Rename pyenv to micromamba submodule and add tests

src/glicid_spawner/micromamba.py

@@ -0,0 +1,75 @@
+"""Micromamba environments module."""
+
+from dataclasses import dataclass
+from operator import itemgetter
+from pathlib import Path
+
+MICROMAMBA_ROOT = Path('/micromamba')  # default micromamba root location
+
+GLOBAL_USER = 'operator'
+GLOBAL_EXCLUDED = 'glicid-jupyterhub'
+
+
+@dataclass
+class MicromambaEnv:
+    """Generic micromamba environment."""
+
+    scope: str
+    name: str
+    path: str
+
+
+def _envs(folder, excluded=None) -> list:
+    """List micromamba environments."""
+    # Convert excluded as as list
+    if excluded is None:
+        excluded = []
+    elif isinstance(excluded, str):
+        excluded = [excluded]
+
+    # Get micromamba envs as pathlib.Path
+    envs = MICROMAMBA_ROOT / folder / 'envs'
+
+    if not envs.exists():
+        return []
+
+    return sorted(
+        [
+            (env.name, str(env))
+            for env in envs.iterdir()
+            if env.is_dir() and env.name not in excluded
+        ],
+        key=itemgetter(0),
+    )
+
+
+def _envs_user(username: str) -> list:
+    """Micromamba environment(s) available to the user."""
+    return [MicromambaEnv('USER', name, path) for name, path in _envs(username)]
+
+
+def _envs_team(username: str) -> list:
+    """Micromamba environment(s) available to the user's team.
+
+    Warning
+    -------
+    At the moment micromamba team environments is not available on GLiCID.
+
+    """
+    teams = []  # FIXME: pull user teams list from groups
+    return [
+        MicromambaEnv('TEAM', name, path) for team in teams for name, path in _envs(f'teams/{team}')
+    ]
+
+
+def _envs_global() -> list:
+    """Micromamba environment(s) available globally."""
+    return [
+        MicromambaEnv('GLOBAL', name, path)
+        for name, path in _envs(GLOBAL_USER, excluded=GLOBAL_EXCLUDED)
+    ]
+
+
+def get_envs(username: str) -> list:
+    """List of all the micromamba environment available to a user."""
+    return _envs_user(username) + _envs_team(username) + _envs_global()

src/glicid_spawner/pyenv.py

@@ -1,74 +0,0 @@
-"""Python environment module."""
-
-from dataclasses import dataclass
-from operator import itemgetter
-from pathlib import Path
-
-
-@dataclass
-class PyEnv:
-    """Python environment generic class."""
-
-    name: str
-    path: str
-
-    def __eq__(self, item):
-        return self.path == str(item)
-
-
-class UserPyEnv(PyEnv):
-    """User python environment."""
-
-    scope = 'USER'
-
-
-class TeamPyEnv(PyEnv):
-    """Team python environment."""
-
-    scope = 'TEAM'
-
-
-class GlobalPyEnv(PyEnv):
-    """Global python environment."""
-
-    scope = 'GLOBAL'
-
-
-def _micromamba_path(path: str) -> Path:
-    """Micromamba path environments locations."""
-    return Path(f'/micromamba/{path}/envs')
-
-
-def _micromamba_envs(path, excluded=None) -> list:
-    """List micromamba environment list."""
-    if excluded is None:
-        excluded = []
-    elif isinstance(excluded, str):
-        excluded = [excluded]
-
-    envs = _micromamba_path(path)
-    return sorted(
-        [(f.name, f.absolute()) for f in envs.iterdir() if f.is_dir() and f.name not in excluded],
-        key=itemgetter(0),
-    )
-
-
-def get_pyenv_user(username: str) -> list:
-    """List of python environment available to the user."""
-    return [UserPyEnv(*env) for env in _micromamba_envs(username)]
-
-
-def get_pyenv_team(username: str) -> list:
-    """List of python environment available to the user's team."""
-    teams = []  # FIXME: pull user teams list from groups
-    return [TeamPyEnv(*env) for team in teams for env in _micromamba_envs(f'teams/{team}')]
-
-
-def get_pyenv_global() -> list:
-    """List of python environment available globally."""
-    return [GlobalPyEnv(*env) for env in _micromamba_envs('operator', excluded='glicid-jupyterhub')]
-
-
-def get_pyenv(username: str) -> list:
-    """List of all the python environment available to a user."""
-    return get_pyenv_user(username) + get_pyenv_team(username) + get_pyenv_global()

src/glicid_spawner/spawner.py

@@ -3,7 +3,7 @@
 from batchspawner import SlurmSpawner
 from jinja2 import Environment, PackageLoader, select_autoescape
 
-from .pyenv import get_pyenv
+from .micromamba import get_envs
 from .resources import CPU, GPU, RAM
 
 
@@ -20,16 +20,14 @@ class GlicidSpawner(SlurmSpawner):
 
         return template.render(
             username=self.user.name,
-            python_envs=get_pyenv(self.user.name),
+            python_envs=get_envs(self.user.name),
             cpu_available=CPU,
             ram_available=RAM,
             gpu_available=GPU,
         )
 
     def options_from_form(self, formdata) -> dict:
-        options = {}
+        """Export options from form."""
-        options['pyenv'] = formdata['python-env'][0]
-
         # Index of user resources choices
         i_cpu = int(formdata['cpu'][0])
         i_ram = int(formdata['ram'][0])
@@ -42,8 +40,12 @@ class GlicidSpawner(SlurmSpawner):
         )
 
         # Export options
+        options = {}
+
+        options['pyenv'] = formdata['python-env'][0]
+
         options['cpus-per-task'] = CPU[i_cpu].description
-        options['mem'] = RAM[i_ram].description + 'GB'
+        options['mem'] = RAM[i_ram].description.replace(' ', '')
 
         if i_gpu:
             options['gres'] = 'gpu:' + GPU[i_gpu].description

tests/test_micromamba.py

@@ -0,0 +1,36 @@
+"""Test python environment module."""
+
+from pathlib import Path
+
+from glicid_spawner import micromamba
+
+MICROMAMBA_ROOT = Path(__file__).parent / 'data' / 'micromamba'
+
+
+def test_micromamba_envs_getter(monkeypatch):
+    """Test micromamba envs getter."""
+    monkeypatch.setattr(micromamba, 'MICROMAMBA_ROOT', MICROMAMBA_ROOT)
+    monkeypatch.setattr(micromamba, 'GLOBAL_USER', 'global')
+    monkeypatch.setattr(micromamba, 'GLOBAL_EXCLUDED', 'qux')
+
+    # User with micromamba envs
+    envs = micromamba.get_envs('john-doe')
+
+    assert len(envs) == 3
+    assert [env.scope for env in envs] == ['USER', 'USER', 'GLOBAL']
+    assert [env.name for env in envs] == ['bar', 'foo', 'baz']
+    assert [env.path for env in envs] == [
+        str(MICROMAMBA_ROOT / 'john-doe' / 'envs' / 'bar'),
+        str(MICROMAMBA_ROOT / 'john-doe' / 'envs' / 'foo'),
+        str(MICROMAMBA_ROOT / 'global' / 'envs' / 'baz'),
+    ]
+
+    # User without micromamba envs, only global envs listed
+    envs = micromamba.get_envs('jane-smith')
+
+    assert len(envs) == 1
+    assert [env.scope for env in envs] == ['GLOBAL']
+    assert [env.name for env in envs] == ['baz']
+    assert [env.path for env in envs] == [
+        str(MICROMAMBA_ROOT / 'global' / 'envs' / 'baz'),
+    ]