Merge pull request #545 from xylar/fix_mamba_init

Fix deployment with latest conda (23.1.0)

conda/bootstrap.py

@@ -229,10 +229,10 @@ 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/conda.sh && ' \
         f'source {conda_base}/etc/profile.d/mamba.sh'
 
-    activate_env = f'{source_activation_scripts}; conda activate {env_name}'
+    activate_env = f'{source_activation_scripts} && mamba activate {env_name}'
 
     return python, recreate, conda_mpi, activ_suffix, env_suffix, \
         activ_path, env_path, env_name, activate_env, spack_env
@@ -264,11 +264,12 @@ def build_conda_env(env_type, recreate, machine, mpi, conda_mpi, version,
     channels = f'--override-channels {" ".join(channels)}'
     packages = f'python={python}'
 
-    base_activation_script = os.path.abspath(
-        f'{conda_base}/etc/profile.d/conda.sh')
+    conda_base = os.path.abspath(conda_base)
 
     activate_env = \
-        f'source {base_activation_script}; conda activate {env_name}'
+        f'source {conda_base}/etc/profile.d/conda.sh &&' \
+        f'source {conda_base}/etc/profile.d/mamba.sh &&' \
+        f'mamba activate {env_name}'
 
     with open(f'{conda_template_path}/spec-file.template', 'r') as f:
         template = Template(f.read())
@@ -296,37 +297,37 @@ def build_conda_env(env_type, recreate, machine, mpi, conda_mpi, version,
         if env_type == 'dev':
             # install dev dependencies and compass itself
             commands = \
-                f'{activate_base}; ' \
+                f'{activate_base} && ' \
                 f'mamba create -y -n {env_name} {channels} ' \
                 f'--file {spec_filename} {packages}'
             check_call(commands, logger=logger)
 
             commands = \
-                f'{activate_env}; ' \
-                f'cd {source_path}; ' \
+                f'{activate_env} && ' \
+                f'cd {source_path} && ' \
                 f'python -m pip install -e .'
             check_call(commands, logger=logger)
 
         else:
             # conda packages don't like dashes
             version_conda = version.replace('-', '')
             packages = f'{packages} "compass={version_conda}={mpi_prefix}_*"'
-            commands = f'{activate_base}; ' \
+            commands = f'{activate_base} && ' \
                        f'mamba 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 compass itself
             commands = \
-                f'{activate_base}; ' \
+                f'{activate_base} && ' \
                 f'mamba install -y -n {env_name} {channels} ' \
                 f'--file {spec_filename} {packages}'
             check_call(commands, logger=logger)
 
             commands = \
-                f'{activate_env}; ' \
-                f'cd {source_path}; ' \
+                f'{activate_env} && ' \
+                f'cd {source_path} && ' \
                 f'python -m pip install -e .'
             check_call(commands, logger=logger)
         else:
@@ -493,9 +494,9 @@ def build_spack_env(config, update_spack, machine, compiler, mpi, spack_env,
 
 def set_ld_library_path(spack_branch_base, spack_env, logger):
     commands = \
-        f'source {spack_branch_base}/share/spack/setup-env.sh; ' \
-        f'spack env activate {spack_env}; ' \
-        f'spack config add modules:prefix_inspections:lib:[LD_LIBRARY_PATH]; ' \
+        f'source {spack_branch_base}/share/spack/setup-env.sh && ' \
+        f'spack env activate {spack_env} && ' \
+        f'spack config add modules:prefix_inspections:lib:[LD_LIBRARY_PATH] && ' \
         f'spack config add modules:prefix_inspections:lib64:[LD_LIBRARY_PATH]'  # noqa: E501
     check_call(commands, logger=logger)
 
@@ -597,12 +598,12 @@ def check_env(script_filename, env_name, logger):
                 ['compass', 'clean', '--help']]
 
     for import_name in imports:
-        command = '{}; python -c "import {}"'.format(activate, import_name)
+        command = '{} && python -c "import {}"'.format(activate, import_name)
         test_command(command, os.environ, import_name, logger)
 
     for command in commands:
         package = command[0]
-        command = '{}; {}'.format(activate, ' '.join(command))
+        command = '{} && {}'.format(activate, ' '.join(command))
         test_command(command, os.environ, package, logger)
 
 
@@ -827,10 +828,10 @@ 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/conda.sh && ' \
         f'source {conda_base}/etc/profile.d/mamba.sh'
 
-    activate_base = f'{source_activation_scripts}; conda activate'
+    activate_base = f'{source_activation_scripts} && mamba activate'
 
     compilers, mpis = get_compilers_mpis(config, machine, args.compilers,
                                          args.mpis, source_path)
@@ -952,7 +953,7 @@ def main():  # noqa: C901
                 check_call(f'ln -sfn {script_filename} {link}')
         os.chdir(source_path)
 
-    commands = '{}; conda clean -y -p -t'.format(activate_base)
+    commands = '{} && conda clean -y -p -t'.format(activate_base)
     check_call(commands, logger=logger)
 
     if args.update_spack or env_type != 'dev':

conda/configure_compass_env.py

@@ -8,16 +8,21 @@
 try:
     from configparser import ConfigParser
 except ImportError:
-    from six.moves import configparser
     import six
+    from six.moves import configparser
 
     if six.PY2:
         ConfigParser = configparser.SafeConfigParser
     else:
         ConfigParser = configparser.ConfigParser
 
-from shared import parse_args, get_conda_base, check_call, install_miniconda, \
-    get_logger
+from shared import (
+    check_call,
+    get_conda_base,
+    get_logger,
+    install_miniconda,
+    parse_args,
+)
 
 
 def get_config(config_file):
@@ -37,7 +42,7 @@ def bootstrap(activate_install_env, source_path, local_conda_build):
 
     print('Creating the compass conda environment\n')
     bootstrap_command = '{}/conda/bootstrap.py'.format(source_path)
-    command = '{}; ' \
+    command = '{} && ' \
               '{} {}'.format(activate_install_env, bootstrap_command,
                              ' '.join(sys.argv[1:]))
     if local_conda_build is not None:
@@ -56,13 +61,13 @@ def setup_install_env(env_name, activate_base, use_local, logger, recreate,
     packages = 'progressbar2 jinja2 "mache=1.10.0"'
     if recreate or not os.path.exists(env_path):
         print('Setting up a conda environment for installing compass\n')
-        commands = '{}; ' \
+        commands = '{} && ' \
                    'mamba create -y -n {} {} {}'.format(activate_base,
                                                         env_name, channels,
                                                         packages)
     else:
         print('Updating conda environment for installing compass\n')
-        commands = '{}; ' \
+        commands = '{} && ' \
                    'mamba install -y -n {} {} {}'.format(activate_base,
                                                          env_name, channels,
                                                          packages)
@@ -82,14 +87,14 @@ def main():
     env_name = 'compass_bootstrap'
 
     source_activation_scripts = \
-        'source {}/etc/profile.d/conda.sh; ' \
+        'source {}/etc/profile.d/conda.sh && ' \
         'source {}/etc/profile.d/mamba.sh'.format(conda_base, conda_base)
 
-    activate_base = '{}; conda activate'.format(source_activation_scripts)
+    activate_base = '{} && mamba activate'.format(source_activation_scripts)
 
     activate_install_env = \
-        '{}; ' \
-        'conda activate {}'.format(source_activation_scripts, env_name)
+        '{} && ' \
+        'mamba activate {}'.format(source_activation_scripts, env_name)
     try:
         os.makedirs('conda/logs')
     except OSError:

conda/shared.py

@@ -1,17 +1,17 @@
 from __future__ import print_function
 
-import os
-import sys
 import argparse
-import subprocess
-import platform
 import logging
+import os
+import platform
 import shutil
+import subprocess
+import sys
 
 try:
-    from urllib.request import urlopen, Request
+    from urllib.request import Request, urlopen
 except ImportError:
-    from urllib2 import urlopen, Request
+    from urllib2 import Request, urlopen
 
 
 def parse_args(bootstrap):
@@ -116,7 +116,7 @@ def get_spack_base(spack_base, config):
 
 
 def check_call(commands, env=None, logger=None):
-    print_command = '\n   '.join(commands.split('; '))
+    print_command = '\n   '.join(commands.split(' && '))
     if logger is None:
         print('\n Running:\n   {}\n'.format(print_command))
     else:
@@ -155,7 +155,7 @@ def install_miniconda(conda_base, activate_base, logger):
         else:
             system = 'Linux'
         miniconda = 'Mambaforge-{}-x86_64.sh'.format(system)
-        url = 'https://github.com/conda-forge/miniforge/releases/latest/download/{}'.format(miniconda)
+        url = 'https://github.com/conda-forge/miniforge/releases/latest/download/{}'.format(miniconda)  # noqa: E501
         print(url)
         req = Request(url, headers={'User-Agent': 'Mozilla/5.0'})
         f = urlopen(req)
@@ -171,11 +171,23 @@ def install_miniconda(conda_base, activate_base, logger):
     backup_bashrc()
 
     print('Doing initial setup\n')
-    commands = '{}; ' \
-               'conda config --add channels conda-forge; ' \
-               'conda config --set channel_priority strict; ' \
-               'conda install -y boa; ' \
-               'conda update -y --all; ' \
+
+    commands = '{} && ' \
+               'conda config --add channels conda-forge && ' \
+               'conda config --set channel_priority strict' \
+               ''.format(activate_base)
+
+    check_call(commands, logger=logger)
+
+    commands = '{} && ' \
+               'conda remove -y boa'.format(activate_base)
+    try:
+        check_call(commands, logger=logger)
+    except subprocess.CalledProcessError:
+        pass
+
+    commands = '{} && ' \
+               'mamba update -y --all && ' \
                'mamba init'.format(activate_base)
 
     check_call(commands, logger=logger)