dayhoff-tools 1.11.4__py3-none-any.whl → 1.11.6__py3-none-any.whl

dayhoff_tools/cli/utility_commands.py

@@ -544,6 +544,10 @@ def sync_with_toml(
             mac_pyproject = mac_uv_dir / "pyproject.toml"
             mac_pyproject.write_text(mac_manifest.read_text())
 
+            # Copy README.md if it exists (required by some build backends)
+            if Path("README.md").exists():
+                (mac_uv_dir / "README.md").write_text(Path("README.md").read_text())
+
             # Ensure lock matches manifest (in mac temp dir)
             print("Ensuring lock file matches pyproject.mac.toml (Mac devcon)…")
             lock_cmd = ["uv", "lock"]
@@ -555,12 +559,19 @@ def sync_with_toml(
             # Sync into the active environment
             if install_project:
                 print(
-                    "Syncing dependencies into ACTIVE env and installing project [full]…"
+                    "Syncing dependencies into ACTIVE env (project installed separately)…"
                 )
-                sync_cmd = ["uv", "sync", "--all-groups", "--active"]
+                sync_cmd = [
+                    "uv",
+                    "sync",
+                    "--all-groups",
+                    "--no-install-project",
+                    "--active",
+                ]
                 print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
                 subprocess.run(sync_cmd, check=True, cwd=str(mac_uv_dir))
-                # Install project from repo root
+                # Install project from repo root (where source code actually is)
+                print("Installing project with 'full' extras from repo root…")
                 pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
                 print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
                 subprocess.run(pip_install_cmd, check=True)
@@ -587,6 +598,10 @@ def sync_with_toml(
                 aws_pyproject = aws_uv_dir / "pyproject.toml"
                 aws_pyproject.write_text(aws_manifest.read_text())
 
+                # Copy README.md if it exists (required by some build backends)
+                if Path("README.md").exists():
+                    (aws_uv_dir / "README.md").write_text(Path("README.md").read_text())
+
                 # Ensure lock matches manifest (in aws temp dir)
                 print("Ensuring lock file matches pyproject.aws.toml (AWS devcon)…")
                 lock_cmd = ["uv", "lock"]
@@ -598,12 +613,19 @@ def sync_with_toml(
                 # Sync into the active environment
                 if install_project:
                     print(
-                        "Syncing dependencies into ACTIVE env and installing project [full]…"
+                        "Syncing dependencies into ACTIVE env (project installed separately)…"
                     )
-                    sync_cmd = ["uv", "sync", "--all-groups", "--active"]
+                    sync_cmd = [
+                        "uv",
+                        "sync",
+                        "--all-groups",
+                        "--no-install-project",
+                        "--active",
+                    ]
                     print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
                     subprocess.run(sync_cmd, check=True, cwd=str(aws_uv_dir))
-                    # Install project from repo root
+                    # Install project from repo root (where source code actually is)
+                    print("Installing project with 'full' extras from repo root…")
                     pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
                     print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
                     subprocess.run(pip_install_cmd, check=True)
@@ -994,6 +1016,9 @@ def update_dependencies(
         if platform == "mac" and mac_manifest.exists():
             mac_uv_dir.mkdir(parents=True, exist_ok=True)
             (mac_uv_dir / "pyproject.toml").write_text(mac_manifest.read_text())
+            # Copy README.md if it exists (required by some build backends)
+            if Path("README.md").exists():
+                (mac_uv_dir / "README.md").write_text(Path("README.md").read_text())
             uv_cwd = str(mac_uv_dir)
             lock_file_path = mac_uv_dir / "uv.lock"
             manifest_path_for_constraint = mac_manifest
@@ -1001,6 +1026,9 @@ def update_dependencies(
             # AWS platform (default)
             aws_uv_dir.mkdir(parents=True, exist_ok=True)
             (aws_uv_dir / "pyproject.toml").write_text(aws_manifest.read_text())
+            # Copy README.md if it exists (required by some build backends)
+            if Path("README.md").exists():
+                (aws_uv_dir / "README.md").write_text(Path("README.md").read_text())
             uv_cwd = str(aws_uv_dir)
             lock_file_path = aws_uv_dir / "uv.lock"
             manifest_path_for_constraint = aws_manifest

{dayhoff_tools-1.11.4.dist-info → dayhoff_tools-1.11.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.11.4
+Version: 1.11.6
 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
 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-1.11.4.dist-info → dayhoff_tools-1.11.6.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=46WAySWDFUgwP_Vkr1L4g1xpZOu38r-9UHJhJpRPMnA,42640
+dayhoff_tools/cli/utility_commands.py,sha256=tU6fv8wnchxj8xuBR6lXI1_3tpyxcDxzqO7zyBXAfoY,44012
 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-1.11.4.dist-info/METADATA,sha256=3aHs-3Zmst0iz9G1VmPuLPHgmBjkVoG7Y-PESX5AlzM,2980
-dayhoff_tools-1.11.4.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-dayhoff_tools-1.11.4.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.11.4.dist-info/RECORD,,
+dayhoff_tools-1.11.6.dist-info/METADATA,sha256=4z45zpr5kaL-2WFPAxStOG5hpgm_23EgsyDWW_rUt58,3003
+dayhoff_tools-1.11.6.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+dayhoff_tools-1.11.6.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.11.6.dist-info/RECORD,,