dayhoff-tools 1.0.22__py3-none-any.whl → 1.1.1__py3-none-any.whl

dayhoff_tools/cli/main.py

@@ -8,20 +8,28 @@ from dayhoff_tools.cli.utility_commands import (
     delete_local_branch,
     get_ancestry,
     import_from_warehouse_typer,
+    install_dependencies,
     rebuild_devcontainer_file,
     test_github_actions_locally,
-    update_dayhoff_tools,
-    sync_dependencies,
+    update_dependencies,
 )
 
 app = typer.Typer()
 
 # Utility commands
 app.command("clean")(delete_local_branch)
-app.command("deps")(sync_dependencies)
+
+# Dependency Management
+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)
+
+# Other Utilities
 app.command("gha")(test_github_actions_locally)
 app.command("rebuild")(rebuild_devcontainer_file)
-app.command("update")(update_dayhoff_tools)
 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

@@ -365,156 +365,197 @@ def build_and_upload_wheel(bump_part: str = "patch"):
                 )
 
 
-def update_dayhoff_tools():
-    """Update dayhoff-tools to latest, update pyproject.toml, and sync.
+# --- Dependency Management Commands ---
 
-    1. Runs `uv lock --upgrade-package dayhoff-tools`
-    2. Parses uv.lock to find the new version.
-    3. Updates the version constraint in pyproject.toml to `>=<new_version>`.
-    4. Runs `uv sync --no-install-project`.
+
+def install_dependencies(
+    install_project: bool = typer.Option(
+        False,
+        "--install-project",
+        "-p",
+        help="Install the local project package itself into the environment.",
+    ),
+):
+    """Install dependencies based on pyproject.toml.
+
+    Ensures uv.lock matches pyproject.toml and syncs the environment.
+    This is the command to run after changing pyproject.toml manually
+    or cloning/pulling a repository.
     """
     # ANSI color codes
     BLUE = "\033[94m"
     RESET = "\033[0m"
 
-    lock_file_path = Path("uv.lock")
-    pyproject_path = Path("pyproject.toml")
-
     try:
-        print("Updating dayhoff-tools lock...")
-
-        # Step 1: Update lock file for dayhoff-tools
-        lock_cmd = ["uv", "lock", "--upgrade-package", "dayhoff-tools"]
+        # Step 1: Ensure lock file matches pyproject.toml
+        print("Ensuring lock file matches pyproject.toml...")
+        lock_cmd = ["uv", "lock"]
         print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
-        subprocess.run(lock_cmd, check=True)
-
-        # Step 2: Parse uv.lock to find the new version
-        print(f"Reading {lock_file_path} to find new version...")
-        if not lock_file_path.exists():
-            print(f"Error: {lock_file_path} not found after lock command.")
-            return
-
-        locked_version = None
-        try:
-            lock_data = toml.load(lock_file_path)
-            # Find dayhoff-tools in the lock file packages
-            for package in lock_data.get("package", []):
-                if package.get("name") == "dayhoff-tools":
-                    locked_version = package.get("version")
-                    break
-        except toml.TomlDecodeError as e:
-            print(f"Error parsing {lock_file_path}: {e}")
-            return
-        except Exception as e:
-            print(f"Error reading lock file: {e}")
-            return
-
-        if not locked_version:
-            print(f"Error: Could not find dayhoff-tools version in {lock_file_path}.")
-            return
-
-        print(f"Found dayhoff-tools version {locked_version} in lock file.")
+        subprocess.run(lock_cmd, check=True, capture_output=True)
 
-        # Step 3: Update pyproject.toml
-        print(f"Updating {pyproject_path} version constraint...")
-        try:
-            content = pyproject_path.read_text()
-            # Regex: Find the line with "dayhoff-tools" dependency,
-            # capture leading space/quote (1), package name, optional specifier, closing quote/rest (2).
-            pattern = re.compile(
-                "^(\\s*['\\\"])dayhoff-tools(?:[><=~^][^'\\\"\\[,]*)?(['\\\"].*)$",
-                re.MULTILINE,
-            )
-            # Note: This pattern intentionally avoids matching extras like [full]
-            # because the specifier part `[^'\"\[,]` excludes '['.
-
-            package_name = "dayhoff-tools"
-            new_constraint_text = f">={locked_version}"
-
-            # Replace the matched line using captured groups:
-            # group 1 (leading space/quote) + package name + new constraint + group 2 (closing quote/rest)
-            replacement_string = f"\\g<1>{package_name}{new_constraint_text}\\g<2>"
-            new_content, num_replacements = pattern.subn(
-                replacement_string,
-                content,
-            )
-
-            if num_replacements > 0:
-                pyproject_path.write_text(new_content)
-                print(
-                    f"Updated dayhoff-tools constraint in {pyproject_path} to '{new_constraint_text}'"
-                )
-            else:
-                print(
-                    f"Warning: Could not find dayhoff-tools dependency line in {pyproject_path} to update constraint."
-                )
-
-        except FileNotFoundError:
-            print(f"Error: {pyproject_path} not found.")
-            return
-        except Exception as e:
-            print(f"Error updating {pyproject_path}: {e}")
-            # Continue to sync step even if pyproject update fails?
-            # For now, let's proceed to sync.
-            print("Proceeding with sync despite pyproject.toml update error.")
-
-        # Step 4: Sync environment based on updated lock file
-        print("Syncing environment...")
-        # Adding --all-groups to ensure dev dependencies are synced too
-        sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project"]
+        # Step 2: Sync environment
+        print("Syncing environment with lock file...")
+        sync_cmd = ["uv", "sync", "--all-groups"]
+        if not install_project:
+            sync_cmd.append("--no-install-project")
         print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
         subprocess.run(sync_cmd, check=True)
 
-        print(
-            "dayhoff-tools updated, pyproject.toml modified, and environment synced successfully."
-        )
+        print("Dependencies installed/synced successfully.")
 
     except subprocess.CalledProcessError as e:
-        print(f"Error occurred during update/sync process: {e}")
+        stderr_output = e.stderr.decode() if e.stderr else "No stderr output."
+        print(f"Error occurred during dependency installation/sync: {e}")
+        print(f"Stderr: {stderr_output}")
+        if "NoSolution" in stderr_output:
+            print(
+                "\nHint: Could not find a compatible set of dependencies. Check constraints in pyproject.toml."
+            )
+        sys.exit(1)
     except FileNotFoundError:
-        # This catches if uv command itself is not found
         print("Error: 'uv' command not found. Is uv installed and in PATH?")
         sys.exit(1)
     except Exception as e:
-        # Catch any other unexpected errors
         print(f"An unexpected error occurred: {e}")
+        sys.exit(1)
 
 
-def sync_dependencies(
-    install_project: bool = typer.Option(
+def update_dependencies(
+    update_all: bool = typer.Option(
         False,
-        "--install-project",
-        help="Install the local project package itself into the environment.",
-    )
+        "--all",
+        "-a",
+        help="Update all dependencies instead of just dayhoff-tools.",
+    ),
 ):
-    """Update uv.lock and sync dependencies based on pyproject.toml.
+    """Update dependencies to newer versions.
 
-    By default, installs all declared dependencies without building/installing
-    the local project itself (--no-install-project). Use --install-project to
-    include the local project.
+    Default Action (no flags): Updates only 'dayhoff-tools' package to latest,
+                               updates pyproject.toml, and syncs.
+
+    Flags:
+    --all/-a: Updates all dependencies to latest compatible versions (`uv lock --upgrade`)
+              and syncs the environment. Overrides the default.
     """
     # ANSI color codes
     BLUE = "\033[94m"
     RESET = "\033[0m"
 
+    lock_file_path = Path("uv.lock")
+    pyproject_path = Path("pyproject.toml")
+
+    # Determine action based on flags
+    lock_cmd = ["uv", "lock"]
+    action_description = ""
+    run_pyproject_update = False
+
+    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:
-        lock_cmd = ["uv", "lock"]
-        # Print command in blue
+        # Step 1: Run the update lock command
+        print(action_description)
         print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
-        subprocess.run(lock_cmd, check=True)
-
-        sync_cmd = ["uv", "sync", "--all-groups"]
-        if not install_project:
-            sync_cmd.append("--no-install-project")
+        subprocess.run(lock_cmd, check=True, capture_output=True)
+
+        # 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
+            locked_version = None
+            try:
+                lock_data = toml.load(lock_file_path)
+                for package in lock_data.get("package", []):
+                    if package.get("name") == "dayhoff-tools":
+                        locked_version = package.get("version")
+                        break
+            except toml.TomlDecodeError as e:
+                print(f"Error parsing {lock_file_path}: {e}")
+                return
+            except Exception as e:
+                print(f"Error reading lock file: {e}")
+                return
+
+            if not locked_version:
+                print(
+                    f"Error: Could not find dayhoff-tools version in {lock_file_path}."
+                )
+                return
 
-        # Print command in blue
+            print(f"Found dayhoff-tools version {locked_version} in lock file.")
+            print(f"Updating {pyproject_path} version constraint...")
+            try:
+                content = pyproject_path.read_text()
+                pattern = re.compile(
+                    "^(\s*['\"])dayhoff-tools(?:[><=~^][^'\"\\[,]*)?(['\"]\S*)$",
+                    re.MULTILINE,
+                )
+                package_name = "dayhoff-tools"
+                new_constraint_text = f">={locked_version}"
+                replacement_string = f"\g<1>{package_name}{new_constraint_text}\g<2>"
+                new_content, num_replacements = pattern.subn(
+                    replacement_string, content
+                )
+                if num_replacements > 0:
+                    pyproject_path.write_text(new_content)
+                    print(
+                        f"Updated dayhoff-tools constraint in {pyproject_path} to '{new_constraint_text}'"
+                    )
+                else:
+                    print(
+                        f"Warning: Could not find dayhoff-tools dependency line in {pyproject_path} to update constraint."
+                    )
+            except FileNotFoundError:
+                print(f"Error: {pyproject_path} not found.")
+                return
+            except Exception as e:
+                print(f"Error updating {pyproject_path}: {e}")
+                print("Proceeding with sync despite pyproject.toml update error.")
+
+        # Step 3: Sync environment
+        print("Syncing environment with updated lock file...")
+        # Always use --no-install-project for updates
+        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("Dependencies synced successfully.")
+        # Final status message
+        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."
+            )
+
     except subprocess.CalledProcessError as e:
-        print(f"Error occurred during dependency sync: {e}")
+        stderr_output = e.stderr.decode() if e.stderr else "No stderr output."
+        print(f"Error occurred during dependency update/sync: {e}")
+        print(f"Stderr: {stderr_output}")
+        if "NoSolution" in stderr_output:
+            print(
+                "\nHint: Could not find a compatible set of dependencies. Check constraints in pyproject.toml."
+            )
+        elif "unrecognized arguments: --upgrade" in stderr_output:
+            print(
+                "\nHint: Your version of 'uv' might be too old to support '--upgrade'. Try updating uv."
+            )
         sys.exit(1)
     except FileNotFoundError:
         print("Error: 'uv' command not found. Is uv installed and in PATH?")
         sys.exit(1)
+    except Exception as e:
+        print(f"An unexpected error occurred: {e}")
+        sys.exit(1)

{dayhoff_tools-1.0.22.dist-info → dayhoff_tools-1.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.0.22
+Version: 1.1.1
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.0.22.dist-info → dayhoff_tools-1.1.1.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=yorL117hknzhNybt7CTz4oKXVuQRIDXPl7huIEWga-M,3666
+dayhoff_tools/cli/main.py,sha256=O-kPX0Di3_W0yBd-jSzQrOKm4K3deV_-jQhOom6Ir5g,3875
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=GePENwZ6u1wjJlrAHZ_M7eaRyhD8ZraFgjpDFQqFgCk,19563
+dayhoff_tools/cli/utility_commands.py,sha256=KgF_shWIfzZyKVl9VKqhVm5WJwp0YCvYFadnN3fLZeU,21211
 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-1.0.22.dist-info/METADATA,sha256=tHgvSVGwT3cLDSDXulJVw5Tet95g3JzJMQLNFarIr0g,2214
-dayhoff_tools-1.0.22.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.0.22.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.0.22.dist-info/RECORD,,
+dayhoff_tools-1.1.1.dist-info/METADATA,sha256=UQv5qilixD2tR0TaF5UHN22BZKPqg7L2bd9my01EyqM,2213
+dayhoff_tools-1.1.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.1.1.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.1.1.dist-info/RECORD,,