Reviewing files that changed from the base of the PR and between 7b45be3 and 130b411.

• src/snakemake/logging.py (5 hunks)

src/snakemake/logging.py (5)

246-246: Excellent simplification of shell command formatting.

The removal of conditional logic from format_shellcmd aligns perfectly with the architectural improvement of moving shell command filtering to the DefaultFilter class. This ensures cleaner separation of concerns.

---

369-369: Good architectural improvement by adding shell command control to the filter.

Adding the printshellcmds parameter to DefaultFilter is the correct approach for controlling shell command visibility at the filtering stage rather than in formatting.

Also applies to: 375-375

---

399-402: Excellent implementation of shell command filtering logic.

This is the core fix that addresses the blank line issue. By filtering out shell command events when printshellcmds is False, the formatter never receives empty messages to format, eliminating the blank lines.

The logic is clear and follows the filtering pattern used elsewhere in the class.

---

618-622: Proper integration of shell command filtering in logger setup.

The addition of self.settings.printshellcmds to the DefaultFilter constructor completes the refactoring by ensuring the filter receives the necessary configuration. This maintains the existing API while enabling the new filtering behavior.

---

393-393:

Details

❓ Verification inconclusive

Verify that changing shell command quietness level aligns with user expectations.

Changing LogEvent.SHELLCMD from Quietness.PROGRESS to Quietness.RULES means shell commands will now be suppressed when using --quiet rules instead of --quiet progress. This addresses the blank line issue mentioned in the PR objectives.

However, this is a behavioral change that might affect existing user workflows.

Please verify that this change aligns with user expectations by checking existing documentation or usage patterns:

---

🏁 Script executed:

#!/bin/bash
# Description: Check for documentation or examples that mention shell command quietness behavior

# Search for documentation about shell command logging and quietness levels
rg -A 3 -B 3 "shell.*command.*quiet|quiet.*shell.*command" --type md --type rst --type txt

# Search for test cases that might verify shell command quietness behavior
rg -A 5 -B 5 "SHELLCMD.*quiet|quiet.*SHELLCMD" --type py

# Search for any mentions of the old PROGRESS mapping for shell commands
rg -A 3 -B 3 "SHELLCMD.*PROGRESS|PROGRESS.*SHELLCMD" --type py

Length of output: 216

---

🏁 Script executed:

#!/bin/bash
# Inspect Quietness enum definition
rg -n "class Quietness" -A 10 -B 0 src/snakemake/logging.py

# Inspect CLI parser references to --quiet flag
rg -n "\-\-quiet" -A 5 -B 5 src/snakemake

# Inspect use of PROGRESS and RULES in logging.py
rg -n "PROGRESS" -A 5 -B 5 src/snakemake/logging.py
rg -n "RULES" -A 5 -B 5 src/snakemake/logging.py

Length of output: 8120

---

Confirm shell-command quietness mapping
We changed LogEvent.SHELLCMD from Quietness.PROGRESS to Quietness.RULES (src/snakemake/logging.py:393), so shell commands will now be suppressed by --quiet rules instead of --quiet progress.

• No user documentation or examples mention shell-command quietness behavior.
• No existing unit tests cover how --quiet progress vs. --quiet rules affects shell-command output.

Please verify that this new mapping matches intended workflows, update any user-facing docs or CLI help accordingly, and add a unit test to cover shell-command suppression under both --quiet progress and --quiet rules.

Reviewing files that changed from the base of the PR and between 130b411 and 077f989.

• src/snakemake/dag.py (2 hunks)
• src/snakemake/logging.py (5 hunks)
• src/snakemake/scheduler.py (2 hunks)

src/snakemake/dag.py (1)

33-33: LGTM!

The import of Quietness enum is necessary for the conditional logging logic implemented in the handle_temp method.

🧰 Tools

🪛 Pylint (3.3.7)

[convention] 33-33: Imports from package snakemake are not grouped

(C0412)

src/snakemake/scheduler.py (1)

73-73: LGTM: Improved granular quietness control for progress printing

This change enhances the quietness handling by allowing progress printing when the specific Quietness.PROGRESS flag is not set, even if other quietness flags are present. This provides more fine-grained control over what gets suppressed and aligns well with the broader logging improvements in this PR.

🧰 Tools

🪛 Pylint (3.3.7)

[convention] 73-73: Line too long (106/100)

(C0301)

src/snakemake/logging.py (5)

246-246: LGTM: Simplified shell command formatting

The shell command formatter now unconditionally returns the message, which is correct since the filtering logic has been moved to the DefaultFilter class. This separation of concerns makes the code cleaner and more maintainable.

---

369-369: LGTM: Enhanced filter constructor for shell command control

The addition of the printshellcmds parameter to the DefaultFilter constructor enables proper filtering of shell command messages based on the CLI flag. This is a much cleaner approach than the previous method of setting messages to empty strings.

Also applies to: 375-375

---

393-393: LGTM: Corrected quietness mapping for shell commands

Moving LogEvent.SHELLCMD from Quietness.PROGRESS to Quietness.RULES aligns shell command log events with the rules quietness level. This addresses the root cause of blank lines appearing when running snakemake --quiet rules, as mentioned in the PR discussion.

---

399-401: LGTM: Proper shell command filtering implementation

This filtering logic correctly implements the approach discussed in the PR comments. Shell command messages are now filtered out when printshellcmds is False, preventing empty messages from reaching the emit method and causing blank lines.

---

618-621: LGTM: Consistent parameter passing to filter

The LoggerManager correctly passes the printshellcmds setting to the DefaultFilter constructor, enabling the new filtering logic. This completes the implementation of the shell command filtering approach discussed in the PR.

Reviewing files that changed from the base of the PR and between 077f989 and c9327dc.

• src/snakemake/dag.py (2 hunks)
• src/snakemake/logging.py (5 hunks)
• src/snakemake/scheduler.py (2 hunks)

• src/snakemake/scheduler.py

src/snakemake/logging.py (5)

244-246: LGTM! Proper separation of concerns.

The simplification of format_shellcmd to unconditionally return the message is correct. Moving the conditional logic to the filtering stage improves the architecture by keeping formatters focused on formatting and filters focused on filtering decisions.

---

369-375: LGTM! Necessary infrastructure for shell command filtering.

The addition of the printshellcmds parameter to the DefaultFilter constructor and its storage as an instance attribute properly supports the new filtering logic for shell commands.

---

393-393: LGTM! Improved quietness level alignment.

Mapping LogEvent.SHELLCMD to Quietness.RULES instead of Quietness.PROGRESS properly aligns shell command logging with rule-related quietness control. This change ensures that --quiet rules will suppress shell commands as expected.

Note: This may change behavior for users who previously used --quiet progress to suppress shell commands.

---

399-401: LGTM! Correct implementation of shell command filtering.

The new filtering logic properly filters out shell command log events when printshellcmds is False. This addresses the core issue of blank lines appearing in quiet mode by preventing shell command messages from reaching the formatter when they shouldn't be displayed.

---

618-621: LGTM! Proper wiring of printshellcmds setting.

The addition of self.settings.printshellcmds to the DefaultFilter constructor call correctly connects the settings to the filtering logic, enabling the new shell command filtering behavior.

Reviewing files that changed from the base of the PR and between c9327dc and d62dd50.

• src/snakemake/dag.py (2 hunks)
• src/snakemake/logging.py (5 hunks)

• src/snakemake/dag.py

src/snakemake/logging.py (5)

246-246: LGTM! Shell command formatting now unconditional.

This change aligns with the PR objective to move shell command filtering from the formatting stage to the filtering stage. The formatter now always returns the message, allowing the filter to handle visibility logic.

---

369-375: LGTM! Filter now handles printshellcmds parameter.

Good refactor moving the printshellcmds logic from the formatter to the filter. This allows proper filtering of shell command messages instead of setting them to empty strings, which was causing the blank lines issue.

---

397-397: LGTM! Correct quietness level mapping for shell commands.

This change fixes the root cause identified in the PR comments. Mapping SHELLCMD to Quietness.RULES instead of Quietness.PROGRESS ensures shell command messages are properly filtered when using --quiet rules.

---

403-406: LGTM! Proper shell command filtering based on printshellcmds flag.

This is the key fix that prevents blank lines. Instead of setting shell command messages to empty strings in the formatter, they are now properly filtered out when printshellcmds is False.

---

622-626: LGTM! LoggerManager now passes printshellcmds to filter.

Correct update to pass the printshellcmds parameter to the DefaultFilter constructor, completing the refactor that moves shell command filtering logic from formatter to filter.