Merge pull request #161 from xylar/remove-mamba

Remove `mamba` command and switch to Miniforge3

.github/workflows/build_workflow.yml

@@ -76,13 +76,10 @@ jobs:
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Conda Environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: "polaris_ci"
-          miniforge-variant: Mambaforge
           miniforge-version: latest
-          use-mamba: true
-          mamba-version: "*"
           channels: conda-forge,e3sm/label/polaris,defaults
           channel-priority: strict
           auto-update-conda: true

.github/workflows/docs_workflow.yml

@@ -32,13 +32,10 @@ jobs:
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Conda Environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: "polaris_ci"
-          miniforge-variant: Mambaforge
           miniforge-version: latest
-          use-mamba: true
-          mamba-version: "*"
           channels: conda-forge,e3sm/label/polaris,defaults
           channel-priority: strict
           auto-update-conda: true

configure_polaris_envs.py

@@ -7,7 +7,7 @@
     check_call,
     get_conda_base,
     get_logger,
-    install_mambaforge,
+    install_miniforge,
     parse_args,
 )
 
@@ -47,11 +47,11 @@ def setup_install_env(env_name, activate_base, use_local, logger, recreate,
     if recreate or not os.path.exists(env_path):
         print('Setting up a conda environment for installing polaris\n')
         commands = f'{activate_base} && ' \
-                   f'mamba create -y -n {env_name} {channels} {packages}'
+                   f'conda create -y -n {env_name} {channels} {packages}'
     else:
         print('Updating conda environment for installing polaris\n')
         commands = f'{activate_base} && ' \
-                   f'mamba install -y -n {env_name} {channels} {packages}'
+                   f'conda install -y -n {env_name} {channels} {packages}'
 
     check_call(commands, logger=logger)
 
@@ -74,8 +74,7 @@ def main():
     env_name = 'polaris_bootstrap'
 
     source_activation_scripts = \
-        f'source {conda_base}/etc/profile.d/conda.sh && ' \
-        f'source {conda_base}/etc/profile.d/mamba.sh'
+        f'source {conda_base}/etc/profile.d/conda.sh'
 
     activate_base = f'{source_activation_scripts} && conda activate'
 
@@ -93,8 +92,8 @@ def main():
         logger = get_logger(log_filename='deploy_tmp/logs/prebootstrap.log',
                             name=__name__)
 
-    # install mambaforge if needed
-    install_mambaforge(conda_base, activate_base, logger)
+    # install miniforge if needed
+    install_miniforge(conda_base, activate_base, logger)
 
     local_mache = args.mache_fork is not None and args.mache_branch is not None
     if local_mache:

deploy/bootstrap.py

@@ -22,7 +22,7 @@
     get_conda_base,
     get_logger,
     get_spack_base,
-    install_mambaforge,
+    install_miniforge,
     parse_args,
 )
 
@@ -227,8 +227,7 @@ def get_env_setup(args, config, machine, compiler, mpi, env_type, source_path,
     env_path = os.path.join(conda_base, 'envs', env_name)
 
     source_activation_scripts = \
-        f'source {conda_base}/etc/profile.d/conda.sh && ' \
-        f'source {conda_base}/etc/profile.d/mamba.sh'
+        f'source {conda_base}/etc/profile.d/conda.sh'
 
     activate_env = f'{source_activation_scripts} && conda activate {env_name}'
 
@@ -242,7 +241,7 @@ def build_conda_env(config, env_type, recreate, mpi, conda_mpi, version,
                     local_conda_build, logger, local_mache):
 
     if env_type != 'dev':
-        install_mambaforge(conda_base, activate_base, logger)
+        install_miniforge(conda_base, activate_base, logger)
 
     if conda_mpi == 'nompi':
         mpi_prefix = 'nompi'
@@ -304,7 +303,7 @@ def build_conda_env(config, env_type, recreate, mpi, conda_mpi, version,
             # install dev dependencies and polaris itself
             commands = \
                 f'{activate_base} && ' \
-                f'mamba create -y -n {env_name} {channels} ' \
+                f'conda create -y -n {env_name} {channels} ' \
                 f'--file {spec_filename} {packages}'
             check_call(commands, logger=logger)
 
@@ -319,15 +318,15 @@ def build_conda_env(config, env_type, recreate, mpi, conda_mpi, version,
             version_conda = version.replace('-', '')
             packages = f'{packages} "polaris={version_conda}={mpi_prefix}_*"'
             commands = f'{activate_base} && ' \
-                       f'mamba create -y -n {env_name} {channels} {packages}'
+                       f'conda create -y -n {env_name} {channels} {packages}'
             check_call(commands, logger=logger)
     else:
         if env_type == 'dev':
             print(f'Updating {env_name}\n')
             # install dev dependencies and polaris itself
             commands = \
                 f'{activate_base} && ' \
-                f'mamba install -y -n {env_name} {channels} ' \
+                f'conda install -y -n {env_name} {channels} ' \
                 f'--file {spec_filename} {packages}'
             check_call(commands, logger=logger)
 
@@ -921,8 +920,7 @@ def main():  # noqa: C901
     conda_base = os.path.abspath(conda_base)
 
     source_activation_scripts = \
-        f'source {conda_base}/etc/profile.d/conda.sh && ' \
-        f'source {conda_base}/etc/profile.d/mamba.sh'
+        f'source {conda_base}/etc/profile.d/conda.sh'
 
     activate_base = f'{source_activation_scripts} && conda activate'
 
@@ -993,7 +991,6 @@ def main():  # noqa: C901
             if local_mache:
                 print('Install local mache\n')
                 commands = f'source {conda_base}/etc/profile.d/conda.sh && ' \
-                           f'source {conda_base}/etc/profile.d/mamba.sh && ' \
                            f'conda activate {conda_env_name} && ' \
                            'cd ../build_mache/mache && ' \
                            'python -m pip install .'
@@ -1008,7 +1005,7 @@ def main():  # noqa: C901
         if compiler is not None:
             env_vars = get_env_vars(machine, compiler, mpi)
             if spack_base is not None:
-                spack_branch_base, spack_script, env_vars = build_spack_env(
+                _, spack_script, env_vars = build_spack_env(
                     config, args.update_spack, machine, compiler, mpi,
                     spack_env, spack_base, spack_template_path, env_vars,
                     args.tmpdir, logger)

deploy/load_polaris.template

@@ -1,7 +1,6 @@
 echo Loading conda environment
 source {{ conda_base }}/etc/profile.d/conda.sh
-source {{ conda_base }}/etc/profile.d/mamba.sh
-mamba activate {{ polaris_env }}
+conda activate {{ polaris_env }}
 echo Done.
 echo
 

deploy/shared.py

@@ -150,36 +150,36 @@ def check_call(commands, env=None, logger=None):
         raise subprocess.CalledProcessError(process.returncode, commands)
 
 
-def install_mambaforge(conda_base, activate_base, logger):
+def install_miniforge(conda_base, activate_base, logger):
     if not os.path.exists(conda_base):
-        print('Installing Mambaforge')
+        print('Installing Miniforge3')
         if platform.system() == 'Linux':
             system = 'Linux'
         elif platform.system() == 'Darwin':
             system = 'MacOSX'
         else:
             system = 'Linux'
-        mambaforge = f'Mambaforge-{system}-x86_64.sh'
-        url = f'https://github.com/conda-forge/miniforge/releases/latest/download/{mambaforge}'  # noqa: E501
+        miniforge = f'Miniforge3-{system}-x86_64.sh'
+        url = f'https://github.com/conda-forge/miniforge/releases/latest/download/{miniforge}'  # noqa: E501
         print(url)
         req = Request(url, headers={'User-Agent': 'Mozilla/5.0'})
         f = urlopen(req)
         html = f.read()
-        with open(mambaforge, 'wb') as outfile:
+        with open(miniforge, 'wb') as outfile:
             outfile.write(html)
         f.close()
 
-        command = f'/bin/bash {mambaforge} -b -p {conda_base}'
+        command = f'/bin/bash {miniforge} -b -p {conda_base}'
         check_call(command, logger=logger)
-        os.remove(mambaforge)
+        os.remove(miniforge)
 
     print('Doing initial setup\n')
     commands = f'{activate_base} && ' \
                f'conda config --add channels conda-forge && ' \
                f'conda config --set channel_priority strict && ' \
-               f'mamba update -y "mamba>1.3.1" "conda>=23.1.0" && ' \
-               f'mamba update -y --all && ' \
-               f'mamba init --no-user'
+               f'conda install -y "conda>=23.1.0" && ' \
+               f'conda update -y --all && ' \
+               f'conda init --no-user'
 
     check_call(commands, logger=logger)
 

docs/developers_guide/deploying_spack.md

@@ -122,27 +122,27 @@ cd ../simplify_local_mache/
 ```
 
 You will also need a local installation of
-[Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+[Miniforge3](https://github.com/conda-forge/miniforge#miniforge3).
 Polaris can do this for you if you haven't already installed it.  If you want
 to download it manually, use the Linux x86_64 version for all our supported
 machines.
 
 :::{note}
 We have found that an existing Miniconda3 installation **does not** always
-work well for polaris, so please start with Mambaforge instead.
+work well for polaris, so please start with Miniforge3 instead.
 :::
 
 :::{note}
-You definitely need your own local Mambaforge installation -- you can’t use
+You definitely need your own local Miniforge3 installation -- you can’t use
 a system version or a shared one like E3SM-Unified.
 :::
 
-Define a location where Mambaforge is installed or where you want to install
+Define a location where Miniforge3 is installed or where you want to install
 it:
 
 ```bash
 # change to your conda installation
-export CONDA_BASE=${HOME}/mambaforge
+export CONDA_BASE=${HOME}/miniforge3
 ```
 
 Okay, we're finally ready to do a test spack build for polaris.
@@ -166,7 +166,7 @@ export TMPDIR=/lcrc/group/e3sm/${USER}/spack_temp
 ```
 
 The directory you point to with `--conda` either doesn't exist or contains
-your existing installation of Mambaforge.
+your existing installation of Miniforge3.
 
 When you supply `--mache_fork` and `--mache_branch`, polaris will clone
 a fork of the `mache` repo and check out the requested branch, then install