dayhoff-tools 1.1.20__py3-none-any.whl → 1.1.22__py3-none-any.whl

dayhoff_tools/__init__.py

@@ -0,0 +1,10 @@
+import importlib.metadata
+
+try:
+    # The package name here should match the 'name' field in your pyproject.toml
+    __version__ = importlib.metadata.version("dayhoff-tools")
+except importlib.metadata.PackageNotFoundError:
+    # This is a fallback for when the package might not be installed (e.g., running from source
+    # without installation, or during development). You can set it to None, "unknown",
+    # or handle it as you see fit.
+    __version__ = "unknown"

dayhoff_tools/cli/utility_commands.py

@@ -465,16 +465,7 @@ def install_dependencies(
             print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
             subprocess.run(pip_install_cmd, check=True)
 
-            # Step 2b: Sync other dependency groups (e.g., dev)
-            # We use --no-install-project here because the project itself was just installed.
-            # --all-groups will ensure other groups like 'dev' are synced.
-            print("Syncing other dependency groups (e.g., dev)...")
-            sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project"]
-            print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
-            subprocess.run(sync_cmd, check=True)
-            print(
-                "Project installed with 'full' extras and other dependency groups synced successfully."
-            )
+            print("Project installed with 'full' extras successfully.")
         else:
             # Original behavior: Sync environment without installing the project
             print(
@@ -582,13 +573,16 @@ def update_dependencies(
             print(f"Updating {pyproject_path} version constraint...")
             try:
                 content = pyproject_path.read_text()
+                package_name_re = re.escape(
+                    "dayhoff-tools"
+                )  # Use the actual package name
                 pattern = re.compile(
-                    "^(\s*['\"])dayhoff-tools(?:[><=~^][^'\"\[,]*)?(['\"].*)$",  # Match rest of line
+                    rf"^(\\s*['\"])({package_name_re})(\\[[^\\]]+\\])?(?:[^'\"[\,\\s]*)?(['\"].*)$",
                     re.MULTILINE,
                 )
-                package_name = "dayhoff-tools"
+                # package_name variable is still 'dayhoff-tools'
                 new_constraint_text = f">={locked_version}"
-                replacement_string = f"\g<1>{package_name}{new_constraint_text}\g<2>"
+                replacement_string = rf"\\g<1>\\g<2>\\g<3>{new_constraint_text}\\g<4>"
                 new_content, num_replacements = pattern.subn(
                     replacement_string, content
                 )

dayhoff_tools/deployment/processors.py

@@ -175,6 +175,10 @@ class MMSeqsProfileProcessor(Processor):
         else:
             self.mmseqs_args = default_mmseqs_args
 
+        # Log dayhoff-tools version
+        from dayhoff_tools import __version__
+
+        logger.info(f"dayhoff-tools version: {__version__}")
         logger.info(
             f"MMSeqsProfileProcessor initialized with query: {self.query_fasta_path}"
         )

dayhoff_tools/deployment/swarm.py

@@ -439,6 +439,11 @@ class Operator:
         - For AWS spot instances, uses IMDSv2 to check instance-action metadata
         - For GCP preemptible VMs, checks both maintenance-event and preempted metadata
         """
+        logger.info(
+            "DEBUG: _check_for_termination has been temporarily disabled for testing."
+        )
+        return  # DEBUG: Temporarily disable to test if this is causing premature shutdown
+
         while not _shutdown_requested.is_set():
             try:
                 # Check AWS spot termination using IMDSv2 (token-based auth)

{dayhoff_tools-1.1.20.dist-info → dayhoff_tools-1.1.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.20
+Version: 1.1.22
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.1.20.dist-info → dayhoff_tools-1.1.22.dist-info}/RECORD

@@ -1,18 +1,18 @@
-dayhoff_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+dayhoff_tools/__init__.py,sha256=M5zThPyEBRYa5CfwlzKhcqTevWn3OKu62cjV6Zqie2A,469
 dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf2ElfZDXEpY,11188
 dayhoff_tools/chemistry/utils.py,sha256=jt-7JgF-GeeVC421acX-bobKbLU_X94KNOW24p_P-_M,2257
 dayhoff_tools/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dayhoff_tools/cli/cloud_commands.py,sha256=NGux28-cjDyCADF-L1tjdEMzkCMYX8V4xNvpK6EWcZA,40802
 dayhoff_tools/cli/main.py,sha256=47EGb28ALaYFc7oAUGlY1D66AIDmc4RZiXxN-gPVrpQ,4519
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=_8l5o0il_wyC96Bx_UHvHRrdnaJUgji7D0L6VYsdops,24918
+dayhoff_tools/cli/utility_commands.py,sha256=vB6WLAq_VNqN00cvCUnPBdo_b_1poM8jH6ZRhIp8Qn4,24500
 dayhoff_tools/deployment/base.py,sha256=8tXwsPYvRo-zV-aNhHw1c7Rji-KWg8S5xoCCznFnVVI,17412
 dayhoff_tools/deployment/deploy_aws.py,sha256=O0gQxHioSU_sNU8T8MD4wSOPvWc--V8eRRZzlRu035I,16446
 dayhoff_tools/deployment/deploy_gcp.py,sha256=DxBM4sUzwPK9RWLP9bSfr38n1HHl-TVrp4TsbdN8pUA,5795
 dayhoff_tools/deployment/deploy_utils.py,sha256=StFwbqnr2_FWiKVg3xnJF4kagTHzndqqDkpaIOaAn_4,26027
 dayhoff_tools/deployment/job_runner.py,sha256=4tmdplpvqSE9bVxRWHo2U5kwkYrYod0Uwzpg2Q7qG5o,4850
-dayhoff_tools/deployment/processors.py,sha256=0D2r2-NgVcFfxF0QSqLZy86cxEWSn78jLTKYf60fLBQ,25519
-dayhoff_tools/deployment/swarm.py,sha256=MGcS2_x4RNFtnVjWlU_SwNfhICz8NlGYr9cYBK4ZKDA,21688
+dayhoff_tools/deployment/processors.py,sha256=LhI-TnQWTtG3tJsBMYVRoqCRlME_C6Hd4E6VUmxIed0,25663
+dayhoff_tools/deployment/swarm.py,sha256=Xoe-lLQYDT3FwCrPzImgpbHdWRmsK6WERh1IMMNWb2c,21898
 dayhoff_tools/embedders.py,sha256=CRgcb2z7KeeFrRQawyUZuJ4Yi0-J5jSr0hwuRhjG_FI,36513
 dayhoff_tools/fasta.py,sha256=e7xw3pInoupqCGE0-fJTOzmW_earL1M7qPyoqIPfUT4,46269
 dayhoff_tools/file_ops.py,sha256=JlGowvr-CUJFidV-4g_JmhUTN9bsYuaxtqKmnKomm-Q,8506
@@ -26,7 +26,7 @@ dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJq
 dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
 dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
 dayhoff_tools/warehouse.py,sha256=TqV8nex1AluNaL4JuXH5zuu9P7qmE89lSo6f_oViy6U,14965
-dayhoff_tools-1.1.20.dist-info/METADATA,sha256=FfqFxLcWkWI83uz38_0HKCCwfOB2uHt4q2u2VnZuRXQ,2225
-dayhoff_tools-1.1.20.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.1.20.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.1.20.dist-info/RECORD,,
+dayhoff_tools-1.1.22.dist-info/METADATA,sha256=TjPBmiCLL-GmIM8gPhhD2g4W0IEKY5gYEQhDX3-XVbc,2225
+dayhoff_tools-1.1.22.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.1.22.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.1.22.dist-info/RECORD,,