Merge branch 'devel'. Bring 'main' to version 1.4.1

README.md

@@ -7,7 +7,7 @@
 [![ADS](https://img.shields.io/badge/ads-2022MNRAS.509.4344A-blue.svg)](https://ui.adsabs.harvard.edu/abs/2022MNRAS.509.4344A/abstract)
 [![DOI](https://img.shields.io/badge/doi-10.1093/mnras/stab2911-orange.svg)](https://doi.org/10.1093/mnras/stab2911)
 
-Current stable version: v1.4.0
+Current stable version: v1.4.1
 
 **Important note:** BASTA is currently developed for Python 3.12, but Python >= 3.9 should in principle suffice. *Please be aware that Python 3.12 will not* work if you need to fit glitches (please see the installation instructions) due to to known build issues in NumPy/f2py (as the glitch fitting relies on Fortran-routines) and we recommend 3.11 in that case.
 

basta/__about__.py

@@ -1 +1 @@
-__version__ = "1.4.0"
+__version__ = "1.4.1"

basta/fileio.py

@@ -952,6 +952,11 @@ def read_allseismic(
 def freqs_ascii_to_xml(
     directory,
     starid,
+    freqsfile: str | None = None,
+    covfile: str | None = None,
+    ratiosfile: str | None = None,
+    cov010file: str | None = None,
+    cov02file: str | None = None,
     symmetric_errors=True,
     check_radial_orders=False,
     quiet=False,
@@ -984,11 +989,16 @@ def freqs_ascii_to_xml(
     """
 
     # (Potential) filepaths
-    freqsfile = os.path.join(directory, starid + ".fre")
-    covfile = os.path.join(directory, starid + ".cov")
-    ratiosfile = os.path.join(directory, starid + ".ratios")
-    cov010file = os.path.join(directory, starid + ".cov010")
-    cov02file = os.path.join(directory, starid + ".cov02")
+    if freqsfile is None:
+        freqsfile = os.path.join(directory, starid + ".fre")
+    if covfile is None:
+        covfile = os.path.join(directory, starid + ".cov")
+    if ratiosfile is None:
+        ratiosfile = os.path.join(directory, starid + ".ratios")
+    if cov010file is None:
+        cov010file = os.path.join(directory, starid + ".cov010")
+    if cov02file is None:
+        cov02file = os.path.join(directory, starid + ".cov02")
 
     # Flags for existence of ratios and covariances
     cov_flag, ratios_flag, cov010_flag, cov02_flag = 1, 1, 1, 1
@@ -1237,8 +1247,8 @@ def freqs_ascii_to_xml(
 
 
 def _read_freq_ascii(
-    filename,
-    symmetric_errors=True,
+    filename: str,
+    symmetric_errors: bool = True,
 ):
     """
     Read individual frequencies from an ascii file
@@ -1260,45 +1270,95 @@ def _read_freq_ascii(
     """
     cols = []
     data = np.genfromtxt(filename, dtype=None, encoding=None, names=True)
+
+    rdict = {
+        "frequency": {
+            "dtype": "float",
+            "recognisednames": [
+                "f",
+                "freq",
+                "freqs",
+                "frequency",
+                "modefrequency",
+            ],
+        },
+        "order": {
+            "dtype": "int",
+            "recognisednames": [
+                "n",
+                "ns",
+                "order",
+                "radialorder",
+            ],
+        },
+        "degree": {
+            "dtype": "int",
+            "recognisednames": [
+                "l",
+                "ls",
+                "ell",
+                "ells",
+                "degree",
+                "angulardegree",
+            ],
+        },
+        "error": {
+            "dtype": "float",
+            "recognisednames": [
+                "error",
+                "err",
+                "e",
+                "uncertainty",
+                "uncert",
+            ],
+        },
+        "error_plus": {
+            "dtype": "float",
+            "recognisednames": [
+                "error_plus",
+                "err_plus",
+                "error_upper",
+                "upper_error",
+            ],
+        },
+        "error_minus": {
+            "dtype": "float",
+            "recognisednames": [
+                "error_minus",
+                "err_minus",
+                "error_lower",
+                "lower_error",
+            ],
+        },
+        "flag": {
+            "dtype": "int",
+            "recognisednames": [
+                "flag",
+            ],
+        },
+        "frequency_mode": {
+            "dtype": "float",
+            "recognisednames": [
+                "frequency_mode",
+            ],
+        },
+    }
+
     for colname in data.dtype.names:
-        if colname.lower() in ["f", "freq", "frequency"]:
-            cols.append(
-                ("frequency", "float"),
-            )
-        elif colname.lower() in ["n", "order"]:
-            cols.append(
-                ("order", "int"),
-            )
-        elif colname.lower() in ["l", "ell", "degree"]:
-            cols.append(
-                ("degree", "int"),
-            )
-        elif colname.lower() in ["error_plus", "err_plus", "error_upper"]:
-            cols.append(
-                ("error_plus", "float"),
-            )
-        elif colname.lower() in ["error_minus", "err_minus", "error_lower"]:
-            cols.append(
-                ("error_minus", "float"),
-            )
-        elif colname.lower() in [
-            "error",
-            "err",
-        ]:
-            cols.append(("error", "float"))
-        elif colname.lower() in [
-            "flag",
-        ]:
-            cols.append(("flag", "int"))
-        elif colname.lower() in [
-            "frequency_mode",
-        ]:
-            cols.append(("frequency_mode", "float"))
-        else:
+        param = [p for p in rdict if colname.lower() in rdict[p]["recognisednames"]]
+        if not param:
             raise ValueError(f"BASTA cannot recognize {colname}")
+        assert len(param) == 1, (colname, param)
+        cols.append((param[0], rdict[param[0]]["dtype"]))
 
     sym = np.any([col[0] == "error" for col in cols])
-    asym = all(item in col[0] for col in l for item in ["error_plus", "error_minus"])
+    asym = all(
+        [
+            item in col[0]
+            for col in cols
+            for item in rdict["error_plus"]["recognisednames"]
+        ]
+    )
     if not sym ^ asym:
         if sym | asym:
             raise ValueError(
@@ -1318,10 +1378,22 @@ def _read_freq_ascii(
     )
 
     if not np.any(["order" in col[0] for col in cols]):
-        print("BASTA did not find n orders, they are generated")
-        freqcol = [col for col in data.dtype.names if col in ["f", "freq", "frequency"]]
-        assert len(freqcol) == 1, print(freqcol)
-        dnu = data[freqcol[0]][1] - data[freqcol[0]][0]
+        print("BASTA did not find column with radial orders, they will be generated")
+
+        freqcol = [
+            col
+            for col in data.dtype.names
+            if col in rdict["frequency"]["recognisednames"]
+        ]
+        lcol = [
+            col for col in data.dtype.names if col in rdict["degree"]["recognisednames"]
+        ]
+        assert len(freqcol) == 1, freqcol
+        assert len(lcol) == 1, lcol
+        mask = data[lcol[0]] == 0
+        l0s = data[freqcol[0]][mask]
+        assert len(l0s) > 1, "More than 1 l=0 mode is required for estimation of dnu"
+        dnu = np.median(np.diff(l0s))
         ns = np.asarray(data[freqcol[0]]) // dnu - 1
         from numpy.lib.recfunctions import append_fields
 
@@ -1330,7 +1402,7 @@ def _read_freq_ascii(
     return freqs
 
 
-def _read_freq_cov_ascii(filename):
+def _read_freq_cov_ascii(filename: str):
     """
     Read covariance and correlations for individual frequencies from an
     ascii file

docs/conf.py

@@ -26,10 +26,10 @@
 author = "The BASTA Team"
 
 # The short X.Y version.
-version = "1.4.0"
+version = "1.4.1"
 
 # The full version, including alpha/beta/rc tags.
-release = "1.4.0"
+release = "1.4.1"
 
 
 # -- General configuration ------------------------------------------------

docs/index.rst

@@ -7,7 +7,7 @@ BASTA is a Python-based fitting tool designed to determine properties of stars u
 models. It calculates the probability density function of a given stellar property based on a set of observational
 constraints defined by the user.
 
-Current stable version: v1.4.0
+Current stable version: v1.4.1
 
 *Please follow the repository on* `GitHub <https://github.com/BASTAcode/BASTA>`_ *to get notifications on new releases: Click "Watch" then "Custom" and tick "Releases.*