ararpy 0.2.4__tar.gz → 0.2.7__tar.gz

{ararpy-0.2.4 → ararpy-0.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.2.4
+Version: 0.2.7
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/__init__.py

@@ -16,10 +16,10 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.2.4'
+version = '0.2.7'
 __version__ = version
 full_version = version
-last_update = '2026-01-07'
+last_update = '2026-02-03'
 
 """ ArArPy Functions """
 

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/calc/age.py

@@ -93,7 +93,7 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
         BB = 1
         KK = np.exp(t / V) - 1  # 40Arr / 40K Use standard age
     else:  # use Ar40* and K concentrations of primary standard
-        # not fanished, this function is wrong
+        # not finished, this function is wrong
         BB = (Ab + Ae) / Ae
         KK = Ap / Kp / f
         raise TypeError(f"Not use standard age. Not supported.")

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/files/arr_file.py

@@ -27,12 +27,12 @@ def save(file_path, sample):
     str, file name
     """
     if not file_path.endswith(".arr"):
-        file_path = os.path.join(file_path, f"{sample.Info.sample.name}.arr")
+        file_path = os.path.join(file_path, f"{sample.Info.experiment.name}.arr")
     with open(file_path, 'wb') as f:
         f.write(pickle.dumps(sample))
     # with open(file_path, 'w') as f:
     # # save serialized json data to a readable text
     #     f.write(basic_funcs.getJsonDumps(sample))
-    return f"{sample.Info.sample.name}.arr"
+    return f"{sample.Info.experiment.name}.arr"
 
 

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/files/raw_file.py

@@ -411,39 +411,42 @@ def get_sample_info(file_contents: list, index_list: list, default="", base: Uni
     """
     sample_info = DEFAULT_SAMPLE_INFO.copy()
     sample_info.update({
-        "ExpName": get_item(file_contents, index_list[0:3], default=default, base=base).strip(),
-        "StepName": get_item(file_contents, index_list[3:6], default=default, base=base).strip(),
-        "StepType": get_item(file_contents, index_list[6:9], default=default, base=base).strip(),
-        "StepLabel": get_item(file_contents, index_list[9:12], default=default, base=base).strip(),
-        "ZeroYear": get_item(file_contents, index_list[12:15], default=default, base=base).strip(),
-        "ZeroHour": get_item(file_contents, index_list[15:18], default=default, base=base).strip(),
-        "ZeroMon": get_item(file_contents, index_list[18:21], default=default, base=base).strip(),
-        "ZeroMin": get_item(file_contents, index_list[21:24], default=default, base=base).strip(),
-        "ZeroDay": get_item(file_contents, index_list[24:27], default=default, base=base).strip(),
-        "ZeroSec": get_item(file_contents, index_list[27:30], default=default, base=base).strip(),
-        "SmpName": get_item(file_contents, index_list[30:33], default=default, base=base).strip(),
-        "SmpLoc": get_item(file_contents, index_list[33:36], default=default, base=base).strip(),
-        "SmpMatr": get_item(file_contents, index_list[36:39], default=default, base=base).strip(),
-        "ExpType": get_item(file_contents, index_list[39:42], default=default, base=base).strip(),
-        "SmpWeight": get_item(file_contents, index_list[42:45], default=default, base=base).strip(),
-        "Stepunit": get_item(file_contents, index_list[45:48], default=default, base=base).strip(),
-        "HeatingTime": get_item(file_contents, index_list[48:51], default=default, base=base).strip(),
-        "InstrName": get_item(file_contents, index_list[51:54], default=default, base=base).strip(),
-        "Researcher": get_item(file_contents, index_list[54:57], default=default, base=base).strip(),
-        "Analyst": get_item(file_contents, index_list[57:60], default=default, base=base).strip(),
-        "Lab": get_item(file_contents, index_list[60:63], default=default, base=base).strip(),
-        "Jv": get_item(file_contents, index_list[63:66], default=default, base=base).strip(),
-        "Jsig": get_item(file_contents, index_list[66:69], default=default, base=base).strip(),
-        "MDF": get_item(file_contents, index_list[69:72], default=default, base=base).strip(),
-        "MDFSig": get_item(file_contents, index_list[72:75], default=default, base=base).strip(),
-        "CalcName": get_item(file_contents, index_list[75:78], default=default, base=base).strip(),
-        "IrraName": get_item(file_contents, index_list[78:81], default=default, base=base).strip(),
-        "IrraLabel": get_item(file_contents, index_list[81:84], default=default, base=base).strip(),
-        "IrraPosH": get_item(file_contents, index_list[84:87], default=default, base=base).strip(),
-        "IrraPosX": get_item(file_contents, index_list[87:90], default=default, base=base).strip(),
-        "IrraPosY": get_item(file_contents, index_list[90:93], default=default, base=base).strip(),
-        "StdName": get_item(file_contents, index_list[93:96], default=default, base=base).strip(),
-        "StdAge": get_item(file_contents, index_list[96:99], default=default, base=base).strip(),
-        "StdAgeSig": get_item(file_contents, index_list[99:102], default=default, base=base).strip(),
+        "ExpName": get_item(file_contents, index_list[0:3], default=default, base=base),
+        "StepName": get_item(file_contents, index_list[3:6], default=default, base=base),
+        "StepType": get_item(file_contents, index_list[6:9], default=default, base=base),
+        "StepLabel": get_item(file_contents, index_list[9:12], default=default, base=base),
+        "ZeroYear": get_item(file_contents, index_list[12:15], default=default, base=base),
+        "ZeroHour": get_item(file_contents, index_list[15:18], default=default, base=base),
+        "ZeroMon": get_item(file_contents, index_list[18:21], default=default, base=base),
+        "ZeroMin": get_item(file_contents, index_list[21:24], default=default, base=base),
+        "ZeroDay": get_item(file_contents, index_list[24:27], default=default, base=base),
+        "ZeroSec": get_item(file_contents, index_list[27:30], default=default, base=base),
+        "SmpName": get_item(file_contents, index_list[30:33], default=default, base=base),
+        "SmpLoc": get_item(file_contents, index_list[33:36], default=default, base=base),
+        "SmpMatr": get_item(file_contents, index_list[36:39], default=default, base=base),
+        "ExpType": get_item(file_contents, index_list[39:42], default=default, base=base),
+        "SmpWeight": get_item(file_contents, index_list[42:45], default=default, base=base),
+        "Stepunit": get_item(file_contents, index_list[45:48], default=default, base=base),
+        "HeatingTime": get_item(file_contents, index_list[48:51], default=default, base=base),
+        "InstrName": get_item(file_contents, index_list[51:54], default=default, base=base),
+        "Researcher": get_item(file_contents, index_list[54:57], default=default, base=base),
+        "Analyst": get_item(file_contents, index_list[57:60], default=default, base=base),
+        "Lab": get_item(file_contents, index_list[60:63], default=default, base=base),
+        "Jv": get_item(file_contents, index_list[63:66], default=default, base=base),
+        "Jsig": get_item(file_contents, index_list[66:69], default=default, base=base),
+        "MDF": get_item(file_contents, index_list[69:72], default=default, base=base),
+        "MDFSig": get_item(file_contents, index_list[72:75], default=default, base=base),
+        "CalcName": get_item(file_contents, index_list[75:78], default=default, base=base),
+        "IrraName": get_item(file_contents, index_list[78:81], default=default, base=base),
+        "IrraLabel": get_item(file_contents, index_list[81:84], default=default, base=base),
+        "IrraPosH": get_item(file_contents, index_list[84:87], default=default, base=base),
+        "IrraPosX": get_item(file_contents, index_list[87:90], default=default, base=base),
+        "IrraPosY": get_item(file_contents, index_list[90:93], default=default, base=base),
+        "StdName": get_item(file_contents, index_list[93:96], default=default, base=base),
+        "StdAge": get_item(file_contents, index_list[96:99], default=default, base=base),
+        "StdAgeSig": get_item(file_contents, index_list[99:102], default=default, base=base),
     })
+    for key, val in sample_info.items():
+        if isinstance(val, str):
+            sample_info[key] = val.strip()
     return sample_info

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/smp/basic.py

@@ -161,6 +161,18 @@ def calc_j(ar40ar39=None, params: dict = None, smp: Sample = None, index: list =
 
 
 def calc_mdf(ar40ar36=None, params: dict = None, smp: Sample = None, index: list = None):
+    """
+    Parameters
+    ----------
+    ar40ar36
+    params
+    smp
+    index
+
+    Returns
+    -------
+
+    """
     params_index_dict = {
         71: 'M36', 72: 'sM36', 79: 'M40', 80: 'sM40', 93: 'Air', 94: 'rsAir', 100: 'Discr'
     }
@@ -193,7 +205,7 @@ def calc_mdf(ar40ar36=None, params: dict = None, smp: Sample = None, index: list
     for i in range(len(index)):
         k = calc.corr.mdf(ar40ar36[0][i], ar40ar36[1][i], params['M36'][i], params['M40'][i],
                           params['Air'][i], params['rsAir'][i])  # linear, exp, pow
-        mdf.append({"linear": k[0:4], "exp": k[4:8], "pow": k[8:12]}[params['Discr'][i].lower()])
+        mdf.append({"l": k[0:4], "e": k[4:8], "p": k[8:12]}[params['Discr'][i].lower()[0]])
 
     if len(index) == 1:
         return np.transpose(mdf).squeeze().tolist()

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/smp/export.py

@@ -1980,10 +1980,10 @@ class CreatePDF:
             self.color_rgb_normalized(self.color_hex_to_rgb(plot.set3.border_color))
         ]
         for (x, sx, y, sy, r, i) in data:
-            if (i - 1) in set1.data:
+            if i in set1.data:
                 pt.scatter(x, y, stroke_color=stroke_colors[0], fill_color=colors[0], line_width=int(float(plot.set1.border_width) / 2),
                            size=int(float(plot.set1.symbol_size) / 3), z_index=10)
-            elif (i - 1) in set2.data:
+            elif i in set2.data:
                 pt.scatter(x, y, stroke_color=stroke_colors[1], fill_color=colors[1], line_width=int(float(plot.set2.border_width) / 2),
                            size=int(float(plot.set2.symbol_size) / 3), z_index=10)
             else:

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/smp/initial.py

@@ -300,14 +300,18 @@ def check_version(smp: Sample):
     -------
 
     """
-    if smp.version != samples.VERSION:
-        std = initial(Sample())
-        basic.get_merged_smp(smp, std)
 
     try:
         version = int(smp.version)
     except ValueError:
         return smp
+    except AttributeError:
+        smp.version = "20240701"
+        return check_version(smp)
+
+    if smp.version != samples.VERSION:
+        std = initial(Sample())
+        basic.get_merged_smp(smp, std)
 
     # 20250328:  # Experiment info
     smp.Info.experiment.name = smp.name()
@@ -328,7 +332,7 @@ def check_version(smp: Sample):
 
     # 20250404:  # Normalization for steps with different J values
     # always check
-    if version < 1120250405:
+    if version < 99990101:
         doNormalize = True
         v, sv = [], []
         try:

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/smp/plots.py

@@ -129,7 +129,7 @@ def get_iso_init(sample: Sample, figure: Plot):
     if figure.id != 'figure_7':
         for point in calc.arr.transpose(data[:5]):
             if '' not in point and None not in point:
-                ellipse_data.append(calc.isochron.get_ellipse(*point))
+                ellipse_data.append(calc.isochron.get_ellipse(*point, plt_sfactor=sample.Info.preference.confidence_level))
     return data, ellipse_data
 
 

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/smp/sample.py

@@ -799,7 +799,7 @@ DEFAULT_PLOT_STYLES = lambda sample_type, age_unit: {
     },
 }
 
-VERSION = '20251231'
+VERSION = '20260101'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy/smp/table.py

@@ -133,10 +133,10 @@ def update_handsontable(smp: Sample, data: list, id: str):
         data = _normalize_data(data, len(samples.SPECTRUM_TABLE_HEADERS), n, 3)
         smp.ApparentAgeValues = _digitize_data(data)
     elif id == '7':  # 等时线
-        data = _normalize_data(data, len(samples.ISOCHRON_TABLE_HEADERS), n, 3)
+        data = _normalize_data(data, len(samples.ISOCHRON_TABLE_HEADERS), n, 3, 0, smp.IsochronsTable.text_indexes)
         smp.IsochronValues = _digitize_data(data)
     elif id == '8':  # 总参数
-        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), n, 3)
+        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), n, 3, 0, smp.TotalParamsTable.text_indexes)
         data = _digitize_data(data)
         data[101: 112] = [_strToBool(i) for i in data[101: 112]]
         smp.TotalParam = data
@@ -232,4 +232,5 @@ def _strToBool(cols):
     bools_dict = {
         'true': True, 'false': False, 'True': True, 'False': False, '1': True, '0': False, 'none': False,
     }
+    cols = [int(col) if isinstance(col, float) else col for col in cols]
     return [bools_dict.get(str(col).lower(), False) for col in cols]

{ararpy-0.2.4 → ararpy-0.2.7}/ararpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.2.4
+Version: 0.2.7
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.2.4 → ararpy-0.2.7}/setup.py

@@ -16,7 +16,7 @@ long_description = (here / 'README.md').read_text(encoding='utf-8')
 
 setuptools.setup(
     name='ararpy',  #
-    version='0.2.4',  # version
+    version='0.2.7',  # version
     author='Yang Wu',
     author_email='wuycug@hotmail.com',
     description='A project for Ar-Ar geochronology',  # short description