Fix minor path filter bug

Author: tovrstra

docs/changelog.md

@@ -10,6 +10,10 @@ and this project adheres to [Effort-based Versioning](https://jacobtomlinson.dev
 
 ## [Unreleased][]
 
+(no changes yet)
+
+## [3.0.5][] - 2025-08-25 {: #v3.0.5 }
+
 This is a minor bugfix release.
 
 ### Fixed
@@ -19,6 +23,8 @@ This is a minor bugfix release.
   When the `optional=True` option is used, the plan step must be mandatory,
   which was not the case.
   With this fix, StepUp can decide which optional run steps need to be executed.
+- Use StepUp's `getenv` to access the `STEPUP_PATH_FILTER` variable,
+  so steps relying on it are re-executed when the variable is updated.
 
 ## [3.0.4][] - 2025-06-25 {: #v3.0.4 }
 
@@ -601,6 +607,7 @@ This release fixes several bugs.
 Initial release
 
 [Unreleased]: https://github.com/reproducible-reporting/stepup-core
+[3.0.5]: https://github.com/reproducible-reporting/stepup-core/releases/tag/v3.0.5
 [3.0.4]: https://github.com/reproducible-reporting/stepup-core/releases/tag/v3.0.4
 [3.0.3]: https://github.com/reproducible-reporting/stepup-core/releases/tag/v3.0.3
 [3.0.2]: https://github.com/reproducible-reporting/stepup-core/releases/tag/v3.0.2

stepup/core/step.py

@@ -386,7 +386,13 @@ def get_rescheduled_info(self) -> str:
         return self.con.execute(sql, (self.i,)).fetchone()[0]
 
     def set_rescheduled_info(self, info: str):
-        self.con.execute("UPDATE step SET rescheduled_info = ? WHERE node = ?", (info, self.i))
+        self.con.execute(
+            "UPDATE step SET rescheduled_info = ? WHERE node = ? AND rescheduled_info = ''",
+            (info, self.i),
+        )
+
+    def clear_rescheduled_info(self):
+        self.con.execute("UPDATE step SET rescheduled_info = '' WHERE node = ?", (self.i,))
 
     def get_validate_amended(self) -> bool:
         sql = "SELECT validate_amended FROM step WHERE node = ?"
@@ -735,7 +741,7 @@ def queue_if_appropriate(self):
         # Queue the job.
         logger.info("Queue %s", job.name)
         self.set_state(StepState.QUEUED)
-        self.set_rescheduled_info("")
+        self.clear_rescheduled_info()
         self.set_validate_amended(False)
         self.workflow.job_queue.put_nowait(job)
         self.workflow.job_queue_changed.set()
@@ -765,7 +771,7 @@ def clean_before_run(self):
         - output files that are in state BUILT
         """
         # Clear rescheduled_info
-        self.set_rescheduled_info("")
+        self.clear_rescheduled_info()
 
         # Drop amended suppliers.
         rows = list(

stepup/core/utils.py

@@ -236,8 +236,12 @@ def filter_dependencies(paths: Collection[str]) -> set[Path]:
     filtered_paths
         A collection of paths relative to `${STEPUP_ROOT}` that were retained by the filter.
     """
+    # The getenv function from StepUp amends the current step to depend on the variable,
+    # to make sure that all steps using it get re-executed properly.
+    from stepup.core.api import getenv  # noqa: PLC0415
+
     # Parse the ${STEPUP_PATH_FILTER} environment variable.
-    filter_str = os.environ.get("STEPUP_PATH_FILTER", "-venv")
+    filter_str = getenv("STEPUP_PATH_FILTER", "-venv")
     filter_str += ":+.:-/"
     rules = []
     stepup_root = Path(os.getenv("STEPUP_ROOT", os.getcwd()))

stepup/core/workflow.py

@@ -1062,6 +1062,7 @@ def amend_step(
                 itertools.chain(["Missing inputs and/or required directories:"], sorted(missing))
             )
         )
+        print(missing)
         return len(missing) == 0, self._build_to_check(deferred)
 
     def _amend_dep(self, idep):

tests/examples/amend/expected_graph1.txt

@@ -23,6 +23,7 @@ file:plan.py
 
 step:runpy ./plan.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   root:
             consumes   file:./
@@ -39,6 +40,7 @@ file:inp1.txt
 
 step:runpy ./work.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   step:runpy ./plan.py
             consumes   file:./

tests/examples/amend/expected_graph2.txt

@@ -23,6 +23,7 @@ file:plan.py
 
 step:runpy ./plan.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   root:
             consumes   file:./
@@ -39,6 +40,7 @@ file:inp1.txt
 
 step:runpy ./work.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   step:runpy ./plan.py
             consumes   file:./

tests/examples/amend/expected_graph3.txt

@@ -23,6 +23,7 @@ file:plan.py
 
 step:runpy ./plan.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   root:
             consumes   file:./
@@ -39,6 +40,7 @@ file:inp1.txt
 
 step:runpy ./work.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   step:runpy ./plan.py
             consumes   file:./

tests/examples/amend/expected_graph4.txt

@@ -23,6 +23,7 @@ file:plan.py
 
 step:runpy ./plan.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   root:
             consumes   file:./
@@ -39,6 +40,7 @@ file:inp1.txt
 
 step:runpy ./work.py
                state = SUCCEEDED
+             env_var = STEPUP_PATH_FILTER [amended]
            explained = yes
           created by   step:runpy ./plan.py
             consumes   file:./

tests/examples/amend/expected_stdout2.txt

@@ -1,5 +1,6 @@
         0/0 |    STARTUP │ Making failed steps pending
         0/0 |    STARTUP │ Watching 1 director(y|ies) from initial database
+        0/0 |    STARTUP │ Making steps pending that use changed environment variables
         0/0 |    STARTUP │ Scanning initial database for changed files
         0/0 |    STARTUP │ Scanning initial database for new nglob matches
         0/0 |   DIRECTOR │ Launched worker 0

tests/examples/amend/expected_stdout3.txt

@@ -1,5 +1,6 @@
         0/0 |    STARTUP │ Making failed steps pending
         0/0 |    STARTUP │ Watching 1 director(y|ies) from initial database
+        0/0 |    STARTUP │ Making steps pending that use changed environment variables
         0/0 |    STARTUP │ Scanning initial database for changed files
         0/0 |    UPDATED │ inp2.txt (digest 55af8bcf ➜ 705a962e, size 6 ➜ 16)
         0/0 |    STARTUP │ Scanning initial database for new nglob matches