dayhoff-tools 1.11.2__tar.gz → 1.11.3__tar.gz

{dayhoff_tools-1.11.2 → dayhoff_tools-1.11.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.11.2
+Version: 1.11.3
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.11.2 → dayhoff_tools-1.11.3}/dayhoff_tools/cli/utility_commands.py

@@ -423,58 +423,79 @@ def sync_with_toml(
             with open("pyproject.workstation.toml", "r") as f:
                 content = f.read()
 
-            # Extract dependencies list
-            deps_match = re.search(r"dependencies\s*=\s*\[(.*?)\]", content, re.DOTALL)
-            if deps_match:
-                deps_text = deps_match.group(1)
-                deps = []
-                for line in deps_text.split("\n"):
-                    line = line.strip()
-                    if line.startswith('"') or line.startswith("'"):
-                        dep = re.sub(r'["\']', "", line)
-                        dep = re.sub(r",?\s*#.*$", "", dep)
-                        dep = dep.strip().rstrip(",")
-                        if dep:
-                            deps.append(dep)
-
-                if deps:
-                    pip_cmd = (
-                        [sys.executable, "-m", "pip", "install"]
-                        + deps
-                        + ["-c", "constraints.txt"]
-                    )
-                    print(
-                        f"Running command: {BLUE}{' '.join(pip_cmd[:5])} ... -c constraints.txt{RESET}"
-                    )
-                    subprocess.run(pip_cmd, check=True)
+            # Extract dependencies list using line-by-line parsing to handle [] in package names
+            lines = content.split("\n")
+            in_deps = False
+            deps_lines = []
+
+            for line in lines:
+                if re.match(r"\s*dependencies\s*=\s*\[", line):
+                    in_deps = True
+                    continue
+                if in_deps:
+                    if re.match(r"^\s*\]\s*$", line):
+                        break
+                    deps_lines.append(line)
+
+            deps = []
+            for line in deps_lines:
+                line = line.strip()
+                if line.startswith('"') or line.startswith("'"):
+                    dep = re.sub(r'["\']', "", line)
+                    dep = re.sub(r",?\s*#.*$", "", dep)
+                    dep = dep.strip().rstrip(",")
+                    if dep:
+                        deps.append(dep)
+
+            if deps:
+                pip_cmd = (
+                    [sys.executable, "-m", "pip", "install"]
+                    + deps
+                    + ["-c", "constraints.txt"]
+                )
+                print(
+                    f"Running command: {BLUE}{' '.join(pip_cmd[:5])} ... -c constraints.txt{RESET}"
+                )
+                subprocess.run(pip_cmd, check=True)
 
-            # Install dev dependencies
-            dev_match = re.search(
-                r"\[dependency-groups\]\s*dev\s*=\s*\[(.*?)\]", content, re.DOTALL
-            )
-            if dev_match:
-                dev_text = dev_match.group(1)
-                dev_deps = []
-                for line in dev_text.split("\n"):
-                    line = line.strip()
-                    if line.startswith('"') or line.startswith("'"):
-                        dep = re.sub(r'["\']', "", line)
-                        dep = re.sub(r",?\s*#.*$", "", dep)
-                        dep = dep.strip().rstrip(",")
-                        if dep:
-                            dev_deps.append(dep)
-
-                if dev_deps:
-                    print("Installing dev dependencies...")
-                    pip_cmd = (
-                        [sys.executable, "-m", "pip", "install"]
-                        + dev_deps
-                        + ["-c", "constraints.txt"]
-                    )
-                    print(
-                        f"Running command: {BLUE}{' '.join(pip_cmd[:5])} ... -c constraints.txt{RESET}"
-                    )
-                    subprocess.run(pip_cmd, check=True)
+            # Install dev dependencies using line-by-line parsing
+            in_dev_groups = False
+            in_dev_list = False
+            dev_lines = []
+
+            for line in lines:
+                if re.match(r"\s*\[dependency-groups\]", line):
+                    in_dev_groups = True
+                    continue
+                if in_dev_groups and re.match(r"\s*dev\s*=\s*\[", line):
+                    in_dev_list = True
+                    continue
+                if in_dev_list:
+                    if re.match(r"^\s*\]\s*$", line):
+                        break
+                    dev_lines.append(line)
+
+            dev_deps = []
+            for line in dev_lines:
+                line = line.strip()
+                if line.startswith('"') or line.startswith("'"):
+                    dep = re.sub(r'["\']', "", line)
+                    dep = re.sub(r",?\s*#.*$", "", dep)
+                    dep = dep.strip().rstrip(",")
+                    if dep:
+                        dev_deps.append(dep)
+
+            if dev_deps:
+                print("Installing dev dependencies...")
+                pip_cmd = (
+                    [sys.executable, "-m", "pip", "install"]
+                    + dev_deps
+                    + ["-c", "constraints.txt"]
+                )
+                print(
+                    f"Running command: {BLUE}{' '.join(pip_cmd[:5])} ... -c constraints.txt{RESET}"
+                )
+                subprocess.run(pip_cmd, check=True)
 
             # Install project if requested
             if install_project:
@@ -728,48 +749,62 @@ def add_dependency(
 
             if dev:
                 # Add to [dependency-groups] dev section
-                # Find the dev = [ ... ] block
-                dev_match = re.search(
-                    r"(\[dependency-groups\]\s*dev\s*=\s*\[)(.*?)(\])",
-                    content,
-                    re.DOTALL,
-                )
-                if not dev_match:
+                # Use line-by-line parsing to handle [] in dependency names like dayhoff-tools[full]
+                lines = content.split("\n")
+                in_dev_groups = False
+                in_dev_list = False
+                dev_start_idx = None
+                dev_end_idx = None
+
+                for idx, line in enumerate(lines):
+                    if re.match(r"\s*\[dependency-groups\]", line):
+                        in_dev_groups = True
+                        continue
+                    if in_dev_groups and re.match(r"\s*dev\s*=\s*\[", line):
+                        in_dev_list = True
+                        dev_start_idx = idx
+                        continue
+                    if in_dev_list and re.match(r"^\s*\]\s*$", line):
+                        dev_end_idx = idx
+                        break
+
+                if dev_start_idx is None or dev_end_idx is None:
                     print(
                         f"Warning: Could not find [dependency-groups] dev section in {manifest_file}"
                     )
                     continue
 
-                # Insert new dependency at the end of the list
-                before = dev_match.group(1)
-                deps_block = dev_match.group(2)
-                after = dev_match.group(3)
-
-                # Add with proper indentation
-                new_dep = f'    "{package}",\n'
-                new_content = content.replace(
-                    dev_match.group(0), f"{before}{deps_block}{new_dep}{after}"
-                )
+                # Insert new dependency before the closing ]
+                new_dep = f'    "{package}",'
+                lines.insert(dev_end_idx, new_dep)
+                new_content = "\n".join(lines)
             else:
                 # Add to [project] dependencies section
-                deps_match = re.search(
-                    r"(dependencies\s*=\s*\[)(.*?)(\])", content, re.DOTALL
-                )
-                if not deps_match:
+                # Use line-by-line parsing to handle [] in dependency names like dayhoff-tools[full]
+                lines = content.split("\n")
+                in_deps = False
+                deps_start_idx = None
+                deps_end_idx = None
+
+                for idx, line in enumerate(lines):
+                    if re.match(r"\s*dependencies\s*=\s*\[", line):
+                        in_deps = True
+                        deps_start_idx = idx
+                        continue
+                    if in_deps and re.match(r"^\s*\]\s*$", line):
+                        deps_end_idx = idx
+                        break
+
+                if deps_start_idx is None or deps_end_idx is None:
                     print(
                         f"Warning: Could not find dependencies section in {manifest_file}"
                     )
                     continue
 
-                before = deps_match.group(1)
-                deps_block = deps_match.group(2)
-                after = deps_match.group(3)
-
-                # Add with proper indentation
-                new_dep = f'    "{package}",\n'
-                new_content = content.replace(
-                    deps_match.group(0), f"{before}{deps_block}{new_dep}{after}"
-                )
+                # Insert new dependency before the closing ]
+                new_dep = f'    "{package}",'
+                lines.insert(deps_end_idx, new_dep)
+                new_content = "\n".join(lines)
 
             manifest_file.write_text(new_content)
             print(f"✅ Added '{package}' to {manifest_file}")

{dayhoff_tools-1.11.2 → dayhoff_tools-1.11.3}/pyproject.toml

@@ -1,5 +1,3 @@
-# This Mac-specific pyproject uses CPU-friendly pins and removes CUDA index mapping.
-
 # This block is needed because we package DHT for PyPi.
 [build-system]
 requires = ["poetry-core>=2.0"]
@@ -7,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.11.2"
+version = "1.11.3"
 description = "Common tools for all the repos at Dayhoff Labs"
 authors = [
     {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
@@ -51,9 +49,17 @@ embedders = [
     "transformers>=4.36.2",
 ]
 
-# Use CPU variants for dev dependencies on Mac
-[tool.uv]
-dev-dependencies = [
+[[tool.uv.index]]
+name = "torch-cuda"
+url = "https://download.pytorch.org/whl/cu121"
+explicit = true
+
+[tool.uv.sources]
+torch = { index = "torch-cuda" }
+torchvision = { index = "torch-cuda" }
+
+[dependency-groups]
+dev = [
     "black>=25.1.0,<26",
     "boto3>=1.36.8",
     "colorlog>=6.8.2,<7",
@@ -73,8 +79,8 @@ dev-dependencies = [
     "pytest>=8.0.2,<9",
     "pytest-cov>=4.1.0,<5",
     "pytest-mock>=3.12.0,<4",
-    "torch==2.4.*",
-    "torchvision==0.19.*",
+    "torch==2.4.0+cu121",
+    "torchvision==0.19.0+cu121",
 ]
 
 [project.scripts]