From 5fc2c26ffa0b9b2d51b286e11ae16b90bc3a10e0 Mon Sep 17 00:00:00 2001 From: kvrigor Date: Wed, 30 Apr 2025 15:06:35 +0200 Subject: [PATCH 01/10] docs.yml updates - Locked Ubuntu version to 24.04 - Upgraded to Python 3.12 - Created a separate 'deploy' job --- .github/workflows/docs.yml | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4637cf6d68..d8f16c5340 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -17,7 +17,7 @@ concurrency: jobs: deploy-docs: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04 environment: name: github-pages url: ${{ steps.deployment.outputs.page_url }} @@ -27,10 +27,10 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@v5 with: - python-version: 3.11 + python-version: 3.12 cache: 'pip' - name: Install dependencies @@ -50,7 +50,23 @@ jobs: uses: actions/upload-pages-artifact@v3 with: path: "docs/_build/html" + name: eCLM_docs - - name: Deploy to GitHub Pages - id: deployment - uses: actions/deploy-pages@v4 + deploy: + if: github.event_name != 'pull_request' + needs: build + runs-on: ubuntu-24.04 + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + + permissions: + pages: write + id-token: write + + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 + with: + artifact_name: eCLM_docs From a8ef42087c2dcb4c42fa984cb2261b8aef434852 Mon Sep 17 00:00:00 2001 From: kvrigor Date: Wed, 30 Apr 2025 15:10:36 +0200 Subject: [PATCH 02/10] docs.yml: Fixed wrong job IDs --- .github/workflows/docs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index d8f16c5340..248be9a89f 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -16,7 +16,7 @@ concurrency: cancel-in-progress: false jobs: - deploy-docs: + build-docs: runs-on: ubuntu-24.04 environment: name: github-pages @@ -52,9 +52,9 @@ jobs: path: "docs/_build/html" name: eCLM_docs - deploy: + deploy-docs: if: github.event_name != 'pull_request' - needs: build + needs: build-docs runs-on: ubuntu-24.04 environment: name: github-pages From fd7038b55c7bfb00b8b35dcd34a018fda7d87e0a Mon Sep 17 00:00:00 2001 From: kvrigor Date: Wed, 30 Apr 2025 15:12:34 +0200 Subject: [PATCH 03/10] docs.yml: build-docs should run everytime --- .github/workflows/docs.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 248be9a89f..9bd725e07d 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -18,12 +18,6 @@ concurrency: jobs: build-docs: runs-on: ubuntu-24.04 - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} - permissions: - pages: write - id-token: write steps: - uses: actions/checkout@v4 From 59eabae0ca83c2d67cba17b08e11138bfe9d5a06 Mon Sep 17 00:00:00 2001 From: kvrigor Date: Tue, 6 May 2025 11:03:37 +0200 Subject: [PATCH 04/10] Replaced jupyter-book with mystmd --- docs/Makefile | 4 +-- docs/_config.yml | 40 ---------------------------- docs/_toc.yml | 59 ----------------------------------------- docs/myst.yml | 68 ++++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 70 insertions(+), 101 deletions(-) delete mode 100644 docs/_config.yml delete mode 100644 docs/_toc.yml create mode 100644 docs/myst.yml diff --git a/docs/Makefile b/docs/Makefile index 7c40135a30..a3cc515061 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -4,7 +4,7 @@ SRC_DIR = ../src all: docs src-browser docs: - jupyter-book build -W -n --keep-going . + myst build --html src-browser: ford -d $(SRC_DIR) -o $(BUILD_DIR)/html/src FORD_options.md @@ -12,4 +12,4 @@ src-browser: .PHONY: clean clean: - jupyter-book clean . \ No newline at end of file + myst clean -ya \ No newline at end of file diff --git a/docs/_config.yml b/docs/_config.yml deleted file mode 100644 index 33cb3e794f..0000000000 --- a/docs/_config.yml +++ /dev/null @@ -1,40 +0,0 @@ -####################################################################################### -# A default configuration that will be loaded for all jupyter books -# See the documentation for help and more options: -# https://jupyterbook.org/customize/config.html - -####################################################################################### -# Book settings -title : eCLM Documentation # The title of the book. Will be placed in the left navbar. -author : HPSC TerrSys # The author of the book -copyright : "2024" # Copyright year to be placed in the footer -logo : "" # A path to the book logo - -# Force re-execution of notebooks on each build. -# See https://jupyterbook.org/content/execute.html -execute: - execute_notebooks: force - -# Define the name of the latex output file for PDF builds -latex: - latex_documents: - targetname: book.tex - -sphinx: - config: - language: en - -# Information about where the book exists on the web -repository: - url: https://github.com/HPSCTerrSys/eCLM # Online location of your book - path_to_book: docs # Optional path to your book, relative to the repository root - branch: master # Which branch of the repository should be used when creating links (optional) - -# Add GitHub buttons to your book -# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository -html: - use_issues_button: true - use_repository_button: true - -# Do not parse these files -exclude_patterns: [FORD_options.md, README.md] diff --git a/docs/_toc.yml b/docs/_toc.yml deleted file mode 100644 index e5ccdeed6f..0000000000 --- a/docs/_toc.yml +++ /dev/null @@ -1,59 +0,0 @@ -# https://hpscterrsys.github.io/eCLM - -format: jb-book -root: INDEX -parts: - - caption: User's Guide - chapters: - - - file: users_guide/introduction_to_eCLM/README - title: Introduction to eCLM - sections: - - file: users_guide/introduction_to_eCLM/introduction - - file: users_guide/introduction_to_eCLM/prerequisites - - file: users_guide/introduction_to_eCLM/how_to_use_this_document - - - file: users_guide/building_eCLM/README - title: Building eCLM - sections: - - file: users_guide/building_eCLM/Ubuntu - - file: users_guide/building_eCLM/JSC/README - title: JSC - sections: - - file: users_guide/building_eCLM/JSC/prerequisites_JSC_users - - file: users_guide/building_eCLM/JSC/setting_up_eCLM - - file: users_guide/building_eCLM/Levante - - - file: users_guide/case_examples/README - title: Running example cases - sections: - - file: users_guide/case_examples/Wuestebach - - file: users_guide/case_examples/NRW - - file: users_guide/case_examples/EURO-CORDEX - - - file: users_guide/case_creation/README - title: Creating a custom case - sections: - - file: users_guide/case_creation/1_create_grid_file - - file: users_guide/case_creation/2_create_mapping_file - - file: users_guide/case_creation/3_create_domain_file - - file: users_guide/case_creation/4_create_surface_file - - file: users_guide/case_creation/5_modifications_surface_domain_file - - file: users_guide/case_creation/6_create_atm_forcings - - - file: users_guide/running_eCLM/README - title: Running eCLM - sections: - - file: users_guide/running_eCLM/basic_commands - - file: users_guide/running_eCLM/case_customization - - - file: users_guide/analyzing_model_output - title: Analyzing model output - - - caption: Reference - chapters: - - file: reference/history_fields - - url: https://escomp.github.io/ctsm-docs/versions/release-clm5.0/html/tech_note/index.html - title: Technical Note - - url: https://hpscterrsys.github.io/eCLM/src - title: eCLM Source Code Browser \ No newline at end of file diff --git a/docs/myst.yml b/docs/myst.yml new file mode 100644 index 0000000000..7925d8cc7b --- /dev/null +++ b/docs/myst.yml @@ -0,0 +1,68 @@ +version: 1 +project: + title: eCLM Documentation + authors: + - name: HPSC TerrSys + copyright: '2024' + exclude: + - FORD_options.md + - README.md + github: HPSCTerrSys/eCLM + exports: + - format: pdf + template: plain_latex_book + output: exports/book.pdf + toc: + - file: INDEX.md + - title: User's Guide + children: + - file: users_guide/introduction_to_eCLM/README.md + title: Introduction to eCLM + children: + - file: users_guide/introduction_to_eCLM/introduction.md + - file: users_guide/introduction_to_eCLM/prerequisites.md + - file: users_guide/introduction_to_eCLM/how_to_use_this_document.md + - file: users_guide/building_eCLM/README.md + title: Building eCLM + children: + - file: users_guide/building_eCLM/Ubuntu.md + - file: users_guide/building_eCLM/JSC/README.md + title: JSC + children: + - file: users_guide/building_eCLM/JSC/prerequisites_JSC_users.md + - file: users_guide/building_eCLM/JSC/setting_up_eCLM.md + - file: users_guide/building_eCLM/Levante.md + - file: users_guide/case_examples/README.md + title: Running example cases + children: + - file: users_guide/case_examples/Wuestebach.md + - file: users_guide/case_examples/NRW.md + - file: users_guide/case_examples/EURO-CORDEX.md + - file: users_guide/case_creation/README.md + title: Creating a custom case + children: + - file: users_guide/case_creation/1_create_grid_file.md + - file: users_guide/case_creation/2_create_mapping_file.md + - file: users_guide/case_creation/3_create_domain_file.md + - file: users_guide/case_creation/4_create_surface_file.md + - file: users_guide/case_creation/5_modifications_surface_domain_file.md + - file: users_guide/case_creation/6_create_atm_forcings.md + - file: users_guide/running_eCLM/README.md + title: Running eCLM + children: + - file: users_guide/running_eCLM/basic_commands.md + - file: users_guide/running_eCLM/case_customization.md + - file: users_guide/analyzing_model_output.md + title: Analyzing model output + - title: Reference + children: + - file: reference/history_fields + - url: https://escomp.github.io/ctsm-docs/versions/release-clm5.0/html/tech_note/index.html + title: Technical Note + - url: https://hpscterrsys.github.io/eCLM/src + title: eCLM Source Code Browser +site: + options: + logo: '' + folders: true + template: book-theme From 25f03ecaa6076d4209fb291ab16372197d6590ee Mon Sep 17 00:00:00 2001 From: kvrigor Date: Tue, 6 May 2025 11:04:33 +0200 Subject: [PATCH 05/10] docs.yml: Installed mystmd dependencies --- .github/workflows/docs.yml | 9 ++++++++- docs/requirements.txt | 2 +- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 9bd725e07d..26b011e079 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -27,7 +27,14 @@ jobs: python-version: 3.12 cache: 'pip' - - name: Install dependencies + - name: Install Ubuntu dependencies + uses: awalsh128/cache-apt-pkgs-action@latest + with: + packages: nodejs npm + version: 1.0 + execute_install_scripts: true + + - name: Install pip packages run: pip install -r ${GITHUB_WORKSPACE}/docs/requirements.txt - name: Build eCLM doc homepage diff --git a/docs/requirements.txt b/docs/requirements.txt index b497855c3e..f4fda67817 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ -jupyter-book +mystmd matplotlib numpy ghp-import From 21099cda80819741ae6be62c9b06386d751c9c21 Mon Sep 17 00:00:00 2001 From: kvrigor Date: Fri, 18 Jul 2025 09:39:19 +0200 Subject: [PATCH 06/10] Merged latest commits from master --- .github/workflows/CI.yml | 38 ++++- .github/workflows/docs.yml | 13 +- cmake/SetBuildOptions.cmake | 9 +- docs/INDEX.md | 4 +- docs/Makefile | 6 +- docs/_config.yml | 40 +++++ docs/_toc.yml | 53 ++++++ docs/users_guide/building_eCLM/JSC/README.md | 3 - .../JSC/prerequisites_JSC_users.md | 11 -- .../building_eCLM/JSC/setting_up_eCLM.md | 154 ------------------ docs/users_guide/building_eCLM/Levante.md | 5 - docs/users_guide/building_eCLM/README.md | 61 ------- docs/users_guide/building_eCLM/Ubuntu.md | 36 ---- docs/users_guide/installation/README.md | 13 ++ .../installation/source_installation.md | 37 +++++ .../introduction.md | 0 .../introduction_to_eCLM/README.md | 5 - .../how_to_use_this_document.md | 16 -- .../introduction_to_eCLM/prerequisites.md | 19 --- .../case_customization.md | 0 docs/users_guide/running_eCLM/README.md | 7 - .../running_eCLM/basic_commands.md | 32 ---- src/clm5/biogeochem/ch4Mod.F90 | 9 +- src/eclm/cime_comp_mod.F90 | 6 +- 24 files changed, 204 insertions(+), 373 deletions(-) create mode 100644 docs/_config.yml create mode 100644 docs/_toc.yml delete mode 100644 docs/users_guide/building_eCLM/JSC/README.md delete mode 100644 docs/users_guide/building_eCLM/JSC/prerequisites_JSC_users.md delete mode 100644 docs/users_guide/building_eCLM/JSC/setting_up_eCLM.md delete mode 100644 docs/users_guide/building_eCLM/Levante.md delete mode 100644 docs/users_guide/building_eCLM/README.md delete mode 100644 docs/users_guide/building_eCLM/Ubuntu.md create mode 100644 docs/users_guide/installation/README.md create mode 100644 docs/users_guide/installation/source_installation.md rename docs/users_guide/{introduction_to_eCLM => introduction}/introduction.md (100%) delete mode 100644 docs/users_guide/introduction_to_eCLM/README.md delete mode 100644 docs/users_guide/introduction_to_eCLM/how_to_use_this_document.md delete mode 100644 docs/users_guide/introduction_to_eCLM/prerequisites.md rename docs/users_guide/{running_eCLM => running_cases}/case_customization.md (100%) delete mode 100644 docs/users_guide/running_eCLM/README.md delete mode 100644 docs/users_guide/running_eCLM/basic_commands.md diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index fbacc61f54..cf289d4b4e 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -1,7 +1,12 @@ name: eCLM CI Test -# Controls when the action will run. -on: [push, pull_request] +on: + push: + branches: + - master + pull_request: + branches: + - master jobs: eclm_build_job: @@ -13,6 +18,15 @@ jobs: config: - { name: "eCLM-Standalone", + build_type: "RELEASE", + use_oasis: "False", + coup_oas_icon: "False", + coup_oas_pfl: "False", + use_pdaf: "False" + } + - { + name: "eCLM-Standalone_DEBUG", + build_type: "DEBUG", use_oasis: "False", coup_oas_icon: "False", coup_oas_pfl: "False", @@ -20,6 +34,15 @@ jobs: } - { name: "eCLM-ParFlow-ICON", + build_type: "RELEASE", + use_oasis: "True", + coup_oas_icon: "True", + coup_oas_pfl: "True", + use_pdaf: "False" + } + - { + name: "eCLM-ParFlow-ICON_DEBUG", + build_type: "DEBUG", use_oasis: "True", coup_oas_icon: "True", coup_oas_pfl: "True", @@ -27,6 +50,15 @@ jobs: } - { name: "eCLM-PDAF", + build_type: "RELEASE", + use_oasis: "False", + coup_oas_icon: "False", + coup_oas_pfl: "False", + use_pdaf: "True" + } + - { + name: "eCLM-PDAF_DEBUG", + build_type: "DEBUG", use_oasis: "False", coup_oas_icon: "False", coup_oas_pfl: "False", @@ -77,7 +109,7 @@ jobs: - name: Configure eCLM run: | cmake -S src -B $BUILD_DIR \ - -DCMAKE_BUILD_TYPE="RELEASE" \ + -DCMAKE_BUILD_TYPE=${{ matrix.config.build_type }} \ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \ -DCMAKE_PREFIX_PATH="$HOME/.local" \ -DCMAKE_C_COMPILER=$CC \ diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 26b011e079..f05e4a36b4 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -4,7 +4,9 @@ on: push: branches: - master - - 'docs-**' + pull_request: + branches: + - master env: BASE_URL: /${{ github.event.repository.name }} @@ -27,13 +29,6 @@ jobs: python-version: 3.12 cache: 'pip' - - name: Install Ubuntu dependencies - uses: awalsh128/cache-apt-pkgs-action@latest - with: - packages: nodejs npm - version: 1.0 - execute_install_scripts: true - - name: Install pip packages run: pip install -r ${GITHUB_WORKSPACE}/docs/requirements.txt @@ -70,4 +65,4 @@ jobs: id: deployment uses: actions/deploy-pages@v4 with: - artifact_name: eCLM_docs + artifact_name: eCLM_docs \ No newline at end of file diff --git a/cmake/SetBuildOptions.cmake b/cmake/SetBuildOptions.cmake index 74160066a7..c6b932369c 100644 --- a/cmake/SetBuildOptions.cmake +++ b/cmake/SetBuildOptions.cmake @@ -35,7 +35,14 @@ elseif(COMPILER STREQUAL "Intel" OR COMPILER STREQUAL "IntelLLVM") set(CMAKE_C_FLAGS_DEBUG "-O0 -g") set(CMAKE_C_FLAGS_RELEASE "-O2 -debug minimal") set(CMAKE_Fortran_FLAGS "-free -qno-opt-dynamic-align -ftz -traceback -convert big_endian -assume byterecl -assume realloc_lhs -fp-model source -qopenmp") - set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -fpe0 -check all") + if(USE_PDAF) + # PDAF does not pass all checks from "-check all" + # TODO: Resolve the PDAF/non-PDAF difference by either adapting + # the compile options or debugging the source code + set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -fpe0") #-check all + else() + set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -fpe0 -check all") + endif() set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -debug minimal") else() message(FATAL_ERROR "COMPILER='${COMPILER}' is not supported.") diff --git a/docs/INDEX.md b/docs/INDEX.md index 7da1a37179..76c7c62cff 100644 --- a/docs/INDEX.md +++ b/docs/INDEX.md @@ -4,5 +4,5 @@ **Welcome!** You are viewing the first version of the documentation for eCLM. This is a living document, which means it will be continuously updated and improved. Please check back regularly for the latest information and updates. ``` -```{tableofcontents} -``` \ No newline at end of file +eCLM is based on version 5.0 of the Community Land Model ([CLM5](https://www.cesm.ucar.edu/models/clm)) with simplified infrastructure for build and namelist generation. The build system is handled entirely by Cmake and namelists are generated through a small set of Python scripts. Similar to CLM5, eCLM is forced with meteorological data and uses numerous input streams on soil properties, land cover and land use, as well as complex parameter sets on crop phenology, and plant hydraulics for simulations. + diff --git a/docs/Makefile b/docs/Makefile index a3cc515061..e1bf337d7a 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,15 +1,15 @@ BUILD_DIR = ./_build SRC_DIR = ../src -all: docs src-browser - docs: myst build --html src-browser: ford -d $(SRC_DIR) -o $(BUILD_DIR)/html/src FORD_options.md +all: docs src-browser + .PHONY: clean clean: - myst clean -ya \ No newline at end of file + jupyter-book clean . diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 0000000000..3c1416a0f3 --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,40 @@ +####################################################################################### +# A default configuration that will be loaded for all jupyter books +# See the documentation for help and more options: +# https://jupyterbook.org/customize/config.html + +####################################################################################### +# Book settings +title : eCLM Documentation # The title of the book. Will be placed in the left navbar. +author : HPSC TerrSys # The author of the book +copyright : "2025" # Copyright year to be placed in the footer +logo : "" # A path to the book logo + +# Force re-execution of notebooks on each build. +# See https://jupyterbook.org/content/execute.html +execute: + execute_notebooks: force + +# Define the name of the latex output file for PDF builds +latex: + latex_documents: + targetname: book.tex + +sphinx: + config: + language: en + +# Information about where the book exists on the web +repository: + url: https://github.com/HPSCTerrSys/eCLM # Online location of your book + path_to_book: docs # Optional path to your book, relative to the repository root + branch: master # Which branch of the repository should be used when creating links (optional) + +# Add GitHub buttons to your book +# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository +html: + use_issues_button: true + use_repository_button: true + +# Do not parse these files +exclude_patterns: [FORD_options.md, README.md] diff --git a/docs/_toc.yml b/docs/_toc.yml new file mode 100644 index 0000000000..7f74453e61 --- /dev/null +++ b/docs/_toc.yml @@ -0,0 +1,53 @@ +# https://hpscterrsys.github.io/eCLM + +format: jb-book +root: INDEX +parts: +- caption: Introduction + chapters: + - file: users_guide/installation/README + title: Installing eCLM + - file: users_guide/introduction/introduction + title: Scientific Background + +- caption: User's Guide + chapters: + - file: users_guide/case_examples/README + title: Running example cases + sections: + - file: users_guide/case_examples/Wuestebach + - file: users_guide/case_examples/NRW + - file: users_guide/case_examples/EURO-CORDEX + + - file: users_guide/running_cases/case_customization + title: Customizing eCLM namelists + + - file: users_guide/analyzing_model_output + title: Analyzing model output + + - file: users_guide/case_creation/README + title: Creating a custom case + sections: + - file: users_guide/case_creation/1_create_grid_file + - file: users_guide/case_creation/2_create_mapping_file + - file: users_guide/case_creation/3_create_domain_file + - file: users_guide/case_creation/4_create_surface_file + - file: users_guide/case_creation/5_modifications_surface_domain_file + - file: users_guide/case_creation/6_create_atm_forcings + +- caption: Developer's Guide + chapters: + - file: users_guide/installation/source_installation + title: Building eCLM from source + - url: https://hpscterrsys.github.io/eCLM/src + title: eCLM Source Code Browser + +- caption: Reference + chapters: + - file: reference/history_fields + - url: https://escomp.github.io/CTSM/release-clm5.0/tech_note/index.html + title: CLM5 Technical Note + - url: https://github.com/HPSCTerrSys/eCLM_static-file-generator/blob/main/README.md) + title: eCLM static file generator + - url: https://hpscterrsys.github.io/TSMP2_workflow-engine + title: TSMP2 Workflow Engine diff --git a/docs/users_guide/building_eCLM/JSC/README.md b/docs/users_guide/building_eCLM/JSC/README.md deleted file mode 100644 index b97a98c468..0000000000 --- a/docs/users_guide/building_eCLM/JSC/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# JSC - -The following section will explain the necessary steps to download the model from the official repository and get eCLM to run on JSC machines (Juwels or Jureca-DC). diff --git a/docs/users_guide/building_eCLM/JSC/prerequisites_JSC_users.md b/docs/users_guide/building_eCLM/JSC/prerequisites_JSC_users.md deleted file mode 100644 index b711f3e450..0000000000 --- a/docs/users_guide/building_eCLM/JSC/prerequisites_JSC_users.md +++ /dev/null @@ -1,11 +0,0 @@ -# Prerequisites for JSC users - -Before building and running eCLM on JSC machines, the following prerequisites should be fulfilled: - -* Create a JSC/JuDoor account -* Join a compute time project -* Logging in to JSC machines - -Follow the startup-guide for creating a JSC/JuDoor account, joining a compute time project and logging in to JSC machines. - -See also additional links and pages, e.g. Software tips for Windows users: https://gitlab.jsc.fz-juelich.de/sdlts/general-organisation/jsc-supercomputer-wiki-for-ibg-3/-/wikis/Software-for-Windows-users diff --git a/docs/users_guide/building_eCLM/JSC/setting_up_eCLM.md b/docs/users_guide/building_eCLM/JSC/setting_up_eCLM.md deleted file mode 100644 index 3ac68c0381..0000000000 --- a/docs/users_guide/building_eCLM/JSC/setting_up_eCLM.md +++ /dev/null @@ -1,154 +0,0 @@ -# Setting up eCLM - -Once you created a JSC account and have access to a compute time project, follow these steps which will guide you on how to download and build eCLM on a JSC system. This guide involves four major steps: - -1. Prepare the environment -2. Download eCLM -3. Build eCLM - - Loading dependencies - - Configuring build settings - - Building eCLM -4. Verify that eCLM works - -Begin by logging in to the JSC system on your local machine using the ssh key. -(Windows users: open a terminal with Putty) - -For juwels for example do this: - -```sh -ssh -X -i ~/.ssh/id_ed25519 user1@juwels.fz-juelich.de # replace user1 with your JuDoor username! -``` - -## Step 1: Prepare the environment - -First, if not already done, you will create your own folders within the `project1` and `scratch` directories of your compute project on the supercomputer. - -```sh -# Check your projects and select a compute project with a non-empty 'budget-accounts'. Use it to replace projectID below! -jutil user projects -u $USER - -# Activate your project -jutil env activate -p projectID - -# Create folders -MYPROJECT="$PROJECT/$USER" -MYSCRATCH="$SCRATCH/$USER" -mkdir -p $MYPROJECT $MYSCRATCH -``` - -## Step 2: Download eCLM - -Navigate to your `$MYPROJECT` directory and clone the eCLM repository from Github. Next you will navigate into the main model folder and set the `eCLM_ROOT` environment variable. - -```sh -# Clone eCLM Github repository -cd $MYPROJECT -git clone https://github.com/HPSCTerrSys/eCLM.git - -# Navigate into eCLM folder and export environment variable -cd eCLM -eCLM_ROOT=$(pwd) -``` -## Step 3: Build eCLM - -### Loading dependencies - -Next, you need to load the software libraries required by eCLM. This is important as eCLM would fail to build nor run without knowing the location of its dependencies on the supercomputer. As this step needs to be done each time you start a new session, it is convenient to create a shell script that automates this step. Run this command to create a shell script named `load-eclm-variables.sh` in your `$HOME` directory: - -```sh -cat << EOF > $HOME/load-eclm-variables.sh -``` - -Then copy the following in the shell file: -```{attention} -Before you copy, replace 'projectID' with your compute project! -``` - -```sh -#!/usr/bin/env bash - -# Activate compute project -jutil env activate -p projectID - -# Set helper variables -MYPROJECT=${MYPROJECT} -MYSCRATCH=${MYSCRATCH} -eCLM_ROOT=${eCLM_ROOT} - -# Load eCLM dependencies -module load Stages/2024 -module load Intel -module load ParaStationMPI -module load netCDF -module load netCDF-Fortran -module load PnetCDF -module load imkl -module load Python -module load Perl -module load CMake - -# Display environment variables -module li -echo MYPROJECT=${MYPROJECT} -echo MYSCRATCH=${MYSCRATCH} -echo eCLM_ROOT=${eCLM_ROOT} - -# Navigate into eCLM model folder -cd $eCLM_ROOT -EOF -``` - -Now, source the environment file by running: - -```sh -source $HOME/load-eclm-variables.sh -``` - -You should get an output similar to this one: - -```{figure} ../../images/load_env.png -:width: 100% -``` -

- -### Configuring build settings - -eCLM is built using the CMake build system. Initially, you need to pass some build settings to `cmake`, such as which C/Fortran compilers to be used and the location of the install folder. This is accomplished by running the following commands: - -```sh -# Set variables -BUILD_DIR="${eCLM_ROOT}/build" -INSTALL_DIR="${eCLM_ROOT}/install" - -# CMake configure step -cmake -S "${eCLM_ROOT}/src" \ - -B "${BUILD_DIR}" \ - -D CMAKE_INSTALL_PREFIX="${INSTALL_DIR}" \ - -D CMAKE_BUILD_TYPE="RELEASE" \ - -D CMAKE_C_COMPILER=mpicc \ - -D CMAKE_Fortran_COMPILER=mpifort -``` - -### Building eCLM - -Finally, you can build eCLM. The commands below should take approximately 15-20 minutes to finish. - -```sh -cmake --build "${BUILD_DIR}" && cmake --install "${BUILD_DIR}" -``` - -## Step 4: Verify that eCLM works - -You can check if eCLM has been properly installed. The following command will display a directory tree showing the eCLM executable `eclm.exe` and library files in the `lib` directory: - -```sh -tree $eCLM_ROOT/install -``` -You should get something similar to: - -```{figure} ../../images/eclm_build.png -:height: 300px -``` -

- -**Congratulations!** You have successfully built and installed eCLM. diff --git a/docs/users_guide/building_eCLM/Levante.md b/docs/users_guide/building_eCLM/Levante.md deleted file mode 100644 index ecb8893007..0000000000 --- a/docs/users_guide/building_eCLM/Levante.md +++ /dev/null @@ -1,5 +0,0 @@ -# Levante - -```{warning} -Page under construction -``` \ No newline at end of file diff --git a/docs/users_guide/building_eCLM/README.md b/docs/users_guide/building_eCLM/README.md deleted file mode 100644 index 4d4e679097..0000000000 --- a/docs/users_guide/building_eCLM/README.md +++ /dev/null @@ -1,61 +0,0 @@ -# Building eCLM - -## Installation - -This section shows you how to build eCLM. - -### Minimum system requirements - -* MPI 3.1 -* netCDF-C 4.7.4 -* netCDF-Fortran 4.5.2 -* PnetCDF 1.12.1 -* LAPACK -* CMake 3.16 -* Supported compilers - - GCC 9.3.0 - - Intel 19.1.2 - -### Building eCLM - -1. Configure CMake build options. - -```sh -# User-specific variables -BUILD_DIR="bld" -INSTALL_DIR="eclm" - -# Run cmake -cmake -S src -B "$BUILD_DIR" \ - -DCMAKE_INSTALL_PREFIX="$INSTALL_DIR" \ - -DCMAKE_C_COMPILER=mpicc \ - -DCMAKE_Fortran_COMPILER=mpifort -``` - -Additionally, you may specify these optional build variables. - -* `CMAKE_BUILD_TYPE=DEBUG|RELEASE`. Defaults to `RELEASE`. -* `CMAKE_PREFIX_PATH`. Semicolon-separated list of paths (i.e. *install prefixes*) where external libraries might be found. You may need to specify this if CMake cannot find some of the required libraries (e.g. NetCDF, PnetCDF, LAPACK). - -2. Build and install eCLM. - -```sh -cmake --build "$BUILD_DIR" -cmake --install "$BUILD_DIR" -``` - -* adding the flag `--parallel 8` can potentially speed up the build - process (full command: `cmake --build "$BUILD_DIR" --parallel 8`), - https://cmake.org/cmake/help/latest/manual/cmake.1.html#cmdoption-cmake-build-j - -### Install namelist generator Python package - -The namelist generator scripts require Python 3.X. - -```sh -# Upgrade to latest version of pip -python3 -m pip install --upgrade pip - -# Install package -pip3 install --user ./namelist_generator -``` diff --git a/docs/users_guide/building_eCLM/Ubuntu.md b/docs/users_guide/building_eCLM/Ubuntu.md deleted file mode 100644 index c246ca41d1..0000000000 --- a/docs/users_guide/building_eCLM/Ubuntu.md +++ /dev/null @@ -1,36 +0,0 @@ -# Ubuntu - -```{warning} -Page under construction -``` - -## Minimum system requirements for Ubuntu - -On Ubuntu the following command should load the necessary system -requirements - -```sh -# Update `apt` -sudo apt update - -# Install packages -# ---------------- - -# Utilities -sudo apt install libxml2-utils wget - -# Python -sudo apt install python3 python3-pip pylint - -# Compiler -sudo apt install gfortran openmpi-bin libopenmpi-dev cmake - -# Linear algebra -sudo apt install libblas-dev liblapack-dev - -# NetCDF -sudo apt install netcdf-bin libnetcdf-dev libnetcdff-dev libpnetcdf-dev -``` - -Have a look in `.github/workflows/CI.yml` to find the Ubuntu packages -installed for CI-testing eCLM. diff --git a/docs/users_guide/installation/README.md b/docs/users_guide/installation/README.md new file mode 100644 index 0000000000..5599edd686 --- /dev/null +++ b/docs/users_guide/installation/README.md @@ -0,0 +1,13 @@ +# Installing eCLM + +The easiest way to install eCLM is through [TSMP2 build system](https://github.com/HPSCTerrSys/TSMP2). + +```sh +# Download TSMP2 +git clone https://github.com/HPSCTerrSys/TSMP2.git +cd TSMP2 + +# Build and install eCLM +./build_tsmp2.sh --eCLM +``` + diff --git a/docs/users_guide/installation/source_installation.md b/docs/users_guide/installation/source_installation.md new file mode 100644 index 0000000000..2a2a304d6b --- /dev/null +++ b/docs/users_guide/installation/source_installation.md @@ -0,0 +1,37 @@ +# Installing eCLM from source + +```{warning} +For advanced users. +``` + +## Requirements + +* MPI compilers (e.g. OpenMPI) +* CMake +* LAPACK +* [netCDF C and Fortran libraries](https://downloads.unidata.ucar.edu/netcdf) +* [PnetCDF](https://github.com/Parallel-NetCDF/PnetCDF) + +## Steps + +```sh +# Download eCLM +git clone https://github.com/HPSCTerrSys/eCLM.git +cd eCLM + +# Create eCLM install directory +mkdir install + +# Set compilers +export CC=mpicc FC=mpifort + +# Build and install eCLM +cmake -S src -B bld -DCMAKE_INSTALL_PREFIX=install +cmake --build bld --parallel +cmake --install bld +``` + +## Reference build scripts + +- [eCLM build on Ubuntu](https://github.com/HPSCTerrSys/eCLM/blob/4d567d2d68cac0fba977914b4a9c3ba199afd0ff/.github/workflows/CI.yml#L70-L121) +- [eCLM build on TSMP2](https://github.com/HPSCTerrSys/TSMP2/blob/master/cmake/BuildeCLM.cmake) diff --git a/docs/users_guide/introduction_to_eCLM/introduction.md b/docs/users_guide/introduction/introduction.md similarity index 100% rename from docs/users_guide/introduction_to_eCLM/introduction.md rename to docs/users_guide/introduction/introduction.md diff --git a/docs/users_guide/introduction_to_eCLM/README.md b/docs/users_guide/introduction_to_eCLM/README.md deleted file mode 100644 index be9f55838f..0000000000 --- a/docs/users_guide/introduction_to_eCLM/README.md +++ /dev/null @@ -1,5 +0,0 @@ -# Introduction to eCLM - -eCLM is based on version 5.0 of the Community Land Model ([CLM5](https://www.cesm.ucar.edu/models/clm)) with simplified infrastructure for build and namelist generation. The build system is handled entirely by Cmake and namelists are generated through a small set of Python scripts. Similar to CLM5, eCLM is forced with meteorological data and uses numerous input streams on soil properties, land cover and land use, as well as complex parameter sets on crop phenology, and plant hydraulics for simulations. - -The following section will give you a brief overview of CLM5. diff --git a/docs/users_guide/introduction_to_eCLM/how_to_use_this_document.md b/docs/users_guide/introduction_to_eCLM/how_to_use_this_document.md deleted file mode 100644 index 4d93e1be07..0000000000 --- a/docs/users_guide/introduction_to_eCLM/how_to_use_this_document.md +++ /dev/null @@ -1,16 +0,0 @@ -# How to use this document - -Throughout the document, the following style is used: - -``` -this is code to be executed in the shell command line -``` -```sh -# this is a comment -``` - -This is a name of a `variable` or a `command` and this in an example for a `script.sh`. - -This indicates a path and a specific file that the path leads to: `this/is/a/path/file.nc`. - -This is a link to a website. \ No newline at end of file diff --git a/docs/users_guide/introduction_to_eCLM/prerequisites.md b/docs/users_guide/introduction_to_eCLM/prerequisites.md deleted file mode 100644 index 02fe47b301..0000000000 --- a/docs/users_guide/introduction_to_eCLM/prerequisites.md +++ /dev/null @@ -1,19 +0,0 @@ -# Prerequisites - -## Linux systems - -If you are new to using Linux systems, it’s helpful to get familiar with a couple of things which will make setting up and working in this environment easier. - -### 1. Get familiar with linux command line -There are many good resources on the internet to get familiar with the basic command line arguments to navigate through different directories, create folders and files, move or manipulate files etc.. - -Resources: -- https://www.linuxcommand.org/ -- Jülich Supercomputing Centre: https://go.fzj.de/JSC-usertips - -### 2. Get familiar with a text editor -A text editor is very useful for quick and effective editing of files on Linux systems. There are different options for text editors like vim, [Emacs](https://www.gnu.org/software/emacs/) or nano. Vim and Emacs are already installed on the JSC systems. Look for a cheat sheet or a tutorial online or check the documentation on their official websites. - -## netCDF files - -NetCDF (network Common Data Form) is a file format for storing multidimensional scientific data (variables). In order to handle model input and output data for eCLM, you will need to be able to work with this file format. If you are not familiar with it yet, look for some resources or tutorials online. A quick introduction to netCDF can, for example, be found here. diff --git a/docs/users_guide/running_eCLM/case_customization.md b/docs/users_guide/running_cases/case_customization.md similarity index 100% rename from docs/users_guide/running_eCLM/case_customization.md rename to docs/users_guide/running_cases/case_customization.md diff --git a/docs/users_guide/running_eCLM/README.md b/docs/users_guide/running_eCLM/README.md deleted file mode 100644 index 97539a9383..0000000000 --- a/docs/users_guide/running_eCLM/README.md +++ /dev/null @@ -1,7 +0,0 @@ -# Running eCLM - -This section will explain how to run and customize your own eCLM cases. - -```{attention} -This workflow is still being further developed and is likely to change in the future. So make sure you check this website for updates! -``` \ No newline at end of file diff --git a/docs/users_guide/running_eCLM/basic_commands.md b/docs/users_guide/running_eCLM/basic_commands.md deleted file mode 100644 index 9241b7f851..0000000000 --- a/docs/users_guide/running_eCLM/basic_commands.md +++ /dev/null @@ -1,32 +0,0 @@ -# Basic commands to run eCLM - -Begin by logging in to the JSC (or another) system. Then, source the eCLM environment file. - -```sh -source load-eclm-variables.sh -``` - -You can create a folder called `cases` or similar in your main eCLM directory in which you create a new directory for every new case. - -```sh -mkdir -p cases/"your case name" -``` - -For the moment, copy the namelists from one of the test cases to use as a starting point for your new case. - -```sh -cd cases/"your case name" # replace with your case name -cp ../../test_cases/"test case"/. . # replace with the name of the test case -``` - -In the next step, you will customize the namelist files to your new case. - - - - - - - - - - diff --git a/src/clm5/biogeochem/ch4Mod.F90 b/src/clm5/biogeochem/ch4Mod.F90 index a35d92c7f7..b42d268415 100644 --- a/src/clm5/biogeochem/ch4Mod.F90 +++ b/src/clm5/biogeochem/ch4Mod.F90 @@ -2473,12 +2473,14 @@ subroutine ch4_prod (bounds, num_methc, filter_methc, num_methp, & end if ! If switched on, use pH factor for production based on spatial pH data defined in surface data. - if (.not. lake .and. usephfact .and. pH(c) > pHmin .and.pH(c) < pHmax) then + if (.not. lake .and. usephfact) then + if (pH(c) > pHmin .and.pH(c) < pHmax) then pH_fact_ch4 = 10._r8**(-0.2235_r8*pH(c)*pH(c) + 2.7727_r8*pH(c) - 8.6_r8) ! fitted function using data from Dunfield et al. 1993 ! Strictly less than one, with optimum at 6.5 ! From Lei Meng f_ch4_adj = f_ch4_adj * pH_fact_ch4 + end if else ! if no data, then no pH effects end if @@ -3552,10 +3554,11 @@ subroutine ch4_tran (bounds, & pondz = h2osfc(c) / 1000._r8 / frac_h2osfc(c) ! Assume all h2osfc corresponds to sat area ! mm / mm/m pondres = pondres + pondz / ponddiff - else if (.not. lake .and. sat == 1 .and. frac_h2osfc(c) > 0._r8 .and. & - h2osfc(c)/frac_h2osfc(c) > capthick) then ! Assuming short-circuit logic will avoid FPE here. + else if (.not. lake .and. sat == 1 .and. frac_h2osfc(c) > 0._r8) then + if (h2osfc(c)/frac_h2osfc(c) > capthick) then ! Assuming short-circuit logic will avoid FPE here. ! assume surface ice is impermeable pondres = 1/smallnumber + end if end if spec_grnd_cond(c,s) = 1._r8/(1._r8/grnd_ch4_cond(c) + snowres(c) + pondres) diff --git a/src/eclm/cime_comp_mod.F90 b/src/eclm/cime_comp_mod.F90 index 3a343a7bd5..ada3780b31 100644 --- a/src/eclm/cime_comp_mod.F90 +++ b/src/eclm/cime_comp_mod.F90 @@ -4059,7 +4059,7 @@ subroutine cime_run() ice(ens1)%iamroot_compid .or. & glc(ens1)%iamroot_compid .or. & wav(ens1)%iamroot_compid) then - call shr_mem_getusage(msize,mrss,.true.) + call shr_mem_getusage(msize,mrss,.false.) write(logunit,105) ' memory_write: model date = ',ymd,tod, & ' memory = ',msize,' MB (highwater) ',mrss,' MB (usage)', & @@ -4119,12 +4119,12 @@ subroutine cime_run() endif #ifdef USE_PDAF - ! TSMP specific stop condition: + ! TSMP-PDAF specific stop condition: counter = counter + 1 if (present(ntsteps) .and. counter == ntsteps) then if (iamroot_CPLID) then write(logunit,*) ' ' - write(logunit,103) subname,' NOTE: Stopping from TSMP-PDAF alarm ntsteps' + write(logunit,'(A, A, i10.8, i8)') subname,' NOTE: Stopping from TSMP-PDAF alarm ntsteps at model date = ',ymd,tod write(logunit,*) ' ' endif stop_alarm = .true. From 53e8fdc35821821287f82c29d27e9e96534131fc Mon Sep 17 00:00:00 2001 From: kvrigor Date: Fri, 18 Jul 2025 10:04:09 +0200 Subject: [PATCH 07/10] CI: Installed nodejs --- .github/workflows/docs.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f05e4a36b4..9c5d9021b7 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -29,6 +29,13 @@ jobs: python-version: 3.12 cache: 'pip' + - name: Install Ubuntu dependencies + uses: awalsh128/cache-apt-pkgs-action@latest + with: + packages: nodejs npm + version: 1.0 + execute_install_scripts: true + - name: Install pip packages run: pip install -r ${GITHUB_WORKSPACE}/docs/requirements.txt @@ -65,4 +72,4 @@ jobs: id: deployment uses: actions/deploy-pages@v4 with: - artifact_name: eCLM_docs \ No newline at end of file + artifact_name: eCLM_docs From 8077388119a4ee6ee0a8e486785cb8d5f2fcae01 Mon Sep 17 00:00:00 2001 From: kvrigor Date: Fri, 18 Jul 2025 10:05:42 +0200 Subject: [PATCH 08/10] Regenerated myst.yml --- docs/myst.yml | 75 +++++++++++++++++++++------------------------------ 1 file changed, 30 insertions(+), 45 deletions(-) diff --git a/docs/myst.yml b/docs/myst.yml index 7925d8cc7b..49479483d3 100644 --- a/docs/myst.yml +++ b/docs/myst.yml @@ -1,45 +1,30 @@ +# See docs at: https://mystmd.org/guide/frontmatter version: 1 project: - title: eCLM Documentation - authors: - - name: HPSC TerrSys - copyright: '2024' - exclude: - - FORD_options.md - - README.md - github: HPSCTerrSys/eCLM - exports: - - format: pdf - template: plain_latex_book - output: exports/book.pdf + id: 0cb7f824-8ccf-46a1-9ffe-0e41f6058eff + # title: + # description: + # keywords: [] + # authors: [] + github: https://github.com/HPSCTerrSys/eCLM + # To autogenerate a Table of Contents, run "myst init --write-toc" toc: + # Auto-generated by `myst init --write-toc` - file: INDEX.md + - title: Introduction + children: + - file: users_guide/installation/README.md + - file: users_guide/introduction/introduction.md - title: User's Guide children: - - file: users_guide/introduction_to_eCLM/README.md - title: Introduction to eCLM - children: - - file: users_guide/introduction_to_eCLM/introduction.md - - file: users_guide/introduction_to_eCLM/prerequisites.md - - file: users_guide/introduction_to_eCLM/how_to_use_this_document.md - - file: users_guide/building_eCLM/README.md - title: Building eCLM - children: - - file: users_guide/building_eCLM/Ubuntu.md - - file: users_guide/building_eCLM/JSC/README.md - title: JSC - children: - - file: users_guide/building_eCLM/JSC/prerequisites_JSC_users.md - - file: users_guide/building_eCLM/JSC/setting_up_eCLM.md - - file: users_guide/building_eCLM/Levante.md - file: users_guide/case_examples/README.md - title: Running example cases children: - file: users_guide/case_examples/Wuestebach.md - file: users_guide/case_examples/NRW.md - file: users_guide/case_examples/EURO-CORDEX.md + - file: users_guide/running_cases/case_customization.md + - file: users_guide/analyzing_model_output.md - file: users_guide/case_creation/README.md - title: Creating a custom case children: - file: users_guide/case_creation/1_create_grid_file.md - file: users_guide/case_creation/2_create_mapping_file.md @@ -47,22 +32,22 @@ project: - file: users_guide/case_creation/4_create_surface_file.md - file: users_guide/case_creation/5_modifications_surface_domain_file.md - file: users_guide/case_creation/6_create_atm_forcings.md - - file: users_guide/running_eCLM/README.md - title: Running eCLM - children: - - file: users_guide/running_eCLM/basic_commands.md - - file: users_guide/running_eCLM/case_customization.md - - file: users_guide/analyzing_model_output.md - title: Analyzing model output + - title: Developer's Guide + children: + - file: users_guide/installation/source_installation.md + - title: eCLM Source Code Browser + url: https://hpscterrsys.github.io/eCLM/src - title: Reference children: - - file: reference/history_fields - - url: https://escomp.github.io/ctsm-docs/versions/release-clm5.0/html/tech_note/index.html - title: Technical Note - - url: https://hpscterrsys.github.io/eCLM/src - title: eCLM Source Code Browser + - title: CLM5 Technical Note + url: https://escomp.github.io/CTSM/release-clm5.0/tech_note/index.html + - title: eCLM static file generator + url: https://github.com/HPSCTerrSys/eCLM_static-file-generator/blob/main/README.md + - title: TSMP2 Workflow Engine + url: https://hpscterrsys.github.io/TSMP2_workflow-engine + site: - options: - logo: '' - folders: true template: book-theme + # options: + # favicon: favicon.ico + # logo: site_logo.png From 50a4f7fd292865399d35669994e11d04e7bcccaf Mon Sep 17 00:00:00 2001 From: kvrigor Date: Fri, 18 Jul 2025 14:17:06 +0200 Subject: [PATCH 09/10] Added webpage title --- docs/myst.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/myst.yml b/docs/myst.yml index 49479483d3..d76daf257c 100644 --- a/docs/myst.yml +++ b/docs/myst.yml @@ -2,8 +2,8 @@ version: 1 project: id: 0cb7f824-8ccf-46a1-9ffe-0e41f6058eff - # title: - # description: + title: eCLM Documentation + description: eCLM Documentation # keywords: [] # authors: [] github: https://github.com/HPSCTerrSys/eCLM From c3a9715add93df62f49b368f2b0cb89990b8b9bc Mon Sep 17 00:00:00 2001 From: kvrigor Date: Fri, 18 Jul 2025 14:20:04 +0200 Subject: [PATCH 10/10] Updated clean command in Makefile --- docs/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Makefile b/docs/Makefile index e1bf337d7a..52e01bda83 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -12,4 +12,4 @@ all: docs src-browser .PHONY: clean clean: - jupyter-book clean . + myst clean -ay