Merge pull request #59 from ericpre/extend_public_API

Extend public API and fix documentation

doc/conf.py

@@ -14,19 +14,14 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
-import hyperspy.api as hs
 import numpydoc
 from packaging.version import Version
 
 
-# Set logging level to `ERROR` to avoid exspy warning in documentation
-hs.set_log_level("ERROR")
-
-
 # -- Project information -----------------------------------------------------
 
 project = "eXSpy"
-copyright = "2023, eSpy Developers"
+copyright = "2024, eXSpy Developers"
 author = "eXSpy Developers"
 
 
@@ -44,6 +39,7 @@
     "sphinx_copybutton",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
     "sphinx.ext.githubpages",
     "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
@@ -54,17 +50,13 @@
 linkcheck_ignore = [
     "https://doi.org/10.1021/acs.nanolett.5b00449",  # 403 Client Error: Forbidden for url
     "https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2006.01549.x",  # 403 Client Error: Forbidden for url
-    # Remove when setup
-    "https://github.com/hyperspy/exspy-demos",
-    "https://www.anaconda.com/blog/understanding-conda-and-pip",  # Transcient?
-    # Remove once it is merged and the links are working
-    "https://exspy.readthedocs.io",
-    "https://github.com/hyperspy/exspy/blob/main/releasing_guide.md",
+    "https://onlinelibrary.wiley.com/doi/10.1002/sia.5789",  # 403 Client Error: Forbidden for url
+    "https://onlinelibrary.wiley.com/doi/10.1002/jemt.20597",  # 403 Client Error: Forbidden for url
 ]
 
 intersphinx_mapping = {
     "dask": ("https://docs.dask.org/en/latest", None),
-    "hyperspy": ("https://hyperspy.org/hyperspy-doc/dev", None),
+    "hyperspy": ("https://hyperspy.org/hyperspy-doc/current", None),
     "kikuchipy": ("https://kikuchipy.org/en/latest/", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
     "numpy": ("https://numpy.org/doc/stable", None),
@@ -159,3 +151,9 @@
 towncrier_draft_autoversion_mode = "draft"
 towncrier_draft_include_empty = False
 towncrier_draft_working_directory = ".."
+
+doctest_global_setup = """
+import hyperspy.api as hs
+import exspy
+import numpy as np
+"""

doc/reference/index.rst

@@ -13,3 +13,5 @@ Reference
    material
    models
    signals
+   utils.eds
+   utils.eels

doc/reference/material.rst

@@ -6,10 +6,58 @@
 .. autosummary::
 
     atomic_to_weight
-    weight_to_atomic
     density_of_mixture
+    elements
     mass_absorption_coefficient
     mass_absorption_mixture
+    weight_to_atomic
 
 .. automodule:: exspy.material
-   :members:
+   :members:
+
+.. autoattribute:: exspy.material.elements
+   :annotation:
+
+Database of element properties. The following properties are included:
+
+.. code::
+
+    ├── Atomic_properties
+    │   ├── Binding_energies
+    │   └── Xray_lines
+    ├── General_properties
+    │   ├── Z
+    │   ├── atomic_weight
+    │   └── name
+    └── Physical_properties
+        └── density_gcm3
+
+Examples:
+
+.. code::
+
+    >>> exspy.material.elements.Fe.General_properties
+    ├── Z = 26
+    ├── atomic_weight = 55.845
+    └── name = iron
+    >>> exspy.material.elements.Fe.Physical_properties
+    └── density (g/cm^3) = 7.874
+    >>> exspy.material.elements.Fe.Atomic_properties.Xray_lines
+    ├── Ka
+    │   ├── energy (keV) = 6.404
+    │   └── weight = 1.0
+    ├── Kb
+    │   ├── energy (keV) = 7.0568
+    │   └── weight = 0.1272
+    ├── La
+    │   ├── energy (keV) = 0.705
+    │   └── weight = 1.0
+    ├── Lb3
+    │   ├── energy (keV) = 0.792
+    │   └── weight = 0.02448
+    ├── Ll
+    │   ├── energy (keV) = 0.615
+    │   └── weight = 0.3086
+    └── Ln
+        ├── energy (keV) = 0.62799
+        └── weight = 0.12525

doc/reference/utils.eds.rst

@@ -0,0 +1,17 @@
+:mod:`exspy.utils.eds`
+----------------------
+
+.. currentmodule:: exspy.utils.eds
+
+
+.. autosummary::
+   cross_section_to_zeta
+   electron_range
+   get_xray_lines_near_energy
+   take_off_angle
+   xray_range
+   zeta_to_cross_section
+
+
+.. automodule:: exspy.utils.eds
+   :members:

doc/reference/utils.eels.rst

@@ -0,0 +1,17 @@
+:mod:`exspy.utils.eels`
+-----------------------
+
+.. currentmodule:: exspy.utils.eels
+
+
+.. autosummary::
+   effective_angle
+   get_edges_near_energy
+   get_info_from_edges
+   iMFP_angular_correction
+   iMFP_Iakoubovskii
+   iMFP_TPP2M
+
+
+.. automodule:: exspy.utils.eels
+   :members: