add sphinxext.remoteliteralinclude to include remote files snippets (fix tracers.rst)

source/conf.py

@@ -14,9 +14,9 @@ author = 'NEMO System Team'
 # The short X.Y version
 version = '4.2.0'
 # The full version, including alpha/beta/rc tags
-release = 'release-4.2.0'
-
-code_repo='https://forge.nemo-ocean.eu/nemo/nemo/-/tree/' + version
+release = 'release-' + version
+# NEMO gitlab repository
+nemo_repo='https://forge.nemo-ocean.eu/nemo/nemo/-/'
 
 
 # -- General configuration ---------------------------------------------------
@@ -25,6 +25,9 @@ code_repo='https://forge.nemo-ocean.eu/nemo/nemo/-/tree/' + version
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.extlinks', 'sphinx.ext.todo', 'sphinxcontrib.bibtex']
+# add pip extensions
+extensions += ['sphinxext.remoteliteralinclude']
+
 bibtex_bibfiles = ['refs.bib', 'cfgs.bib', 'tests.bib']
 
 # Add any paths that contain templates here, relative to this directory.
@@ -105,9 +108,10 @@ extlinks = {
 	'github'  : ('https://github.com/NEMO-ocean/%s'         , None),
 	'xios'    : ('https://forge.ipsl.jussieu.fr/ioserver/%s', None),
 	'website' : ('https://www.nemo-ocean.eu/%s'             , None),
-	'gitlab'  : ('https://forge.nemo-ocean.eu/nemo/core'    , None),
 	'zenodo'  : ('https://zenodo.org/publication/%s'        , None),
-        'coderepo': (code_repo + '%s'                           , None),
+	'gitlab'  : (nemo_repo                                  , None),
+        'coderepo': (nemo_repo + '/tree/'+ version + '%s'       , None),
+        'tarrepo' : (nemo_repo + '/releases/'+ version + '%s'   , None),
 }
 
 # Include common directives for every rst file

source/install.rst

@@ -119,13 +119,11 @@ Instructions on how to install XIOS can be found on its :xios:`wiki<>`.
 Download and install the NEMO code
 **********************************
 
-Checkout the 4.2.0 NEMO source
-------------------------------
+Checkout the NEMO source
+------------------------
 
-  .. _`4.2.0 release site`: https://forge.nemo-ocean.eu/nemo/nemo/-/releases/4.2.0
-  
 There are several ways to obtain the NEMO source code. Users who are not familiar with ``git``
-and simply want a fixed code to compile and run, can download a tarball from the `4.2.0 release site`_
+and simply want a fixed code to compile and run, can download a tarball from the :tarrepo:`4.2.0 release site<>`
 
 Users who are familiar with ``git`` and likely to use it to manage their own local branches and 
 modifications, can clone the repository at the release tag:
@@ -243,9 +241,9 @@ More :file:`makenemo` options
 ``makenemo`` has several other options that can control which source files are selected and
 the operation of the build process itself.
 
-.. literalinclude:: ../../../makenemo
+.. rli:: https://forge.nemo-ocean.eu/nemo/nemo/-/raw/4.2.0/makenemo
    :language: text
-   :lines: 119-143
+   :lines: 119-151
    :caption: Output of ``makenemo -h``
 
 These options can be useful for maintaining several code versions with only minor differences but

source/migration.rst

@@ -28,8 +28,8 @@ the periodicity, see Figure 1.:
    chosen periodicity. Thick black rows delimit the part of the domain included in all
    input/outputs files.
 
-**From NEMO 4.2.0, s the columns and rows that are duplicated because of periodicity (EW, SN
-and NP)  are excluded from all input and output files.**  In practise, when preparing old
+**From NEMO 4.2.0, the columns and rows that are duplicated because of periodicity (EW, SN
+and NP)  are excluded from all input and output files.**  In practice, when preparing old
 configurations for use with 4.2.0, this means:
 
 .. list-table::

source/tracers.rst

@@ -79,10 +79,9 @@ Model initialization (:file:`./src/OCE/nemogcm.F90`)
 
 Call to ``trc_init`` subroutine (:file:`./src/TOP/trcini.F90`) to initialize TOP.
 
-.. literalinclude:: ../../../src/TOP/trcini.F90
+.. rli:: https://forge.nemo-ocean.eu/nemo/nemo/-/raw/4.2.0/src/TOP/trcini.F90
    :language:        fortran
-   :lines:           41-86
-   :emphasize-lines: 21,30-32,38-40
+   :lines:           43-87
    :caption:         ``trc_init`` subroutine
 
 Time marching procedure (:file:`./src/OCE/step.F90`)
@@ -90,27 +89,25 @@ Time marching procedure (:file:`./src/OCE/step.F90`)
 
 Call to ``trc_stp`` subroutine (:file:`./src/TOP/trcstp.F90`) to compute/update passive tracers.
 
-.. literalinclude:: ../../../src/TOP/trcstp.F90
+.. rli:: https://forge.nemo-ocean.eu/nemo/nemo/-/raw/4.2.0/src/TOP/trcstp.F90
    :language:        fortran
-   :lines:           46-125
-   :emphasize-lines: 42,55-57
+   :lines:           48-139
    :caption:         ``trc_stp`` subroutine
 
 BGC trends computation for each submodule (:file:`./src/TOP/trcsms.F90`)
 ------------------------------------------------------------------------
 
-.. literalinclude:: ../../../src/TOP/trcsms.F90
+.. rli:: https://forge.nemo-ocean.eu/nemo/nemo/-/raw/4.2.0/src/TOP/trcsms.F90
    :language:        fortran
-   :lines:           21
-   :caption:         :file:`trcsms` snippet
+   :lines:           36-66
+   :caption:         :file:`trcsms` subroutine
 
 Physical trends computation (:file:`./src/TOP/TRP/trctrp.F90`)
 --------------------------------------------------------------
 
-.. literalinclude:: ../../../src/TOP/TRP/trctrp.F90
+.. rli:: https://forge.nemo-ocean.eu/nemo/nemo/-/raw/4.2.0/src/TOP/TRP/trctrp.F90
    :language:        fortran
-   :lines:           46-95
-   :emphasize-lines: 17,21,29,33-35
+   :lines:           50-111
    :caption:         ``trc_trp`` subroutine
 
 Namelists walkthrough
@@ -237,7 +234,7 @@ the segments defined for the physical core of NEMO
 Here below the description of :file:`namelist_trc_ref` used to handle Carbon tracers modules,
 namely CFC and C14.
 
-.. literalinclude:: ../../../cfgs/SHARED/namelist_trc_ref
+.. rli:: https://forge.nemo-ocean.eu/nemo/nemo/-/raw/4.2.0/cfgs/SHARED/namelist_trc_ref
    :language: fortran
    :lines: 7,17,26,34
    :caption: :file:`../namelist_trc_ref` snippet