dayhoff-tools 1.11.2__py3-none-any.whl → 1.11.3__py3-none-any.whl

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.dist-info → dayhoff_tools-1.11.3.dist-info}/METADATA

@@ -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.dist-info → dayhoff_tools-1.11.3.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=YLNW1u68br4N4RK5TDVYLKlG2b-uMF-qwoW3CZ5bKZs,40929
+dayhoff_tools/cli/utility_commands.py,sha256=Yk2s09Dqkmv1CWJhhMV07Gy0-hZpQhkfiTSmOlykAa8,42185
 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-1.11.2.dist-info/METADATA,sha256=rVpxw6vSBegBs4W3-ukrjnLDX5np40EGzQwjrrPW-eo,2980
-dayhoff_tools-1.11.2.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-dayhoff_tools-1.11.2.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.11.2.dist-info/RECORD,,
+dayhoff_tools-1.11.3.dist-info/METADATA,sha256=tESeKSHZIZHMi5ekLoJRkRTyBTON40yJ0oegecixNnY,2980
+dayhoff_tools-1.11.3.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+dayhoff_tools-1.11.3.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.11.3.dist-info/RECORD,,