From 5180eeb379535d6a803f627af819e6b5eb36a5b3 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 26 Dec 2024 11:47:04 -0500
Subject: [PATCH 01/11] initial commit

---
 news/mu.rst               | 23 +++++++++++++++++++++++
 requirements/conda.txt    |  1 +
 requirements/pip.txt      |  1 +
 src/diffpy/utils/tools.py | 25 +++++++++++++++++++++++++
 tests/test_tools.py       |  8 +++++++-
 5 files changed, 57 insertions(+), 1 deletion(-)
 create mode 100644 news/mu.rst

diff --git a/news/mu.rst b/news/mu.rst
new file mode 100644
index 00000000..bbf9cb1a
--- /dev/null
+++ b/news/mu.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* function to compute x-ray attenuation coefficient (mu) using XrayDB
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/requirements/conda.txt b/requirements/conda.txt
index 24ce15ab..b26085a8 100644
--- a/requirements/conda.txt
+++ b/requirements/conda.txt
@@ -1 +1,2 @@
 numpy
+xraydb
diff --git a/requirements/pip.txt b/requirements/pip.txt
index 24ce15ab..b26085a8 100644
--- a/requirements/pip.txt
+++ b/requirements/pip.txt
@@ -1 +1,2 @@
 numpy
+xraydb
diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index a6c30ed3..ca965e22 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -3,6 +3,8 @@
 from copy import copy
 from pathlib import Path
 
+from xraydb import material_mu
+
 
 def _stringify(obj):
     """
@@ -131,3 +133,26 @@ def get_package_info(package_names, metadata=None):
         pkg_info.update({package: importlib.metadata.version(package)})
     metadata["package_info"] = pkg_info
     return metadata
+
+
+def compute_mu_using_xraydb(sample, energy, density=None):
+    """
+    compute mu using the XrayDB database
+
+    Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu
+
+    Parameters
+    ----------
+    sample str
+        the chemical formula or the name of the material
+    energy float
+        the energy in eV
+    density float or None
+        material density in gr/cm^3
+
+    Returns
+    -------
+    the attenuation coefficient mu in mm^{-1}
+    """
+    mu = material_mu(sample, energy, density=density, kind="total") / 10
+    return mu
diff --git a/tests/test_tools.py b/tests/test_tools.py
index cf730ddd..62b1673c 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -5,7 +5,7 @@
 
 import pytest
 
-from diffpy.utils.tools import get_package_info, get_user_info
+from diffpy.utils.tools import compute_mu_using_xraydb, get_package_info, get_user_info
 
 # def _setup_dirs(monkeypatch, user_filesystem):
 #     home_dir, cwd_dir = user_filesystem.home_dir, user_filesystem.cwd_dir
@@ -189,3 +189,9 @@ def test_get_package_info(monkeypatch, inputs, expected):
     )
     actual_metadata = get_package_info(inputs[0], metadata=inputs[1])
     assert actual_metadata == expected
+
+
+def test_compute_mu_using_xraydb():
+    sample, energy, density = "ZrO2", 17445.362740959618, 1.009
+    actual_mu = compute_mu_using_xraydb(sample, energy, density=density)
+    assert actual_mu == pytest.approx(1.252, rel=1e-4, abs=0.1)

From 5ff2c2312de6d4eab46c201327053f86cd64e829 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 26 Dec 2024 16:49:30 +0000
Subject: [PATCH 02/11] [pre-commit.ci] auto fixes from pre-commit hooks

---
 src/diffpy/utils/tools.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index ca965e22..2440abef 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -136,8 +136,7 @@ def get_package_info(package_names, metadata=None):
 
 
 def compute_mu_using_xraydb(sample, energy, density=None):
-    """
-    compute mu using the XrayDB database
+    """Compute mu using the XrayDB database.
 
     Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu
 

From 182622167e58bc704f15efefa890e021f2981449 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 26 Dec 2024 14:58:40 -0500
Subject: [PATCH 03/11] add packing fraction, add more tests

---
 src/diffpy/utils/tools.py | 24 +++++++++++++++---------
 tests/test_tools.py       | 26 ++++++++++++++++++++++----
 2 files changed, 37 insertions(+), 13 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index ca965e22..3674401a 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -135,24 +135,30 @@ def get_package_info(package_names, metadata=None):
     return metadata
 
 
-def compute_mu_using_xraydb(sample, energy, density=None):
+def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):
     """
-    compute mu using the XrayDB database
+    Compute the attenuation coefficient (mu) using the XrayDB database
 
+    This function calculates mu based on the sample composition and energy.
+    If density is not provided, a standard reference density (e.g., 0.987 g/cm^3 for H2O) is used.
+    User can provide either a measured density or an estimated packing fraction (with a standard density).
+    It is recommended to specify the density, especially for materials like ZrO2, where it can vary.
     Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu
 
     Parameters
     ----------
-    sample str
-        the chemical formula or the name of the material
-    energy float
-        the energy in eV
-    density float or None
-        material density in gr/cm^3
+    sample_composition: str
+        The chemical formula or the name of the material
+    energy: float
+        The energy in eV
+    density: float, optional, Default is None
+        The mass density of the packed powder/sample in gr/cm^3. If None, a standard density from XrayDB is used.
+    packing_fraction: float, optional, Default is 1
+        The fraction of sample in the capillary (between 0 and 1)
 
     Returns
     -------
     the attenuation coefficient mu in mm^{-1}
     """
-    mu = material_mu(sample, energy, density=density, kind="total") / 10
+    mu = material_mu(sample_composition, energy, density=density, kind="total") * packing_fraction / 10
     return mu
diff --git a/tests/test_tools.py b/tests/test_tools.py
index 62b1673c..dd70d347 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -191,7 +191,25 @@ def test_get_package_info(monkeypatch, inputs, expected):
     assert actual_metadata == expected
 
 
-def test_compute_mu_using_xraydb():
-    sample, energy, density = "ZrO2", 17445.362740959618, 1.009
-    actual_mu = compute_mu_using_xraydb(sample, energy, density=density)
-    assert actual_mu == pytest.approx(1.252, rel=1e-4, abs=0.1)
+params_mu = [
+    # C1: user didn't specify density or packing fraction
+    ({"sample_composition": "H2O", "energy": 10000, "density": None, "packing_fraction": 1}, 0.5330),
+    # C2: user specified packing fraction only
+    ({"sample_composition": "H2O", "energy": 10000, "density": None, "packing_fraction": 0.5}, 0.2665),
+    # C3: user specified density only
+    ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 1}, 0.5330),
+    ({"sample_composition": "H2O", "energy": 10000, "density": 0.4985, "packing_fraction": 1}, 0.2665),
+    # C4: user specified a standard density and a packing fraction
+    ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 0.5}, 0.2665),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params_mu)
+def test_compute_mu_using_xraydb(inputs, expected):
+    actual_mu = compute_mu_using_xraydb(
+        inputs["sample_composition"],
+        inputs["energy"],
+        density=inputs["density"],
+        packing_fraction=inputs["packing_fraction"],
+    )
+    assert actual_mu == pytest.approx(expected, rel=0.01, abs=0.1)

From be7c275a66ed254e82f6c772fbee2d21bcea13c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 26 Dec 2024 20:00:29 +0000
Subject: [PATCH 04/11] [pre-commit.ci] auto fixes from pre-commit hooks

---
 src/diffpy/utils/tools.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index 3674401a..611048f1 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -136,8 +136,7 @@ def get_package_info(package_names, metadata=None):
 
 
 def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):
-    """
-    Compute the attenuation coefficient (mu) using the XrayDB database
+    """Compute the attenuation coefficient (mu) using the XrayDB database.
 
     This function calculates mu based on the sample composition and energy.
     If density is not provided, a standard reference density (e.g., 0.987 g/cm^3 for H2O) is used.

From 9e4bc0dc1173978544be084e80ee182311587ccc Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 26 Dec 2024 15:27:55 -0500
Subject: [PATCH 05/11] refine docstring and test comments

---
 src/diffpy/utils/tools.py | 24 +++++++-------
 tests/test_tools.py       | 70 ++++++++++++++++++++++++++++++---------
 2 files changed, 66 insertions(+), 28 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index 3674401a..9b78dec2 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -136,29 +136,29 @@ def get_package_info(package_names, metadata=None):
 
 
 def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):
-    """
-    Compute the attenuation coefficient (mu) using the XrayDB database
+    """Compute the attenuation coefficient (mu) using the XrayDB database.
 
-    This function calculates mu based on the sample composition and energy.
+    Computes mu based on the sample composition and energy.
     If density is not provided, a standard reference density (e.g., 0.987 g/cm^3 for H2O) is used.
     User can provide either a measured density or an estimated packing fraction (with a standard density).
     It is recommended to specify the density, especially for materials like ZrO2, where it can vary.
-    Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu
+    Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu.
 
     Parameters
     ----------
-    sample_composition: str
-        The chemical formula or the name of the material
-    energy: float
-        The energy in eV
-    density: float, optional, Default is None
+    sample_composition : str
+        The chemical formula or the name of the material.
+    energy : float
+        The energy in eV.
+    density : float, optional, Default is None
         The mass density of the packed powder/sample in gr/cm^3. If None, a standard density from XrayDB is used.
-    packing_fraction: float, optional, Default is 1
-        The fraction of sample in the capillary (between 0 and 1)
+    packing_fraction : float, optional, Default is 1
+        The fraction of sample in the capillary (between 0 and 1).
 
     Returns
     -------
-    the attenuation coefficient mu in mm^{-1}
+    mu : float
+        The attenuation coefficient mu in mm^{-1}.
     """
     mu = material_mu(sample_composition, energy, density=density, kind="total") * packing_fraction / 10
     return mu
diff --git a/tests/test_tools.py b/tests/test_tools.py
index dd70d347..28850985 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -191,25 +191,63 @@ def test_get_package_info(monkeypatch, inputs, expected):
     assert actual_metadata == expected
 
 
-params_mu = [
-    # C1: user didn't specify density or packing fraction
-    ({"sample_composition": "H2O", "energy": 10000, "density": None, "packing_fraction": 1}, 0.5330),
-    # C2: user specified packing fraction only
-    ({"sample_composition": "H2O", "energy": 10000, "density": None, "packing_fraction": 0.5}, 0.2665),
-    # C3: user specified density only
-    ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 1}, 0.5330),
-    ({"sample_composition": "H2O", "energy": 10000, "density": 0.4985, "packing_fraction": 1}, 0.2665),
-    # C4: user specified a standard density and a packing fraction
-    ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 0.5}, 0.2665),
-]
-
-
-@pytest.mark.parametrize("inputs, expected", params_mu)
-def test_compute_mu_using_xraydb(inputs, expected):
+@pytest.mark.parametrize(
+    "inputs, expected_mu",
+    [
+        # Test whether the function returns the correct mu
+        (  # C1: No density or packing fraction provided, expect to compute mu based on standard density
+            {
+                "sample_composition": "H2O",
+                "energy": 10000,
+                "density": None,
+                "packing_fraction": 1,
+            },
+            0.5330,
+        ),
+        (  # C2: Packing fraction (=0.5) provided only, expect to return half of mu based on standard density
+            {
+                "sample_composition": "H2O",
+                "energy": 10000,
+                "density": None,
+                "packing_fraction": 0.5,
+            },
+            0.2665,
+        ),
+        (  # C3: Density provided only, expect to compute mu based on density
+            # 1. Standard density provided, expect to return the same mu as C1
+            {
+                "sample_composition": "H2O",
+                "energy": 10000,
+                "density": 0.997,
+                "packing_fraction": 1,
+            },
+            0.5330,
+        ),
+        (  # 2. Lower density for H2O (half of standard), expect to return half of mu based on standard density
+            {
+                "sample_composition": "H2O",
+                "energy": 10000,
+                "density": 0.4985,
+                "packing_fraction": 1,
+            },
+            0.2665,
+        ),
+        (  # C4: Both standard density and packing fraction are provided, expect to compute the same mu as C2
+            {
+                "sample_composition": "H2O",
+                "energy": 10000,
+                "density": 0.997,
+                "packing_fraction": 0.5,
+            },
+            0.2665,
+        ),
+    ],
+)
+def test_compute_mu_using_xraydb(inputs, expected_mu):
     actual_mu = compute_mu_using_xraydb(
         inputs["sample_composition"],
         inputs["energy"],
         density=inputs["density"],
         packing_fraction=inputs["packing_fraction"],
     )
-    assert actual_mu == pytest.approx(expected, rel=0.01, abs=0.1)
+    assert actual_mu == pytest.approx(expected_mu, rel=0.01, abs=0.1)

From 0bdbbb48a8c9fff3e9a2c9a715baa04dd08e9164 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Fri, 27 Dec 2024 21:18:59 -0500
Subject: [PATCH 06/11] enforce requirement to specify either density or
 packing fraction

---
 src/diffpy/utils/tools.py | 31 +++++++++++----
 tests/test_tools.py       | 82 ++++++++++++++++++++-------------------
 2 files changed, 66 insertions(+), 47 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index 7144a9bb..d8b59f10 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -1,5 +1,6 @@
 import importlib.metadata
 import json
+import warnings
 from copy import copy
 from pathlib import Path
 
@@ -210,12 +211,12 @@ def get_package_info(package_names, metadata=None):
     return metadata
 
 
-def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):
+def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None, packing_fraction=None):
     """Compute the attenuation coefficient (mu) using the XrayDB database.
 
     Computes mu based on the sample composition and energy.
-    User can provide a measured density or an estimated packing fraction.
-    Specifying the density is recommended, though not required for some pure or standard materials.
+    User should provide a sample mass density or a packing fraction.
+    If neither density nor packing fraction is specified, or if both are specified, a ValueError will be raised.
     Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu.
 
     Parameters
@@ -223,10 +224,10 @@ def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fr
     sample_composition : str
         The chemical formula or the name of the material.
     energy : float
-        The energy in keV.
-    density : float, optional, Default is None
+        The energy of the incident x-rays in keV.
+    sample_mass_density : float, optional, Default is None
         The mass density of the packed powder/sample in gr/cm^3.
-    packing_fraction : float, optional, Default is 1
+    packing_fraction : float, optional, Default is None
         The fraction of sample in the capillary (between 0 and 1).
 
     Returns
@@ -234,5 +235,21 @@ def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fr
     mu : float
         The attenuation coefficient mu in mm^{-1}.
     """
-    mu = material_mu(sample_composition, energy * 1000, density=density, kind="total") * packing_fraction / 10
+    if (sample_mass_density is None and packing_fraction is None) or (
+        sample_mass_density is not None and packing_fraction is not None
+    ):
+        raise ValueError(
+            "You must specify either sample_mass_density or packing_fraction, but not both. "
+            "Please rerun specifying only one."
+        )
+    if sample_mass_density is not None:
+        mu = material_mu(sample_composition, energy * 1000, density=sample_mass_density, kind="total") / 10
+    else:
+        warnings.warn(
+            "Warning: Density is set to None if a packing fraction is specified, "
+            "which may cause errors for some materials. "
+            "We recommend specifying sample mass density for now. "
+            "Auto-density calculation is coming soon."
+        )
+        mu = material_mu(sample_composition, energy * 1000, density=None, kind="total") * packing_fraction / 10
     return mu
diff --git a/tests/test_tools.py b/tests/test_tools.py
index 06202cdf..a3363320 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -171,59 +171,61 @@ def test_get_package_info(monkeypatch, inputs, expected):
     "inputs, expected_mu",
     [
         # Test whether the function returns the correct mu
-        (  # C1: No density or packing fraction (only for known material), expect to get mu from database
+        (  # C1: Composition, energy, and mass density provided, expect to get mu based on mass density
+            # 1. Fully dense mass density
+            {"sample_composition": "quartz", "energy": 10, "sample_mass_density": 2.65},
+            5.0368,
+        ),
+        (  # 2. Measured mass density
             {
-                "sample_composition": "H2O",
-                "energy": 10,
+                "sample_composition": "ZrO2",
+                "energy": 17.445,
+                "sample_mass_density": 1.009,
             },
-            0.5330,
+            1.2522,
         ),
-        (  # C2: Packing fraction (=0.5) provided only (only for known material)
+        (  # C2: Composition, energy, and packing fraction provided, expect to get mu based on packing fraction
+            # Reuse pattern from C1.1 here
             {
-                "sample_composition": "H2O",
+                "sample_composition": "quartz",
                 "energy": 10,
                 "packing_fraction": 0.5,
             },
-            0.2665,
+            2.5184,
         ),
-        (  # C3: Density provided only, expect to compute mu based on it
-            # 1. Known material
+    ],
+)
+def test_compute_mu_using_xraydb(inputs, expected_mu):
+    actual_mu = compute_mu_using_xraydb(**inputs)
+    assert actual_mu == pytest.approx(expected_mu, rel=1e-6, abs=1e-4)
+
+
+@pytest.mark.parametrize(
+    "inputs",
+    [
+        # Test when the function raises ValueError
+        # C1: Both mass density and packing fraction are provided
+        (
             {
-                "sample_composition": "H2O",
+                "sample_composition": "quartz",
                 "energy": 10,
-                "density": 0.987,
-            },
-            0.5330,
+                "sample_mass_density": 2.65,
+                "packing_fraction": 1,
+            }
         ),
-        (  # 2. Unknown material
-            {
-                "sample_composition": "ZrO2",
-                "energy": 17,
-                "density": 1.009,
-            },
-            1.252,
-        ),
-        (  # C4: Both density and packing fraction are provided, expect to compute mu based on both
-            # 1. Known material
+        # C2: None of mass density or packing fraction are provided
+        (
             {
-                "sample_composition": "H2O",
+                "sample_composition": "quartz",
                 "energy": 10,
-                "density": 0.997,
-                "packing_fraction": 0.5,
-            },
-            0.2665,
-        ),
-        (  # 2. Unknown material
-            {
-                "sample_composition": "ZrO2",
-                "energy": 17,
-                "density": 1.009,
-                "packing_fraction": 0.5,
-            },
-            0.626,
+            }
         ),
     ],
 )
-def test_compute_mu_using_xraydb(inputs, expected_mu):
-    actual_mu = compute_mu_using_xraydb(**inputs)
-    assert actual_mu == pytest.approx(expected_mu, rel=0.01, abs=0.1)
+def test_compute_mu_using_xraydb_bad(inputs):
+    with pytest.raises(
+        ValueError,
+        match="You must specify either sample_mass_density or packing_fraction, but not both. "
+        "Please rerun specifying only one.",
+    ):
+        compute_mu_using_xraydb(**inputs)

From 00f36ad2ff38985ce74c26563cc13887abd7e735 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Sat, 28 Dec 2024 23:35:37 -0500
Subject: [PATCH 07/11] add notimplementederror

---
 src/diffpy/utils/tools.py | 29 +++++++++++++++++++----------
 tests/test_tools.py       |  9 ---------
 2 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index d8b59f10..e1e7ad0a 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -211,6 +211,14 @@ def get_package_info(package_names, metadata=None):
     return metadata
 
 
+def get_density_from_cloud(sample_composition, mp_token=""):
+    """Function to get material density from the MP database.
+
+    It is not implemented yet.
+    """
+    raise NotImplementedError
+
+
 def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None, packing_fraction=None):
     """Compute the attenuation coefficient (mu) using the XrayDB database.
 
@@ -242,14 +250,15 @@ def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None
             "You must specify either sample_mass_density or packing_fraction, but not both. "
             "Please rerun specifying only one."
         )
-    if sample_mass_density is not None:
-        mu = material_mu(sample_composition, energy * 1000, density=sample_mass_density, kind="total") / 10
-    else:
-        warnings.warn(
-            "Warning: Density is set to None if a packing fraction is specified, "
-            "which may cause errors for some materials. "
-            "We recommend specifying sample mass density for now. "
-            "Auto-density calculation is coming soon."
-        )
-        mu = material_mu(sample_composition, energy * 1000, density=None, kind="total") * packing_fraction / 10
+    if packing_fraction is None:
+        packing_fraction = 1
+        try:
+            sample_mass_density = get_density_from_cloud(sample_composition) * packing_fraction
+        except NotImplementedError:
+            warnings.warn(
+                "Density computation is not implemented right now. "
+                "Please rerun specifying a sample mass density."
+            )
+    energy_eV = energy * 1000
+    mu = material_mu(sample_composition, energy_eV, density=sample_mass_density, kind="total") / 10
     return mu
diff --git a/tests/test_tools.py b/tests/test_tools.py
index a3363320..d02996ca 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -184,15 +184,6 @@ def test_get_package_info(monkeypatch, inputs, expected):
             },
             1.2522,
         ),
-        (  # C2: Composition, energy, and packing fraction provided, expect to get mu based on packing fraction
-            # Reuse pattern from C1.1 here
-            {
-                "sample_composition": "quartz",
-                "energy": 10,
-                "packing_fraction": 0.5,
-            },
-            2.5184,
-        ),
     ],
 )
 def test_compute_mu_using_xraydb(inputs, expected_mu):

From 255c603a54ccc0d680a8a851308355114663ca6c Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Sun, 29 Dec 2024 15:07:29 -0500
Subject: [PATCH 08/11] refactor: rearrange error msg and docstring, update
 condition in function

---
 src/diffpy/utils/tools.py | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index e1e7ad0a..9c963e14 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -1,6 +1,5 @@
 import importlib.metadata
 import json
-import warnings
 from copy import copy
 from pathlib import Path
 
@@ -212,11 +211,15 @@ def get_package_info(package_names, metadata=None):
 
 
 def get_density_from_cloud(sample_composition, mp_token=""):
-    """Function to get material density from the MP database.
+    """Function to get material density from the MP or COD database.
 
     It is not implemented yet.
     """
-    raise NotImplementedError
+    raise NotImplementedError(
+        "So sorry, density computation from composition is not implemented right now. "
+        "We hope to have this implemented in the next release. "
+        "Please rerun specifying a sample mass density."
+    )
 
 
 def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None, packing_fraction=None):
@@ -250,15 +253,8 @@ def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None
             "You must specify either sample_mass_density or packing_fraction, but not both. "
             "Please rerun specifying only one."
         )
-    if packing_fraction is None:
-        packing_fraction = 1
-        try:
-            sample_mass_density = get_density_from_cloud(sample_composition) * packing_fraction
-        except NotImplementedError:
-            warnings.warn(
-                "Density computation is not implemented right now. "
-                "Please rerun specifying a sample mass density."
-            )
+    if packing_fraction is not None:
+        sample_mass_density = get_density_from_cloud(sample_composition) * packing_fraction
     energy_eV = energy * 1000
     mu = material_mu(sample_composition, energy_eV, density=sample_mass_density, kind="total") / 10
     return mu

From 5492ad8718b46854c8fc0530e9f1d28be4dba89e Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Sun, 29 Dec 2024 21:08:09 -0500
Subject: [PATCH 09/11] test: remove test for the correct mu, improve test
 comment for invalid inputs

---
 tests/test_tools.py | 30 +++---------------------------
 1 file changed, 3 insertions(+), 27 deletions(-)

diff --git a/tests/test_tools.py b/tests/test_tools.py
index d02996ca..d3f7cf16 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -167,35 +167,11 @@ def test_get_package_info(monkeypatch, inputs, expected):
     assert actual_metadata == expected
 
 
-@pytest.mark.parametrize(
-    "inputs, expected_mu",
-    [
-        # Test whether the function returns the correct mu
-        (  # C1: Composition, energy, and mass density provided, expect to get mu based on mass density
-            # 1. Fully dense mass density
-            {"sample_composition": "quartz", "energy": 10, "sample_mass_density": 2.65},
-            5.0368,
-        ),
-        (  # 2. Measured mass density
-            {
-                "sample_composition": "ZrO2",
-                "energy": 17.445,
-                "sample_mass_density": 1.009,
-            },
-            1.2522,
-        ),
-    ],
-)
-def test_compute_mu_using_xraydb(inputs, expected_mu):
-    actual_mu = compute_mu_using_xraydb(**inputs)
-    assert actual_mu == pytest.approx(expected_mu, rel=1e-6, abs=1e-4)
-
-
 @pytest.mark.parametrize(
     "inputs",
     [
-        # Test when the function raises ValueError
-        # C1: Both mass density and packing fraction are provided
+        # Test when the function has invalid inputs
+        # C1: Both mass density and packing fraction are provided, expect ValueError exception
         (
             {
                 "sample_composition": "quartz",
@@ -204,7 +180,7 @@ def test_compute_mu_using_xraydb(inputs, expected_mu):
                 "packing_fraction": 1,
             }
         ),
-        # C2: None of mass density or packing fraction are provided
+        # C2: None of mass density or packing fraction are provided, expect ValueError exception
         (
             {
                 "sample_composition": "quartz",

From a4a217d482af895970ea4934745b95fc45bd6497 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Sun, 29 Dec 2024 21:29:17 -0500
Subject: [PATCH 10/11] test: reformat tests

---
 tests/test_tools.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/tests/test_tools.py b/tests/test_tools.py
index d3f7cf16..91bf63bb 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -171,19 +171,17 @@ def test_get_package_info(monkeypatch, inputs, expected):
     "inputs",
     [
         # Test when the function has invalid inputs
-        # C1: Both mass density and packing fraction are provided, expect ValueError exception
-        (
+        (  # C1: Both mass density and packing fraction are provided, expect ValueError exception
             {
-                "sample_composition": "quartz",
+                "sample_composition": "SiO2",
                 "energy": 10,
                 "sample_mass_density": 2.65,
                 "packing_fraction": 1,
             }
         ),
-        # C2: None of mass density or packing fraction are provided, expect ValueError exception
-        (
+        (  # C2: None of mass density or packing fraction are provided, expect ValueError exception
             {
-                "sample_composition": "quartz",
+                "sample_composition": "SiO2",
                 "energy": 10,
             }
         ),

From dd52ad9b401eb9475fccfb57ee09297a02bafa58 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Sun, 29 Dec 2024 21:48:37 -0500
Subject: [PATCH 11/11] docs: improve docstring

---
 src/diffpy/utils/tools.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
index c562a2dd..036cc696 100644
--- a/src/diffpy/utils/tools.py
+++ b/src/diffpy/utils/tools.py
@@ -218,13 +218,14 @@ def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None
     Parameters
     ----------
     sample_composition : str
-        The chemical formula or the name of the material.
+        The chemical formula of the material.
     energy : float
         The energy of the incident x-rays in keV.
     sample_mass_density : float, optional, Default is None
-        The mass density of the packed powder/sample in gr/cm^3.
+        The mass density of the packed powder/sample in g/cm*3.
     packing_fraction : float, optional, Default is None
         The fraction of sample in the capillary (between 0 and 1).
+        Specify either sample_mass_density or packing_fraction but not both.
 
     Returns
     -------