omicslab 2.5.1__tar.gz → 2.6.0__tar.gz

{omicslab-2.5.1 → omicslab-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omicslab
-Version: 2.5.1
+Version: 2.6.0
 Summary: Python SDK and CLI for the OmicsLab Platform
 Project-URL: Homepage, https://platform.omicslab.io
 Project-URL: Repository, https://github.com/vieomics/omicslab-platform
@@ -52,7 +52,7 @@ omicslab use
 omicslab ls && omicslab upload ./data.csv
 
 # 4. Launch a job
-omicslab jobs launch --workspace <ws_id> --analysis <id> --compute <id>
+omicslab ws analysis launch --workspace <ws_id> --analysis <id> --compute <id>
 ```
 
 ## Storage Commands
@@ -148,12 +148,13 @@ Analysis and studio jobs share one backend namespace:
 `/workspaces/{workspace_id}/jobs/...` — `job_type` ("analysis" | "studio")
 is part of the launch payload / list filter, not a separate URL space.
 `client.jobs` exposes generic methods (`launch`, `list_jobs`, `get_job`,
-`get_job_manifest`, `terminate_job`, `delete_job`, `connect_job`,
-`disconnect_job`, `check_job_ready`, ...) plus the domain aliases
-(`launch_analysis`, `launch_studio`, `list_analysis`, `list_studio`, ...)
-for convenience. Job resources (`time`/`cpu`/`memory`/`disk`) and the
-launch config live in the per-job manifest on S3, retrievable via
-`get_job_manifest` / `get_job_audit_params` / `get_job_audit_config`.
+`get_job_manifest`, `rerun_job`, `terminate_job`, `delete_job`,
+`connect_job`, `disconnect_job`, `check_job_ready`, ...) plus the domain
+aliases (`launch_analysis`, `launch_studio`, `rerun_analysis`,
+`rerun_studio`, `list_analysis`, `list_studio`, ...) for convenience. Job
+resources (`time`/`cpu`/`memory`/`disk`) and the launch config live in the
+per-job manifest on S3, retrievable via `get_job_manifest` /
+`get_job_audit_params` / `get_job_audit_config`.
 
 ```python
 from omicslab import Client
@@ -180,6 +181,52 @@ studio = client.jobs.launch_studio(
     compute_id="cloud-comp-...",
 )
 access = client.jobs.connect_job("ws-...", studio["id"])  # {"access_url": ...}
+
+# Rerun a job from its resolved launch manifest. Only the overrides below
+# change; tool/tag/pinned commit/versioning/config stay fixed to the source.
+rerun = client.jobs.rerun_analysis(
+    "ws-...",
+    job_id,
+    cpu=8,
+    time=7200,
+    params={"max_cpus": 8},  # merged per top-level key
+)
+# Masked secret params must be supplied again, otherwise the API returns 400.
+```
+
+The same rerun is available for studio sessions via
+`client.jobs.rerun_studio(...)`; the generic `client.jobs.rerun_job(...)`
+works for both. The response carries `old_job_id` and
+`changed_parameters` so callers can show what changed.
+
+```python
+# Estimate the max cost before launching
+estimate = client.jobs.estimate_job(
+    "ws-...",
+    compute_type="cloud",
+    compute_id="cloud-comp-...",
+    time=7200,
+    cpu=8,
+    memory=32,
+    disk=100,
+)
+
+# Status counts + per-period launch trend (workspace or organization scope)
+counts = client.jobs.get_job_counts("ws-...", job_type="analysis", granularity="daily")
+org_counts = client.orgs.get_job_counts("org-...", job_type="analysis")
+
+# Snapshot a RUNNING studio session into workspace storage
+client.jobs.snapshot_studio("ws-...", studio["id"], outdir="snapshots")
+
+# Server-side search/filter/sort (exact statuses need filter_column="status")
+client.jobs.list_analysis(
+    "ws-...",
+    search="bacass",
+    filter_column="status",
+    filter_value="running,failed",
+    sort_column="created_at",
+    sort_desc=True,
+)
 ```
 
 ## Testing

{omicslab-2.5.1 → omicslab-2.6.0}/README.developer.md

@@ -92,11 +92,11 @@ and then hand the raw token to `Client`.
 
 | Property   | Class                    | Purpose |
 |------------|--------------------------|---------|
-| `orgs`     | `OrgResource`            | Org CRUD + members + roles |
+| `orgs`     | `OrgResource`            | Org CRUD + members + roles + job counts |
 | `workspaces` | `WorkspaceResource`    | Workspace CRUD, members, pin, linked resources, budget/storage-quota (read-only) |
 | `analysis` | `AnalysisResource`       | Tool catalog (batch tools) CRUD/tags/profiles/schema |
 | `studio`   | `StudioResource`         | Tool catalog (interactive tools) CRUD + tags/profiles/schema |
-| `jobs`     | `JobResource`            | Launch/list/get/terminate analysis + studio jobs |
+| `jobs`     | `JobResource`            | Launch/list/get/rerun/estimate/counts/snapshot/terminate analysis + studio jobs |
 | `storage`  | `StorageResource`        | Upload/download list/delete/rename vs workspace S3 |
 | `credentials` | `CredentialResource`  | S3/GitHub/Cloud credentials (user + org scopes) |
 | `tokens`   | `TokenResource`          | Create/list/revoke API tokens |
@@ -248,15 +248,16 @@ bootstraps one session-scoped user via raw `httpx`:
 ```
 POST /api/auth/register/   (unique email)
 POST /api/auth/standard/   → access_token cookie
-GET  /api/organizations/            → take first (auto-provisioned Sponsor org)
+POST /api/organizations/            → create the test org
 POST /api/credentials/organization/{org}/storage/base/ + link s3   (storage cred)
 POST /api/organizations/{org}/workspaces/                             (workspace)
 POST /api/tokens/          → omx_ token scoped to org (admin)
 Client(token=..., base_url=...)
 ```
 
-Registration auto-provisions a **Sponsor org + Free subscription + workspace**
-(`service_auth/utils/provisioning.py`), so no payment step is needed.
+Registration does not create any organization; the conftest creates the org
+explicitly. A subscription is still activated for it through the payment flow
+(see `test_subscription`).
 
 ### 7.2 Fixtures
 
@@ -475,8 +476,11 @@ Studio session mounts (no token exposure, snapshot-safe):
   `history`; the copy lives in the job dir and is never snapshotted.
 - Users can create their own project envs in the writable workspace
   (`pixi init` + `pixi add`); those envs are in the writable layer and **are**
-  included in snapshots. The pixi package cache goes to a RAM-backed tmpfs
-  (`PIXI_CACHE_DIR=/run/omicslab-cache`) so downloads never bloat snapshots.
+  included in snapshots. Pixi keeps its default package cache under the
+  session user's home, so that cache is part of the writable layer too and is
+  included in snapshots. No cache directory is mounted: sessions need no extra
+  mount, the cache never runs out of a fixed size cap, and pixi works for any
+  image user without permission fixes.
 - The staged CLI config is mounted from the host into
   `OMICSLAB_CONFIG_DIR=/run/omicslab` before the container starts. The token
   is replaced with a placeholder first; the SDK talks to a host-side

{omicslab-2.5.1 → omicslab-2.6.0}/README.md

@@ -24,7 +24,7 @@ omicslab use
 omicslab ls && omicslab upload ./data.csv
 
 # 4. Launch a job
-omicslab jobs launch --workspace <ws_id> --analysis <id> --compute <id>
+omicslab ws analysis launch --workspace <ws_id> --analysis <id> --compute <id>
 ```
 
 ## Storage Commands
@@ -120,12 +120,13 @@ Analysis and studio jobs share one backend namespace:
 `/workspaces/{workspace_id}/jobs/...` — `job_type` ("analysis" | "studio")
 is part of the launch payload / list filter, not a separate URL space.
 `client.jobs` exposes generic methods (`launch`, `list_jobs`, `get_job`,
-`get_job_manifest`, `terminate_job`, `delete_job`, `connect_job`,
-`disconnect_job`, `check_job_ready`, ...) plus the domain aliases
-(`launch_analysis`, `launch_studio`, `list_analysis`, `list_studio`, ...)
-for convenience. Job resources (`time`/`cpu`/`memory`/`disk`) and the
-launch config live in the per-job manifest on S3, retrievable via
-`get_job_manifest` / `get_job_audit_params` / `get_job_audit_config`.
+`get_job_manifest`, `rerun_job`, `terminate_job`, `delete_job`,
+`connect_job`, `disconnect_job`, `check_job_ready`, ...) plus the domain
+aliases (`launch_analysis`, `launch_studio`, `rerun_analysis`,
+`rerun_studio`, `list_analysis`, `list_studio`, ...) for convenience. Job
+resources (`time`/`cpu`/`memory`/`disk`) and the launch config live in the
+per-job manifest on S3, retrievable via `get_job_manifest` /
+`get_job_audit_params` / `get_job_audit_config`.
 
 ```python
 from omicslab import Client
@@ -152,6 +153,52 @@ studio = client.jobs.launch_studio(
     compute_id="cloud-comp-...",
 )
 access = client.jobs.connect_job("ws-...", studio["id"])  # {"access_url": ...}
+
+# Rerun a job from its resolved launch manifest. Only the overrides below
+# change; tool/tag/pinned commit/versioning/config stay fixed to the source.
+rerun = client.jobs.rerun_analysis(
+    "ws-...",
+    job_id,
+    cpu=8,
+    time=7200,
+    params={"max_cpus": 8},  # merged per top-level key
+)
+# Masked secret params must be supplied again, otherwise the API returns 400.
+```
+
+The same rerun is available for studio sessions via
+`client.jobs.rerun_studio(...)`; the generic `client.jobs.rerun_job(...)`
+works for both. The response carries `old_job_id` and
+`changed_parameters` so callers can show what changed.
+
+```python
+# Estimate the max cost before launching
+estimate = client.jobs.estimate_job(
+    "ws-...",
+    compute_type="cloud",
+    compute_id="cloud-comp-...",
+    time=7200,
+    cpu=8,
+    memory=32,
+    disk=100,
+)
+
+# Status counts + per-period launch trend (workspace or organization scope)
+counts = client.jobs.get_job_counts("ws-...", job_type="analysis", granularity="daily")
+org_counts = client.orgs.get_job_counts("org-...", job_type="analysis")
+
+# Snapshot a RUNNING studio session into workspace storage
+client.jobs.snapshot_studio("ws-...", studio["id"], outdir="snapshots")
+
+# Server-side search/filter/sort (exact statuses need filter_column="status")
+client.jobs.list_analysis(
+    "ws-...",
+    search="bacass",
+    filter_column="status",
+    filter_value="running,failed",
+    sort_column="created_at",
+    sort_desc=True,
+)
 ```
 
 ## Testing

{omicslab-2.5.1 → omicslab-2.6.0}/scripts/bootstrap-env.sh

@@ -37,13 +37,32 @@ PIXI_LOCK="${PIXI_LOCK:-pixi.lock}"
 PIXI_VERSION="${PIXI_VERSION:-v0.76.1}"
 RETRIES=3
 
+# Download helper. Every fetch is bounded and retried so a stalled connection
+# fails in minutes with a clear message instead of hanging until the platform's
+# SSH bootstrap deadline (900s) kills the job with no diagnostics. The bucket
+# sits behind a single gateway that also serves the conda/pypi payload, so
+# transient 5xx/timeouts must be retried rather than abort the whole bootstrap.
+FETCH_CONNECT_TIMEOUT="${FETCH_CONNECT_TIMEOUT:-10}"
+FETCH_MAX_TIME="${FETCH_MAX_TIME:-300}"
+FETCH_RETRIES="${FETCH_RETRIES:-5}"
+fetch() {
+    local url="$1" out="$2"
+    curl -fsSL \
+        --connect-timeout "${FETCH_CONNECT_TIMEOUT}" \
+        --max-time "${FETCH_MAX_TIME}" \
+        --retry "${FETCH_RETRIES}" \
+        --retry-delay 5 \
+        --retry-connrefused \
+        "$url" -o "$out"
+}
+
 # ── 1. pixi (from the tools bucket, absolute path under $HOME) ────────────
 PIXI_BIN="${HOME}/.pixi/bin/pixi"
 if [ ! -x "${PIXI_BIN}" ]; then
     PIXI_URL="$TOOLS_BASE/pixi/bin/pixi-${PIXI_VERSION}-linux-amd64.tar.gz"
     echo "Installing pixi ${PIXI_VERSION} from: $PIXI_URL"
     mkdir -p "$(dirname "${PIXI_BIN}")"
-    curl -fsSL "$PIXI_URL" -o /tmp/pixi.tar.gz
+    fetch "$PIXI_URL" /tmp/pixi.tar.gz
     tar -xzf /tmp/pixi.tar.gz -C "$(dirname "${PIXI_BIN}")"
     rm -f /tmp/pixi.tar.gz
 else
@@ -136,23 +155,32 @@ echo "Fetching manifest:"
 echo "  TOML: $TOML_URL"
 echo "  LOCK: $LOCK_URL"
 mkdir -p "$OMICSLAB_HOME"
-curl -fsSL "$TOML_URL" -o "$OMICSLAB_HOME/pixi.toml"
-curl -fsSL "$LOCK_URL" -o "$OMICSLAB_HOME/pixi.lock"
+fetch "$TOML_URL" "$OMICSLAB_HOME/pixi.toml"
+fetch "$LOCK_URL" "$OMICSLAB_HOME/pixi.lock"
 
 # ── 3. pixi install + SDK wheel (with retries) ────────────────────────────
 cd "$OMICSLAB_HOME"
+env_ready=0
 for i in $(seq 1 $RETRIES); do
     if "${PIXI_BIN}" install --frozen; then
+        env_ready=1
         break
     fi
     echo "bootstrap-retry-$i"
     sleep 5
 done
+# `set -e` does not fire for a command used as an `if` condition, so without an
+# explicit check the script would carry on with a half-installed environment
+# and fail later at the wheel step with a misleading message.
+if [ "$env_ready" -ne 1 ]; then
+    echo "ERROR: pixi install --frozen failed after ${RETRIES} attempts" >&2
+    exit 1
+fi
 
 # Download the stable alias and resolve the real version from wheel
 # metadata so pip gets a valid PEP 427 filename.
 echo "Installing omicslab SDK wheel..."
-curl -fsSL "$TOOLS_BASE/omicslab-latest.whl" -o /tmp/omicslab.whl
+fetch "$TOOLS_BASE/omicslab-latest.whl" /tmp/omicslab.whl
 VERSION=$("${PIXI_BIN}" run python3 -c "
 import zipfile, os
 z = zipfile.ZipFile('/tmp/omicslab.whl')

omicslab-2.6.0/src/omicslab/_version.py

@@ -0,0 +1 @@
+__version__ = "2.6.0"

{omicslab-2.5.1 → omicslab-2.6.0}/src/omicslab/cli/main.py

@@ -265,13 +265,13 @@ def pwd():
     parts = []
     if org:
         org_name = config.get_org_name() or org[:8]
-        parts.append(f"[cyan]{org_name}[/cyan]")
+        parts.append(f"[bold]{org_name}[/bold]")
     if ws:
         ws_name = config.get_workspace_name() or ws[:8]
-        parts.append(f"[green]{ws_name}[/green]")
+        parts.append(f"[bold]{ws_name}[/bold]")
     if stored_prefix is not None:
         p = "/" if not stored_prefix else stored_prefix.rstrip("/")
-        parts.append(f"[yellow]{p}[/yellow]")
+        parts.append(f"[bold]{p}[/bold]")
 
     if parts:
         console.print("  ".join(parts))

{omicslab-2.5.1 → omicslab-2.6.0}/src/omicslab/cli/runner_commands.py

@@ -121,18 +121,18 @@ def generate_token(
             output(result, format="json")
         else:
             success("Registration token created")
-            console.print(f"[cyan]Token:[/cyan] [bold]{result['token']}[/bold]")
-            console.print(f"[cyan]Expires:[/cyan] {result['expires_at']}")
-            console.print(f"[cyan]Scope:[/cyan] {scope}")
+            console.print(f"[bold]Token:[/bold] [bold]{result['token']}[/bold]")
+            console.print(f"[bold]Expires:[/bold] {result['expires_at']}")
+            console.print(f"[bold]Scope:[/bold] {scope}")
             console.print("")
             console.print("Register a runner with:")
             console.print(
-                f"  [green]omicslab runner register --token '{result['token']}' --server {config.get_base_url()}[/green]"
+                f"  [bold]omicslab runner register --token '{result['token']}' --server {config.get_base_url()}[/bold]"
             )
             console.print("")
             console.print("Then start the daemon:")
-            console.print("  [green]omicslab runner start --daemon[/green]")
-            console.print("  [green]omicslab runner status[/green]")
+            console.print("  [bold]omicslab runner start --daemon[/bold]")
+            console.print("  [bold]omicslab runner status[/bold]")
     except Exception as e:
         error(f"Failed to create registration token: {e}")
         raise typer.Exit(1)
@@ -199,11 +199,11 @@ def register(
             output(result, format="json")
         else:
             success(f"Registered as runner: {runner_name}")
-            console.print(f"[cyan]Runner ID:[/cyan] {runner_id}")
-            console.print(f"[cyan]Server:[/cyan] {server}")
+            console.print(f"[bold]Runner ID:[/bold] {runner_id}")
+            console.print(f"[bold]Server:[/bold] {server}")
             console.print("")
             console.print("Next, start the runner daemon:")
-            console.print("  [green]omicslab runner start[/green]")
+            console.print("  [bold]omicslab runner start[/bold]")
 
     except typer.Exit:
         raise
@@ -249,17 +249,17 @@ def start(
         if not tool_info.get(t, {}).get("available")
     ]
     if missing_critical and has_slurm:
-        console.print("[yellow]═══ Pre-flight Tool Check ═══[/yellow]")
+        console.print("[bold]═══ Pre-flight Tool Check ═══[/bold]")
         for t in missing_critical:
             console.print(f"  [red]✗ {t}[/red] — not found in PATH")
-        console.print("  [yellow]Install on HPC:[/yellow]")
+        console.print("  [bold]Install on HPC:[/bold]")
         console.print(
-            "    [green]pixi global install nextflow[/green]"
+            "    [bold]pixi global install nextflow[/bold]"
             if "nextflow" in missing_critical
             else ""
         )
         console.print(
-            "    [green]pixi global install apptainer[/green]"
+            "    [bold]pixi global install apptainer[/bold]"
             if "apptainer" in missing_critical
             else ""
         )
@@ -377,14 +377,14 @@ def status_command():
     server_url = config.get_base_url()
 
     if not runner_id:
-        console.print("[yellow]Runner is not registered.[/yellow]")
+        console.print("[bold]Runner is not registered.[/bold]")
         console.print("  Run `omicslab runner register` first.")
         return
 
     console.print("[bold]OmicsLab Runner Status[/bold]")
-    console.print(f"  Runner ID:   [cyan]{runner_id}[/cyan]")
-    console.print(f"  Name:        [cyan]{runner_name}[/cyan]")
-    console.print(f"  Server URL:  [cyan]{server_url}[/cyan]")
+    console.print(f"  Runner ID:   [bold]{runner_id}[/bold]")
+    console.print(f"  Name:        [bold]{runner_name}[/bold]")
+    console.print(f"  Server URL:  [bold]{server_url}[/bold]")
 
     running, pid = _runner_is_running()
     if running:

{omicslab-2.5.1 → omicslab-2.6.0}/src/omicslab/cli/utils.py

@@ -134,7 +134,7 @@ _COST_KEYS = frozenset(
 def _format_value(key: str, val):
     """Convert a raw value to a human-readable string."""
     if val is None:
-        return "[dim]—[/dim]"
+        return "—"
     if isinstance(val, (dict, list)):
         return json.dumps(val)[:60]
     if isinstance(val, str) and key in _DATETIME_KEYS:
@@ -158,8 +158,12 @@ def get_client() -> Client:
         raise typer.Exit(1)
 
 
-def output(data, format: str = "table"):
-    """Output data in the specified format."""
+def output(data, format: str = "table", columns: list[str] | None = None):
+    """Output data in the specified format.
+
+    ``columns`` selects and orders table columns; when omitted the generic
+    display-key heuristic is used.
+    """
     if format == "json":
         console.print(json.dumps(data, indent=2, default=str))
         return
@@ -171,14 +175,14 @@ def output(data, format: str = "table"):
         if not data:
             console.print("[dim]No items found.[/dim]")
             return
-        _print_table(data)
+        _print_table(data, columns=columns)
     elif isinstance(data, dict):
         if "items" in data and isinstance(data["items"], list):
             items = data["items"]
             if not items:
                 console.print("[dim]No items found.[/dim]")
                 return
-            _print_table(items)
+            _print_table(items, columns=columns)
             if "total" in data:
                 console.print(
                     f"[dim]Page {data.get('page', '?')} of {data.get('total_pages', '?')} — {data['total']} total items[/dim]"
@@ -187,18 +191,21 @@ def output(data, format: str = "table"):
             _print_dict(data)
 
 
-def _print_table(items: list[dict]):
-    """Print a list of dicts as a rich table."""
+def _print_table(items: list[dict], columns: list[str] | None = None):
+    """Print a list of dicts as a rich table.
+
+    Data cells deliberately keep the terminal's default foreground so the
+    table stays readable on both light and dark backgrounds. Only the header
+    is emphasised (bold).
+    """
     if not items:
         return
 
-    keys = _get_display_keys(items)
-    table = Table(box=box.SIMPLE_HEAVY)
+    keys = columns or _get_display_keys(items)
+    table = Table(box=box.SIMPLE_HEAVY, header_style="bold")
 
     for key in keys:
-        table.add_column(
-            key, style="cyan", no_wrap=key in ("id", "role", "state", "type")
-        )
+        table.add_column(key, no_wrap=key in ("id", "role", "state", "type"))
 
     for item in items:
         row = []
@@ -215,12 +222,12 @@ def _print_dict(data: dict, indent: int = 0):
     prefix = "  " * indent
     for key, val in data.items():
         if isinstance(val, dict):
-            console.print(f"{prefix}[cyan]{key}:[/cyan]")
+            console.print(f"{prefix}[bold]{key}:[/bold]")
             _print_dict(val, indent + 1)
         elif isinstance(val, list):
-            console.print(f"{prefix}[cyan]{key}:[/cyan] {json.dumps(val)[:120]}")
+            console.print(f"{prefix}[bold]{key}:[/bold] {json.dumps(val)[:120]}")
         else:
-            console.print(f"{prefix}[cyan]{key}:[/cyan] {_format_value(key, val)}")
+            console.print(f"{prefix}[bold]{key}:[/bold] {_format_value(key, val)}")
 
 
 def _get_display_keys(items: list[dict]) -> list[str]:
@@ -293,8 +300,8 @@ def info(msg: str):
 
 
 def print_panel(title: str, data: dict):
-    table = Table(box=box.SIMPLE)
-    table.add_column("Key", style="cyan")
+    table = Table(box=box.SIMPLE, header_style="bold")
+    table.add_column("Key")
     table.add_column("Value")
     for k, v in data.items():
         if isinstance(v, (dict, list)):
@@ -454,11 +461,11 @@ def print_storage_listing(objects: list[dict]):
     sorted_prefixes = sorted(prefixes)
     sorted_files = sorted(files, key=lambda f: f.get("name", ""))
 
-    table = Table(box=box.SIMPLE)
-    table.add_column("Type", style="cyan", width=4)
-    table.add_column("Name", style="white")
-    table.add_column("Size", style="dim", justify="right")
-    table.add_column("Modified", style="dim")
+    table = Table(box=box.SIMPLE, header_style="bold")
+    table.add_column("Type", width=4)
+    table.add_column("Name")
+    table.add_column("Size", justify="right")
+    table.add_column("Modified")
 
     for p in sorted_prefixes:
         table.add_row("DIR", p.rstrip("/"), "", "")