dayhoff-tools 1.1.0__py3-none-any.whl → 1.1.2__py3-none-any.whl

dayhoff_tools/cli/main.py

@@ -9,7 +9,6 @@ from dayhoff_tools.cli.utility_commands import (
     get_ancestry,
     import_from_warehouse_typer,
     install_dependencies,
-    rebuild_devcontainer_file,
     test_github_actions_locally,
     update_dependencies,
 )
@@ -23,13 +22,12 @@ app.command("clean")(delete_local_branch)
 app.command(
     "install", help="Install dependencies based on pyproject.toml and sync environment."
 )(install_dependencies)
-app.command(
-    "update", help="Update dependencies (--all or --dayhoff) and sync environment."
-)(update_dependencies)
+app.command("update", help="Update dayhoff-tools (or all deps) and sync environment.")(
+    update_dependencies
+)
 
 # Other Utilities
 app.command("gha")(test_github_actions_locally)
-app.command("rebuild")(rebuild_devcontainer_file)
 app.command("wadd")(add_to_warehouse_typer)
 app.command("wancestry")(get_ancestry)
 app.command("wimport")(import_from_warehouse_typer)

dayhoff_tools/cli/utility_commands.py

@@ -23,17 +23,6 @@ def test_github_actions_locally():
         print(f"Error occurred while running the script: {e}")
 
 
-def rebuild_devcontainer_file():
-    """Run the script prepare_for_build.py."""
-    script_path = ".devcontainer/scripts/prepare_for_build.py"
-
-    try:
-        subprocess.check_call([sys.executable, script_path])
-        print("Script ran successfully!")
-    except subprocess.CalledProcessError as e:
-        print(f"Error occurred while running the script: {e}")
-
-
 def get_ancestry(filepath: str) -> None:
     """Take a .dvc file created from import, and generate an ancestry entry
     that can be manually copied into other .dvc files."""
@@ -421,28 +410,21 @@ def install_dependencies(
 
 
 def update_dependencies(
-    update_dayhoff: bool = typer.Option(
-        False,
-        "--dayhoff",
-        "-d",
-        help="Update only the dayhoff-tools package to latest, update pyproject.toml, and sync.",
-    ),
     update_all: bool = typer.Option(
         False,
         "--all",
         "-a",
-        help="Update all dependencies to their latest compatible versions and sync.",
+        help="Update all dependencies instead of just dayhoff-tools.",
     ),
 ):
     """Update dependencies to newer versions.
 
-    Requires specifying either --dayhoff/-d or --all/-a.
+    Default Action (no flags): Updates only 'dayhoff-tools' package to latest,
+                               updates pyproject.toml, and syncs.
 
-    Modes:
+    Flags:
     --all/-a: Updates all dependencies to latest compatible versions (`uv lock --upgrade`)
-              and syncs the environment.
-    --dayhoff/-d: Updates only 'dayhoff-tools' to latest, updates its constraint
-                  in pyproject.toml, and syncs the environment.
+              and syncs the environment. Overrides the default.
     """
     # ANSI color codes
     BLUE = "\033[94m"
@@ -451,28 +433,24 @@ def update_dependencies(
     lock_file_path = Path("uv.lock")
     pyproject_path = Path("pyproject.toml")
 
-    # Validate that either -d or -a is provided
-    if not update_dayhoff and not update_all:
-        print(
-            "Error: Must specify either --dayhoff (-d) or --all (-a) to update dependencies."
-        )
-        raise typer.Exit(code=1)
-    if update_dayhoff and update_all:
-        print("Error: Cannot specify both --dayhoff (-d) and --all (-a).")
-        raise typer.Exit(code=1)
-
-    # Determine lock command based on flags
+    # Determine action based on flags
     lock_cmd = ["uv", "lock"]
     action_description = ""
+    run_pyproject_update = False
 
-    if update_dayhoff:
-        lock_cmd.extend(["--upgrade-package", "dayhoff-tools"])
-        action_description = "Updating dayhoff-tools lock and pyproject.toml..."
-    elif update_all:
+    if update_all:
         lock_cmd.append("--upgrade")
         action_description = (
             "Updating lock file for all dependencies to latest versions..."
         )
+    else:  # Default behavior: update dayhoff-tools
+        lock_cmd.extend(["--upgrade-package", "dayhoff-tools"])
+        action_description = (
+            "Updating dayhoff-tools lock and pyproject.toml (default behavior)..."
+        )
+        run_pyproject_update = (
+            True  # Only update pyproject if we are doing the dayhoff update
+        )
 
     try:
         # Step 1: Run the update lock command
@@ -480,13 +458,12 @@ def update_dependencies(
         print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
         subprocess.run(lock_cmd, check=True, capture_output=True)
 
-        # Step 2: If specifically updating dayhoff-tools, update pyproject.toml
-        if update_dayhoff:
+        # Step 2: Update pyproject.toml only if doing the dayhoff update (default)
+        if run_pyproject_update:
             print(f"Reading {lock_file_path} to find new dayhoff-tools version...")
             if not lock_file_path.exists():
                 print(f"Error: {lock_file_path} not found after lock command.")
-                return  # Changed to return instead of exit
-
+                return
             locked_version = None
             try:
                 lock_data = toml.load(lock_file_path)
@@ -496,20 +473,18 @@ def update_dependencies(
                         break
             except toml.TomlDecodeError as e:
                 print(f"Error parsing {lock_file_path}: {e}")
-                return  # Changed to return
+                return
             except Exception as e:
                 print(f"Error reading lock file: {e}")
-                return  # Changed to return
+                return
 
             if not locked_version:
                 print(
                     f"Error: Could not find dayhoff-tools version in {lock_file_path}."
                 )
-                return  # Changed to return
+                return
 
             print(f"Found dayhoff-tools version {locked_version} in lock file.")
-
-            # Update pyproject.toml constraint
             print(f"Updating {pyproject_path} version constraint...")
             try:
                 content = pyproject_path.read_text()
@@ -523,7 +498,6 @@ def update_dependencies(
                 new_content, num_replacements = pattern.subn(
                     replacement_string, content
                 )
-
                 if num_replacements > 0:
                     pyproject_path.write_text(new_content)
                     print(
@@ -535,7 +509,7 @@ def update_dependencies(
                     )
             except FileNotFoundError:
                 print(f"Error: {pyproject_path} not found.")
-                return  # Changed to return
+                return
             except Exception as e:
                 print(f"Error updating {pyproject_path}: {e}")
                 print("Proceeding with sync despite pyproject.toml update error.")
@@ -548,12 +522,12 @@ def update_dependencies(
         subprocess.run(sync_cmd, check=True)
 
         # Final status message
-        if update_dayhoff:
+        if update_all:
+            print("All dependencies updated and environment synced successfully.")
+        else:  # Default case (dayhoff update)
             print(
                 "dayhoff-tools updated, pyproject.toml modified, and environment synced successfully."
             )
-        elif update_all:
-            print("All dependencies updated and environment synced successfully.")
 
     except subprocess.CalledProcessError as e:
         stderr_output = e.stderr.decode() if e.stderr else "No stderr output."

{dayhoff_tools-1.1.0.dist-info → dayhoff_tools-1.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.0
+Version: 1.1.2
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.1.0.dist-info → dayhoff_tools-1.1.2.dist-info}/RECORD

@@ -3,9 +3,9 @@ dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf
 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=KiYEuD3nSg8QPWBYfrhdze2La_CJe4iqK-8uOAHyS8U,35827
-dayhoff_tools/cli/main.py,sha256=O-kPX0Di3_W0yBd-jSzQrOKm4K3deV_-jQhOom6Ir5g,3875
+dayhoff_tools/cli/main.py,sha256=Ae0Bee2VjRzUge1I2DJoDVqoXpQnKfxGhdiMSmIWJwo,3788
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=cpxAVYeSnDJXKhxWJ75X8N1VP6qNLl0TrdYY6BBv1xw,21776
+dayhoff_tools/cli/utility_commands.py,sha256=fauEY2M9NyoW5XeU4wyEw8t5PZlSLx5b9kIRXJ4WGNg,20843
 dayhoff_tools/deployment/base.py,sha256=u-AjbtHnFLoLt33dhYXHIpV-6jcieMEHHGBGN_U9Hm0,15626
 dayhoff_tools/deployment/deploy_aws.py,sha256=O0gQxHioSU_sNU8T8MD4wSOPvWc--V8eRRZzlRu035I,16446
 dayhoff_tools/deployment/deploy_gcp.py,sha256=DxBM4sUzwPK9RWLP9bSfr38n1HHl-TVrp4TsbdN8pUA,5795
@@ -25,7 +25,7 @@ dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
 dayhoff_tools/structure.py,sha256=ufN3gAodQxhnt7psK1VTQeu9rKERmo_PhoxIbB4QKMw,27660
 dayhoff_tools/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJqE4,16456
 dayhoff_tools/warehouse.py,sha256=TqV8nex1AluNaL4JuXH5zuu9P7qmE89lSo6f_oViy6U,14965
-dayhoff_tools-1.1.0.dist-info/METADATA,sha256=a1k_yMC8QdtjTmj0cYhmCG_yAilCrG5WKlnm91Ljukg,2213
-dayhoff_tools-1.1.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.1.0.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.1.0.dist-info/RECORD,,
+dayhoff_tools-1.1.2.dist-info/METADATA,sha256=5tt1iO_M0YddPk-2Ne3b3f6rzYJIkuije8Ad6M4E3aI,2213
+dayhoff_tools-1.1.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.1.2.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.1.2.dist-info/RECORD,,