dayhoff-tools 1.1.17__tar.gz → 1.1.19__tar.gz

{dayhoff_tools-1.1.17 → dayhoff_tools-1.1.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.17
+Version: 1.1.19
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.1.17 → dayhoff_tools-1.1.19}/dayhoff_tools/cli/cloud_commands.py

@@ -902,6 +902,72 @@ def gcp_use_devcon_adc():
         sys.exit(1)
 
 
+@gcp_app.command("logout")
+def gcp_logout():
+    """Clear all GCP credentials for testing or role switching purposes.
+
+    This removes the active user's gcloud login, disables impersonation,
+    and invalidates Application Default Credentials (ADC).
+    """
+    print(f"{BLUE}Clearing all GCP credentials...{NC}")
+
+    try:
+        gcloud_path = _find_executable("gcloud")
+        errors = []
+
+        # 1. Revoke user-level credentials
+        print(f"{BLUE}Revoking active gcloud credentials...{NC}")
+        revoke_cmd = [gcloud_path, "auth", "revoke", "--all", "--quiet"]
+        revoke_code, _, revoke_err = _run_command(revoke_cmd, capture=True, check=False)
+        if revoke_code != 0 and revoke_err:
+            errors.append(f"Failed to revoke credentials: {revoke_err}")
+
+        # 2. Unset impersonation config
+        print(f"{BLUE}Disabling service account impersonation...{NC}")
+        unset_code, _, unset_err = _gcloud_unset_config(
+            "auth/impersonate_service_account"
+        )
+        if unset_code != 0 and unset_err:
+            errors.append(f"Failed to unset impersonation: {unset_err}")
+
+        # 3. Revoke ADC
+        print(f"{BLUE}Revoking Application Default Credentials (ADC)...{NC}")
+        adc_cmd = [gcloud_path, "auth", "application-default", "revoke", "--quiet"]
+        adc_code, _, adc_err = _run_command(adc_cmd, capture=True, check=False)
+
+        # 4. Additionally remove ADC file if it exists (belt-and-suspenders approach)
+        adc_file = (
+            Path.home() / ".config" / "gcloud" / "application_default_credentials.json"
+        )
+        if adc_file.exists():
+            try:
+                adc_file.unlink()
+                print(f"{BLUE}Removed ADC file: {adc_file}{NC}")
+            except Exception as e:
+                errors.append(f"Failed to delete ADC file: {e}")
+
+        if errors:
+            print(f"{YELLOW}Logged out with some warnings:{NC}")
+            for err in errors:
+                print(f"{YELLOW}  - {err}{NC}")
+        else:
+            print(f"{GREEN}Successfully logged out from GCP.{NC}")
+
+        # Always show how to log back in
+        print(f"\n{BLUE}To log back in:{NC}")
+        print(f"  {YELLOW}dh gcp login{NC}")
+
+        # Show current (now-cleared) status
+        print(f"\n{BLUE}Current status:{NC}")
+        gcp_status()
+
+    except Exception as e:
+        print(f"{RED}Error during logout: {e}{NC}", file=sys.stderr)
+        print(f"{YELLOW}You may need to manually run:{NC}")
+        print(f"  {YELLOW}gcloud auth revoke --all{NC}")
+        print(f"  {YELLOW}gcloud auth application-default revoke{NC}")
+
+
 # === End NEW ADC Commands ===
 
 

{dayhoff_tools-1.1.17 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/processors.py

@@ -405,16 +405,20 @@ class MMSeqsProfileProcessor(Processor):
                 run_base_dir,
             )
 
-            # 9. Extract hit sequences directly to FASTA using result2flat
+            # 9. Extract hit sequences directly to FASTA using createseqfiledb
             self._run_mmseqs_command(
                 [
                     "mmseqs",
                     "createseqfiledb",
-                    str(result_db),  # resultDB containing target hits
-                    str(target_db),  # targetDB containing actual sequences
-                    str(intermediate_hits_fasta_file),  # output FASTA
-                    "--db-output",
-                    "1",  # Output in FASTA format
+                    str(target_db),  # <i:sequenceDB> - The DB to pull sequences from
+                    str(
+                        result_db
+                    ),  # <i:resultDB> - Contains IDs of target sequences to pull
+                    str(
+                        intermediate_hits_fasta_file
+                    ),  # <o:fastaDB> - Output FASTA file
+                    "--threads",  # createseqfiledb supports --threads
+                    self.num_threads,
                 ],
                 "Extract hit sequences to FASTA via createseqfiledb",
                 run_base_dir,

{dayhoff_tools-1.1.17 → dayhoff_tools-1.1.19}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.1.17"
+version = "1.1.19"
 description = "Common tools for all the repos at Dayhoff Labs"
 authors = [
     {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}