Improve test coverage

.coveragerc

@@ -8,3 +8,5 @@ source = flamingpy
 
 exclude_lines =
     if __name__ == .__main__.:
+    pragma: no cover
+    plt.show()

.github/workflows/build_tests.yaml

@@ -39,7 +39,7 @@ jobs:
           python setup.py build_cmake --inplace
 
       - name: Run tests
-        run: python -m pytest tests/ --cov=flamingpy --cov-report=xml --cov-report=term-missing -p no:warnings --tb=native --cov-fail-under=90
+        run: python -m pytest tests/ --cov=flamingpy --cov-report=xml --cov-report=term-missing -p no:warnings --tb=native --cov-fail-under=95
 
       - name: Adjust coverage file for Codecov
         run: bash <(sed -i 's/filename=\"/filename=\"flamingpy\//g' coverage.xml)

flamingpy/__init__.py

@@ -29,7 +29,7 @@
 try:
     import flamingpy.cpp.lemonpy as lp
     import flamingpy.cpp.cpp_mc_loop as cmc
-except ImportError:
+except ImportError:  # pragma: no cover
     warnings.warn("Failed to import flamingpy.cpp libraries.", ImportWarning)
 
 

flamingpy/benchmarks/decoding.py

@@ -83,5 +83,6 @@
 plt.xlabel("Times [seconds]")
 plt.ylabel("Count")
 plt.title(f"Decoding for code distance {distance}")
+
 if __name__ == "__main__":
     plt.savefig(f"benchmark_decoding_distance_{distance}.pdf")

flamingpy/benchmarks/lemon.py

@@ -58,5 +58,6 @@
 plt.ylabel("Time")
 plt.yscale("log")
 plt.legend(loc="best")
+
 if __name__ == "__main__":
     plt.savefig("lemon_benchmark.pdf")

flamingpy/benchmarks/matching.py

@@ -91,5 +91,6 @@
 plt.xlabel("Times [seconds]")
 plt.ylabel("Count")
 plt.title(f"Matching for code distance {distance}")
+
 if __name__ == "__main__":
     plt.savefig(f"benchmark_matching_distance_{distance}.pdf")

flamingpy/benchmarks/shortest_path.py

@@ -79,5 +79,6 @@
 plt.xlabel("Times [seconds]")
 plt.ylabel("Count")
 plt.title(f"Building matching graph for code distance {distance}")
+
 if __name__ == "__main__":
     plt.savefig(f"benchmark_shortest_path_distance_{distance}.pdf")

flamingpy/benchmarks/simulations.py

@@ -14,7 +14,9 @@
 """Benchmark for the Monte Carlo simulations estimating FT thresholds and
 comparing python and cpp loops."""
 
-# pylint: disable=too-many-arguments
+
+# pylint: disable=no-self-use,protected-access,redefined-outer-name
+
 
 import csv
 import warnings
@@ -29,7 +31,7 @@
 
 try:
     import flamingpy.cpp.cpp_mc_loop as cmc
-except ImportError:
+except ImportError:  # pragma: no cover
     warnings.warn("Failed to import flamingpy.cpp.cpp_mc_loop library.", ImportWarning)
 
 
@@ -92,79 +94,90 @@ def ec_monte_carlo(code, trials, delta, p_swap, passive_objects=None, backend="c
     return errors
 
 
-# The Monte Carlo simulations
-
-# Arguments
-distance = 2
-ec = "primal"
-boundaries = "open"
-delta = 0.01
-p_swap = 0.5
-trials = 100
-passive = True
-
-# The qubit code
-RHG_code = SurfaceCode(distance, ec, boundaries)
-RHG_lattice = RHG_code.graph
-RHG_lattice.index_generator()
-if passive:
-    # The lattice with macronodes.
-    pad_bool = boundaries != "periodic"
-    RHG_macro = RHG_lattice.macronize(pad_boundary=pad_bool)
-    RHG_macro.index_generator()
-    RHG_macro.adj_generator(sparse=True)
-    # The empty CV state, uninitiated with any error model.
-    CVRHG_reduced = CVLayer(RHG_lattice)
-    # Define the 4X4 beamsplitter network for a given macronode.
-    # star at index 0, planets at indices 1-3.
-    bs_network = BS_network(4)
-    passive_objects = [RHG_macro, RHG_lattice, CVRHG_reduced, bs_network]
-else:
-    passive_objects = None
-
-tic = process_time()
-errors = ec_monte_carlo(RHG_code, trials, delta, p_swap, passive_objects, backend="python")
-walltime_py = process_time() - tic
-
-tic = process_time()
-ec_monte_carlo(RHG_code, trials, delta, p_swap, passive_objects, backend="cpp")
-walltime_cpp = process_time() - tic
-
-# Store results in a sims_data directory in the file simulations_results.csv.
-file_name = "./flamingpy/sims_data/sims_benchmark_results.csv"
-# Create a CSV file if it doesn't already exist.
-try:
-    file = open(file_name, "x", newline="", encoding="utf8")
-    writer = csv.writer(file)
+def run_sims_benchmark(distance, ec, boundaries, delta, p_swap, trials, passive, fname=None):
+    """Run full Monte Carlo error-correction simulations benchmarks.
+
+    Compare the Cython and regular Python backends. Results are stored
+    in a file in the sims_data directory (with name fname, if supplied).
+    """
+
+    # The qubit code
+    RHG_code = SurfaceCode(distance, ec, boundaries)
+    RHG_lattice = RHG_code.graph
+    RHG_lattice.index_generator()
+    if passive:
+        # The lattice with macronodes.
+        pad_bool = boundaries != "periodic"
+        RHG_macro = RHG_lattice.macronize(pad_boundary=pad_bool)
+        RHG_macro.index_generator()
+        RHG_macro.adj_generator(sparse=True)
+        # The empty CV state, uninitiated with any error model.
+        CVRHG_reduced = CVLayer(RHG_lattice)
+        # Define the 4X4 beamsplitter network for a given macronode.
+        # star at index 0, planets at indices 1-3.
+        bs_network = BS_network(4)
+        passive_objects = [RHG_macro, RHG_lattice, CVRHG_reduced, bs_network]
+    else:
+        passive_objects = None
+
+    # Monte Carlo simulations
+    tic = process_time()
+    errors = ec_monte_carlo(RHG_code, trials, delta, p_swap, passive_objects, backend="python")
+    walltime_py = process_time() - tic
+
+    tic = process_time()
+    ec_monte_carlo(RHG_code, trials, delta, p_swap, passive_objects, backend="cpp")
+    walltime_cpp = process_time() - tic
+
+    # Store results in a sims_data directory in the file simulations_results.csv.
+    file_name = fname or "./flamingpy/sims_data/sims_benchmark_results.csv"
+    # Create a CSV file if it doesn't already exist.
+    try:
+        file = open(file_name, "x", newline="", encoding="utf8")
+        writer = csv.writer(file)
+        writer.writerow(
+            [
+                "distance",
+                "ec",
+                "boundaries",
+                "delta",
+                "p_swap",
+                "errors_py",
+                "trials",
+                "current_time",
+                "cpp_to_py_speedup",
+            ]
+        )
+    # Open the file for appending if it already exists.
+    except FileExistsError:
+        file = open(file_name, "a", newline="", encoding="utf8")
+        writer = csv.writer(file)
+    current_time = datetime.now().time().strftime("%H:%M:%S")
     writer.writerow(
         [
-            "distance",
-            "ec",
-            "boundaries",
-            "delta",
-            "p_swap",
-            "errors_py",
-            "trials",
-            "current_time",
-            "cpp_to_py_speedup",
+            distance,
+            ec,
+            boundaries,
+            delta,
+            p_swap,
+            errors,
+            trials,
+            current_time,
+            walltime_py / walltime_cpp,
         ]
     )
-# Open the file for appending if it already exists.
-except FileExistsError:
-    file = open(file_name, "a", newline="", encoding="utf8")
-    writer = csv.writer(file)
-current_time = datetime.now().time().strftime("%H:%M:%S")
-writer.writerow(
-    [
-        distance,
-        ec,
-        boundaries,
-        delta,
-        p_swap,
-        errors,
-        trials,
-        current_time,
-        walltime_py / walltime_cpp,
-    ]
-)
-file.close()
+    file.close()
+
+
+if __name__ == "__main__":
+
+    # Arguments
+    distance = 2
+    ec = "primal"
+    boundaries = "open"
+    delta = 0.01
+    p_swap = 0.5
+    trials = 100
+    passive = True
+
+    run_sims_benchmark(ec_monte_carlo, distance, ec, boundaries, delta, p_swap, trials, passive)

flamingpy/decoders/mwpm/lemon.py

@@ -18,7 +18,7 @@
 
 try:
     import flamingpy.cpp.lemonpy as lp
-except ImportError:
+except ImportError:  # pragma: no cover
     warnings.warn("Failed to import flamingpy.cpp.lemonpy library.", ImportWarning)