From 93dc0c8cdfdb4ebda7ba82c1f84bf99540d1f166 Mon Sep 17 00:00:00 2001 From: Andreas Pauling Date: Mon, 27 Nov 2023 14:17:46 +0100 Subject: [PATCH] Update of README.md (removal of Tsa support) --- README.md | 5 +++- requirements/environment.yml | 57 ++++++++++++++++++------------------ tools/setup_env.sh | 13 ++------ 3 files changed, 34 insertions(+), 41 deletions(-) diff --git a/README.md b/README.md index 99d90c1..b7f6411 100644 --- a/README.md +++ b/README.md @@ -3,11 +3,14 @@ This repository calculates the pollen input fields needed for the real-time pollen calibration in ICON-ART. It is very similar to the FORTRAN implementation used in COSMO-ART. More information about the Pollen module currently in the weather model COSMO can be found here: -And in this paper: (currently under review :) +And in this paper: Adamov, S & Pauling, A (2023): A real-time calibration method for the numerical pollen forecast model COSMO-ART +Aerobiologia, 39, 327-344. Available open access from https://link.springer.com/article/10.1007/s10453-023-09796-5 This specific project also has a confluence page here: +The package has been tested on Balfrin at CSCS only. + ## Data Import In the /data folder are case studies for four Species: diff --git a/requirements/environment.yml b/requirements/environment.yml index 24a67a8..9d8a8c0 100644 --- a/requirements/environment.yml +++ b/requirements/environment.yml @@ -1,4 +1,4 @@ -name: RTcalib +name: RTcal channels: - conda-forge - defaults @@ -22,7 +22,7 @@ dependencies: - brotli-python=1.1.0 - bzip2=1.0.8 - c-ares=1.22.1 - - ca-certificates=2023.11.17 + - ca-certificates=2023.08.22 - certifi=2023.11.17 - cffi=1.16.0 - cfgrib=0.9.10.4 @@ -60,13 +60,13 @@ dependencies: - hdf5=1.12.1 - icu=73.2 - identify=2.5.32 - - idna=3.4 + - idna=3.6 - imagesize=1.4.1 - importlib-metadata=4.13.0 - importlib_resources=6.1.1 - iniconfig=2.0.0 - ipdb=0.13.13 - - ipython=8.17.2 + - ipython=8.18.0 - isort=5.12.0 - jasper=2.0.33 - jedi=0.19.1 @@ -82,7 +82,7 @@ dependencies: - keyutils=1.6.1 - krb5=1.21.2 - lcms2=2.15 - - ld_impl_linux-64=2.40 + - ld_impl_linux-64=2.38 - lerc=4.0.0 - libaec=1.1.2 - libarchive=3.7.2 @@ -92,7 +92,7 @@ dependencies: - libdeflate=1.17 - libedit=3.1.20191231 - libev=4.33 - - libffi=3.4.2 + - libffi=3.4.4 - libgcc-ng=13.2.0 - libgfortran-ng=13.2.0 - libgfortran5=13.2.0 @@ -105,15 +105,13 @@ dependencies: - libmambapy=1.5.3 - libnetcdf=4.8.1 - libnghttp2=1.58.0 - - libnsl=2.0.1 - libopenblas=0.3.25 - libpng=1.6.39 - - libsolv=0.7.26 - - libsqlite=3.44.1 + - libsolv=0.7.27 - libssh2=1.11.0 - libstdcxx-ng=13.2.0 - libtiff=4.5.0 - - libuuid=2.38.1 + - libuuid=1.41.5 - libwebp-base=1.3.2 - libxcb=1.13 - libxml2=2.11.6 @@ -129,14 +127,14 @@ dependencies: - mccabe=0.7.0 - mdurl=0.1.0 - more-itertools=10.1.0 - - mypy=1.7.0 + - mypy=1.7.1 - mypy_extensions=1.0.0 - nbformat=5.9.2 - ncurses=6.4 - nodeenv=1.8.0 - - numpy=1.26.0 + - numpy=1.26.2 - openjpeg=2.5.0 - - openssl=3.1.4 + - openssl=3.2.0 - packaging=23.2 - pandas=2.1.3 - parso=0.8.3 @@ -196,7 +194,7 @@ dependencies: - ruamel.yaml=0.18.5 - ruamel.yaml.clib=0.2.7 - ruamel_yaml=0.15.80 - - setuptools=68.2.2 + - setuptools=68.0.0 - shellingham=1.5.4 - six=1.16.0 - sniffio=1.3.0 @@ -210,8 +208,9 @@ dependencies: - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.6 - sphinxcontrib-serializinghtml=1.1.9 + - sqlite=3.41.2 - stack_data=0.6.2 - - tk=8.6.13 + - tk=8.6.12 - toml=0.10.2 - tomli=2.0.1 - tomlkit=0.12.3 @@ -221,7 +220,7 @@ dependencies: - truststore=0.8.0 - typer=0.9.0 - types-docutils=0.20.0.3 - - types-setuptools=68.2.0.1 + - types-setuptools=68.2.0.2 - types-toml=0.10.8.7 - typing-extensions=4.8.0 - typing_extensions=4.8.0 @@ -231,7 +230,7 @@ dependencies: - virtualenv=20.24.7 - watchgod=0.8.2 - wcwidth=0.2.12 - - wheel=0.41.3 + - wheel=0.41.2 - xarray=2023.11.0 - xorg-fixesproto=5.0 - xorg-inputproto=2.3.2 @@ -244,7 +243,7 @@ dependencies: - xorg-libxi=1.7.10 - xorg-xextproto=7.3.0 - xorg-xproto=7.0.31 - - xz=5.2.6 + - xz=5.4.2 - yaml=0.2.5 - yaml-cpp=0.8.0 - zipp=3.17.0 @@ -252,14 +251,14 @@ dependencies: - zstandard=0.22.0 - zstd=1.5.5 - pip: - - copier==9.0.1 - - dunamai==1.19.0 - - flake8-pyproject==1.2.3 - - funcy==2.0 - - jinja2-ansible-filters==1.3.2 - - mistune==2.0.5 - - plumbum==1.8.2 - - prompt-toolkit==3.0.36 - - pyyaml-include==1.3.1 - - questionary==2.0.1 - - sphinx-mdinclude==0.5.3 + - copier==9.0.1 + - dunamai==1.19.0 + - flake8-pyproject==1.2.3 + - funcy==2.0 + - jinja2-ansible-filters==1.3.2 + - mistune==2.0.5 + - plumbum==1.8.2 + - prompt-toolkit==3.0.36 + - pyyaml-include==1.3.1 + - questionary==2.0.1 + - sphinx-mdinclude==0.5.3 diff --git a/tools/setup_env.sh b/tools/setup_env.sh index a9015f7..003d52e 100755 --- a/tools/setup_env.sh +++ b/tools/setup_env.sh @@ -77,18 +77,9 @@ ${CONDA} env config vars set GRIB_DEFINITION_PATH=${conda_eccodes}/definitions/: # fieldextra path -if [[ $(hostname -s) == *'tsa'* ]]; then - echo 'Setting FIELDEXTRA_PATH for tsa' - ${CONDA} env config vars set FIELDEXTRA_PATH=/project/s83c/fieldextra/tsa/bin/fieldextra_gnu_opt_omp +echo 'Setting FIELDEXTRA_PATH for balfrin' +${CONDA} env config vars set FIELDEXTRA_PATH=/users/oprusers/osm/bin/fieldextra -elif [[ $(hostname -s) == *'daint'* ]]; then - echo 'Setting FIELDEXTRA_PATH for daint' - ${CONDA} env config vars set FIELDEXTRA_PATH=/project/s83c/fieldextra/daint/bin/fieldextra_gnu_opt_omp - -elif [[ $(hostname -s) == *'balfrin'* ]]; then - echo 'Setting FIELDEXTRA_PATH for balfrin' - ${CONDA} env config vars set FIELDEXTRA_PATH=/users/oprusers/osm/bin/fieldextra -fi # # cartopy setup