latch 2.76.3__tar.gz → 2.76.4__tar.gz

{latch-2.76.3 → latch-2.76.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: latch
-Version: 2.76.3
+Version: 2.76.4
 Summary: The Latch SDK
 Project-URL: Homepage, https://latch.bio
 Project-URL: Documentation, https://latch.wiki
@@ -41,7 +41,6 @@ Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Build Tools
 Requires-Python: >=3.9
-Requires-Dist: aioconsole==0.6.1
 Requires-Dist: apscheduler>=3.10.0
 Requires-Dist: asyncssh==2.13.2
 Requires-Dist: boto3>=1.26.0
@@ -53,20 +52,22 @@ Requires-Dist: gql==3.5.0
 Requires-Dist: graphql-core==3.2.3
 Requires-Dist: kubernetes>=24.2.0
 Requires-Dist: latch-persistence>=0.1.5
-Requires-Dist: lytekit==0.15.35
+Requires-Dist: lytekit==0.16
 Requires-Dist: lytekitplugins-pods==0.7.4
 Requires-Dist: orjson>=3.10.12
 Requires-Dist: paramiko>=3.4.0
+Requires-Dist: pydantic<3,>=2
 Requires-Dist: pyjwt>=0.2.0
 Requires-Dist: python-dateutil>=2.8
 Requires-Dist: pyxattr>=0.8.1
 Requires-Dist: requests-toolbelt==1.0.0
 Requires-Dist: requests>=2.28.1
+Requires-Dist: rich>=14.0.0
 Requires-Dist: scp>=0.14.0
 Requires-Dist: tqdm>=4.63.0
 Requires-Dist: typing-extensions>=4.12.0
 Requires-Dist: watchfiles==1.1.1
-Requires-Dist: websockets>=15.0.1
+Requires-Dist: websockets<16,>=11
 Provides-Extra: pandas
 Requires-Dist: pandas>=2.0.0; extra == 'pandas'
 Provides-Extra: snakemake

{latch-2.76.3 → latch-2.76.4}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.sdist]
-include = ["src/**/*.py", "src/**/py.typed", "src/latch_cli/services/init/*"]
+include = ["src/**/*.py", "src/**/*.graphql", "src/**/py.typed", "src/latch_cli/services/init/*"]
 
 [tool.hatch.build.targets.wheel.force-include]
 "src/latch_cli" = "latch_cli"
@@ -12,7 +12,7 @@ include = ["src/**/*.py", "src/**/py.typed", "src/latch_cli/services/init/*"]
 
 [project]
 name = "latch"
-version = "2.76.3"
+version = "2.76.4"
 description = "The Latch SDK"
 authors = [{ name = "Kenny Workman", email = "kenny@latch.bio" }]
 maintainers = [{ name = "Kenny Workman", email = "kenny@latch.bio" }]
@@ -31,7 +31,7 @@ dependencies = [
   "scp>=0.14.0",
   "boto3>=1.26.0",
   "tqdm>=4.63.0",
-  "lytekit==0.15.35",
+  "lytekit==0.16",
   "lytekitplugins-pods==0.7.4",
   "typing-extensions>=4.12.0",
   "apscheduler>=3.10.0",
@@ -39,11 +39,12 @@ dependencies = [
   "graphql-core==3.2.3",
   "requests-toolbelt==1.0.0",
   "python-dateutil>=2.8",
+  "pydantic>=2,<3",
+  "rich>=14.0.0",
   "GitPython==3.1.40",
   # for old latch develop, to be removed
-  "aioconsole==0.6.1",
   "asyncssh==2.13.2",
-  "websockets>=15.0.1",
+  "websockets>=11,<16",
   "watchfiles==1.1.1",
   "pyxattr>=0.8.1",
   "orjson>=3.10.12",

{latch-2.76.3 → latch-2.76.4}/src/latch/types/file.py

@@ -1,7 +1,7 @@
 import os
 from os import PathLike
 from pathlib import Path
-from typing import Annotated, Optional, Union, get_args, get_origin
+from typing import Annotated, Optional, Union
 from urllib.parse import urlparse
 
 import gql
@@ -249,9 +249,6 @@ class LatchFilePathTransformer(FlyteFilePathTransformer):
                 "Casting from Pathlike to LatchFile is currently not supported."
             )
 
-        while get_origin(expected_python_type) == Annotated:
-            expected_python_type = get_args(expected_python_type)[0]
-
         if not issubclass(expected_python_type, LatchFile):
             raise TypeError(
                 f"Neither os.PathLike nor LatchFile specified {expected_python_type}"

{latch-2.76.3 → latch-2.76.4}/src/latch/utils.py

@@ -4,27 +4,39 @@ from typing import Dict, TypedDict
 
 import gql
 import jwt
+
 from latch_sdk_config.user import user_config
 from latch_sdk_gql.execute import execute
 
 
 def account_id_from_token(token: str) -> str:
-    """Exchanges a valid JWT for a Latch account ID.
+    """Resolve the Latch account ID associated with ``token``.
 
     Latch account IDs are needed for any user-specific request, eg. register
     workflows or copy files to Latch.
 
     Args:
-        token: JWT
+        token: A Latch SDK token.
 
     Returns:
-        A Latch account ID (UUID).
+        A Latch account ID.
     """
-    decoded_jwt = jwt.decode(token, options={"verify_signature": False})
-    try:
-        return decoded_jwt.get("id")
-    except KeyError as e:
-        raise ValueError("Your Latch access token is malformed") from e
+
+    res = execute(
+        gql.gql("""
+            query AccountIdFromToken {
+                accountInfoCurrent {
+                    id
+                }
+            }
+        """)
+    )
+    aic = res.get("accountInfoCurrent")
+    if aic is None or aic.get("id") is None:
+        raise ValueError(
+            "Your Latch access token is invalid or could not be resolved to an account."
+        )
+    return aic["id"]
 
 
 def retrieve_or_login() -> str:
@@ -170,7 +182,7 @@ def current_workspace() -> str:
                     }
                 }
             }
-        """),
+        """)
     )["accountInfoCurrent"]
 
     if res is not None:

{latch-2.76.3 → latch-2.76.4}/src/latch_cli/centromere/ctx.py

@@ -1,3 +1,4 @@
+from logging import getLogger
 import re
 import sys
 import traceback
@@ -30,6 +31,8 @@ from latch_cli.utils import (
 )
 from latch_sdk_config.latch import config
 
+log = getLogger(__name__)
+
 
 @dataclass
 class _Container:
@@ -91,12 +94,14 @@ class _CentromereCtx:
         use_new_centromere: bool = False,
         overwrite: bool = False,
         dockerfile_path: Optional[Path] = None,
+        account_id: Optional[str] = None,
     ):
         self.use_new_centromere = use_new_centromere
         self.remote = remote
         self.disable_auto_version = disable_auto_version
         self.wf_module = wf_module if wf_module is not None else "wf"
 
+        log.debug("Initializing CentromereCtx")
         if self.wf_module.startswith("."):
             click.secho(
                 dedent(f"""\
@@ -107,10 +112,15 @@ class _CentromereCtx:
             raise click.exceptions.Exit(1)
 
         try:
+            log.debug("retrieve_or_login")
             self.token = retrieve_or_login()
-            self.account_id = current_workspace()
+            log.debug("current_workspace")
+            self.account_id = (
+                account_id if account_id is not None else current_workspace()
+            )
 
             self.dkr_repo = config.dkr_repo
+            log.debug("resolving pkg_root")
             self.pkg_root = pkg_root.resolve()
 
             if snakefile is not None and nf_script is not None:
@@ -131,6 +141,7 @@ class _CentromereCtx:
             else:
                 self.workflow_type = WorkflowType.latchbiosdk
 
+            log.debug("Determining version")
             version_file = self.pkg_root / "version"
             try:
                 self.version = version_file.read_text()
@@ -143,6 +154,7 @@ class _CentromereCtx:
 
             self.version = self.version.strip()
 
+            log.debug("Loading the git repo")
             try:
                 from git import GitError, Repo
 
@@ -162,6 +174,7 @@ class _CentromereCtx:
                     fg="yellow",
                 )
 
+            log.debug("Auto-versioning")
             if not self.disable_auto_version:
                 hash = ""
 
@@ -198,6 +211,7 @@ class _CentromereCtx:
                     ),
                 )
 
+                log.debug("Loading Flyte objects")
                 try:
                     if not module_path.exists():
                         click.secho(error_msg, fg="red")
@@ -426,6 +440,7 @@ class _CentromereCtx:
                     self.ssh_key_path, add_to_agent=False
                 )
 
+                log.debug("use_new_centromere=%s", use_new_centromere)
                 if use_new_centromere:
                     self.internal_ip, self.username = (
                         self.provision_register_deployment()
@@ -448,6 +463,7 @@ class _CentromereCtx:
                 def _patched_connect(self): ...
 
                 def _patched_create_paramiko_client(self, base_url):
+                    log.debug("_patched_create_paramiko_client")
                     self.ssh_client = ssh_client
 
                 SSHHTTPAdapter._create_paramiko_client = _patched_create_paramiko_client
@@ -514,6 +530,7 @@ class _CentromereCtx:
         return f"{self.image}:{self.version}"
 
     def task_image_name(self, task_name: str) -> str:
+        log.debug("task_image_name: %s", task_name)
         task_name = identifier_suffix_from_str(task_name).lower()
         task_name = docker_image_name_illegal_pat.sub("_", task_name)
 
@@ -555,6 +572,7 @@ class _CentromereCtx:
 
     def provision_register_deployment(self) -> Tuple[str, str]:
         """Retrieve centromere IP + username."""
+        log.debug("provision_register_deployment")
         click.echo("Provisioning register instance. This may take a few minutes.")
 
         assert self.ssh_key_path is not None
@@ -610,9 +628,11 @@ class _CentromereCtx:
     def nucleus_check_version(self, version: str, workflow_name: str) -> bool:
         """Check if version has already been registered for given workflow"""
 
+        log.debug("nucleus_check_version")
+
         headers = {"Authorization": f"Bearer {self.token}"}
 
-        ws_id = current_workspace()
+        ws_id = self.account_id
         if ws_id is None or ws_id == "":
             ws_id = account_id_from_token(retrieve_or_login())
 

{latch-2.76.3 → latch-2.76.4}/src/latch_cli/centromere/utils.py

@@ -6,6 +6,7 @@ import string
 import sys
 import tempfile
 from dataclasses import dataclass
+from logging import getLogger
 from pathlib import Path
 from types import ModuleType
 from typing import Callable, Iterator, List, Optional, TypeVar
@@ -17,6 +18,8 @@ from typing_extensions import ParamSpec
 
 from latch_cli.constants import latch_constants
 
+log = getLogger(__name__)
+
 
 @dataclass
 class RemoteConnInfo:
@@ -109,6 +112,7 @@ def _construct_dkr_client(ssh_host: Optional[str] = None):
     If `ssh_host` is passed, we attempt to make a connection with a remote
     machine.
     """
+    log.debug("Creating docker client: %s", ssh_host)
 
     def _from_env():
         host = environment.get("DOCKER_HOST")
@@ -124,6 +128,8 @@ def _construct_dkr_client(ssh_host: Optional[str] = None):
 
         enable_tls = tls_verify or cert_path is not None
 
+        log.debug("Determined Docker host from environment: %s", host)
+
         dkr_client = None
         try:
             if not enable_tls:
@@ -164,8 +170,19 @@ def _construct_dkr_client(ssh_host: Optional[str] = None):
     if host is not None and host != "":
         return _from_env()
     else:
+        try:
+            base_url = f"unix:/{Path.home()}/.docker/run/docker.sock"
+            log.debug(
+                "Using default Docker host: unix://$HOME/run/docker.sock (%s)", base_url
+            )
+            return docker.APIClient(base_url=base_url)
+        except docker.errors.DockerException:
+            tracebac
+            pass
+
         try:
             # TODO: platform specific socket defaults
+            log.debug("Using default Docker host: unix://var/run/docker.sock")
             return docker.APIClient(base_url="unix://var/run/docker.sock")
         except docker.errors.DockerException as de:
             raise OSError(
@@ -177,40 +194,66 @@ def _construct_dkr_client(ssh_host: Optional[str] = None):
 def _construct_ssh_client(
     remote_conn_info: RemoteConnInfo, *, use_gateway: bool = True
 ) -> paramiko.SSHClient:
+    log.debug(
+        "_construct_ssh_client conn_info=%s use_gateway=%s",
+        remote_conn_info,
+        use_gateway,
+    )
+
     if use_gateway:
         gateway = paramiko.SSHClient()
+
+        log.debug("Loading system host keys")
         gateway.load_system_host_keys()
+
+        log.debug("Setting missing host key policy")
         gateway.set_missing_host_key_policy(paramiko.MissingHostKeyPolicy)
 
-        gateway_pkey = paramiko.PKey.from_path(
-            path=str(remote_conn_info.jump_key_path.resolve())
-        )
+        path = str(remote_conn_info.jump_key_path.resolve())
+        log.debug("Loading public key from %s", path)
+        gateway_pkey = paramiko.PKey.from_path(path=path)
 
+        log.debug(
+            "Connecting to gateway: %s@%s",
+            latch_constants.jump_user,
+            latch_constants.jump_host,
+        )
         gateway.connect(
             latch_constants.jump_host,
             username=latch_constants.jump_user,
             pkey=gateway_pkey,
         )
 
+        log.debug("Getting gateway transport")
         gateway_transport = gateway.get_transport()
         if gateway_transport is None:
             raise ConnectionError("unable to create connection to jump host")
 
+        log.debug("Opening gateway channel")
         sock = gateway_transport.open_channel(
             kind="direct-tcpip", dest_addr=(remote_conn_info.ip, 22), src_addr=("", 0)
         )
     else:
         sock = None
 
-    pkey = paramiko.PKey.from_path(path=str(remote_conn_info.ssh_key_path.resolve()))
+    path = str(remote_conn_info.ssh_key_path.resolve())
+    log.debug("Loading public key")
+    pkey = paramiko.PKey.from_path(path=path)
 
     ssh = paramiko.SSHClient()
+
+    log.debug("Loading system host keys")
     ssh.load_system_host_keys()
+
+    log.debug("Setting missing host key policy")
     ssh.set_missing_host_key_policy(paramiko.MissingHostKeyPolicy)
+
+    log.debug("Connecting to remote")
     ssh.connect(
         remote_conn_info.ip, username=remote_conn_info.username, sock=sock, pkey=pkey
     )
 
+    log.debug("Getting transport")
     transport = ssh.get_transport()
     if transport is None:
         raise ConnectionError(
@@ -219,6 +262,7 @@ def _construct_ssh_client(
 
     # (kenny) Equivalent of OpenSSH configuration `ServerAliveInterval`
     # No analogue for `ServerAliveCountMax` in paramiko I could find.
+    log.debug("Setting Keep-Alive")
     transport.set_keepalive(latch_constants.centromere_keepalive_interval)
 
     return ssh
@@ -242,6 +286,7 @@ class MaybeRemoteDir:
         self.reconnect_info = reconnect_info
 
     def __enter__(self):
+        log.debug("MaybeRemoteDir.__enter__")
         return self.create()
 
     def __exit__(self, exc_type, exc_value, tb):

{latch-2.76.3 → latch-2.76.4}/src/latch_cli/constants.py

@@ -57,10 +57,11 @@ latch_constants = LatchConstants()
 
 @dataclass(frozen=True)
 class OAuth2Constants:
-    client_id: str = "jzFBOhIbfp4EPRYZ8wmx4YyvL27LFDeB"
+    client_id: str = "UQs8mV2SvKLrPkcI5dt3nmsnrdZvPUs0"
     """Identifies the authentication server in 0Auth2.0 flow"""
 
-    authz_server_host: str = "https://latchai.us.auth0.com"
+    authz_server_host: str = "https://auth.latch.bio"
+
     """Host of the authentication server used in 0Auth2.0 flow."""
 
     redirect_url: str = "http://127.0.0.1:5050/callback"