tpattern 0.1.9__tar.gz → 0.1.11__tar.gz

{tpattern-0.1.9/tpattern.egg-info → tpattern-0.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tpattern
-Version: 0.1.9
+Version: 0.1.11
 Summary: Open, auditable temporal & sequential pattern analysis (T-patterns) for sport and behaviour
 Author-email: Andrew Callaway <acallaway@bournemouth.ac.uk>
 License-Expression: MIT

{tpattern-0.1.9 → tpattern-0.1.11}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tpattern"
-version = "0.1.9"
+version = "0.1.11"
 description = "Open, auditable temporal & sequential pattern analysis (T-patterns) for sport and behaviour"
 readme = "README.md"
 requires-python = ">=3.9"

tpattern-0.1.11/tests/test_outputs.py

@@ -0,0 +1,86 @@
+"""Tests for the 0.1.11 output layer: per-pattern timing, and the THEME-style
+tables (durations, event-type roles, connections, data summary, interval counts)."""
+import os
+from tpattern import (Observation, Engine, Config, calibrate, patterns_table,
+                      duration_stats, pattern_durations, event_type_roles,
+                      connections, data_summary, interval_counts, report,
+                      occurrence_plot, duration_plot)
+
+
+def sample():
+    # A -> B at a fixed 300 ms lag in every observation; half also carry a later C, so
+    # (A B) survives standalone (not fully absorbed) alongside the longer ((A B) C).
+    obs = []
+    for i in range(8):
+        ev = [(0, "A"), (300, "B")]
+        if i < 4:
+            ev.append((600, "C"))
+        obs.append(Observation(name=f"o{i}", start=0, end=1000, events=ev))
+    return obs
+
+
+def patterns():
+    return Engine(sample(), Config(min_lag=1)).detect()
+
+
+def test_duration_stats_from_instances():
+    p = next(p for p in patterns() if p.signature() == "(A B)")
+    d = duration_stats(p)
+    assert d["n"] == 8 and d["median"] == 300 and d["min"] == 300 and d["max"] == 300
+
+
+def test_patterns_table_has_timing_columns():
+    rows = patterns_table(patterns(), n_observations=8)
+    ab = next(r for r in rows if r["signature"] == "(A B)")
+    assert ab["duration_median_ms"] == 300
+    assert ab["critical_interval"].endswith("ms")          # unit is labelled
+    assert ab["duration_range_ms"] == "[300,300]"
+
+
+def test_pattern_durations_one_row_per_occurrence():
+    rows = pattern_durations(patterns())
+    ab = [r for r in rows if r["signature"] == "(A B)"]
+    assert len(ab) == 8
+    assert all(r["duration_ms"] == r["end_ms"] - r["start_ms"] for r in rows)
+
+
+def test_event_type_roles_first_and_last():
+    roles = {r["event_type"]: r for r in event_type_roles(patterns())}
+    # A only ever starts a pattern; C only ever ends one
+    assert roles["A"]["pct_first"] == 1.0 and roles["A"]["as_last"] == 0
+    assert roles["C"]["pct_last"] == 1.0 and roles["C"]["as_first"] == 0
+
+
+def test_connections_direction():
+    conn = {r["event_type"]: r for r in connections(patterns())}
+    assert "B" in conn["A"]["followed_by"] and "C" in conn["A"]["followed_by"]
+    assert conn["A"]["n_followed_by"] >= 2
+
+
+def test_data_summary_counts():
+    rows = data_summary(sample())
+    a = next(r for r in rows if r["event_type"] == "A")
+    assert a["count"] == 8 and a["observations"] == 8 and a["mean_per_observation"] == 1.0
+
+
+def test_interval_counts_split():
+    rows = interval_counts(patterns(), [(0, 100), (100, 1000)], split_time=100)
+    ab = next(r for r in rows if r["signature"] == "(A B)")
+    # every A->B occurrence starts at t=0, so all are in [0,100] and before the split
+    assert ab["in[0,100]"] == 8 and ab["before_split"] == 8 and ab["after_split"] == 0
+
+
+def test_report_writes_all_default_outputs(tmp_path):
+    res = calibrate(sample(), Config(min_lag=1), null="profile", B=50, q_target=0.05, seed=1)
+    w = report(res, str(tmp_path), observations=sample(), title="unit test")
+    for key in ("table", "durations", "roles", "connections", "data_summary",
+                "dendrograms", "durations_plot", "occurrence_plot", "summary"):
+        assert key in w and os.path.getsize(w[key]) > 0
+
+
+def test_plots_render(tmp_path):
+    res = calibrate(sample(), Config(min_lag=1), null="profile", B=50, q_target=0.05, seed=1)
+    f1 = str(tmp_path / "occ.png"); f2 = str(tmp_path / "dur.png")
+    occurrence_plot(sample(), f1)
+    duration_plot(res, f2)
+    assert os.path.getsize(f1) > 0 and os.path.getsize(f2) > 0

tpattern-0.1.11/tests/test_read_table_validation.py

@@ -0,0 +1,121 @@
+"""Data-check tests for read_table: the E/W/I codes, and that the clean path
+stays silent and unchanged. See tpattern/io.py CHECKS."""
+import pytest
+from tpattern import read_table, DataFormatError, CHECKS, check_reference
+
+
+def write(tmp_path, name, text):
+    p = tmp_path / name
+    p.write_text(text)
+    return str(p)
+
+
+# ---- E codes: raise, nothing loaded ----
+
+def test_E01_missing_column(tmp_path):
+    f = write(tmp_path, "m.csv", "observation,event,time\np1,pass,0\np1,shot,3\n")
+    with pytest.raises(DataFormatError) as e:
+        read_table(f)
+    assert "E01" in str(e.value) and "start" in str(e.value)
+
+
+def test_E01_suggests_close_column(tmp_path):
+    f = write(tmp_path, "m.csv", "observation,event,Start\np1,pass,0\np1,shot,3\n")
+    with pytest.raises(DataFormatError) as e:
+        read_table(f)
+    assert "Start" in str(e.value)  # suggested the near-match
+
+
+def test_E02_wrong_separator(tmp_path):
+    f = write(tmp_path, "s.csv", "observation;event;start\np1;pass;0\np1;shot;3\n")
+    with pytest.raises(DataFormatError) as e:
+        read_table(f)
+    assert "E02" in str(e.value)
+
+
+def test_E03_header_only(tmp_path):
+    f = write(tmp_path, "h.csv", "observation,event,start\n")
+    with pytest.raises(DataFormatError) as e:
+        read_table(f)
+    assert "E03" in str(e.value)
+
+
+def test_E04_all_rows_blank(tmp_path):
+    f = write(tmp_path, "b.csv", "observation,event,start\n,pass,0\n,shot,3\n")
+    with pytest.raises(DataFormatError) as e:
+        read_table(f)
+    assert "E04" in str(e.value)
+
+
+def test_E05_no_pattern_capable_observation(tmp_path):
+    # every observation has exactly one event
+    f = write(tmp_path, "one.csv",
+              "observation,event,start\np1,pass,0\np2,shot,0\np3,cross,0\n")
+    with pytest.raises(DataFormatError) as e:
+        read_table(f)
+    assert "E05" in str(e.value)
+
+
+# ---- W codes: load anyway, reported ----
+
+def test_W10_non_numeric_times_dropped(tmp_path, capsys):
+    f = write(tmp_path, "c.csv",
+              "observation,event,start\np1,pass,0\np1,cross,01:03\np1,shot,5\n"
+              "p2,pass,1\np2,shot,4\n")
+    obs = read_table(f)                       # default report: a W fired, so it prints
+    out = capsys.readouterr().out
+    assert "W10" in out and "left out" in out
+    # the one good p1 row + p2 both loaded; the mm:ss row dropped
+    assert sum(len(o.events) for o in obs) == 4
+
+
+def test_W13_near_duplicate_labels(tmp_path, capsys):
+    f = write(tmp_path, "d.csv",
+              "observation,event,start\np1,Pass,0\np1,pass,1\np1,shot,2\n"
+              "p2,Pass,0\np2,shot,2\n")
+    read_table(f)
+    assert "W13" in capsys.readouterr().out
+
+
+def test_clean_file_is_silent(tmp_path, capsys):
+    f = write(tmp_path, "ok.csv",
+              "observation,event,start\np1,pass,0\np1,shot,2\np2,pass,0\np2,shot,3\n")
+    obs = read_table(f)
+    assert capsys.readouterr().out == ""       # nothing to warn about
+    assert len(obs) == 2
+
+
+# ---- I codes: only shown with report="all" ----
+
+def test_I20_effective_sample_only_with_all(tmp_path, capsys):
+    f = write(tmp_path, "e.csv",
+              "observation,event,start\np1,pass,0\np1,shot,2\np2,pass,0\n")  # p2 has 1 event
+    read_table(f)                              # default: I-only, stays silent
+    assert capsys.readouterr().out == ""
+    read_table(f, report="all")                # report='all' surfaces the info note
+    assert "I20" in capsys.readouterr().out
+
+
+def test_report_false_silences_warnings(tmp_path, capsys):
+    f = write(tmp_path, "c.csv",
+              "observation,event,start\np1,pass,0\np1,x,bad\np1,shot,5\np2,a,0\np2,b,1\n")
+    read_table(f, report=False)
+    assert capsys.readouterr().out == ""
+
+
+# ---- BOM (Excel) handled ----
+
+def test_utf8_bom_is_stripped(tmp_path):
+    p = tmp_path / "bom.csv"
+    p.write_bytes("observation,event,start\np1,pass,0\np1,shot,2\n".encode("utf-8"))
+    obs = read_table(str(p))                   # must not see the BOM as part of the column name
+    assert len(obs) == 1 and len(obs[0].events) == 2
+
+
+# ---- registry integrity (Appendix A generates from this) ----
+
+def test_check_reference_covers_every_code():
+    rows = check_reference()
+    assert {r["code"] for r in rows} == set(CHECKS)
+    for r in rows:
+        assert r["condition"] and r["fix"] and r["severity"]

{tpattern-0.1.9 → tpattern-0.1.11}/tpattern/__init__.py

@@ -6,17 +6,20 @@ behavior: T-patterns and their detection. Behavior Research Methods,
 Instruments, & Computers, 32(1), 93-110.
 """
 
-__version__ = "0.1.9"   # defined before submodule imports (methods.py reads it)
+__version__ = "0.1.11"   # defined before submodule imports (methods.py reads it)
 
-from .io import Observation, read_observation, read_sample, read_table, read_sofcoder
+from .io import (Observation, read_observation, read_sample, read_table,
+                 read_sofcoder, DataFormatError, check_reference, CHECKS)
 from .pattern import Instance, Pattern
 from .ci import find_critical_interval, CIResult
 from .detect import Config, Engine
 from .randomise import run_null, NullResult, rotate, shuffle
 from .significance import calibrate, CalibrationResult, compare_nulls, NullComparison
-from .report import patterns_table, forest_plot, report
+from .report import (patterns_table, forest_plot, report, interpret, duration_stats,
+                     pattern_durations, event_type_roles, connections, data_summary,
+                     interval_counts)
 from .viz import (pattern_dendrogram, patterns_overview, support_profile,
-                  null_comparison_plot)
+                  null_comparison_plot, occurrence_plot, duration_plot, STYLE)
 from .advisor import recommend
 from .methods import methods_text
 from .guided import run_analysis, launch
@@ -24,12 +27,15 @@ from .contrast import group_contrast, contrast_items
 
 __all__ = [
     "Observation", "read_observation", "read_sample", "read_table", "read_sofcoder",
+    "DataFormatError", "check_reference", "CHECKS",
     "Instance", "Pattern",
     "find_critical_interval", "CIResult",
     "Config", "Engine",
     "run_null", "NullResult", "rotate", "shuffle",
     "calibrate", "CalibrationResult",
-    "patterns_table", "forest_plot", "report",
+    "patterns_table", "forest_plot", "report", "interpret", "duration_stats",
+    "pattern_durations", "event_type_roles", "connections", "data_summary",
+    "interval_counts", "occurrence_plot", "duration_plot", "STYLE",
     "pattern_dendrogram", "patterns_overview", "support_profile",
     "recommend", "methods_text",
     "run_analysis", "launch",