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Commit f0c66a62 authored by Tomas Lovato's avatar Tomas Lovato
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add sphinxext.remoteliteralinclude to include remote files snippets (fix tracers.rst)

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1 merge request!2Fix several wrong linkages
This commit is part of merge request !2. Comments created here will be created in the context of that merge request.
......@@ -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
......
......@@ -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
......
......@@ -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::
......
......@@ -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
......
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