fix-rtd-formatting (#257)

fixes failed rendering on rtd for matlab and python Updates to the build system on readthedocs.org, changes to sphinx-contrib for matlab, and now explicitly copying over some metadata (on this author) so that it's available on the read the docs vm during build. * refactoring and small formatting changes to docs * update rtd yaml and conf.py * copy over metadata to pypet2bids/pypet2bids folder * update sphinx-contrib version to 0.21.4
openneuropet · Jan 18, 2024 · d4da7f3 · d4da7f3
1 parent 1c6928f
commit d4da7f3
Show file tree

Hide file tree

Showing 13 changed files with 78 additions and 98 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -14,27 +14,22 @@ submodules:
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
   jobs:
     post_create_environment:
+      - cp -r metadata pypet2bids/pypet2bids/
       # install poetry
-      # https://python-poetry.org/docs/#osx--linux--bashonwindows-install-instructions
-      - curl -sSL https://install.python-poetry.org | python3 -
-      # Tell poetry to not use a virtual environment
-      - $HOME/.local/bin/poetry config virtualenvs.create false
+      - pip install poetry
+      - poetry config virtualenvs.create false
       # just use poetry to export a requirements.txt as that worked much better than the previous attempts
-      - cd pypet2bids && $HOME/.local/bin/poetry export --with dev --without-hashes -o requirements.txt
+      - cd pypet2bids && poetry lock && poetry export --without-hashes --with dev --format=requirements.txt > requirements.txt
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py
 
-# If using Sphinx, optionally build your docs in additional formats such as PDF
-# formats:
-#    - pdf
-
 # Optionally declare the Python requirements required to build your docs
 python:
    install:

diff --git a/Makefile b/Makefile
@@ -43,3 +43,6 @@ installpackage:
 
 testphantoms:
 	@scripts/testphantoms
+
+html:
+	@cd docs && make html
diff --git a/docs/index.rst b/docs/index.rst
@@ -11,7 +11,6 @@ Welcome to PET2BIDS's documentation!
    installation
    usage
    modules
-   matlab
    spreadsheets
    :maxdepth: 2
    :caption: Contents:

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -40,10 +40,11 @@ If you wish to contribute, are unable to install from PyPi, or simply wish to ru
 reading the `Additional Install Notes`_ section below.
 
 Additional Install Notes
-========================
+------------------------
 
-Matlab
-------
+**Matlab**
+
+------------------------------------------------------------------------------------------------------------------------
 
 **Dependencies**
 
@@ -76,8 +77,7 @@ all arguments in although this is also possible). You can find templates of such
 
 ------------------------------------------------------------------------------------------------------------------------
 
-Python
-------
+**Python**
 
 If you are unable to install this library from PyPi you can clone this repository to build and install the package
 as distributed on PyPi yourself with poetry.

diff --git a/docs/matlab.rst b/docs/matlab.rst
@@ -9,7 +9,7 @@ matlab
 
 .. mat:autofunction:: dcm2niix4pet
 
-.. mat:autofunction:: updatjsonpetfile
+.. mat:autofunction:: updatejsonpetfile
 
 .. mat:autofunction:: ecat2nii
 

diff --git a/docs/modules.rst b/docs/modules.rst
@@ -1,7 +1,8 @@
-pypet2bids
-==========
+Code
+====
 
 .. toctree::
    :maxdepth: 4
 
    pypet2bids
+   matlab
diff --git a/docs/pypet2bids.rst b/docs/pypet2bids.rst
@@ -1,10 +1,7 @@
 .. _pypet2bids-package:
 
-pypet2bids package
-==================
-
-Submodules
-----------
+pypet2bids
+==========
 
 pypet2bids.ecat\_cli module
 ---------------------------

diff --git a/matlab/get_pet_metadata.m b/matlab/get_pet_metadata.m
@@ -1,5 +1,4 @@
 function metadata = get_pet_metadata(varargin)
-
 % Routine that outputs PET scanner metadata following
 % `BIDS <https://bids.neuroimaging.io/ BIDS>`_.
 %
@@ -16,16 +15,16 @@
 %    all info is necessarily needed\)
 % :param inputs: a series of key/value pairs are expected
 % :returns metadata: a structure with BIDS fields filled \(such structure is ready
-%                   to be writen as json file using e.g. the bids matlab jsonwrite 
-%                   function, typically associated with the *_pet.nii file\)
+%   to be writen as json file using e.g. the bids matlab jsonwrite
+%   function, typically associated with the \*_pet.nii file\)
 %
 % :format:  metadata = get_pet_metadata(key,value)
 %
 % .. note::
 %
 %  Mandatory inputs are as follows\:
 %
-%   - *Scanner* name of scanner, map to a *parameters.txt file  e.g. 'Scanner', 'SiemensBiograph'
+%   - *Scanner* name of scanner, map to a \*parameters.txt file  e.g. 'Scanner', 'SiemensBiograph'
 %   - *TimeZero* when was the tracer injected                   e.g. 'TimeZero','11:05:01'
 %   - *ModeOfAdministration*                                    e.g. 'ModeOfAdministration', 'bolus'
 %   - *TracerName* which tracer was used                        e.g. 'TracerName','DASB'
@@ -55,7 +54,7 @@
 %    FrameTimesStart            = 0;
 %
 % .. note::
-%   TimeZero also can be [] or 'ScanStart' indicating that the scanning time 
+%   TimeZero also can be [] or 'ScanStart' indicating that the scanning time
 %   should be used as TimeZero. If TimeZero is not the scan time, we strongly
 %   advice to input ScanStart and InjectionStart making sure timing is correct
 %

diff --git a/pypet2bids/poetry.lock b/pypet2bids/poetry.lock
diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -28,7 +28,6 @@
 from tempfile import TemporaryDirectory
 import shutil
 from dateutil import parser
-from termcolor import colored
 import argparse
 import importlib
 import dotenv