Merge branch 'develop' into hp

Author: martinkilbinger

.github/workflows/ci-build.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8]
+        python-version: [3.10.12]
 
     steps:
       - name: Checkout
@@ -29,29 +29,15 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Set up Conda with Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
-
-      - name: Check Conda
-        shell: bash -l {0}
-        run: |
-          conda info
-          conda list
-          python --version
+      - name: Install Poetry
+        run: pip install poetry
 
       - name: Install Dependencies
         shell: bash -l {0}
-        run: |
-          python --version
-          python -m pip install --upgrade pip
-          python -m pip install -r develop.txt
-          python -m pip install -r docs/requirements.txt
-          python -m pip install twine
-          python -m pip install .
+        run: poetry install
+
+      - name: Build Package
+        run: poetry build
 
       - name: Run Tests
         shell: bash -l {0}
@@ -66,12 +52,6 @@ jobs:
           name: unit-test-results-${{ matrix.os }}-${{ matrix.python-version }}
           path: pytest.xml
 
-      - name: Check Distribution
-        shell: bash -l {0}
-        run: |
-          python setup.py sdist
-          twine check dist/*
-
       - name: Check API Documentation build
         shell: bash -l {0}
         run: |

cs_util/args.py

@@ -9,6 +9,7 @@
 
 import sys
 import os
+import shlex
 
 from optparse import OptionParser
 
@@ -103,6 +104,9 @@ def my_string_split(string, num=-1, verbose=False, stop=False, sep=None):
     the first in the list [space, underscore] that occurs in the string.
     (Thus, if both occur, use space.)
 
+    Handles quoted strings: entries containing spaces can be enclosed
+    in double quotes, e.g., 'value1 "entry with spaces" value3'.
+
     Parameters
     ----------
     string : str
@@ -131,6 +135,19 @@ def my_string_split(string, num=-1, verbose=False, stop=False, sep=None):
     if string is None:
         return None
 
+    # Handle quoted strings with shlex
+    if '"' in string or "'" in string:
+        try:
+            res = shlex.split(string)
+            if num != -1 and num != len(res) and stop:
+                raise ValueError(
+                    f"String has {len(res)} elements, required is {num}"
+                )
+            return res
+        except ValueError:
+            # Fall through to regular splitting if shlex fails
+            pass
+
     if sep is None:
         has_space = string.find(" ")
         has_underscore = string.find("_")
@@ -162,7 +179,7 @@ def my_string_split(string, num=-1, verbose=False, stop=False, sep=None):
 
     if num != -1 and num != len(res) and stop:
         raise ValueError(
-            f"String '{len(res)}' has length {num}, required is {num}"
+            f"String has {len(res)} elements, required is {num}"
         )
 
     return res

cs_util/cat.py

@@ -11,14 +11,21 @@
 import os
 from datetime import datetime
 
+from importlib.metadata import version
+import numpy as np
 import healpy as hp
 
 from astropy.io import fits
 from astropy.io import ascii
 from astropy.table import Table
 
 
-def write_header_info_sp(primary_header, name="unknown", version="unknown"):
+def write_header_info_sp(
+    primary_header,
+    software_name="cs_util",
+    software_version="unknown",
+    author=None,
+):
     """Write Header Info sp_validation.
 
     Write information about software and run to FITS header
@@ -27,27 +34,37 @@ def write_header_info_sp(primary_header, name="unknown", version="unknown"):
     ----------
     primary_header : dict
        FITS header information
-    name : str
-        software name, default is 'unknown'
-    version : str
-        version, default is 'unknown'
+    software_name : str, optional
+        software name; default is "cs_util"
+    software_version : str, optional
+        version; default is current cs_util version
+    author : str, optional
+        author name; if ``None`` (default), read from os.environ["USER"],
+        or if not set in env, "unknown"
 
     Returns
     -------
     dict
         updated FITS header information
 
     """
-    if "USER" in os.environ:
-        author = os.environ["USER"]
+    if software_version is None:
+        software_version = version("cs_util")
+
+    if author is None:
+        if "USER" in os.environ:
+            author = os.environ["USER"]
+        else:
+            author = "unknown"
     else:
         author = "unknown"
+
     primary_header["AUTHOR"] = (author, "Who ran the software")
-    primary_header["SOFTNAME"] = (name, "Name of the software")
-    primary_header["SOFTVERS"] = (version, "Version of the software")
+    primary_header["SOFTNAME"] = (software_name, "Software name")
+    primary_header["SOFTVERS"] = (software_version, "software version")
     primary_header["DATE"] = (
         datetime.now().strftime("%Y-%m-%d_%H-%M-%S"),
-        "When it was started",
+        "Creation date",
     )
 
     return primary_header
@@ -171,6 +188,39 @@ def write_fits_BinTable_file(
     hdu_list.writeto(output_path, overwrite=True)
 
 
+def read_fits_to_dict(file_path):
+    """Read Fits To Dict.
+
+    Read FITS file and return dictionary.
+
+    Parameters
+    ----------
+    file_path : str
+        input file path
+
+    Returns
+    -------
+    dict
+        file content
+
+    Raises
+    ------
+    IOError
+        if input file is not found
+    """
+    if not os.path.exists(file_path):
+        raise IOError(f"Input file '{file_path}' not found")
+
+    hdu_list = fits.open(file_path)
+    data_input = hdu_list[1].data
+    col_names = hdu_list[1].data.dtype.names
+    data = {}
+    for col_name in col_names:
+        data[col_name] = data_input[col_name]
+
+    return data
+
+
 def bin_edges2centers(bin_edges):
     """Bin Edges To Centers.
 
@@ -204,19 +254,36 @@ def read_dndz(file_path):
 
     Returns
     -------
-    list :
+    np.array
         redshift bin centers
-    list :
+    np.array
         number densities
-    list :
-        redshift bin edges
+    np.array
+        redshift bin edges; one less than centers and density arrays
 
     """
-    dat = ascii.read(file_path, format="commented_header")
+    try:
+        # Expecting header line "# z dn_dz"
+        dat = ascii.read(file_path, format="commented_header")
+        missing = [col for col in ("z", "dn_dz") if col not in dat.dtype.names]
+        if missing:
+            raise ValueError(
+                f"Missing columns in dndz path {file_path}: {missing}"
+            )
+    except:
+        # No header line
+        dat = ascii.read(file_path)
+        dat.rename_column("col1", "z")
+        dat.rename_column("col2", "dn_dz")
+
+    # Remove last n(z) value which should be zero, to match bin centers
+    tolerance = 1e-5
+    if dat["dn_dz"][-1] / sum(dat["dn_dz"]) > tolerance:
+        raise ValueError("dn_dz at last z-edge = {dat['dn_dz'][-1]}, no zero")
 
-    # Remove last n(z) value which is zero, to match bin centers
     nz = dat["dn_dz"][:-1]
     z_edges = dat["z"]
+
     z_centers = bin_edges2centers(z_edges)
 
     return z_centers, nz, z_edges

cs_util/cosmo.py

@@ -79,9 +79,9 @@ def sigma_crit(z_lens, z_source, cos, d_lens=None, d_source=None):
 
     a_lens = 1 / (1 + z_lens)
     a_source = 1 / (1 + z_source)
-    if not d_lens:
+    if d_lens is None:
         d_lens = cos.angular_diameter_distance(a_lens) * units.Mpc
-    if not d_source:
+    if d_source is None:
         d_source = cos.angular_diameter_distance(a_source) * units.Mpc
 
     d_lens_source = cos.angular_diameter_distance(a_lens, a_source) * units.Mpc