dayhoff-tools 1.11.8__py3-none-any.whl → 1.11.9__py3-none-any.whl

dayhoff_tools/cli/utility_commands.py

@@ -862,6 +862,8 @@ def add_dependency(
     package_name = re.split(r"[<>=~!\[]", package)[0].strip()
     has_version_spec = any(c in package for c in ["<", ">", "=", "~", "!"])
 
+    added_count = 0
+
     for manifest_file in manifest_files:
         try:
             content = manifest_file.read_text()
@@ -939,11 +941,17 @@ def add_dependency(
 
             manifest_file.write_text(new_content)
             print(f"✅ Added '{package}' to {manifest_file}")
+            added_count += 1
 
         except Exception as e:
             print(f"Error updating {manifest_file}: {e}")
 
-    print(f"\n✅ Added '{package}' to all platform manifests")
+    # If nothing was added, exit early
+    if added_count == 0:
+        print(f"\n⚠️  Package '{package_name}' already exists in all manifests")
+        return
+
+    print(f"\n✅ Added '{package}' to {added_count} platform manifest(s)")
 
     # If no version specified, resolve and add version constraint
     if not has_version_spec:
@@ -981,7 +989,7 @@ def add_dependency(
                     print(f"Warning: Could not update version in {manifest_file}: {e}")
 
             print(
-                f"\n✅ Added '{package_name}>={resolved_version}' to all platform manifests"
+                f"\n✅ Added '{package_name}>={resolved_version}' to {added_count} platform manifest(s)"
             )
         else:
             print(
@@ -1031,17 +1039,19 @@ def remove_dependency(
             content = manifest_file.read_text()
 
             # Pattern to match the dependency line (with optional version spec)
-            # Matches:  "package...",  or  "package...",\n
+            # Matches:  "package...",  or  "package...",\n (including the newline)
             pattern = re.compile(
-                rf'^\s*["\']({package_esc}[<>=~!\[].+?|{package_esc})["\'],?\s*(?:#.*)?$',
+                rf'^\s*["\']({package_esc}[<>=~!\[].+?|{package_esc})["\'],?\s*(?:#.*)?$\n?',
                 re.MULTILINE,
             )
 
             new_content, num_removed = pattern.subn("", content)
 
             if num_removed > 0:
-                # Clean up any double blank lines
+                # Clean up any consecutive blank lines (more than one)
                 new_content = re.sub(r"\n\n\n+", "\n\n", new_content)
+                # Also clean up trailing whitespace on lines
+                new_content = re.sub(r"[ \t]+$", "", new_content, flags=re.MULTILINE)
                 manifest_file.write_text(new_content)
                 print(f"✅ Removed '{package}' from {manifest_file}")
                 removed_count += 1

{dayhoff_tools-1.11.8.dist-info → dayhoff_tools-1.11.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.11.8
+Version: 1.11.9
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -29,6 +29,7 @@ Requires-Dist: pyyaml (>=6.0)
 Requires-Dist: questionary (>=2.0.1)
 Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
 Requires-Dist: requests (>=2.31.0)
+Requires-Dist: seaborn (>=0.13.2)
 Requires-Dist: sentencepiece (>=0.2.0) ; extra == "embedders"
 Requires-Dist: sentencepiece (>=0.2.0) ; extra == "full"
 Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"

{dayhoff_tools-1.11.8.dist-info → dayhoff_tools-1.11.9.dist-info}/RECORD

@@ -12,7 +12,7 @@ dayhoff_tools/cli/engine/shared.py,sha256=Ecx6I1jtzmxQDn3BezKpgpQ4SJeZf4SZjUCLg-
 dayhoff_tools/cli/engine/studio_commands.py,sha256=VwTQujz32-uMcYusDRE73SdzRpgvIkv7ZAF4zRv6AzA,30266
 dayhoff_tools/cli/main.py,sha256=Ii5boey--93yGthB_eS2LC7ZR3WHGsJXDHY7uElEtso,6169
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=iMj2Oj6Q9LcUTwwZismFqc2QTW_oSeIDR1o_eC7kj-Q,50331
+dayhoff_tools/cli/utility_commands.py,sha256=e2P4dCCtoqMUGNyb0lFBZ6GZpl5Zslm1qqE5qIvsy38,50765
 dayhoff_tools/deployment/base.py,sha256=48KE76QlWMeIZJefcBOZVbyChS2V_mgs7IQ31odPV2o,17806
 dayhoff_tools/deployment/deploy_aws.py,sha256=gfqh09hGbz0q3oPqVm0imd_CEjKF2k8moGNRIL26qqE,18614
 dayhoff_tools/deployment/deploy_gcp.py,sha256=xgaOVsUDmP6wSEMYNkm1yRNcVskfdz80qJtCulkBIAM,8860
@@ -33,7 +33,7 @@ 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=UETBtZD3r7WgvURqfGbyHlT7cxoiVq8isjzMuerKw8I,24475
-dayhoff_tools-1.11.8.dist-info/METADATA,sha256=BVSPi89Q4l1JH1DPOXHcwbxq9U1jJ66KJCaqsz5Sqrg,2980
-dayhoff_tools-1.11.8.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-dayhoff_tools-1.11.8.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.11.8.dist-info/RECORD,,
+dayhoff_tools-1.11.9.dist-info/METADATA,sha256=POBxTDcl6NafsxeUli-dgk5-CZ7SvytEjEONN8OEazA,3014
+dayhoff_tools-1.11.9.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+dayhoff_tools-1.11.9.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.11.9.dist-info/RECORD,,