Merge branch 'master' into accept_variant_as_a_list

.pre-commit-config.yaml

@@ -1,24 +1,24 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.5.0'
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 'v5.0.0'
     hooks:
-      - id: check-merge-conflict
-      - id: check-toml
-      - id: check-yaml
-      - id: debug-statements
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
+    -   id: check-merge-conflict
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
 
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: '24.3.0'
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: '24.10.0'
     hooks:
-      - id: black
+    -   id: black
         args: ['--config=./pyproject.toml']
 
-  - repo: https://github.com/pycqa/isort
+-   repo: https://github.com/pycqa/isort
     rev: '5.13.2'
     hooks:
-      - id: isort
+    -   id: isort
         args: ['--settings-path=./pyproject.toml']

conda-recipe/meta.yaml

@@ -39,8 +39,8 @@ requirements:
         - pineappl >=0.8.2
         - eko >=0.14.2
         - fiatlux
-        - sphinx >=5.0.2,<6 # documentation. Needs pinning temporarily due to markdown
-        - recommonmark
+        - sphinx >=5.0.2
+        - joblib
         - sphinx_rtd_theme >0.5
         - sphinxcontrib-bibtex
         - ruamel.yaml <0.18

doc/README.md

@@ -3,181 +3,5 @@
 Here we store the [documentation](https://docs.nnpdf.science/) (user / developer
 guides)
 
-## Sphinx Documentation
-
-### Generating the Documentation
-
-The NNPDF documentation is produced by the
-[sphinx](http://www.sphinx-doc.org/en/master/) resource. To generate the sphinx
-documentation, navigate to the `sphinx/` directory and execute the command `make
-html`. This produces the documentation in the `build/index/` directory. The
-`index.html` can be viewed with any appropriate browser.
-
-It is required to install `recommonmark` to interpret markdown. To add the
-dependencies to your environment, run
-
-```
-conda install sphinx recommonmark
-```
-
-### Adding to the Documentation
-
-New documentation can be added in markdown (`.md` or `.txt` suffices) or
-restructured text (`.rst` suffix) formats. To add a new section to the
-documentation, create an appropriately named directory in the `sphinx/source/`
-directory.  Inside the new directory, add all relevant documentation in the
-markdown or restructured text formats. In addition to these files, create an
-`index.rst` file containing:
-
-```
-Chapter Name
-============
-
-.. toctree::
-   :maxdepth: 1
-
-   ./file1.md
-   ./file2.rst
-```
-ensuring that the number of `=` signs is the same as the number of characters in
-`Chapter Name`.
-
-The next step is to reference the newly made `index.rst` in the main
-`sphinx/source/index.rst` file:
-
-```
-.. NNPDF documentation master file, created by
-   sphinx-quickstart on Mon Oct 29 10:53:50 2018.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-NNPDF documentation
-===================
-
-.. toctree::
-   :maxdepth: 2
-
-   get-started/index
-   theory/index
-   vp/index
-   code/index
-   tutorials/index
-   QA/index
-   <NEW CHAPTER>/index
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-```
-
-### Useful Markdown and Restructured Text Tools
-
-Various
-[markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) and
-[restructured text](http://docutils.sourceforge.net/docs/user/rst/quickref.html)
-cheatsheets exist online.
-
-In restructured text, a $\LaTeX$ block can be generated using
-
-```
-.. math::
-
-   \frac{1}{2}
-```
-
-while inline maths is generated using
-
-```
-:math:`\frac{1}{2}`
-```
-with attention being brought to the backticks. Note: the markdown intepreter
-being used here does not support inline maths, so if formula dense documentation
-is being implemented, it is advised to use restructured text instead.
-
-One can cross reference various parts of their markdown file using `anchors`,
-which provide clickable pieces of text which transport the reader to a
-particular part of the document.
-
-To do this: add an anchor point in the text. This may look like the following:
-```
-Lorem ipsum dolor sit amet <a name="label"</a> consectetur adipiscing elit, sed do
-```
-
-we can then jump to `label` from an arbitrary point in the text by using
-`[text](#label)`
-
-As an example, clicking [this](#top) will take the reader to the top of the
-page.
-
-This was done by having the following lines of code:
-
-```
-For example, clicking [this](#top) will take the reader to the top of the page.
-```
-as well as
-```
-# NNPDF code and standards documentation <a name="top"></a>
-```
-at the top of this file.
-
-
-In addition, one can link to other pages within the documentation by
-`[text](<relative-path-to-md-or-rst-file>.<extension>)`.
-
-One can define "lables" for RestructuredText, which can be referred to from
-anywhere, like this:
-```
-    .. _my-reference-label:
-
-    Section to cross-reference
-    --------------------------
-
-    This is the text of the section.
-
-    It refers to the section itself, see :ref:`my-reference-label`.
-```
-
-Such labels can also be defined in Markdown by using `rst` syntax embedded in
-code markers in markdown:
-
-
-	```eval_rst
-	.. _my-reference-label:
-	```
-
-Labels can be linked to from anywhere using  the syntax
-
-```
-[lint text](my-refence-label)
-```
-for Markdown and
-
-```
-:ref:`my-reference-label`.
-```
-for RestructuredText, as described in its
-[documentation](https://www.sphinx-doc.org/en/master/usage/restructuredtext/roles.html?highlight=cross%20reference#role-ref).
-
-## Installation using conda
-
-
-
-### Adding indices for modules
-
-Sphinx has the capability of automatically documenting any python package. It
-produces these under the `index` and `module index` sections. The functions and
-modules are documented using their corresponding docstrings.
-
-To add a new module to document, add a new line in `sphinx/Makefile` under:
-
-```
-%: Makefile
-	@if test $@ != "clean"; then
-            sphinx-apidoc -o ./source/modules/validphys ../../validphys2/src/validphys/ ; \
-            sphinx-apidoc -o ./source/modules/<MODULE-NAME> <PATH-TO-MODULE>  ;\
-	fi
-
-```
+For instructions on how to contribute to the documentation see the
+[documentation](https://docs.nnpdf.science/contributing/sphinx-documentation.html)