dayhoff-tools 1.13.10__tar.gz → 1.13.12__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/PKG-INFO +1 -1
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/deployment/base.py +8 -2
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/deployment/deploy_aws.py +49 -40
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/pyproject.toml +1 -1
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/README.md +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/__init__.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/chemistry/standardizer.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/chemistry/utils.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/__init__.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/cloud_commands.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/__init__.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/engine_core.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/engine_lifecycle.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/engine_maintenance.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/engine_management.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/shared.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/studio_commands.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/__init__.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/api_client.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/auth.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/engine-studio-cli.md +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/engine_commands.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/progress.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/cli-simulators.md +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/demo.sh +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/engine_list_simulator.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/engine_status_simulator.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/idle_status_simulator.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/simulator_utils.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/studio_list_simulator.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/studio_status_simulator.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/studio_commands.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/main.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/swarm_commands.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/utility_commands.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/deployment/deploy_utils.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/deployment/job_runner.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/deployment/processors.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/deployment/swarm.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/embedders.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/fasta.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/file_ops.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/h5.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/intake/gcp.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/intake/gtdb.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/intake/kegg.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/intake/mmseqs.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/intake/structure.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/intake/uniprot.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/logs.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/sqlite.py +0 -0
- {dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/warehouse.py +0 -0
|
@@ -177,8 +177,14 @@ def build_job_image(config: dict) -> str:
|
|
|
177
177
|
platform = docker_config.get("platform", "linux/amd64")
|
|
178
178
|
build_image_command.extend(["--platform", platform])
|
|
179
179
|
|
|
180
|
-
# Add build
|
|
181
|
-
|
|
180
|
+
# Add build args if provided (for parameterized Dockerfiles)
|
|
181
|
+
build_args = docker_config.get("build_args", {})
|
|
182
|
+
for arg_name, arg_value in build_args.items():
|
|
183
|
+
build_image_command.extend(["--build-arg", f"{arg_name}={arg_value}"])
|
|
184
|
+
|
|
185
|
+
# Add build context (defaults to "." for backward compatibility)
|
|
186
|
+
build_context = docker_config.get("build_context", ".")
|
|
187
|
+
build_image_command.append(build_context)
|
|
182
188
|
subprocess.run(build_image_command, check=True)
|
|
183
189
|
|
|
184
190
|
# Get and print image size
|
|
@@ -344,46 +344,55 @@ def create_or_update_job_definition(
|
|
|
344
344
|
f"Adding mount points to job definition: {batch_job_config['mountPoints']}"
|
|
345
345
|
)
|
|
346
346
|
|
|
347
|
-
#
|
|
348
|
-
#
|
|
349
|
-
|
|
350
|
-
if
|
|
351
|
-
|
|
352
|
-
|
|
353
|
-
|
|
354
|
-
|
|
355
|
-
|
|
356
|
-
"
|
|
357
|
-
|
|
358
|
-
|
|
359
|
-
|
|
360
|
-
|
|
361
|
-
|
|
362
|
-
|
|
363
|
-
|
|
364
|
-
|
|
365
|
-
|
|
366
|
-
|
|
367
|
-
|
|
368
|
-
|
|
369
|
-
|
|
370
|
-
|
|
371
|
-
|
|
372
|
-
|
|
373
|
-
|
|
374
|
-
|
|
375
|
-
|
|
376
|
-
|
|
377
|
-
|
|
378
|
-
|
|
379
|
-
|
|
380
|
-
|
|
381
|
-
|
|
382
|
-
|
|
383
|
-
|
|
384
|
-
|
|
385
|
-
|
|
386
|
-
|
|
347
|
+
# Mount Primordial Drive if explicitly enabled via feature flag
|
|
348
|
+
# Add 'mount_primordial_drive' to features list to mount shared EFS at /primordial/
|
|
349
|
+
features = config.get("features", []) or []
|
|
350
|
+
features_set = {f if isinstance(f, str) else next(iter(f)) for f in features}
|
|
351
|
+
mount_primordial = "mount_primordial_drive" in features_set
|
|
352
|
+
|
|
353
|
+
if mount_primordial:
|
|
354
|
+
primordial_fs_id = get_primordial_fs_id(session)
|
|
355
|
+
if primordial_fs_id:
|
|
356
|
+
print(f"Adding Primordial Drive configuration (fs_id: {primordial_fs_id})")
|
|
357
|
+
|
|
358
|
+
# Add volume configuration
|
|
359
|
+
efs_volume = {
|
|
360
|
+
"name": "primordial",
|
|
361
|
+
"efsVolumeConfiguration": {
|
|
362
|
+
"fileSystemId": primordial_fs_id,
|
|
363
|
+
"rootDirectory": "/",
|
|
364
|
+
},
|
|
365
|
+
}
|
|
366
|
+
|
|
367
|
+
if "volumes" not in container_properties:
|
|
368
|
+
container_properties["volumes"] = []
|
|
369
|
+
|
|
370
|
+
# Check if already added to avoid duplicates
|
|
371
|
+
if not any(
|
|
372
|
+
v.get("name") == "primordial" for v in container_properties["volumes"]
|
|
373
|
+
):
|
|
374
|
+
container_properties["volumes"].append(efs_volume)
|
|
375
|
+
|
|
376
|
+
# Add mount point
|
|
377
|
+
mount_point = {
|
|
378
|
+
"sourceVolume": "primordial",
|
|
379
|
+
"containerPath": "/primordial",
|
|
380
|
+
"readOnly": False,
|
|
381
|
+
}
|
|
382
|
+
|
|
383
|
+
if "mountPoints" not in container_properties:
|
|
384
|
+
container_properties["mountPoints"] = []
|
|
385
|
+
|
|
386
|
+
# Check if already added
|
|
387
|
+
if not any(
|
|
388
|
+
mp.get("containerPath") == "/primordial"
|
|
389
|
+
for mp in container_properties["mountPoints"]
|
|
390
|
+
):
|
|
391
|
+
container_properties["mountPoints"].append(mount_point)
|
|
392
|
+
else:
|
|
393
|
+
print(
|
|
394
|
+
"Warning: mount_primordial_drive enabled but Primordial Drive not found in this environment"
|
|
395
|
+
)
|
|
387
396
|
|
|
388
397
|
# Check if job definition already exists using the session client
|
|
389
398
|
try:
|
|
@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
|
|
|
5
5
|
|
|
6
6
|
[project]
|
|
7
7
|
name = "dayhoff-tools"
|
|
8
|
-
version = "1.13.
|
|
8
|
+
version = "1.13.12"
|
|
9
9
|
description = "Common tools for all the repos at Dayhoff Labs"
|
|
10
10
|
authors = [
|
|
11
11
|
{name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/engine_lifecycle.py
RENAMED
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/engine_maintenance.py
RENAMED
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/engine_management.py
RENAMED
|
File without changes
|
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engine1/studio_commands.py
RENAMED
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/__init__.py
RENAMED
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/api_client.py
RENAMED
|
File without changes
|
|
File without changes
|
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/engine_commands.py
RENAMED
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/progress.py
RENAMED
|
File without changes
|
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/simulators/demo.sh
RENAMED
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
{dayhoff_tools-1.13.10 → dayhoff_tools-1.13.12}/dayhoff_tools/cli/engines_studios/studio_commands.py
RENAMED
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|