astro-otter 0.2.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

{astro_otter-0.2.0.dist-info → astro_otter-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: astro-otter
-Version: 0.2.0
+Version: 0.3.0
 Author-email: Noah Franz <nfranz@arizona.edu>
 License: MIT License
         
@@ -36,7 +36,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Development Status :: 2 - Pre-Alpha
-Requires-Python: <3.12,>=3.10
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy<2,>=1.20

{astro_otter-0.2.0.dist-info → astro_otter-0.3.0.dist-info}/RECORD

@@ -1,18 +1,18 @@
-astro_otter-0.2.0.dist-info/licenses/LICENSE,sha256=s9IPE8A3CAMEaZpDhj4eaorpmfLYGB0mIGphq301PUY,1067
+astro_otter-0.3.0.dist-info/licenses/LICENSE,sha256=s9IPE8A3CAMEaZpDhj4eaorpmfLYGB0mIGphq301PUY,1067
 otter/__init__.py,sha256=pvX-TN7nLVmvKpkDi89Zxe-jMfHNiVMD3zsd_bPEK9Y,535
-otter/_version.py,sha256=Hwps5WC9_lYJO5SVIdnlMYP1MbeluDR9sJvlFgSiQjg,76
+otter/_version.py,sha256=XDCAY_avI84JEWPKHKBF9kXkCGBGi2CjNGEItozNsk4,76
 otter/exceptions.py,sha256=3lQF4AXVTfs9VRsVePQoIrXnramsPZbUL5crvf1s9Ng,1702
 otter/schema.py,sha256=eOxlrtp9TTbiENy38ueE2HcYlI-M56g0Ohg7zQeTxjk,10631
 otter/util.py,sha256=xKsNkkxGajML1rZZnR9d5rJV1_z1KeAlIdAs8t0814M,22440
 otter/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 otter/io/data_finder.py,sha256=v3jZCOhvysHUQG1FOwHdeJ-psTT-MsdO_GZalBpMBGc,38218
 otter/io/host.py,sha256=xv_SznZuvMoMVsZLqlcmlOyaqKCMZqlTQ_gkN4VBSTw,7139
-otter/io/otter.py,sha256=75YHnYN6NznFi8O9YzMAM8AJQNXqByUSDkmzEOaFro4,46766
-otter/io/transient.py,sha256=0Z2G9uvv0xl4sJSj43cwFfOj6qkhlmRfBIh4XCYUHVU,41416
+otter/io/otter.py,sha256=HiYQ5hgAvPYSHmU6taF6NumpElYzFgjjA0oIgLEo9_4,47471
+otter/io/transient.py,sha256=b_gOQxjk8z3VylZ9ZrAv-Dhqp_d2iXPICL65Hq3kYGg,41846
 otter/plotter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 otter/plotter/otter_plotter.py,sha256=OQhuLgnMSzgtAjJF8SYBuQOyYcu7Pr0uia5P0G_7z5Q,2144
 otter/plotter/plotter.py,sha256=z09NwQVJS2tuwH3sv95DZv8xogjvf-7Gvj6iWCEx-gQ,9635
-astro_otter-0.2.0.dist-info/METADATA,sha256=uyREDToWRYbZ0hYeQAz3PZKLqdz4pmLQYQVhZWAN36w,7134
-astro_otter-0.2.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-astro_otter-0.2.0.dist-info/top_level.txt,sha256=Wth72sCwBRUk3KZGknSKvLQDMFuJk6qiaAavMDOdG5k,6
-astro_otter-0.2.0.dist-info/RECORD,,
+astro_otter-0.3.0.dist-info/METADATA,sha256=7qokfMceKHN1Ai0FNKqY95LYiil9jf3BzAX_7_A5KVI,7127
+astro_otter-0.3.0.dist-info/WHEEL,sha256=ooBFpIzZCPdw3uqIQsOo4qqbA4ZRPxHnOH7peeONza0,91
+astro_otter-0.3.0.dist-info/top_level.txt,sha256=Wth72sCwBRUk3KZGknSKvLQDMFuJk6qiaAavMDOdG5k,6
+astro_otter-0.3.0.dist-info/RECORD,,

{astro_otter-0.2.0.dist-info → astro_otter-0.3.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

otter/_version.py

@@ -2,4 +2,4 @@
 Just define the package version in one place
 """
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"

otter/io/otter.py

@@ -280,7 +280,7 @@ class Otter(Database):
 
         WARNING! This does not do any conversions for you!
         This is how it differs from the `get_meta` method. Users should prefer to use
-        `get_meta`, `getPhot`, and `getSpec` independently because it is a better
+        `get_meta`, and `get_phot` independently because it is a better
         workflow and can return the data in an astropy table with everything in the
         same units.
 
@@ -816,8 +816,32 @@ class Otter(Database):
         # read in the metadata and photometry file
         meta = pd.read_csv(metafile)
         phot = None
+
+        required_phot_cols = [
+            "name",
+            "date",
+            "date_format",
+            "filter",
+            "filter_eff",
+            "filter_eff_units",
+            "flux",
+            "flux_err",
+            "flux_unit",
+        ]
+
         if photfile is not None:
-            phot = pd.read_csv(photfile)
+            phot_unclean = pd.read_csv(photfile)
+
+            phot = phot_unclean.dropna(subset=required_phot_cols)
+            if len(phot) != len(phot_unclean):
+                warn("""
+                Filtered out rows with nan in the photometry file! Make sure you
+                expect this behaviour!
+                """)
+
+            if "bibcode" not in phot:
+                phot["bibcode"] = "private"
+                warn("Setting the bibcode column to the special keyword 'private'!")
 
             # we need to generate columns of wave_eff and freq_eff
             wave_eff = []

otter/io/transient.py

@@ -662,6 +662,12 @@ class Transient(MutableMapping):
             try:
                 if isvegamag:
                     astropy_units = VEGAMAG
+                elif unit == "AB":
+                    # In astropy "AB" is a magnitude SYSTEM not unit and while
+                    # u.Unit("AB") will succeed without error, it will not produce
+                    # the expected result!
+                    # We can assume here that this unit really means astropy's "mag(AB)"
+                    astropy_units = u.Unit("mag(AB)")
                 else:
                     astropy_units = u.Unit(unit)
 
@@ -806,20 +812,19 @@ class Transient(MutableMapping):
             # magnitude upperlimits are independent of the actual measurement!)
             # sigma_m > (1/3) * (ln(10)/2.5)
             def is_upperlimit(row):
-                if pd.isna(row.upperlimit):
+                if "upperlimit" in row and pd.isna(row.upperlimit):
                     return row.converted_flux_err > np.log(10) / (3 * 2.5)
                 else:
                     return row.upperlimit
         else:
 
             def is_upperlimit(row):
-                if pd.isna(row.upperlimit):
+                if "upperlimit" in row and pd.isna(row.upperlimit):
                     return row.converted_flux < 3 * row.converted_flux_err
                 else:
                     return row.upperlimit
 
         outdata["upperlimit"] = outdata.apply(is_upperlimit, axis=1)
-
         return outdata
 
     def _merge_names(t1, t2, out):  # noqa: N805