From 75ef1c9e61f044306652901fcc5722158a85f2b2 Mon Sep 17 00:00:00 2001
From: yokochin <naiya_yokochi@yokochilab.org>
Date: Wed, 4 Dec 2024 16:19:40 -0600
Subject: [PATCH 1/2] Fixed xarray_wrappers.py and test, removed demos

---
 autoreact/ktp_xarray/xarray_demo_DataArray.py | 60 -------------------
 autoreact/ktp_xarray/xarray_demo_DataSet.py   | 26 --------
 autoreact/ktp_xarray/xarray_wrappers.py       |  4 +-
 autoreact/ktp_xarray/xarray_wrappers_test.py  | 22 ++++---
 4 files changed, 17 insertions(+), 95 deletions(-)
 delete mode 100644 autoreact/ktp_xarray/xarray_demo_DataArray.py
 delete mode 100644 autoreact/ktp_xarray/xarray_demo_DataSet.py

diff --git a/autoreact/ktp_xarray/xarray_demo_DataArray.py b/autoreact/ktp_xarray/xarray_demo_DataArray.py
deleted file mode 100644
index 7015ed96..00000000
--- a/autoreact/ktp_xarray/xarray_demo_DataArray.py
+++ /dev/null
@@ -1,60 +0,0 @@
-import xarray
-import numpy
-
-temps = [1000, 1500, 2000, 2500]
-press = [1, 10, numpy.inf]
-
-# Define the array of rates (note: it makes sense to structure it as a list 
-# of rates at a given P based on how the MESS parser is written, though it
-# doesn't really matter) 
-ktp_vals = [[1e1, 1e2, 1e3, 1e4], [1e5, 1e6, 1e7, 1e8], [1e9, 1e10, 1e11, 1e12]]
-
-# Create the DataArray
-ktp = xarray.DataArray(ktp_vals, [("pres", press), ("temp", temps)])
-print(ktp)
-
-# Get a slice at a selected pressure or temperature value
-print('\nPressure slice by value')
-print(ktp.sel(pres=numpy.inf))  # the fact that you can use np.inf is very convenient!
-print('\nTemperature slice by value')
-print(ktp.sel(temp=1500))
-
-# Get a specific value at a selected temperature value and pressure value
-print('\nTemperature slice by value')
-print(ktp.sel(temp=1500, pres=1))
-
-# Get a slice at a selected pressure or temperature index
-print('\nPressure slice by index')
-print(ktp.isel(pres=0))
-print('\nTemperature slice by index')
-print(ktp.isel(temp=0))
-
-# Can also add some metadata (probably unnecessary for ktp objects, but cool)
-ktp.attrs["units"] = "s^-1"  # any number of arbitrary attributes can be added
-ktp.name = "N2O=N2+O"
-
-# Can do various arithmetic operations
-print('\nVarious operations')
-print(ktp + ktp)
-print(3 * ktp)
-
-# To get the actual values, use the values OR data attribute
-print('\nGet the values, which should be a numpy array')
-print(ktp.values)
-print('type of ktp.values: ', type(ktp.values))
-print('\nTemperature slice by value, as an array')
-print(ktp.sel(temp=1500, pres=1).data)
-print(type(ktp.sel(temp=1500, pres=1).data))
-
-# Can get all dimensions associated with an array usings the dims attribute
-print('\nNames of all dimensions, as a tuple')
-print(ktp.dims)
-
-# Can get the coordinates associated with a dimension by using that coordinate name
-print('\nPressure values: ', ktp.pres.data)
-print('\nTemperature values: ', ktp.temp.data)
-
-# Can do lookup on values with the nearest value
-# This is giving an error even though I thought I copied it from the website?
-#print('\nTemperature slice by nearest lookup')
-#print(ktp.sel(temp=1600), method='nearest')
diff --git a/autoreact/ktp_xarray/xarray_demo_DataSet.py b/autoreact/ktp_xarray/xarray_demo_DataSet.py
deleted file mode 100644
index 2148424e..00000000
--- a/autoreact/ktp_xarray/xarray_demo_DataSet.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import xarray
-import numpy
-
-temps = [1000, 1500, 2000, 2500]
-enthalpy = [60, 70, 80, 90]
-gibbs = [10, 15, 20, 25]
-c_p = [1, 1.1, 1.2, 1.3]
-entropy = [3, 4, 5, 6]
-
-therm = xarray.Dataset(
-    {
-        "enthalpy": (["temp"], enthalpy),
-        "gibbs": (["temp"], gibbs),
-        "c_p": (["temp"], c_p),
-        "entropy": (["temp"], entropy),
-    },
-    coords={
-        "temp": temps,
-    },
-)
-
-print(therm)
-print(therm.temp)
-print(therm.temp.values)
-
-
diff --git a/autoreact/ktp_xarray/xarray_wrappers.py b/autoreact/ktp_xarray/xarray_wrappers.py
index a0d3098d..8496b256 100644
--- a/autoreact/ktp_xarray/xarray_wrappers.py
+++ b/autoreact/ktp_xarray/xarray_wrappers.py
@@ -10,7 +10,7 @@ def from_data(temps, press, rates):
     Construct a KTP DataArray from data
     """
 
-    ktp = xarray.DataArray(rates, [("pres", press), ("temp", temps)])
+    ktp = xarray.DataArray(rates, (("pres", press), ("temp", temps)))
 
     return ktp
 
@@ -88,5 +88,5 @@ def set_rates(ktp, rates, pres, temp):
     Sets the KTP values
     """
 
-    ktp.loc[dict(pres=pres, temp=temp)] = rates
+    ktp.loc[{"pres": pres, "temp": temp}] = rates
     return ktp
diff --git a/autoreact/ktp_xarray/xarray_wrappers_test.py b/autoreact/ktp_xarray/xarray_wrappers_test.py
index 06c4cba5..60b9c0f8 100644
--- a/autoreact/ktp_xarray/xarray_wrappers_test.py
+++ b/autoreact/ktp_xarray/xarray_wrappers_test.py
@@ -1,6 +1,7 @@
-import xarray_wrappers
-import xarray
+"""Tests xarray_wrappers.py's functions"""
+
 import numpy
+from autoreact.ktp_xarray import xarray_wrappers
 
 Temps = [1000, 1500, 2000, 2500]
 Press = [1, 10, numpy.inf]
@@ -9,53 +10,60 @@
 Ktp = xarray_wrappers.from_data(Temps, Press, Rates)
 print(Ktp)
 
-def test_set_rates():
-    ktp = xarray_wrappers.set_rates(Ktp, Rates)
-    print(ktp)
-
 def test_get_temperatures():
+    """Tests the get_temperatures function"""
     temp = xarray_wrappers.get_temperatures(Ktp)
     print(temp)
 
 
 def test_get_pressures():
+    """Tests the get_pressures function"""
     pres = xarray_wrappers.get_pressures(Ktp)
     print(pres)
 
 
 def test_get_values():
+    """Tests the get_values function"""
     vals = xarray_wrappers.get_values(Ktp)
     print(vals)
 
 
 def test_get_pslice():
+    """Tests the get_pslice function"""
     pslice = xarray_wrappers.get_pslice(Ktp, numpy.inf)
     print(pslice)
 
 
 def test_get_tslice():
+    """Tests the get_tslice function"""
     tslice = xarray_wrappers.get_tslice(Ktp, 1500)
     print(tslice)
 
 
 def test_get_spec_vals():
+    """Tests the get_spec_values function"""
     vals = xarray_wrappers.get_spec_vals(Ktp, 1500, 1)
     print(vals)
 
 
 def test_get_ipslice():
+    """Tests the get_ipslice function"""
     ipslice = xarray_wrappers.get_ipslice(Ktp, 0)
     print(ipslice)
 
 
 def test_get_itslice():
+    """Tests the get_itslice function"""
     itslice = xarray_wrappers.get_itslice(Ktp, 0)
     print(itslice)
 
+
 def test_set_rates():
+    """Tests the set_rates function"""
     new_rates = xarray_wrappers.set_rates(Ktp, 1e11, 10, 2000)
     print(new_rates)
-    
+
+
 test_get_pressures()
 test_get_temperatures()
 test_get_values()

From d0b03a52f1ee586570d2291ffd32304bdde91f9a Mon Sep 17 00:00:00 2001
From: yokochin <naiya_yokochi@yokochilab.org>
Date: Wed, 4 Dec 2024 16:25:03 -0600
Subject: [PATCH 2/2] Fixed ktp_xarray/__init__.py

---
 autoreact/ktp_xarray/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/autoreact/ktp_xarray/__init__.py b/autoreact/ktp_xarray/__init__.py
index 4d45d0c4..64660ddd 100644
--- a/autoreact/ktp_xarray/__init__.py
+++ b/autoreact/ktp_xarray/__init__.py
@@ -1,3 +1,5 @@
+"""Initializes the ktp_xarray folder"""
+
 from autoreact.ktp_xarray import xarray_wrappers
 
 __all__ = [