Fix/check append rep (#277)

* add option that the headers of an append-mode file can have different format

* add tests for irregular headers in append mode

* hotfix: fix bug in append start read implementation

* lint

* lint II

pyerrors/input/sfcf.py

@@ -5,6 +5,7 @@ import numpy as np  # Thinly-wrapped numpy
 from ..obs import Obs
 from .utils import sort_names, check_idl
 import itertools
+import warnings
 
 
 sep = "/"
@@ -603,42 +604,82 @@ def _read_chunk_data(chunk, start_read, T, corr_line, b2b, pattern, im, single):
     return data
 
 
+def _check_append_rep(content, start_list):
+    data_len_list = []
+    header_len_list = []
+    has_regular_len_heads = True
+    for chunk_num in range(len(start_list)):
+        start = start_list[chunk_num]
+        if chunk_num == len(start_list) - 1:
+            stop = len(content)
+        else:
+            stop = start_list[chunk_num + 1]
+        chunk = content[start:stop]
+        for linenumber, line in enumerate(chunk):
+            if line.startswith("[correlator]"):
+                header_len = linenumber
+                break
+        header_len_list.append(header_len)
+        data_len_list.append(len(chunk) - header_len)
+
+    if len(set(header_len_list)) > 1:
+        warnings.warn("Not all headers have the same length. Data parts do.")
+        has_regular_len_heads = False
+
+    if len(set(data_len_list)) > 1:
+        raise Exception("Irregularities in file structure found, not all run data are of the same output length")
+    return has_regular_len_heads
+
+
+def _read_chunk_structure(chunk, pattern, b2b):
+    start_read = 0
+    for linenumber, line in enumerate(chunk):
+        if line.startswith("gauge_name"):
+            gauge_line = linenumber
+        elif line.startswith("[correlator]"):
+            corr_line = linenumber
+            found_pat = ""
+            for li in chunk[corr_line + 1: corr_line + 6 + b2b]:
+                found_pat += li
+            if re.search(pattern, found_pat):
+                start_read = corr_line + 7 + b2b
+                break
+    if start_read == 0:
+        raise ValueError("Did not find pattern\n", pattern)
+    endline = corr_line + 6 + b2b
+    while not chunk[endline] == "\n":
+        endline += 1
+    T = endline - start_read
+    return gauge_line, corr_line, start_read, T
+
+
 def _read_append_rep(filename, pattern, b2b, im, single, idl_func, cfg_func_args):
     with open(filename, 'r') as fp:
         content = fp.readlines()
-        data_starts = []
+        chunk_start_lines = []
         for linenumber, line in enumerate(content):
             if "[run]" in line:
-                data_starts.append(linenumber)
-        if len(set([data_starts[i] - data_starts[i - 1] for i in range(1, len(data_starts))])) > 1:
-            raise Exception("Irregularities in file structure found, not all runs have the same output length")
-        chunk = content[:data_starts[1]]
-        for linenumber, line in enumerate(chunk):
-            if line.startswith("gauge_name"):
-                gauge_line = linenumber
-            elif line.startswith("[correlator]"):
-                corr_line = linenumber
-                found_pat = ""
-                for li in chunk[corr_line + 1: corr_line + 6 + b2b]:
-                    found_pat += li
-                if re.search(pattern, found_pat):
-                    start_read = corr_line + 7 + b2b
-                    break
-                else:
-                    raise ValueError("Did not find pattern\n", pattern, "\nin\n", filename)
-        endline = corr_line + 6 + b2b
-        while not chunk[endline] == "\n":
-            endline += 1
-        T = endline - start_read
-
-        # all other chunks should follow the same structure
+                chunk_start_lines.append(linenumber)
+        has_regular_len_heads = _check_append_rep(content, chunk_start_lines)
+        if has_regular_len_heads:
+            chunk = content[:chunk_start_lines[1]]
+            try:
+                gauge_line, corr_line, start_read, T = _read_chunk_structure(chunk, pattern, b2b)
+            except ValueError:
+                raise ValueError("Did not find pattern\n", pattern, "\nin\n", filename, "lines", 1, "to", chunk_start_lines[1] + 1)
+        # if has_regular_len_heads is true, all other chunks should follow the same structure
         rep_idl = []
         rep_data = []
 
-        for cnfg in range(len(data_starts)):
-            start = data_starts[cnfg]
-            stop = start + data_starts[1]
+        for chunk_num in range(len(chunk_start_lines)):
+            start = chunk_start_lines[chunk_num]
+            if chunk_num == len(chunk_start_lines) - 1:
+                stop = len(content)
+            else:
+                stop = chunk_start_lines[chunk_num + 1]
             chunk = content[start:stop]
+            if not has_regular_len_heads:
+                gauge_line, corr_line, start_read, T = _read_chunk_structure(chunk, pattern, b2b)
             try:
                 idl = idl_func(chunk[gauge_line], *cfg_func_args)
             except Exception:

pyerrors/version.py

@@ -1 +1 @@
-__version__ = "2.16.0"
+__version__ = "2.17.0-dev"

tests/data/sfcf_test/data_ah/data_ah_r0.f_1

@@ -0,0 +1,966 @@
+[run]
+
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+param_hash  686af5e712ee2902180f5428af94c6e7
+data_name   ./output_10519905/data_af_1
+
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@@ -0,0 +1,395 @@
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+

tests/sfcf_in_test.py

@@ -24,7 +24,7 @@ def build_test_environment(path, env_type, cfgs, reps):
             os.mkdir(path + "/data_c/data_c_r"+str(i))
             for j in range(1, cfgs+1):
                 shutil.copy(path + "/data_c/data_c_r0/data_c_r0_n1", path + "/data_c/data_c_r"+str(i)+"/data_c_r"+str(i)+"_n"+str(j))
-    elif env_type in ["a", "apf"]:
+    elif env_type in ["a", "apf", "ah"]:
         for i in range(1, reps):
             for corr in ["f_1", "f_A", "F_V0"]:
                 shutil.copy(path + "/data_" + env_type + "/data_" + env_type + "_r0." + corr, path + "/data_" + env_type + "/data_" + env_type + "_r" + str(i) + "." + corr)
@@ -389,6 +389,30 @@ def test_a_bib_external_idl_func_postfix(tmp_path):
     assert f_V0[2] == 683.6776090081005
 
 
+def test_a_bib_irreg_header(tmp_path):
+    build_test_environment(str(tmp_path), "ah", 5, 3)
+    with pytest.warns(UserWarning):
+        f_V0 = sfin.read_sfcf(str(tmp_path) + "/data_ah", "data_ah", "F_V0", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bib")
+    print(f_V0)
+    assert len(f_V0) == 3
+    assert list(f_V0[0].shape.keys()) == ["data_ah_|r0", "data_ah_|r1", "data_ah_|r2"]
+    assert f_V0[0] == 683.6776090085115
+    assert f_V0[1] == 661.3188585582334
+    assert f_V0[2] == 683.6776090081005
+
+
+def test_a_bi_irreg_header(tmp_path):
+    build_test_environment(str(tmp_path), "ah", 5, 3)
+    with pytest.warns(UserWarning):
+        f_A = sfin.read_sfcf(str(tmp_path) + "/data_ah", "data_ah", "f_A", quarks="lquark lquark", wf=0, version="2.0a", corr_type="bi")
+    print(f_A)
+    assert len(f_A) == 3
+    assert list(f_A[0].shape.keys()) == ["data_ah_|r0", "data_ah_|r1", "data_ah_|r2"]
+    assert f_A[0].value == 65.4711887279723
+    assert f_A[1].value == 1.0447210336915187
+    assert f_A[2].value == -41.025094911185185
+
+
 def test_simple_multi_a(tmp_path):
     build_test_environment(str(tmp_path), "a", 5, 3)
     corrs = sfin.read_sfcf_multi(str(tmp_path) + "/data_a", "data_a", ["F_V0"], quarks_list=["lquark lquark"], wf1_list=[0], wf2_list=[0], version="2.0a", corr_type_list=["bib"])