Merge pull request #115 from xylar/update-to-1.9.3

Update to 1.9.3

README.md

@@ -1,26 +1,26 @@
 # E3SM-Unified
 
-A metapackage for a unified 
+A metapackage for a unified
 [conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
-for analysis an other post-processing of results from Energy Exascale Earth 
+for analysis an other post-processing of results from Energy Exascale Earth
 System Model (E3SM) simulations.
 
 E3SM-Unified currently supports Linux and OSX, and python >=3.9,<3.11.
 Support for Windows is not planned.
 
 To create a new conda environment on a laptop or workstation (or on
 HPC that is not already supported by the E3SM team), first install
-[Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).  Then,
+[Miniforge3](https://github.com/conda-forge/miniforge#miniforge3).  Then,
 create the E3SM-Unified environment (with MPI support from the `mpich` package
 in this example), use:
-```bash 
-mamba create -n e3sm-unified -c conda-forge -c defaults -c e3sm \
+```bash
+conda create -n e3sm-unified -c conda-forge -c defaults -c e3sm \
     python=3.10 "e3sm-unified=*=mpi_mpich_*"
-mamba activate e3sm-unified
+conda activate e3sm-unified
 ```
 Each time you want to use the environment in the future, again run:
 ```bash
-mamba activate e3sm-unified
+conda activate e3sm-unified
 ```
 
 For the full list of packages in the current version of the metapackages, see:

e3sm_supported_machines/bootstrap.py

@@ -139,8 +139,7 @@ def build_env(is_test, recreate, compiler, mpi, conda_mpi, version,
                 channels = f'{channels} -c conda-forge/label/{package}_dev'
 
         # edit if not using a release candidate for a given package
-        dev_labels = ['e3sm_diags', 'e3sm_to_cmip', 'mache', 'mpas_analysis',
-                      'mpas_tools', 'zstash']
+        dev_labels = ['e3sm_diags', 'e3sm_to_cmip', 'mache', 'zppy']
         for package in dev_labels:
             channels = f'{channels} -c conda-forge/label/{package}_dev'
         channels = f'{channels} ' \

e3sm_supported_machines/default.cfg

@@ -22,23 +22,23 @@ ilamb = 2.7
 
 # the version of mache to use during deployment (should match the version used
 # in the package itself)
-mache = 1.18.0
+mache = 1.21.0
 
 # the version of mpi4py to build if using system compilers
 mpi4py = 3.1.5
 
 # the version of esmpy to build if using system compilers (must match esmf from
 # spack below)
-esmpy = 8.4.2
+esmpy = 8.6.0
 
 
 # spack package specs
 [spack_specs]
 
-esmf = esmf@8.4.2+mpi+netcdf~pnetcdf~external-parallelio
+esmf = esmf@8.6.0+mpi+netcdf~pnetcdf~external-parallelio
 hdf5 = [email protected]+cxx+fortran+hl+mpi+shared
 moab = [email protected]+mpi+hdf5+netcdf+pnetcdf+metis+parmetis+tempest
-nco = nco@5.1.9+openmp
+nco = nco@5.2.2+openmp
 netcdf_c = [email protected]+mpi~parallel-netcdf
 netcdf_fortran = [email protected]
 parallel_netcdf = [email protected]

e3sm_supported_machines/deploy_e3sm_unified.py

@@ -50,7 +50,7 @@ def setup_install_env(activate_base, use_local, mache):
     channels = ' '.join(channels)
     commands = f'{activate_base} && ' \
                f'conda create -y -n temp_e3sm_unified_install ' \
-               f'{channels} progressbar2 jinja2 {mache}'
+               f'{channels} progressbar2 jinja2 {mache} pip'
 
     check_call(commands)
 
@@ -67,14 +67,14 @@ def remove_install_env(activate_base):
 def install_mache_from_branch(activate_install_env, fork, branch):
     print('Clone and install local mache\n')
     commands = f'{activate_install_env} && ' \
-                f'rm -rf build_mache && ' \
-                f'mkdir -p build_mache && ' \
-                f'cd build_mache && ' \
-                f'git clone -b {branch} ' \
-                f'[email protected]:{fork}.git mache && ' \
-                f'cd mache && ' \
-                f'conda install -y --file spec-file.txt && ' \
-                f'python -m pip install --no-deps .'
+               f'rm -rf build_mache && ' \
+               f'mkdir -p build_mache && ' \
+               f'cd build_mache && ' \
+               f'git clone -b {branch} ' \
+               f'[email protected]:{fork}.git mache && ' \
+               f'cd mache && ' \
+               f'conda install -y --file spec-file.txt && ' \
+               f'python -m pip install --no-deps .'
 
     check_call(commands)
 

e3sm_supported_machines/shared.py

@@ -14,7 +14,7 @@
 def parse_args(bootstrap):
     parser = argparse.ArgumentParser(
         description='Deploy E3SM-Unified')
-    parser.add_argument("--version", dest="version", default="1.9.2",
+    parser.add_argument("--version", dest="version", default="1.9.3",
                         help="The version of E3SM-Unified to deploy")
     parser.add_argument("--conda", dest="conda_base",
                         help="Path for the  conda base")

e3sm_supported_machines/templates/build.template

@@ -14,7 +14,7 @@ fi
 
 
 if [ "{{ build_ilamb }}" == "True" ]; then
-    mamba install -y {{ ilamb_channels }} --no-deps "ilamb={{ ilamb_version }}"
+    conda install -y {{ ilamb_channels }} --no-deps "ilamb={{ ilamb_version }}"
 fi
 
 if [ "{{ build_esmpy }}" == "True" ]; then
@@ -28,7 +28,7 @@ if [ "{{ build_esmpy }}" == "True" ]; then
     # this is an unused dumping grounds and causes disconcerting warnings
     rm -rf src/esmpy/fragments
 
-    python -m pip install .
+    python -m pip install --no-deps .
 
     cd ${build_dir}
 fi

e3sm_supported_machines/templates/load_e3sm_unified.sh.template

@@ -1,5 +1,4 @@
 source {{ conda_base }}/etc/profile.d/conda.sh
-source {{ conda_base }}/etc/profile.d/mamba.sh
 
 export E3SMU_SCRIPT="{{ script_filename }}"
 export E3SMU_MACHINE="{{ machine }}"
@@ -9,15 +8,15 @@ then
   # we seem to be on a login node, so load the no-MPI environment
 
   export E3SMU_MPI="NOMPI"
-  mamba activate {{ env_nompi }}
+  conda activate {{ env_nompi }}
 
   export HDF5_USE_FILE_LOCKING=FALSE
 
 else
   # we seem to be on a compute node, so load the MPI environment
 
   export E3SMU_MPI="{{ env_type }}"
-  mamba activate {{ env_name }}
+  conda activate {{ env_name }}
 
   {{ spack }}
 

recipes/e3sm-unified/build_and_upload.bash

@@ -2,7 +2,7 @@
 
 set -e
 
-conda_dir=${HOME}/miniforge
+conda_dir=${HOME}/miniforge3
 os_dir=linux-64
 upload=False
 dev=False
@@ -15,14 +15,12 @@ then
   channels="-c conda-forge/label/e3sm_diags_dev \
             -c conda-forge/label/e3sm_to_cmip_dev \
             -c conda-forge/label/mache_dev \
-            -c conda-forge/label/mpas_analysis_dev \
-            -c conda-forge/label/mpas_tools_dev \
-            -c conda-forge/label/zstash_dev \
+            -c conda-forge/label/zppy_dev \
             -c conda-forge"
 
   for file in configs/mpi_mpich_python3.10.yaml configs/mpi_hpc_python3.10.yaml
   do
-    conda mambabuild -m $file --override-channels --use-local $channels .
+    conda build -m $file --override-channels --use-local $channels .
   done
 
   if [ $upload == "True" ]
@@ -35,7 +33,7 @@ else
   channels="-c conda-forge"
   for file in configs/mpi_*_python*.yaml
   do
-    conda mambabuild -m $file --override-channels --use-local $channels .
+    conda build -m $file --override-channels $channels .
   done
 
   if [ $upload == "True" ]

recipes/e3sm-unified/conda_first_failure.py

@@ -79,7 +79,7 @@
          'pandas'
          ]
 
-base_command = ['mamba', 'create', '-y', '-n', 'test', '--dry-run',
+base_command = ['conda', 'create', '-y', '-n', 'dry-run', '--dry-run',
                 '--override-channels',
                 '-c', 'conda-forge/label/mpas_analysis_dev',
                 '-c', 'conda-forge/label/zstash_dev',

recipes/e3sm-unified/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "E3SM-Unified" %}
-{% set version = "1.9.2" %}
+{% set version = "1.9.3" %}
 {% set build = 0 %}
 
 package:
@@ -30,27 +30,35 @@ requirements:
   run:
     ### main packages ###
     - python
-    - chemdyg 0.1.4
-    - e3sm_diags 2.10.1
-    - e3sm_to_cmip 1.11.1
-    - geometric_features 1.2.0
+    - chemdyg 0.1.5
+    - e3sm_diags 2.11.0
+    - e3sm_to_cmip 1.11.2
+    - geometric_features 1.3.0
     # fixes an issues with cryptography <37 constraint
     - globus-cli >=3.15.0
     - ilamb 2.7  # [mpi != 'nompi' and mpi != 'hpc']
     - ipython
     - jupyter
     - livvkit 3.0.1
-    - mache 1.18.0
+    - mache 1.21.0
     - moab 5.5.1 {{ mpi_prefix }}_tempest_*  # [mpi != 'hpc']
-    - mpas-analysis 1.9.1
-    - mpas_tools 0.30.0
-    - nco 5.1.9  # [mpi != 'hpc']
+    - mpas-analysis 1.10.0
+    - mpas_tools 0.32.0
+    - nco 5.2.2  # [mpi != 'hpc']
     - pcmdi_metrics 2.3.1
     - tempest-remap 2.2.0  # [mpi != 'hpc']
     - tempest-extremes 2.2.1 {{ mpi_prefix }}_*  # [mpi != 'hpc']
     - xcdat 0.6.1
-    - zppy 2.3.1
+    - zppy 2.4.0
     - zstash 1.4.2  # [linux]
+
+    ### mkdocs
+    - mkdocs-material
+    - pymdown-extensions
+    - mkdocs-monorepo-plugin
+    - mdutils
+    - mkdocs-bibtex
+
     ### dependencies ###
     - {{ mpi }}  # [mpi != 'nompi' and mpi != 'hpc']
     - blas
@@ -64,8 +72,8 @@ requirements:
     - dask 2023.6.0
     - dogpile.cache
     - eofs
-    - esmf 8.4.2 {{ mpi_prefix }}_*
-    - esmpy 8.4.2
+    - esmf 8.6.0 {{ mpi_prefix }}_*
+    - esmpy 8.6.0
     - f90nml
     - ffmpeg
     - genutil 8.2.1
@@ -75,7 +83,7 @@ requirements:
     - ipygany
     - libnetcdf 4.9.2 {{ mpi_prefix }}_*
     - lxml
-    - matplotlib 3.7.1
+    - matplotlib 3.8.2
     - metpy
     - mpi4py  # [mpi != 'nompi' and mpi != 'hpc']
     - nb_conda