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Create analysis3-23.07 #47

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Aug 24, 2023
Merged

Create analysis3-23.07 #47

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50 changes: 23 additions & 27 deletions scripts/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ channels:
variables:
CARTOPY_USER_BACKGROUNDS: /g/data/hh5/public/apps/cartopy-data/backgrounds
dependencies:
- python>=3.9
- python>=3.10
- pip
- sqlalchemy<2.0 ### cosima cookbook does not import with sqlalchemy 2
- libnetcdf>=4.7.4=mpi_openmpi* # pinned for solver stability
Expand All @@ -30,16 +30,15 @@ dependencies:
- seaborn
- xarray
- jupyter
- notebook<7 ### Roll-back due to some incompatible extensions
- nb_conda
- notebook
- metpy
- windspharm
- python-cdo
- arm_pyart
- bokeh!=3.0.*,>=2.4.2 ### Dask needs bokeh!=3.0.*,>=2.4.2 for the dashboard.
- datashader
- f90nml==1.4.3
- wrf-python>=1.3.4 ### Force update
- f90nml
- wrf-python
- sympy
- sh
- ffmpeg
Expand Down Expand Up @@ -69,7 +68,7 @@ dependencies:
- matplotlib
#- matplotlib>=3.5.2|<=3.4.3 # pinned to solve https://github.com/matplotlib/matplotlib/issues/21917
- dreqpy
- pint<=0.19.2 ### pinned to fix https://github.com/Ouranosinc/xclim/issues/1216
- pint
- pycodestyle
- nc-time-axis
- jq
Expand All @@ -85,7 +84,7 @@ dependencies:
- hupper
- kealib
- mo_pack
- mule==2022.07.1
- mule
- cf-units
- python-stratify
- nbdime
Expand All @@ -100,14 +99,12 @@ dependencies:
- jupyterlab_server
- docrep
- gifsicle
- jupyter_nbextensions_configurator
- nodejs
- cfgrib
- h5netcdf
- jupyter_contrib_nbextensions
- intake #==0.6.5 # pinned to downgrade until intake 0.6.6 issue is solved
- intake
- gridfill
- xgcm>0.5 # pinned for solver stability
- xgcm
- xrft
- doit
- pylint
Expand All @@ -116,7 +113,7 @@ dependencies:
- nchash
- umtools
- cosima-cookbook
- clef>=1.5.1 # pinning to make sure it updates
- clef
- nccmp
- coecms-util
- yamanifest
Expand All @@ -125,7 +122,7 @@ dependencies:
- splitvar
- marineHeatWaves
- holoviews
- geoviews>=1.10 ### force update
- geoviews
- pytest-cov
- panel
- xrft
Expand All @@ -146,9 +143,9 @@ dependencies:
- sphinx
- doc8
- pymunge
- climtas>=0.3.3 # pin to force update
- climtas
- asyncssh
- ants==0.19.0
- ants
- xhistogram
- cartopy_userconfig=1.0.gadi
- geopy
Expand All @@ -157,12 +154,12 @@ dependencies:
- cython
- esmf>=8.0.1=mpi_openmpi*
- esmpy>=8.0.1=mpi_openmpi*
- xesmf>=0.6.2 # https://github.com/pangeo-data/xESMF/issues/127
- xesmf
- sharppy
- docrep
- earthpy
- descartes
- era5grib>=0.3.9 # pinned to force update
- era5grib
- conda-tree
- xmitgcm
- cupy
Expand All @@ -178,11 +175,11 @@ dependencies:
- noise # unlisted dependency of xarray-spatial
- nctoolkit
- geoplot
- dask-ml>=2022.5.27
- dask-ml
- mamba
- intake-esm==2023.07.07
- intake-esm
- pykrige
- nci_intake_catalogue>=1.3 # triggering update
- nci_intake_catalogue
- cmdline_provenance
- mplleaflet
- branca
Expand All @@ -202,8 +199,8 @@ dependencies:
- xmovie
- pymannkendall
- param
- tensorflow>=2.6 # pinned for solver stability
- shap<0.42.0 # https://github.com/shap/shap/issues/3075
- tensorflow
- shap
- gh
- pyqt
- vtk
Expand All @@ -227,7 +224,7 @@ dependencies:
- cdms2
- pygam
- pysal
- xmhw>=0.9.3
- xmhw
- argopy
- dataclasses-json
- ilamb
Expand All @@ -239,13 +236,12 @@ dependencies:
- palettable
- webcolors
- mpl-scatter-density
- benchcab>=1.0
- benchcab
- lmfit
- xclim
- jupyter-resource-usage
- acs_replica_intake
- matchpy
- pytmatrix
- mscorefonts
- opencv
- conda-build
Expand All @@ -262,7 +258,7 @@ dependencies:
- xcdat
- neutralocean
- ipympl
- libtiff<4.5.0 ### 4.4.0 -> 4.5.0 ABI change breaks gdal
- libtiff
- xskillscore
- geocat-comp
- ecgtools
Expand All @@ -277,7 +273,7 @@ dependencies:
- bargeparse
- accessnri::amami
- accessnri::access-nri-intake
- ipynbname>2023.1.0.0
- ipynbname
- shellcheck
- pip:
- railroad-diagrams ### Unlisted dependency of pip and pyparsing
4 changes: 2 additions & 2 deletions scripts/install_config.sh
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Expand Up @@ -22,7 +22,7 @@ export APPS_OWNERS_GROUP=hh5_w

### Version settings
export ENVIRONMENT=analysis3
export VERSION_TO_MODIFY=23.04
export VERSION_TO_MODIFY=23.07
export STABLE_VERSION=23.01
export UNSTABLE_VERSION=23.04
export FULLENV="${ENVIRONMENT}-${VERSION_TO_MODIFY}"
Expand All @@ -36,4 +36,4 @@ export SINGULARITY_BINARY_PATH="/opt/singularity/bin/singularity"
declare -a rpms_to_remove=( "openssh-clients" "openssh-server" "openssh" )
declare -a replace_from_apps=( "openmpi/4.1.5" )
declare -a outside_commands_to_include=( "pbs_tmrsh" "ssh" )
declare -a outside_files_to_copy=( "/g/data/hh5/public/apps/nci-intake-catalogue/catalogue_new.yaml" )
declare -a outside_files_to_copy=( "/g/data/hh5/public/apps/nci-intake-catalogue/catalogue_new.yaml" )
2 changes: 2 additions & 0 deletions scripts/testconfig.yml
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Expand Up @@ -45,6 +45,8 @@ skip:
- xgboost.spark ### Don't think we support spark as a parallel backend
- send2trash.mac ### Gadi is not a mac
- send2trash.win ### Nor is it windows
- attrdict ### Deprecated but still erroneously bought in by wavespectra - not used by anything else
- skimage.future.graph ### Thanks for raising a module error to tell me that you've moved this

# Preload these modules before testing to avoid weird python issues
preload:
Expand Down