Files that changed from the base of the PR and between 387b6df and 8d14d8f.

• setup.cfg (2 hunks)
• snakemake/report/html_reporter/data/packages.py (3 hunks)
• snakemake/report/html_reporter/template/index.html.jinja2 (2 hunks)

snakemake/report/html_reporter/data/packages.py (2)

18-56: LGTM! The get_packages function changes align with offline access goals.

The use of local paths for licenses and sources supports the offline functionality objective of the PR.

---

76-93: LGTM! The Package class constructor changes enhance maintainability.

The use of local paths and a helper function for reading files aligns with the PR objectives and improves code maintainability.

Tools

Ruff

76-76: Missing return type annotation for special method __init__

Add return type annotation: None

(ANN204)

---

77-77: Missing type annotation for self in method

(ANN101)

---

77-77: Missing type annotation for function argument version

(ANN001)

---

77-77: Missing type annotation for function argument license_path

(ANN001)

---

77-77: Missing type annotation for function argument source_path

(ANN001)

---

77-77: Missing type annotation for **source_paths

(ANN003)

---

77-77: Trailing comma missing

Add trailing comma

(COM812)

---

79-79: Missing return type annotation for private function read_source

(ANN202)

snakemake/report/html_reporter/template/index.html.jinja2 (2)

12-12: Streamlined resource inclusion for tailwindcss.

The change to directly use packages["tailwindcss"].source simplifies resource inclusion and aligns with the PR objectives.

---

34-39: Streamlined resource inclusion for JavaScript libraries.

The direct access to sources for React, Prop-Types, Vega, Vega-Lite, and Vega-Embed simplifies the template and aligns with the PR objectives.

setup.cfg (2)

66-66: Addition of setup_requires for setuptools-download.

The inclusion of setuptools-download enhances dependency management by ensuring necessary tools are available during setup.

---

68-117: Addition of [setuptools_download] section for asset management.

The structured list of download_data_files ensures that necessary assets are fetched and verified during setup, aligning with the PR objectives.

Files that changed from the base of the PR and between 8d14d8f and 57d06db.

• .gitignore (1 hunks)
• setup.cfg (2 hunks)
• setup.py (1 hunks)
• snakemake/assets/init.py (1 hunks)
• snakemake/report/html_reporter/data/packages.py (3 hunks)

• .gitignore

setup.py (3)

12-12: LGTM!

The import statement for the Assets class is correct and necessary.

---

14-15: LGTM!

The Assets.deploy() method invocation is correct and ensures that assets are downloaded during the setup process.

---

21-21: LGTM!

The package_data parameter update is correct and ensures that all files within the assets/data directory are included in the package.

setup.cfg (2)

32-32: LGTM!

The change to the include_package_data option is correct and ensures that package data is included in the distribution.

---

53-53: LGTM!

The formatting adjustment in the install_requires section is minor but contributes to a cleaner configuration file.

snakemake/report/html_reporter/data/packages.py (8)

6-6: LGTM!

The import statement for the Assets class is correct and necessary.

---

7-7: LGTM!

The addition of the blank line improves readability by separating the import statements from the function definitions.

---

23-23: LGTM!

The addition of the license_path parameter to the Package instances is correct and ensures that the license information is sourced from local files.

Also applies to: 27-27, 30-30, 34-34, 40-40, 44-44, 48-48, 51-51, 55-55

---

31-31: LGTM!

The addition of the source_path parameter to the Package instances is correct and ensures that the source information is sourced from local files.

Also applies to: 39-39, 43-43, 47-47, 54-54

---

75-77: LGTM!

The update to the __init__ method is correct and ensures that the package information is sourced from local assets.

---

80-80: LGTM!

The assignment of the license attribute using the Assets.get_content method is correct and ensures that the license content is retrieved from local assets.

---

81-82: LGTM!

The conditional assignment of the source attribute using the Assets.get_content method is correct and ensures that the source content is retrieved from local assets if the source_path parameter is provided.

---

84-86: LGTM!

The assignment of the sources attribute using a dictionary comprehension with the Assets.get_content method is correct and ensures that the source contents are retrieved from local assets for each item in the source_paths dictionary.

Files that changed from the base of the PR and between 57d06db and 37e3a06.

• snakemake/assets/init.py (1 hunks)

• snakemake/assets/init.py

Files that changed from the base of the PR and between 37e3a06 and dbff081.

• setup.py (1 hunks)
• snakemake/init.py (1 hunks)
• snakemake/assets/init.py (1 hunks)
• snakemake/common/init.py (2 hunks)

• setup.py

snakemake/__init__.py (2)

8-11: Refactor: Improved version management using get_versions.

The dynamic fetching of the version using get_versions() from snakemake._version is a good practice as it centralizes version management. Deleting the get_versions function after its use helps clean up the namespace, preventing potential conflicts or misuse in the larger codebase.

The changes are well-integrated and improve maintainability.

---

13-13: Consistency Check: PIP_DEPLOYMENTS_PATH remains unchanged.

It's noted that PIP_DEPLOYMENTS_PATH remains unchanged. Ensure this consistency is intentional and well-documented, especially if there are related changes elsewhere in the system that might affect how deployment paths are handled.

Verification successful

---

Consistency of PIP_DEPLOYMENTS_PATH is maintained.

The PIP_DEPLOYMENTS_PATH is consistently used in the codebase to modify the system path and as a target directory for pip installations. This confirms that its usage is intentional and aligns with its purpose as a deployment path. No further action is required.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for references to `PIP_DEPLOYMENTS_PATH` to ensure consistency across the project.

# Test: Search for references to `PIP_DEPLOYMENTS_PATH`. Expect: Consistent usage across the project.
rg --type python 'PIP_DEPLOYMENTS_PATH'

Length of output: 70

---

Script:

#!/bin/bash
# Description: Check for references to `PIP_DEPLOYMENTS_PATH` to ensure consistency across the project.

# Test: Search for references to `PIP_DEPLOYMENTS_PATH`. Expect: Consistent usage across the project.
rg 'PIP_DEPLOYMENTS_PATH'

Length of output: 270

snakemake/assets/__init__.py (2)

15-25: Enhancement: Robust asset fetching with error handling.

The implementation of error handling in the get_content method for assets is robust, using requests.get with proper exception handling and checksum verification. This ensures that asset fetching is reliable and secure, which is crucial for the offline capabilities of the system.

The changes are well-implemented and enhance the system's robustness.

Tools

Ruff

22-22: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

---

97-115: Methodology: Asset deployment and retrieval.

The deploy and get_content class methods in the Assets class handle the deployment and retrieval of assets effectively. The use of Path for file operations and the structured handling of file not found exceptions are good practices that enhance the code's readability and maintainability.

The asset management system is correctly implemented and integrates well with the overall system architecture.

snakemake/common/__init__.py (1)

20-20: Refinement: Simplified version retrieval.

Directly importing __version__ from snakemake simplifies the version management process by eliminating unnecessary function calls, which can reduce overhead and potential errors.

The simplification is a positive change that enhances code clarity and performance.

Files that changed from the base of the PR and between dbff081 and 171128d.

• snakemake/assets/init.py (1 hunks)
• snakemake/report/html_reporter/data/packages.py (3 hunks)

snakemake/report/html_reporter/data/packages.py (2)

18-56: LGTM!

The function is correctly implemented and aligns with the objective of improving offline capabilities.

The code changes are approved.

---

Line range hint 58-66: LGTM!

The class is correctly implemented.

The code changes are approved.

snakemake/assets/__init__.py (4)

1-7: LGTM!

All imports are used in the code.

The code changes are approved.

---

10-11: LGTM!

The class is correctly implemented.

The code changes are approved.

---

35-122: Add error handling for requests.get call.

The requests.get call should handle potential exceptions to ensure robustness.

 def get_content(cls, asset_path: str) -> str:
     try:
-        return (cls.base_path / asset_path).read_text()
+        return (cls.base_path / Path(asset_path)).read_text()
     except FileNotFoundError:
         logger.warning(
             f"Asset {asset_path} not found (development setup?), downloading..."
         )
-        return cls.spec[asset_path].get_content().decode()
+        try:
+            response = requests.get(cls.spec[asset_path].url)
+            response.raise_for_status()
+            content = response.content
+        except requests.RequestException as e:
+            raise ValueError(f"Failed to download asset {cls.spec[asset_path].url}: {e}")
+        if cls.spec[asset_path].sha256 != hashlib.sha256(content).hexdigest():
+            raise ValueError(f"Checksum mismatch when downloading asset {cls.spec[asset_path].url}")
+        return content.decode()

Likely invalid or redundant comment.

---

14-32: Add error handling for urllib.request.urlopen call.

The urllib.request.urlopen call should handle potential exceptions to ensure robustness.

 def get_content(self) -> bytes:
     """Get and validate asset content."""
-    req = urllib.request.Request(self.url, headers={"User-Agent": "snakemake"})
-    try:
-        resp = urllib.request.urlopen(req)
-        content = resp.read()
-    except urllib.error.URLError as e:
-        raise AssetDownloadError(f"Failed to download asset {self.url}: {e}")
-    if self.sha256 != hashlib.sha256(content).hexdigest():
-        raise AssetDownloadError(
-            f"Checksum mismatch when downloading asset {self.url}"
-        )
-    return content
+    req = urllib.request.Request(self.url, headers={"User-Agent": "snakemake"})
+    try:
+        resp = urllib.request.urlopen(req)
+        resp.raise_for_status()
+        content = resp.read()
+    except urllib.error.URLError as e:
+        raise AssetDownloadError(f"Failed to download asset {self.url}: {e}") from e
+    if self.sha256 != hashlib.sha256(content).hexdigest():
+        raise AssetDownloadError(
+            f"Checksum mismatch when downloading asset {self.url}"
+        )
+    return content

Likely invalid or redundant comment.

Tools

Ruff

27-27: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

Files that changed from the base of the PR and between 171128d and 34f1a5f.

• setup.py (1 hunks)
• snakemake/assets/init.py (1 hunks)
• snakemake/report/html_reporter/data/packages.py (3 hunks)

• setup.py

snakemake/report/html_reporter/data/packages.py (2)

74-89: LGTM! But verify the class usage in the codebase.

The class is correctly implemented. However, ensure that all instances of the Package class are updated to reflect the new constructor parameters.

The code changes are approved.

Run the following script to verify the class usage:

Verification successful

---

Class usage is correctly updated.

The Package class constructor changes are correctly reflected in the codebase, with the updated parameters used in snakemake/report/html_reporter/data/packages.py. No other instances require modification.

• snakemake/report/html_reporter/data/packages.py: Correct usage of the updated constructor parameters.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify all instances of the `Package` class are updated to reflect the new constructor parameters.

# Test: Search for the class usage. Expect: Only occurrences of the new implementation.
rg --type python -A 5 $'Package'

Length of output: 62

---

Script:

#!/bin/bash
# Description: Verify all instances of the `Package` class are updated to reflect the new constructor parameters.

# Test: Search for the class usage. Expect: Only occurrences of the new implementation.
rg -A 5 'Package'

Length of output: 9807

Tools

Ruff

89-89: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

---

Line range hint 4-54: LGTM! But verify the function usage in the codebase.

The function is correctly implemented. However, ensure that all function calls to get_packages are updated to reflect the new local paths for licenses and source files.

The code changes are approved.

Run the following script to verify the function usage:

Files that changed from the base of the PR and between 34f1a5f and 470d3a3.

• snakemake/assets/init.py (1 hunks)

snakemake/assets/__init__.py (3)

10-11: LGTM!

The custom exception class AssetDownloadError is correctly implemented.

The code changes are approved.

---

105-113: LGTM!

The deploy method is correctly implemented.

The code changes are approved.

---

128-132: LGTM!

The base_path method is correctly implemented.

The code changes are approved.