Merge pull request #23 from kmnhan/dev

Added new interface for fitting, see #22 for discussions. Made loader argument optional for `erlab.io.loader_context` so it can be used to just change the data directory. Momentum conversion has been rewritten using `xarray.apply_ufunc`, and is now dask-compatible. It also automatically determines the current energy axis (kinetic or binding).
kmnhan · Apr 22, 2024 · 4514a23 · 4514a23
2 parents 3304a18 + 156cef8
commit 4514a23
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diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -33,4 +33,4 @@ qtpy
 igor2>=0.5.6
 ipywidgets
 ipython
--e git+https://github.com/kmnhan/erlabpy.git#egg=erlab
+-e .
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -5,7 +5,9 @@
 # -- Imports -----------------------------------------------------------------
 
 import importlib.metadata
+import inspect
 import os
+import sys
 
 import pybtex.plugin
 import pybtex.style.formatting
@@ -37,7 +39,7 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     # "sphinx_autodoc_typehints",
-    "sphinx.ext.viewcode",
+    "sphinx.ext.linkcode",
     "sphinx.ext.mathjax",
     "sphinx.ext.intersphinx",
     "matplotlib.sphinxext.plot_directive",
@@ -61,6 +63,58 @@
 # nitpicky = False
 # nitpick_ignore = [("py:class", "numpy.float64")]
 
+# -- Linkcode settings -------------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/linkcode.html
+
+
+# based on numpy doc/source/conf.py
+def linkcode_resolve(domain, info):
+    """
+    Determine the URL corresponding to Python object
+    """
+    if domain != "py":
+        return None
+
+    modname = info["module"]
+    fullname = info["fullname"]
+
+    submod = sys.modules.get(modname)
+    if submod is None:
+        return None
+
+    obj = submod
+    for part in fullname.split("."):
+        try:
+            obj = getattr(obj, part)
+        except AttributeError:
+            return None
+
+    try:
+        fn = inspect.getsourcefile(inspect.unwrap(obj))
+    except TypeError:
+        fn = None
+    if not fn:
+        return None
+
+    try:
+        source, lineno = inspect.getsourcelines(obj)
+    except OSError:
+        lineno = None
+
+    if lineno:
+        linespec = f"#L{lineno}-L{lineno + len(source) - 1}"
+    else:
+        linespec = ""
+
+    import erlab
+
+    fn = os.path.relpath(fn, start=os.path.dirname(erlab.__file__))
+
+    return (
+        f"https://github.com/kmnhan/erlabpy/blob/"
+        f"v{version}/src/erlab/{fn}{linespec}"
+    )
+
 
 # -- Autosummary and autodoc settings ----------------------------------------
 
@@ -131,6 +185,7 @@
     "iminuit": ("https://scikit-hep.org/iminuit/", None),
     "cmasher": ("https://cmasher.readthedocs.io/", None),
     "ipywidgets": ("https://ipywidgets.readthedocs.io/en/stable/", None),
+    "joblib": ("https://joblib.readthedocs.io/en/latest/", None),
 }
 
 

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -120,8 +120,7 @@ reflected in the package without having to reinstall it. Before installing:
 
    .. hint::
 
-     | If using conda, replace :code:`mamba` with :code:`conda`.
-     | If on Apple silicon, replace :code:`environment.yml` with :code:`environment_apple.yml` to use `Accelerate <https://developer.apple.com/accelerate/>`_ instead of `OpenBLAS <https://en.wikipedia.org/wiki/OpenBLAS>`_.
+     If using conda, replace :code:`mamba` with :code:`conda`.
 
    .. code-block:: sh
 
@@ -152,8 +151,7 @@ Updating the editable installation
 
   .. hint::
 
-    | If using conda, replace :code:`mamba` with :code:`conda`.
-    | If on Apple silicon, replace :code:`environment.yml` with :code:`environment_apple.yml`.
+    If using conda, replace :code:`mamba` with :code:`conda`.
 
   .. code-block:: bash
 
@@ -305,6 +303,16 @@ Code standards
               super().__init__()
               self.setupUi(self)
 
+- Please try to add type annotations to your code. This will help with code completion
+  and static analysis.
+
+- Although it would be great to enforce static type checking, our code base currently
+  does not pass the tests. It would require a large amount of work to get it to pass, so
+  we are not enforcing it at the moment, and it is unclear whether the extra effort is
+  worth it. See `this article
+  <https://typing.readthedocs.io/en/latest/source/typing_anti_pitch.html>`_ for some
+  reasons to avoid static type checking.
+
 Documentation
 =============
 

diff --git a/docs/source/erlab.parallel.rst b/docs/source/erlab.parallel.rst
@@ -13,6 +13,5 @@
 
    .. autosummary::
 
-      is_notebook
       joblib_progress
       joblib_progress_qt
diff --git a/docs/source/getting-started.rst b/docs/source/getting-started.rst
@@ -5,9 +5,8 @@ Getting Started
 Installing
 ==========
 
-The recommended way to install ERLabPy is via `conda
-<https://docs.conda.io/en/latest/>`_. If you do not have conda installed, follow
-the :ref:`installation instructions <Installing conda>`. Once you have a working
+The recommended way to install ERLabPy is via conda. If you do not have conda installed,
+follow the :ref:`installation instructions <Installing conda>`. Once you have a working
 conda environment, you can install ERLabPy with the conda command line tool: ::
 
   conda install -c conda-forge erlab

diff --git a/docs/source/refs.bib b/docs/source/refs.bib
@@ -1,3 +1,38 @@
+@article{dynes1978dynes,
+  author  = {Dynes, R. C. and Narayanamurti, V. and Garno, J. P.},
+  title   = {Direct Measurement of Quasiparticle-Lifetime Broadening in a Strong-Coupled Superconductor},
+  journal = {Phys. Rev. Lett.},
+  volume  = {41},
+  number  = {21},
+  pages   = {1509-1512},
+  doi     = {10.1103/PhysRevLett.41.1509},
+  year    = {1978},
+  type    = {Journal Article}
+}
+
+@article{he2017mingrad,
+  author  = {He, Y. and Wang, Y. and Shen, Z.-X.},
+  title   = {Visualizing dispersive features in 2D image via minimum gradient method},
+  journal = {Rev. Sci. Instrum.},
+  volume  = {88},
+  number  = {7},
+  pages   = {073903},
+  doi     = {10.1063/1.4993919},
+  year    = {2017},
+  type    = {Journal Article}
+}
+
+@article{hoyer2017xarray,
+  title     = {xarray: {N-D} labeled arrays and datasets in {Python}},
+  author    = {Hoyer, S. and J. Hamman},
+  journal   = {J. Open Res. Softw.},
+  volume    = {5},
+  number    = {1},
+  year      = {2017},
+  publisher = {Ubiquity Press},
+  doi       = {10.5334/jors.148}
+}
+
 @article{ishida2018kconv,
   author  = {Ishida, Y. and Shin, S.},
   title   = {Functions to map photoelectron distributions in a variety of setups in angle-resolved photoemission spectroscopy},
@@ -10,16 +45,14 @@ @article{ishida2018kconv
   type    = {Journal Article}
 }
 
-@article{seah1979imfp,
-  author  = {Seah, M. P. and Dench, W. A.},
-  title   = {Quantitative electron spectroscopy of surfaces: A standard data base for electron inelastic mean free paths in solids},
-  journal = {Surf. Interface Anal.},
-  volume  = {1},
-  number  = {1},
-  pages   = {2-11},
-  issn    = {0142-2421},
-  doi     = {10.1002/sia.740010103},
-  year    = {1979},
+@article{tusche2015spin,
+  author  = {Tusche, Christian and Krasyuk, Alexander and Kirschner, Jürgen},
+  title   = {Spin resolved bandstructure imaging with a high resolution momentum microscope},
+  journal = {Ultramicroscopy},
+  volume  = {159},
+  pages   = {520-529},
+  doi     = {10.1016/j.ultramic.2015.03.020},
+  year    = {2015},
   type    = {Journal Article}
 }
 
@@ -39,6 +72,19 @@ @inproceedings{schirra2008polygon
   type      = {Conference Proceedings}
 }
 
+@article{seah1979imfp,
+  author  = {Seah, M. P. and Dench, W. A.},
+  title   = {Quantitative electron spectroscopy of surfaces: A standard data base for electron inelastic mean free paths in solids},
+  journal = {Surf. Interface Anal.},
+  volume  = {1},
+  number  = {1},
+  pages   = {2-11},
+  issn    = {0142-2421},
+  doi     = {10.1002/sia.740010103},
+  year    = {1979},
+  type    = {Journal Article}
+}
+
 @article{zhang2011curvature,
   author  = {Zhang, P. and Richard, P. and Qian, T. and Xu, Y.-M. and Dai, X. and Ding, H.},
   title   = {A precise method for visualizing dispersive features in image plots},
@@ -50,38 +96,3 @@ @article{zhang2011curvature
   year    = {2011},
   type    = {Journal Article}
 }
-
-@article{he2017mingrad,
-  author  = {He, Y. and Wang, Y. and Shen, Z.-X.},
-  title   = {Visualizing dispersive features in 2D image via minimum gradient method},
-  journal = {Rev. Sci. Instrum.},
-  volume  = {88},
-  number  = {7},
-  pages   = {073903},
-  doi     = {10.1063/1.4993919},
-  year    = {2017},
-  type    = {Journal Article}
-}
-
-@article{hoyer2017xarray,
-  title     = {xarray: {N-D} labeled arrays and datasets in {Python}},
-  author    = {Hoyer, S. and J. Hamman},
-  journal   = {J. Open Res. Softw.},
-  volume    = {5},
-  number    = {1},
-  year      = {2017},
-  publisher = {Ubiquity Press},
-  doi       = {10.5334/jors.148}
-}
-
-@article{dynes1978dynes,
-  author  = {Dynes, R. C. and Narayanamurti, V. and Garno, J. P.},
-  title   = {Direct Measurement of Quasiparticle-Lifetime Broadening in a Strong-Coupled Superconductor},
-  journal = {Phys. Rev. Lett.},
-  volume  = {41},
-  number  = {21},
-  pages   = {1509-1512},
-  doi     = {10.1103/PhysRevLett.41.1509},
-  year    = {1978},
-  type    = {Journal Article}
-}