From 95664b03ab3507c07f1b94628a13a593fe7af704 Mon Sep 17 00:00:00 2001 From: Nikolay Koldunov Date: Sat, 11 Jan 2025 20:42:16 +0100 Subject: [PATCH 01/10] Update Docker instructions for compatibility with Mac Silicon and new image reference --- docs/getting_started/getting_started.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/getting_started/getting_started.rst b/docs/getting_started/getting_started.rst index cf5207da4..eeeb96934 100644 --- a/docs/getting_started/getting_started.rst +++ b/docs/getting_started/getting_started.rst @@ -460,12 +460,16 @@ The best way to run the model locally is to use Docker container. You obviously - Get the image:: - docker pull koldunovn/fesom2_test:refactoring2 + docker pull ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master + # if you use Mac Silicon (M1 M2 etc) use: + docker pull --platform linux/amd64 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master - Go to the folder with your version of fesom2 folder (NOT inside fesom2 folder, one up, the one you run ``git clone https://github.com/FESOM/fesom2.git`` in). - Run:: docker run -it -v "$(pwd)"/fesom2:/fesom/fesom2 koldunovn/fesom2_test:refactoring2 /bin/bash + # if you use Mac Silicon (M1 M2 etc) use: + docker run --platform linux/amd64 -it -v "$(pwd)"/fesom2:/fesom/fesom2 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master /bin/bash - This should get you inside the container. You now can edit the files in your fesom2 folder (on host system), but run compule and run the model inside the container. - When inside the container, to compile do: From 33ebc31b0ccb5d7979652d6b171b1b4314337d2e Mon Sep 17 00:00:00 2001 From: Nikolay Koldunov Date: Sat, 11 Jan 2025 20:43:38 +0100 Subject: [PATCH 02/10] Update Docker run command for consistency and Mac Silicon compatibility --- docs/getting_started/getting_started.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/getting_started/getting_started.rst b/docs/getting_started/getting_started.rst index eeeb96934..1625db117 100644 --- a/docs/getting_started/getting_started.rst +++ b/docs/getting_started/getting_started.rst @@ -467,7 +467,7 @@ The best way to run the model locally is to use Docker container. You obviously - Go to the folder with your version of fesom2 folder (NOT inside fesom2 folder, one up, the one you run ``git clone https://github.com/FESOM/fesom2.git`` in). - Run:: - docker run -it -v "$(pwd)"/fesom2:/fesom/fesom2 koldunovn/fesom2_test:refactoring2 /bin/bash + docker run -it -v "$(pwd)"/fesom2:/fesom/fesom2 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master /bin/bash # if you use Mac Silicon (M1 M2 etc) use: docker run --platform linux/amd64 -it -v "$(pwd)"/fesom2:/fesom/fesom2 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master /bin/bash From 09525552c82fb916948dba24587d10aef06c1b8f Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 11:25:47 +0100 Subject: [PATCH 03/10] remove refactoring branch from getting_started.rst --- docs/getting_started/getting_started.rst | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/getting_started/getting_started.rst b/docs/getting_started/getting_started.rst index 1625db117..afbf37971 100644 --- a/docs/getting_started/getting_started.rst +++ b/docs/getting_started/getting_started.rst @@ -57,13 +57,12 @@ Change to the `fesom2` folder and execute: :: cd fesom2 - git checkout refactoring -As a good practice, if one wants to make modifications to the source code or any of the files, it is advisable to create a branch from refactoring: +As a good practice, if one wants to make modifications to the source code or any of the files, it is advisable to create a branch from main: :: - git checkout -b refactoring + git checkout -b main After confirming that the right FESOM2 branch is being used, compile the model with: @@ -477,7 +476,6 @@ The best way to run the model locally is to use Docker container. You obviously :: cd fesom2 - git checkout refactoring bash -l configure.sh ubuntu - To prepare the run (this will do the test with pi mesh):: From cea2ad426bfcd19633b544c1829fd8bdbe67778f Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 11:51:31 +0100 Subject: [PATCH 04/10] Update requirements.txt with new sphinx version, add applehelp --- docs/requirements.txt | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 302b80753..ec1cd0cb3 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,4 @@ -sphinx==4.1.2 -sphinxcontrib-bibtex==2.3.0 +sphinx>=5.0 +sphinxcontrib-bibtex>=2.5 +sphinxcontrib-applehelp sphinx_rtd_theme From df5d5780838b7fb23f8669cae259d3abf9d99f77 Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 15:56:46 +0100 Subject: [PATCH 05/10] Update requirements.txt add sphinxfortran --- docs/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/requirements.txt b/docs/requirements.txt index ec1cd0cb3..bc88fe290 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,3 +2,4 @@ sphinx>=5.0 sphinxcontrib-bibtex>=2.5 sphinxcontrib-applehelp sphinx_rtd_theme +sphinxfortran From 4cb11eba84077db261b82ba1087a5f94fa65e4bb Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 16:00:12 +0100 Subject: [PATCH 06/10] Update requirements.txt --- docs/requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index bc88fe290..85696f8bc 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,4 @@ sphinx>=5.0 sphinxcontrib-bibtex>=2.5 -sphinxcontrib-applehelp sphinx_rtd_theme sphinxfortran From 4b4473caf53f3892aa8bdf44c36c2daf3f5fa34e Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 16:01:39 +0100 Subject: [PATCH 07/10] Update requirements.txt --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 85696f8bc..837c42d04 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ sphinx>=5.0 sphinxcontrib-bibtex>=2.5 sphinx_rtd_theme -sphinxfortran +sphinx-fortran From dab8dafb06a4f7448ed1f26bc91022659bae6af7 Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 16:04:15 +0100 Subject: [PATCH 08/10] Update requirements.txt --- docs/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/requirements.txt b/docs/requirements.txt index 837c42d04..35c60a0c5 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,3 +2,4 @@ sphinx>=5.0 sphinxcontrib-bibtex>=2.5 sphinx_rtd_theme sphinx-fortran +numpy From b5ae75b9ce08caea81b35c387971c8f6c52b6f23 Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 16:16:28 +0100 Subject: [PATCH 09/10] remove autodoc --- docs/conf.py | 2 -- docs/requirements.txt | 2 -- 2 files changed, 4 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 5550754e0..b61dc871f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -34,10 +34,8 @@ "sphinx.ext.mathjax", "sphinxcontrib.bibtex", "sphinxfortran.fortran_domain", - "sphinxfortran.fortran_autodoc", ] bibtex_bibfiles = ["mybib_fesom2.bib"] -fortran_src = ["../src/"] numfig = True # Add any paths that contain templates here, relative to this directory. diff --git a/docs/requirements.txt b/docs/requirements.txt index 35c60a0c5..81e5e9a0c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,3 @@ sphinx>=5.0 sphinxcontrib-bibtex>=2.5 sphinx_rtd_theme -sphinx-fortran -numpy From 49d30fa7bdca3bc4959c17e0ad2ba69cc620a7eb Mon Sep 17 00:00:00 2001 From: Jan Streffing Date: Mon, 13 Jan 2025 16:17:54 +0100 Subject: [PATCH 10/10] remove autodoc --- docs/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index b61dc871f..fdb38cc5c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -33,7 +33,6 @@ extensions = [ "sphinx.ext.mathjax", "sphinxcontrib.bibtex", - "sphinxfortran.fortran_domain", ] bibtex_bibfiles = ["mybib_fesom2.bib"]