
+requests==2.28.*
+scikit-learn==1.2.*
+scikit-image==0.22.*
+scipy==1.9.*
+sphinx-rtd-theme==2.0.*
+six==1.16.*
+spams==2.6.*
+statsmodels==0.13.*
+trimeshpy==0.0.3
+vtk==9.2.*

docs/source/conf.py

@@ -18,13 +18,6 @@
 sys.path.insert(0, os.path.abspath("../.."))
 sys.path.insert(1, os.path.abspath("../../scripts"))
 
-autodoc_mock_imports = ['numpy', 'dipy', 'fury', 'nibabel', "scipy", "h5py",
-                        "scilpy.tractanalysis.grid_intersections",
-                        "scilpy.tractanalysis.quick_tools",
-                        "sklearn", "scilpy.tractanalysis.streamlines_metrics",
-                        "scilpy.tractograms.uncompress", "matplotlib",
-                        "skimage"]
-
 # -- Project information -----------------------------------------------------
 
 project = 'scilpy'
@@ -217,6 +210,8 @@ def setup(app):
 
         # Loop over scripts
         for i in sorted(os.listdir(path_script)):
+            if 'scil' not in i:
+                continue
             if not isdir(join(path_script, i)):
                 name, ext = i.split(".")
 

scilpy/dwi/operations.py

@@ -226,7 +226,7 @@ def compute_residuals(predicted_data, real_data, b0s_mask=None, mask=None):
 
     If data is a tensor, the residuals computation was introduced in:
     [J-D Tournier, S. Mori, A. Leemans. Diffusion Tensor Imaging and Beyond.
-     MRM 2011].
+    MRM 2011].
 
     Parameters
     ----------

scilpy/io/utils.py

@@ -18,7 +18,6 @@
 from PIL import Image
 from scipy.io import loadmat
 import six
-import importlib.metadata
 
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.gradients.bvec_bval_tools import DEFAULT_B0_THRESHOLD
@@ -231,12 +230,6 @@ def add_verbose_arg(parser):
                              'the provided level. \nDefault level is warning, '
                              'default when using -v is info.')
 
-    version = importlib.metadata.version('scilpy')
-
-    logging.getLogger().setLevel(logging.INFO)
-    logging.info("Scilpy version: {}".format(version))
-    logging.getLogger().setLevel(logging.WARNING)
-
 
 def add_bbox_arg(parser):
     parser.add_argument('--no_bbox_check', dest='bbox_check',