From 81fe4c8718e5965dfa0591e168b147eb2708ad5b Mon Sep 17 00:00:00 2001
From: arjunsavel <asavel@gmail.com>
Date: Thu, 21 Mar 2024 16:46:45 -0400
Subject: [PATCH] the test exo-transmit files are incomplete!

---
 src/cortecs/opac/io.py             |  6 +++--
 src/cortecs/tests/test_chunking.py | 39 ++++++++++++------------------
 2 files changed, 19 insertions(+), 26 deletions(-)

diff --git a/src/cortecs/opac/io.py b/src/cortecs/opac/io.py
index df59dcd..7532b5f 100644
--- a/src/cortecs/opac/io.py
+++ b/src/cortecs/opac/io.py
@@ -388,7 +388,7 @@ def get_lams_and_opacities(self, file):
         except:
             pdb.set_trace()
 
-    def load(self, filename):
+    def load(self, filename, fullfile=True):
         """
         Loads file.
 
@@ -415,7 +415,9 @@ def load(self, filename):
 
         # and now make it log10
         cross_section = np.log10(cross_section)
-        cross_section = cross_section.reshape(len(T), len(P), len(wl))
+
+        if fullfile:  # only reshape if it's not a "test" file.
+            cross_section = cross_section.reshape(len(T), len(P), len(wl))
 
         return wl, T, P, cross_section
 
diff --git a/src/cortecs/tests/test_chunking.py b/src/cortecs/tests/test_chunking.py
index f1c072b..76b41b4 100644
--- a/src/cortecs/tests/test_chunking.py
+++ b/src/cortecs/tests/test_chunking.py
@@ -1,6 +1,7 @@
 """
 just do a few tests for chunking...
 """
+
 import unittest
 import os
 import numpy as np
@@ -9,6 +10,8 @@
 
 
 class TestIntegration(unittest.TestCase):
+    load_kwargs = {"fullfile": False}
+
     opacity_file = os.path.abspath(".") + "/src/cortecs/tests/opacCH4_narrow_wl.dat"
     first_file = os.path.abspath(".") + "/src/cortecs/tests/" + "opacCH4_narrow_wl0.dat"
     second_file = (
@@ -43,12 +46,10 @@ def test_wls_of_each_created_file(self):
         # now get the wavelengths of each file
         opac_obj_ref = Opac(self.opacity_file, loader="exotransmit")
         opac_obj0 = Opac(
-            self.first_file,
-            loader="exotransmit",
+            self.first_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         opac_obj1 = Opac(
-            self.second_file,
-            loader="exotransmit",
+            self.second_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         np.testing.assert_array_equal(
             opac_obj_ref.wl, np.concatenate((opac_obj0.wl, opac_obj1.wl))
@@ -67,12 +68,10 @@ def test_vals_of_each_created_file(self):
         # now get the wavelengths of each file
         opac_obj_ref = Opac(self.opacity_file, loader="exotransmit")
         opac_obj0 = Opac(
-            self.first_file,
-            loader="exotransmit",
+            self.first_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         opac_obj1 = Opac(
-            self.second_file,
-            loader="exotransmit",
+            self.second_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         # pdb.set_trace()
         np.testing.assert_array_equal(
@@ -92,12 +91,10 @@ def test_add_overlap_wl_increase_or_same(self):
 
         chunk_wavelengths(self.opacity_file, wav_per_chunk=2)
         opac_obj0_orig = Opac(
-            self.first_file,
-            loader="exotransmit",
+            self.first_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         opac_obj1_orig = Opac(
-            self.second_file,
-            loader="exotransmit",
+            self.second_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
 
         add_overlap(self.file_base, v_max=0.0)
@@ -105,12 +102,10 @@ def test_add_overlap_wl_increase_or_same(self):
         # now get the wavelengths of each file
         opac_obj_ref = Opac(self.opacity_file, loader="exotransmit")
         opac_obj0 = Opac(
-            self.first_file,
-            loader="exotransmit",
+            self.first_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         opac_obj1 = Opac(
-            self.second_file,
-            loader="exotransmit",
+            self.second_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         # pdb.set_trace()
         self.assertTrue(
@@ -128,12 +123,10 @@ def add_overlap_with_single_overlap_point(self):
 
         chunk_wavelengths(self.opacity_file, wav_per_chunk=2)
         opac_obj0_orig = Opac(
-            self.first_file,
-            loader="exotransmit",
+            self.first_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         opac_obj1_orig = Opac(
-            self.second_file,
-            loader="exotransmit",
+            self.second_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
 
         # calculate the vmax so that one point is changed
@@ -146,12 +139,10 @@ def add_overlap_with_single_overlap_point(self):
         # now get the wavelengths of each file
         opac_obj_ref = Opac(self.opacity_file, loader="exotransmit")
         opac_obj0 = Opac(
-            self.first_file,
-            loader="exotransmit",
+            self.first_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         opac_obj1 = Opac(
-            self.second_file,
-            loader="exotransmit",
+            self.second_file, loader="exotransmit", load_kwargs=self.load_kwargs
         )
         self.assertTrue(
             len(opac_obj1.wl.min) == len(opac_obj0.wl.max())