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Merged
seamm merged 3 commits into from
Oct 3, 2026
Merged

Loops over tables in the job's database #38

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6ba6156
Loop over table rows with seamm.Table; commit after each body step
paulsaxe Oct 3, 2026
8327ae6
Use seamm.step_completed after each body step
paulsaxe Oct 3, 2026
4fdb799
Release 2026.10.3: pin seamm>=2026.10.3; HISTORY; CI on uv (no test_e…
paulsaxe Oct 3, 2026
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7 changes: 7 additions & 0 deletions HISTORY.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,13 @@
=======
History
=======
2026.10.3 -- Loops over tables in the job's database
* Loops over the rows of a table work with tables kept in the job's database (seamm
2026.10.3); the job's database is committed after each step of the loop body.
* Bugfix: selecting rows with a test on a numeric column failed when the second
value was empty, although only "between" uses it.
* Rows can be selected on the table's index column too.
* The values of ``_row`` and of the row variables are plain Python values.
2026.9.18 -- Standard structure selection for loops over systems
* The "For systems in the database" loop now uses SEAMM's standard structure
selection: the systems to loop over (all, the current one, or those whose name
Expand Down
36 changes: 0 additions & 36 deletions devtools/conda-envs/test_env.yaml
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105 changes: 32 additions & 73 deletions loop_step/loop.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,6 @@ def __init__(self, flowchart=None, extension=None):
"""
logger.debug("Creating Loop {}".format(self))

self.table_handle = None
self.table = None
self._loop_count = None
self._loop_value = None
Expand Down Expand Up @@ -317,17 +316,16 @@ def run(self):
self.set_variable("_loop_indices", (None,))
elif P["type"] == "For rows in table":
if self._loop_value is None:
self.table_handle = self.get_variable(P["table"])
self.table = self.table_handle["table"]
self.table_handle["loop index"] = True
self.table = self.get_table(P["table"], create=False)
self.table["loop index"] = True

self.logger.info(
"Initialize loop over {} rows in table {}".format(
self.table.shape[0], P["table"]
self.table.n_rows, P["table"]
)
)
self._loop_value = 0
self._loop_length = self.table.shape[0]
self._loop_length = self.table.n_rows
if self.variable_exists("_loop_indices"):
tmp = self.get_variable("_loop_indices")
self.set_variable(
Expand All @@ -341,77 +339,33 @@ def run(self):
self.set_variable("_loop_indices", (None,))
where = P["where"]
if where == "Use all rows":
table_indices = [*self.table.index]
n_table_indices = len(table_indices)
table_rows = [row for row, _ in self.table.rows()]
elif where == "Select rows where column":
tmp_col = P["query-column"].lower()
column = None
op = P["query-op"]

for col in self.table:
if col.lower() == tmp_col:
column = col
if column is None:
if op not in seamm.table.operators:
raise NotImplementedError(f"Loop query '{op}' not implemented")
try:
selection = (
P["query-column"],
op,
P["query-value"],
P["query-value2"],
)
table_rows = [
row for row, _ in self.table.rows(where=selection)
]
except ValueError as e:
if "has no column" not in str(e):
raise
column = P["query-column"]
raise ValueError(
f"Looping over table with criterion on column '{column}': "
"that column does not exist."
)

dtype = self.table.dtypes[column]
value = dtype.type(P["query-value"])
value2 = dtype.type(P["query-value2"])

# Find the indices
table_indices = []
for i, row_value in zip(self.table.index, self.table[column]):
if op == "==":
if row_value == value:
table_indices.append(i)
elif op == "!=":
if row_value != value:
table_indices.append(i)
elif op == ">":
if row_value > value:
table_indices.append(i)
elif op == ">=":
if row_value >= value:
table_indices.append(i)
elif op == "<":
if row_value < value:
table_indices.append(i)
elif op == "<=":
if row_value <= value:
table_indices.append(i)
elif op == "between":
if row_value >= value and row_value <= value2:
table_indices.append(i)
elif op == "contains":
if value in row_value:
table_indices.append(i)
elif op == "does not contain":
if value not in row_value:
table_indices.append(i)
elif op == "contains regexp":
if re.search(value, row_value) is not None:
table_indices.append(i)
elif op == "does not contain regexp":
if re.search(value, row_value) is None:
table_indices.append(i)
elif op == "is empty":
# Might be numpy.nan, and NaN != NaN hence odd test.
if row_value == "" or row_value != row_value:
table_indices.append(i)
elif op == "is not empty":
if row_value != "" and row_value == row_value:
table_indices.append(i)
else:
raise NotImplementedError(
f"Loop query '{op}' not implemented"
)
n_table_indices = len(table_indices)
else:
raise NotImplementedError(f"Loop cannot handle '{where}'")
table_indices = [self.table.label(row) for row in table_rows]
n_table_indices = len(table_indices)
printer.important(
__(
f"The loop will have {n_table_indices} iterations.\n\n",
Expand Down Expand Up @@ -579,11 +533,10 @@ def run(self):
self.set_variable("_loop_indices", tmp[0:-1])
self.set_variable("_loop_index", tmp[-2])

# and the other info in the table handle
self.table_handle["loop index"] = False
# and the other info in the table
self.table["loop index"] = False

self.table = None
self.table_handle = None

self.logger.info(
"The loop over table "
Expand All @@ -604,15 +557,19 @@ def run(self):
" --> {}".format(self.get_variable("_loop_indices"))
)
self.set_variable("_loop_index", index)
self.table_handle["current index"] = index
self.table.current_row = table_rows[self._loop_value - 1]

# Name of directory is the index (+1 since tends to be 0 based)
if index_is_int:
self._custom_directory_name = f"iter_{index + 1:{fmt}}"
else:
self._custom_directory_name = self.safe_filename(str(index))

row = {k: self.table.at[index, k] for k in self.table}
row = {
k: v
for k, v in self.table.get_row().items()
if k != self.table.index_column
}
self.set_variable("_row", row)
if P["as variables"]:
for key, value in row.items():
Expand Down Expand Up @@ -695,7 +652,9 @@ def run(self):

# Run through the steps in the loop body
try:
node = next_node
next_node = next_node.run()
seamm.step_completed(node)
except DeprecationWarning as e:
printer.normal("\nDeprecation warning: " + str(e))
traceback.print_exc(file=sys.stderr)
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
psutil
seamm>=2026.9.18.1
seamm>=2026.10.3
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