snakemake/deployment/env_modules.py (1)

23-28: LGTM! Hash implementation is appropriate for change detection.

The hash property implementation is clean and efficient, providing a deterministic way to detect changes in environment modules. While MD5 is not cryptographically secure, it's perfectly suitable here as we're using it for change detection rather than security purposes.

The hash computation contributes to the broader software stack tracking system, enabling Snakemake to detect when environment module changes should trigger reruns.

snakemake/persistence.py (1)

515-515: Address the TODO: Move code for retrieval into plugin interface.

There's a TODO comment indicating that the code for retrieval should be moved into the software deployment plugin interface once available.

Would you like assistance in implementing this, or should we open a GitHub issue to track this task?

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snakemake/deployment/conda.py (2)

222-226: LGTM! Consider adding docstring for clarity.

The refactoring of hash computation logic is well-structured. The hash property now correctly differentiates between containerized and non-containerized environments.

Consider adding a docstring to explain the significance of including location in the hash computation, e.g.:

@property
def hash(self):
    """Compute a unique hash for the environment.
    
    For non-containerized environments, this includes the environment location
    to handle cases where conda binaries contain hardcoded absolute RPATHs.
    """

---

237-260: LGTM! Consider adding return type hint.

The _get_hash method effectively consolidates the hash computation logic with clear parameter names and comprehensive comments.

Consider adding a return type hint to improve code maintainability:

-    def _get_hash(self, include_location: bool, include_container_img: bool) -> str:
+    def _get_hash(self, include_location: bool, include_container_img: bool) -> str:
         """Compute a hash for the environment.
         
         Args:
             include_location: Whether to include the environment location in the hash.
             include_container_img: Whether to include the container image in the hash.
         
         Returns:
             str: MD5 hash of the environment configuration.
         """

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snakemake/deployment/conda.py (2)

237-260: Consider adding docstring to document hash computation logic.

The _get_hash method contains complex logic for computing environment hashes. A docstring would help future maintainers understand:

• The purpose of the include_location and include_container_img parameters
• Why absolute paths are included in the hash
• The significance of including pin file content

 def _get_hash(self, include_location: bool, include_container_img: bool) -> str:
+    """Compute a hash for the conda environment.
+    
+    Args:
+        include_location: If True, includes the absolute path of the environment
+            directory in the hash. This is necessary because conda binaries can
+            contain hardcoded absolute RPATHs.
+        include_container_img: If True, includes the container image URL in the
+            hash.
+            
+    Returns:
+        str: MD5 hash of the environment definition
+    """
     if self.is_externally_managed:
         md5hash = hashlib.md5()

---

Include error output in pin file installation failure message

The codebase consistently includes error output in error messages across various error handling blocks. The pin file installation error is an exception where the error output is not shown. Let's align it with the codebase's error handling pattern by including the error output in the warning message.

logger.warning(
-    f"Failed to install conda environment from pin file ({self.pin_file.get_path_or_uri()}). "
-    f"Trying regular environment definition file.{advice}"
+    f"Failed to install conda environment from pin file ({self.pin_file.get_path_or_uri()}): "
+    f"{e.output}\nTrying regular environment definition file.{advice}"
)

🔗 Analysis chain

Line range hint 500-700: Verify error handling in pin file installation.

The error message when pin file installation fails could be more informative. Consider including the actual error output from conda in the warning message to help users diagnose the issue.

             except subprocess.CalledProcessError as e:
                 # remove potential partially installed environment
                 shutil.rmtree(env_path, ignore_errors=True)
                 advice = ""
                 if isinstance(self.file, LocalSourceFile):
                     advice = (
                         " If that works, make sure to update the pin file with "
                         f"'snakedeploy pin-conda-env {self.file.get_path_or_uri()}'."
                     )
                 logger.warning(
-                    f"Failed to install conda environment from pin file ({self.pin_file.get_path_or_uri()}). "
-                    f"Trying regular environment definition file.{advice}"
+                    f"Failed to install conda environment from pin file ({self.pin_file.get_path_or_uri()}): "
+                    f"{e.output}\nTrying regular environment definition file.{advice}"
                 )

Let's verify the error handling:

---

Let me verify if there are any other error handling patterns in the codebase that we should align with:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for other instances of pin file error handling
# to ensure consistent error reporting.

rg -A 5 "Failed to install conda environment from pin file"

Length of output: 647

---

Script:

#!/bin/bash
# Check for similar error handling patterns in conda.py
rg -A 5 "CalledProcessError as e" snakemake/deployment/conda.py

# Check for other error messages in conda.py that include error output
rg "\.output" snakemake/deployment/conda.py

Length of output: 2900

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snakemake/persistence.py (1)

514-524: Consider adding error handling for hash computation.

The hash computation logic is comprehensive, covering conda environments, container images, and environment modules. However, it could benefit from error handling for cases where hash computation fails.

Consider wrapping the hash computation in a try-except block:

 def _software_stack_hash(self, job):
     md5hash = hashlib.md5()
-    if job.conda_env:
-        md5hash.update(job.conda_env.hash.encode())
-    if job.container_img_url:
-        md5hash.update(job.container_img_url.encode())
-    if job.env_modules:
-        md5hash.update(job.env_modules.hash.encode())
-    return md5hash.hexdigest()
+    try:
+        if job.conda_env:
+            md5hash.update(job.conda_env.hash.encode())
+        if job.container_img_url:
+            md5hash.update(job.container_img_url.encode())
+        if job.env_modules:
+            md5hash.update(job.env_modules.hash.encode())
+        return md5hash.hexdigest()
+    except Exception as e:
+        logger.warning(f"Failed to compute software stack hash: {e}")
+        return None

snakemake/deployment/conda.py (2)

224-260: LGTM! Well-structured hash computation logic.

The new _get_hash method nicely consolidates the hash computation logic with clear control over what components to include. The implementation properly handles all environment types and consistently encodes all components.

Consider extracting the hash components into a separate method for better readability:

 def _get_hash(self, include_location: bool, include_container_img: bool) -> str:
     md5hash = hashlib.md5()
+    self._add_location_hash(md5hash, include_location)
+    self._add_container_hash(md5hash, include_container_img)
+    self._add_content_hashes(md5hash)
+    return md5hash.hexdigest()
+
+def _add_location_hash(self, md5hash, include_location: bool):
     if self.name:
         md5hash.update(self.name.encode())
     elif self.dir:
         md5hash.update(self.dir.encode())
     else:
         if include_location:
             env_dir = os.path.realpath(self._envs_dir)
             md5hash.update(env_dir.encode())
+
+def _add_container_hash(self, md5hash, include_container_img: bool):
     if include_container_img and self._container_img:
         md5hash.update(self._container_img.url.encode())
+
+def _add_content_hashes(self, md5hash):
     content_deploy = self.content_deploy
     if content_deploy:
         md5hash.update(content_deploy)
     content_pin = self.content_pin
     if content_pin:
         md5hash.update(content_pin)
     md5hash.update(self.content)
-    return md5hash.hexdigest()

---

Line range hint 516-524: Improve error handling for pin file creation.

The pin file creation could fail silently if the temporary file cannot be written. Consider wrapping it in a try-except block to provide better error handling and cleanup.

Here's a suggested improvement:

             if self.pin_file and not dryrun:
-                with tempfile.NamedTemporaryFile(delete=False, suffix="pin.txt") as tmp:
-                    tmp.write(self.content_pin)
-                    pin_file = tmp.name
-                    tmp_pin_file = tmp.name
+                try:
+                    with tempfile.NamedTemporaryFile(delete=False, suffix="pin.txt") as tmp:
+                        tmp.write(self.content_pin)
+                        pin_file = tmp.name
+                        tmp_pin_file = tmp.name
+                except (IOError, OSError) as e:
+                    logger.warning(f"Failed to create temporary pin file: {e}")
+                    if tmp_pin_file and os.path.exists(tmp_pin_file):
+                        os.unlink(tmp_pin_file)
+                    pin_file = None
+                    tmp_pin_file = None

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