Bump to version 1.2

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "glicid-spawner"
-version = "1.0"
+version = "1.2"
 description = "JupyterHub Batch Spawner for GLiCID"
 authors = ["Benoit Seignovert <benoit.seignovert@univ-nantes.fr>"]
 license = "BSD 3-Clause License"
@@ -90,7 +90,7 @@ exclude_lines = [
 ]
 
 [tool.tbump.version]
-current = "1.0"
+current = "1.2"
 regex = '(?P<major>\d+)\.(?P<patch>\d+)'
 
 [tool.tbump.git]

render/__main__.py

@@ -32,7 +32,7 @@ SINFO = sinfo_from_file(
 )
 
 # Single vs. multi-cluster implementation
-SLURM_SINGLE_CLUSTER = {'N/A': SINFO.pop('N/A')}
+SLURM_SINGLE_CLUSTER = {'cluster': SINFO.pop('cluster')}
 SLURM_MULTI_CLUSTER = SINFO
 GPU_SINGLE_CLUSTER = gpu_max_duration(gres(SLURM_SINGLE_CLUSTER))
 GPU_MULTI_CLUSTER = gpu_max_duration(gres(SLURM_MULTI_CLUSTER))

src/glicid_spawner/micromamba.py

@@ -9,6 +9,7 @@ GLOBAL_USER = 'operator'
 
 MAMBA_ROOT_PREFIX = f'{MICROMAMBA_ROOT}/{GLOBAL_USER}'
 MAMBA_EXE = f'{MAMBA_ROOT_PREFIX}/bin/micromamba'
+MAMBA_USER_BASE = f'{MICROMAMBA_ROOT}/$USER'
 
 
 @dataclass

src/glicid_spawner/slurm.py

@@ -69,7 +69,7 @@ class SlurmNode:
         self.state = state.strip().lower()
         self.cpu = SlurmCpu(*re.findall(r'(\d+)/(\d+)/\d+/(\d+)', cpus_state)[0])
         self.mem = int(memory_mb) // 1000  # in GB
-        self.gpu = SlurmGpu(*re.findall(r'gpu:(\w+):(\d+)', gres)[0] if 'gpu:' in gres else [])
+        self.gpu = SlurmGpu(*re.findall(r'gpu:([\w\.]+):(\d+)', gres)[0] if 'gpu:' in gres else [])
 
     def __str__(self):
         return self.hostname
@@ -141,7 +141,7 @@ class SlurmCluster:
 
 def sinfo_run(username: str = None) -> str:
     """SLURM SINFO run command."""
-    flags = '--federation --noheader --responding'
+    flags = '--federation --noheader --responding --cluster=all'
     fmt = 'Cluster,PartitionName,NodeHost,StateLong,CPUsState,Memory,Gres'
     cmd = f'sinfo {flags} --Format={fmt}'
 

src/glicid_spawner/spawner.py

@@ -9,7 +9,7 @@ from batchspawner import JobStatus, SlurmSpawner
 from traitlets import Bool, Integer, Unicode, default
 
 from .form import options_form, options_from_form
-from .micromamba import MAMBA_EXE, MAMBA_ROOT_PREFIX
+from .micromamba import MAMBA_EXE, MAMBA_ROOT_PREFIX, MAMBA_USER_BASE
 from .progress import ElapseTime, get_progress
 from .templates import get_template_src
 
@@ -24,14 +24,19 @@ class GlicidSpawner(SlurmSpawner):
         help='Spawner singleuser command.',
     ).tag(config=True)
 
+    req_mamba_exe = Unicode(
+        MAMBA_EXE,
+        help='Micromamba global exe',
+    ).tag(config=True)
+
     req_mamba_root_prefix = Unicode(
         MAMBA_ROOT_PREFIX,
         help='Micromamba global root prefix',
     ).tag(config=True)
 
-    req_mamba_exe = Unicode(
-        MAMBA_EXE,
-        help='Micromamba global exe',
+    req_mamba_user_base = Unicode(
+        MAMBA_USER_BASE,
+        help='Micromamba user base prefix',
     ).tag(config=True)
 
     req_job_name = Unicode(
@@ -80,7 +85,7 @@ class GlicidSpawner(SlurmSpawner):
 
     slurm_job_id_re = Unicode(r'(\d+)(?:;(\w+))?').tag(config=True)
 
-    def parse_job_id(self, output):
+    def parse_job_id(self, output) -> str:
         """Parse job id with cluster name support.
 
         If cluster name is present, `job_id` will be a string
@@ -88,10 +93,10 @@ class GlicidSpawner(SlurmSpawner):
 
         """
         for job_id, job_cluster in re.findall(self.slurm_job_id_re, output):
-            return f'{job_id} -M {job_cluster}' if job_cluster else int(job_id)
+            return f'{job_id} -M {job_cluster}' if job_cluster else job_id
 
         self.log.error(f'GlicidSpawner unable to parse job ID from text: {output}')
-        return None
+        return ''
 
     @default('options_form')
     def _options_form_default(self) -> str:

src/glicid_spawner/templates/slurm_script.jinja

@@ -33,6 +33,7 @@ echo "The {{job_name}} logs are located in: ${JUPYTER_LOG_DIR}"
     {# Micromamba config -#}
     export MAMBA_EXE={{mamba_exe}};
     export MAMBA_ROOT_PREFIX={{mamba_root_prefix}};
+    export PYTHONUSERBASE={{ mamba_user_base }};
     source $MAMBA_ROOT_PREFIX/etc/profile.d/micromamba.sh;
 
     {# Activate micromamba env requested by the user -#}

src/glicid_spawner/templates/views/resources.jinja

@@ -41,7 +41,7 @@
                     data-max-duration="{{max_duration}}"
                     {%- if loop.first %} checked{% endif %}>
                 <label for="gpu_{{gpu}}" class="btn btn-default btn-block">
-                    {{ gpu }}
+                    {{ gpu | replace("_"," ") | replace("."," ") | replace("gb","GB") }}
                 </label>
             </div>
             {% endfor -%}

src/glicid_spawner/templates/views/slurm.jinja

@@ -11,7 +11,7 @@
         <div id="cluster-config-collapse" class="panel-collapse collapse" role="tabpanel" aria-labelledby="heading">
             <div class="panel-body">
 
-                {% if 'N/A' not in sinfo %}
+                {% if 'cluster' not in sinfo %}
                 <div class="form-group clusters">
                     <label for="cluster" class="col-sm-3 control-label">Cluster:</label>
                     <div class="col-sm-9 flex-container">

tests/data/sinfo.txt

@@ -1,21 +1,21 @@
-N/A                 Devel               nazare001           idle                0/20/0/20           128000              (null)              
-N/A                 GPU-short           budbud001           mixed               20/20/0/40          184000              gpu:t4:2,mps:t4:2000
-N/A                 A40-short           budbud002           allocated           40/0/0/40           184000              gpu:a40:2,mps:a40:20
-N/A                 AMD-short           cloudbreak001       drained             0/0/32/32           128000              (null)              
-N/A                 lowp                budbud003           down~               0/0/40/40           128000              gpu:p100:2          
-N/A                 lowp                budbud004           drained~            0/0/20/20           128000              gpu:k80:4           
-N/A                 lowp                budbud005           idle~               0/20/0/20           192000              gpu:p100:1          
+cluster             Devel               nazare001           idle                0/20/0/20           128000              (null)              
+cluster             GPU-short           budbud001           mixed               20/20/0/40          184000              gpu:t4:2,mps:t4:2000
+cluster             A40-short           budbud002           allocated           40/0/0/40           184000              gpu:a40:2,mps:a40:20
+cluster             AMD-short           cloudbreak001       drained             0/0/32/32           128000              (null)              
+cluster             lowp                budbud003           down~               0/0/40/40           128000              gpu:p100:2          
+cluster             lowp                budbud004           drained~            0/0/20/20           128000              gpu:k80:4           
+cluster             lowp                budbud005           idle~               0/20/0/20           192000              gpu:p100:1          
 nautilus            standard            cnode001            completing          0/96/0/96           384000              (null)              
 nautilus            bigmem              cnode002            planned             0/96/0/96           768000              (null)              
 nautilus            gpu                 gnode1              mixed               4/92/0/96           768000              gpu:A100:1(S:0-1)   
 nautilus            gpu                 gnode2              idle                0/96/0/96           256000              gpu:A100:2(S:0-1)   
-nautilus            gpu                 gnode3              allocated           96/0/0/96           128000              gpu:A100:4(S:0-1)   
+nautilus            gpu                 gnode3              allocated           96/0/0/96           128000              gpu:A100_2g.10gb:6(S 
 nautilus            visu                visu1               idle                0/96/0/96           768000              (null)              
 nautilus            all                 cnode001            completing          0/96/0/96           384000              (null)              
 nautilus            all                 cnode002            planned             0/96/0/96           768000              (null)              
 nautilus            all                 gnode1              mixed               4/92/0/96           768000              gpu:A100:1(S:0-1)   
 nautilus            all                 gnode2              idle                0/96/0/96           256000              gpu:A100:2(S:0-1)   
-nautilus            all                 gnode3              allocated           96/0/0/96           128000              gpu:A100:4(S:0-1)   
+nautilus            all                 gnode3              allocated           96/0/0/96           128000              gpu:A100_2g.10gb:6(S 
 nautilus            all                 visu1               idle                0/96/0/96           768000              (null)              
 waves               standard            cribbar001          mixed               30/10/0/40          16000               (null)              
 waves               gpu                 budbud006           allocated           64/0/0/64           256000              gpu:a100:2,mps:a100:

tests/test_form.py

@@ -12,7 +12,7 @@ from pytest import fixture
 DATA = Path(__file__).parent / 'data'
 SINFO = sinfo_from_file(DATA / 'sinfo.txt')
 
-SLURM_SINGLE_CLUSTER = {'N/A': SINFO.pop('N/A')}
+SLURM_SINGLE_CLUSTER = {'cluster': SINFO.pop('cluster')}
 SLURM_MULTI_CLUSTER = SINFO
 
 
@@ -81,7 +81,7 @@ def test_options_attrs(mock_cluster):
     # Multi cluster configuration (default)
     sinfo = options['sinfo']
 
-    assert 'N/A' not in sinfo
+    assert 'cluster' not in sinfo
     assert 'nautilus' in sinfo
     assert 'waves' in sinfo
 
@@ -99,11 +99,11 @@ def test_options_attrs_single_cluster(mock_single_cluster):
     # Single cluster configuration
     sinfo = options['sinfo']
 
-    assert 'N/A' in sinfo
+    assert 'cluster' in sinfo
     assert 'nautilus' not in sinfo
     assert 'waves' not in sinfo
 
-    node = sinfo['N/A']['Devel']['nazare001']
+    node = sinfo['cluster']['Devel']['nazare001']
 
     assert node == 'nazare001'
     assert node.cpu.idle == 20
@@ -218,32 +218,32 @@ def test_options_form_slurm_single_cluster(mock_single_cluster):
 
     assert (
         '<div class="flex-item-4 slurm-partition" '
-        'data-cluster="N/A" data-partition="GPU-short" '
+        'data-cluster="cluster" data-partition="GPU-short" '
         'data-cpu="20" data-mem="184" data-gpu="T4">' in html
     )
 
     assert (
-        '<input type="radio" name="partition" id="partition_N/A_GPU-short" value="GPU-short">'
+        '<input type="radio" name="partition" id="partition_cluster_GPU-short" value="GPU-short">'
         in html
     )
     assert (
-        '<label for="partition_N/A_GPU-short" class="btn btn-default btn-block"> Gpu-short </label>'
+        '<label for="partition_cluster_GPU-short" class="btn btn-default btn-block"> Gpu-short </label>'
         in html
     )
 
     # Nodes (hidden by default)
     assert (
         '<div class="flex-item-4 slurm-node" '
-        'data-cluster="N/A" data-partition="GPU-short" data-node="budbud001" '
+        'data-cluster="cluster" data-partition="GPU-short" data-node="budbud001" '
         'data-cpu="20" data-mem="184" data-gpu="T4">' in html
     )
 
     assert (
-        '<input type="radio" name="node" id="node_N/A_GPU-short_budbud001" value="budbud001">'
+        '<input type="radio" name="node" id="node_cluster_GPU-short_budbud001" value="budbud001">'
         in html
     )
     assert (
-        '<label for="node_N/A_GPU-short_budbud001" class="btn btn-default btn-block"> Budbud001 </label>'
+        '<label for="node_cluster_GPU-short_budbud001" class="btn btn-default btn-block"> Budbud001 </label>'
         in html
     )
 

tests/test_slurm.py

@@ -105,6 +105,7 @@ def test_slurm_sinfo_run(monkeypatch):
         '--federation '
         '--noheader '
         '--responding '
+        '--cluster=all '
         '--Format=Cluster,PartitionName,NodeHost,StateLong,CPUsState,Memory,Gres'
     )
 
@@ -114,6 +115,7 @@ def test_slurm_sinfo_run(monkeypatch):
         '--federation '
         '--noheader '
         '--responding '
+        '--cluster=all '
         '--Format=Cluster,PartitionName,NodeHost,StateLong,CPUsState,Memory,Gres'
     )
 
@@ -127,7 +129,7 @@ def test_slurm_sinfo_reader():
 
     node = nodes[0]
 
-    assert node.cluster == 'N/A'
+    assert node.cluster == 'cluster'
     assert node.partition == 'Devel'
     assert node.hostname == 'nazare001'
     assert node.state == 'idle'
@@ -136,7 +138,7 @@ def test_slurm_sinfo_reader():
     assert node.mem == 128
     assert not node.gpu
 
-    assert [node.cluster for node in nodes] == 7 * ['N/A'] + 12 * ['nautilus'] + 6 * ['waves']
+    assert [node.cluster for node in nodes] == 7 * ['cluster'] + 12 * ['nautilus'] + 6 * ['waves']
 
     assert len([node for node in nodes if node.state in ('idle', 'mixed')]) == 10
 
@@ -159,9 +161,17 @@ def test_slurm_sinfo_reader():
         'P100',
         'K80',
         'P100',
-    ] + 8 * ['A100']
+        'A100',
+        'A100',
+        'A100_2g.10gb',
+        'A100',
+        'A100',
+        'A100_2g.10gb',
+        'A100',
+        'A100',
+    ]
 
-    assert [node.gpu.nb for node in nodes if node.gpu] == [2, 2, 2, 4, 1, 1, 2, 4, 1, 2, 4, 2, 2]
+    assert [node.gpu.nb for node in nodes if node.gpu] == [2, 2, 2, 4, 1, 1, 2, 6, 1, 2, 6, 2, 2]
 
 
 def test_slurm_sinfo_filter(monkeypatch):
@@ -172,7 +182,7 @@ def test_slurm_sinfo_filter(monkeypatch):
 
     assert isinstance(clusters, dict)
     assert len(clusters) == 3
-    assert list(clusters) == ['N/A', 'nautilus', 'waves']  # __eq__ on cluster.name
+    assert list(clusters) == ['cluster', 'nautilus', 'waves']  # __eq__ on cluster.name
 
     assert [len(partitions) for partitions in clusters.values()] == [2, 4, 2]
 
@@ -195,7 +205,7 @@ def test_slurm_sinfo_filter(monkeypatch):
     # Get only `idle` nodes
     clusters = sinfo_filter(resources, with_states=('idle'))
 
-    assert list(clusters) == ['N/A', 'nautilus']
+    assert list(clusters) == ['cluster', 'nautilus']
     assert [len(partitions) for partitions in clusters.values()] == [1, 3]
 
     # Discard clusters without partition available
@@ -251,4 +261,4 @@ def test_slurm_gres():
     gpus = gres(resources)
 
     # Sorted and without duplicates
-    assert gpus == ['A100', 'A40', 'None', 'P100', 'T4']
+    assert gpus == ['A100', 'A100_2g.10gb', 'A40', 'None', 'P100', 'T4']

tests/test_spawner.py

@@ -27,8 +27,9 @@ def test_spawner_config():
     assert 'bin/glicid-spawner-singleuser' in cmd
     assert 'bin/jupyterhub-singleuser' in cmd
 
-    assert spawner.req_mamba_root_prefix == '/micromamba/operator'
     assert spawner.req_mamba_exe == '/micromamba/operator/bin/micromamba'
+    assert spawner.req_mamba_root_prefix == '/micromamba/operator'
+    assert spawner.req_mamba_user_base == '/micromamba/$USER'
     assert spawner.req_job_name == 'jupyterhub_glicid'
     assert spawner.req_qos == 'short'
 
@@ -70,8 +71,12 @@ def test_spawner_batch_script(monkeypatch):
 
     assert 'export MAMBA_EXE=/micromamba/operator/bin/micromamba;' in script
     assert 'export MAMBA_ROOT_PREFIX=/micromamba/operator;' in script
+    assert 'export PYTHONUSERBASE=/micromamba/$USER;' in script
     assert 'micromamba activate /micromamba/john-doe/envs/foo;' in script
 
+    assert 'micromamba activate /micromamba/john-doe/envs/foo;' in script
+    assert 'export JUPYTER_PATH=/micromamba/john-doe/envs/foo/share/jupyter;' in script
+
     assert re.search(r'.*/bin/glicid-spawner-singleuser .*/bin/jupyterhub-singleuser', script)
 
 
@@ -79,10 +84,10 @@ def test_spawner_parse_job_id():
     """Test spawner job id parser."""
     spawner = GlicidSpawner()
 
-    assert spawner.parse_job_id('123') == 123
+    assert spawner.parse_job_id('123') == '123'
     assert spawner.parse_job_id('456;nautilus') == '456 -M nautilus'
 
-    assert spawner.parse_job_id('') is None
+    assert spawner.parse_job_id('') == ''
 
 
 def test_spawner_options_form(monkeypatch):