xarpes 0.3.0__tar.gz → 0.3.1__tar.gz

{xarpes-0.3.0 → xarpes-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xarpes
-Version: 0.3.0
+Version: 0.3.1
 Summary: Extraction from angle resolved photoemission spectra
 Author: xARPES Developers
 Requires-Python: >=3.7.0
@@ -17,6 +17,7 @@ Requires-Dist: scipy
 Requires-Dist: lmfit
 Requires-Dist: pyqt5
 Requires-Dist: ipympl
+Requires-Dist: ipykernel<6.32.0
 Project-URL: Documentation, https://xarpes.github.io
 
 # xARPES 
@@ -35,7 +36,7 @@ Contributions to the code are most welcome. xARPES is intended to co-develop alo
 
 # Installation
 
-xARPES can be installed in several ways depending on your workflow:  
+xARPES installation can be divided into graphical package manager instructions, and command-line instructions for either conda or pip. With command-line instructions, an editable installation of xARPES can be created; on Windows, we strongly recommend Windows Powershell to do so. Here is a summary for the three options:
 - via a graphical package manager (Anaconda Navigator, VS Code, PyCharm, Spyder, JupyterLab)  
 - via conda-forge, out-of-the-box or editable installation, sourcing the [conda-forge package](https://anaconda.org/conda-forge/xarpes).  
 - via Pip, out-of-the-box or editable installation, sourcing the [PyPI package](https://pypi.org/project/xarpes).
@@ -89,14 +90,19 @@ Create and activate an environment:
 
 ### Installing xARPES
 
-#### Option A — User installation (from conda-forge)
+#### Option A — Out-of-the-box installation (from conda-forge)
 
     conda install conda-forge::xarpes
 
-#### Option B — Developer installation (GitHub, editable)
+#### Option B — Editable installation (GitHub)
+
+First, clone the repository:
 
     git clone git@github.com:xARPES/xARPES.git  
-    cd xARPES  
+    cd xARPES
+
+Then perform editable installation (this mixes conda and pip):
+
     pip install -e .
 
 ## Pip installation
@@ -120,25 +126,26 @@ Upgrade pip:
 
 ### Installing xARPES
 
-#### Option A — User installation (PyPI)
+#### Option A — Out-of-the-box installation (PyPI)
 
     python3 -m pip install xarpes
 
-#### Option B — Developer installation (GitHub, editable)
+#### Option B — Editable installation (GitHub)
+
+First, clone the repository:
 
     git clone git@github.com:xARPES/xARPES.git  
-    cd xARPES  
-    python3 -m pip install -e .
+    cd xARPES
 
-# Examples
+Then perform editable installation:
 
-After installation of xARPES, the `examples/` folder can be downloaded to the current directory:
+    pip install -e .
 
-    xarpes_download_examples
+# Examples
 
-Equivalently:
+After installation of xARPES, the `examples/` folder can be downloaded to the current directory:
 
-    python3 -c "import xarpes; xarpes.download_examples()"
+    python -c "import xarpes; xarpes.download_examples()"
 
 # Execution
 
@@ -158,3 +165,4 @@ Copyright (C) 2025 xARPES Developers
 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.
 
 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+

{xarpes-0.3.0 → xarpes-0.3.1}/README.md

@@ -14,7 +14,7 @@ Contributions to the code are most welcome. xARPES is intended to co-develop alo
 
 # Installation
 
-xARPES can be installed in several ways depending on your workflow:  
+xARPES installation can be divided into graphical package manager instructions, and command-line instructions for either conda or pip. With command-line instructions, an editable installation of xARPES can be created; on Windows, we strongly recommend Windows Powershell to do so. Here is a summary for the three options:
 - via a graphical package manager (Anaconda Navigator, VS Code, PyCharm, Spyder, JupyterLab)  
 - via conda-forge, out-of-the-box or editable installation, sourcing the [conda-forge package](https://anaconda.org/conda-forge/xarpes).  
 - via Pip, out-of-the-box or editable installation, sourcing the [PyPI package](https://pypi.org/project/xarpes).
@@ -68,14 +68,19 @@ Create and activate an environment:
 
 ### Installing xARPES
 
-#### Option A — User installation (from conda-forge)
+#### Option A — Out-of-the-box installation (from conda-forge)
 
     conda install conda-forge::xarpes
 
-#### Option B — Developer installation (GitHub, editable)
+#### Option B — Editable installation (GitHub)
+
+First, clone the repository:
 
     git clone git@github.com:xARPES/xARPES.git  
-    cd xARPES  
+    cd xARPES
+
+Then perform editable installation (this mixes conda and pip):
+
     pip install -e .
 
 ## Pip installation
@@ -99,25 +104,26 @@ Upgrade pip:
 
 ### Installing xARPES
 
-#### Option A — User installation (PyPI)
+#### Option A — Out-of-the-box installation (PyPI)
 
     python3 -m pip install xarpes
 
-#### Option B — Developer installation (GitHub, editable)
+#### Option B — Editable installation (GitHub)
+
+First, clone the repository:
 
     git clone git@github.com:xARPES/xARPES.git  
-    cd xARPES  
-    python3 -m pip install -e .
+    cd xARPES
 
-# Examples
+Then perform editable installation:
 
-After installation of xARPES, the `examples/` folder can be downloaded to the current directory:
+    pip install -e .
 
-    xarpes_download_examples
+# Examples
 
-Equivalently:
+After installation of xARPES, the `examples/` folder can be downloaded to the current directory:
 
-    python3 -c "import xarpes; xarpes.download_examples()"
+    python -c "import xarpes; xarpes.download_examples()"
 
 # Execution
 
@@ -136,4 +142,4 @@ Copyright (C) 2025 xARPES Developers
 
 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.
 
-This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

{xarpes-0.3.0 → xarpes-0.3.1}/dev_tools/Rmd2py.py

@@ -88,8 +88,11 @@ def convert_rmd_to_py(rmd_path: str) -> None:
                 if "%matplotlib widget" in line or "%matplotlib inline" in line:
                     continue
 
+                # Remove global Jupyter hooks (e.g. get_ipython().events.register(...))
+                if "get_ipython" in line:
+                    continue
+
                 # Replace first Jupyter magic comment with Qt5Agg backend
-                # (lines like "# %load_ext ..." often end up as "#%..." after export)
                 if line.replace(" ", "").startswith("#%"):
                     if first_magic_comment:
                         text.write("import matplotlib as mpl\n")
@@ -99,6 +102,7 @@ def convert_rmd_to_py(rmd_path: str) -> None:
 
                 # Otherwise, write code verbatim
                 text.write(line)
+
             else:
                 # ---- Outside code fence: Markdown -> Python comments ---------------
                 if line.strip() == "":
@@ -146,4 +150,4 @@ def main() -> None:
             convert_rmd_to_py(rmd)
 
 if __name__ == "__main__":
-    main()
+    main()

{xarpes-0.3.0 → xarpes-0.3.1}/examples/graphene/graphene.Rmd

@@ -8,7 +8,7 @@ jupyter:
       format_version: '1.2'
       jupytext_version: 1.15.2
   kernelspec:
-    display_name: Python 3 (ipykernel)
+    display_name: 3.7_env
     language: python
     name: python3
 ---
@@ -23,11 +23,16 @@ jupyter:
 # %load_ext autoreload
 # %autoreload 2
 
+# Necessary packages
 import xarpes
 import matplotlib.pyplot as plt
 import os
 
+# Default plot configuration from xarpes.plotting.py
 xarpes.plot_settings('default')
+
+# If needed, close figures before running other cells, if figures show up in the wrong places.
+# get_ipython().events.register('pre_run_cell', lambda info: plt.close('all'))
 ```
 
 ```{python}
@@ -118,6 +123,11 @@ ax = fig.gca()
 fig = mdcs.visualize_guess(distributions=guess_dists, energy_value=energy_value, ax=ax)
 ```
 
+#### Note on interactive figures
+- Operability of the interactive figure is sensitive to configuration of the plotting backend.
+- With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
+- As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+
 ```{python}
 # %matplotlib widget
 
@@ -129,6 +139,15 @@ mdcs = xarpes.MDCs(*bmap.mdc_set(angle_min, angle_max, energy_range=energy_range
 fig = mdcs.fit_selection(distributions=guess_dists, ax=ax)
 ```
 
+```{python}
+# # %matplotlib widget
+
+# fig = plt.figure(figsize=(7, 5))
+# ax = fig.gca()
+
+# mdcs.plot(energy_range=[-0.15, -0.05], ax=ax)
+```
+
 ```{python}
 # %matplotlib inline
 
@@ -152,6 +171,8 @@ fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 ```
 
 ```{python}
+# %matplotlib inline
+
 fig = plt.figure(figsize=(7, 5))
 ax = fig.gca()
 
@@ -163,7 +184,8 @@ ax.errorbar(self_energy.enel_range, self_energy.real,
             yerr=stdv * self_energy.real_sigma, label =r"$\Sigma'(E)$")
 ax.set_xlabel(r'$E-\mu$ (eV)'); ax.set_ylabel(r"$\Sigma'(E), -\Sigma''(E)$ (eV)")
 
-plt.legend(); plt.show()
+plt.legend()
+plt.show()
 ```
 
 ```{python}
@@ -195,22 +217,7 @@ self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_
 ```
 
 ```{python}
-# %matplotlib inline
-
-fig = plt.figure(figsize=(8, 5))
-ax = fig.gca()
 
-from xarpes.constants import stdv
-
-ax.errorbar(self_left.peak_positions, self_left.enel_range, 
-            xerr=stdv * self_left.peak_positions_sigma,
-           markersize=2, color='tab:red', label=self_left.label)
-
-ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
-            xerr=stdv * self_energy.peak_positions_sigma,
-           markersize=2, color='tab:blue', label=self_energy.label)
-
-fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 ```
 
 ```{python}
@@ -218,11 +225,22 @@ fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 ```
 
 ```{python}
+# # %matplotlib inline
 
-```
+# fig = plt.figure(figsize=(8, 5))
+# ax = fig.gca()
 
-```{python}
+# from xarpes.constants import stdv
 
+# ax.errorbar(self_left.peak_positions, self_left.enel_range, 
+#             xerr=stdv * self_left.peak_positions_sigma,
+#            markersize=2, color='tab:red', label=self_left.label)
+
+# ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
+#             xerr=stdv * self_energy.peak_positions_sigma,
+#            markersize=2, color='tab:blue', label=self_energy.label)
+
+# fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 ```
 
 ```{python}
@@ -288,8 +306,6 @@ fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 ```
 
 ```{python}
-
-
 # # %matplotlib inline
 
 # fig = plt.figure(figsize=(8, 6)); ax = fig.gca()
@@ -398,7 +414,3 @@ fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
 # fig = mdcs.plot(distributions=guess_dists, ax=ax, energy_value=-0.003)
 ```
-
-```{python}
-
-```

{xarpes-0.3.0 → xarpes-0.3.1}/examples/graphene/graphene.py

@@ -9,12 +9,16 @@
 import matplotlib as mpl
 mpl.use('Qt5Agg')
 
+# Necessary packages
 import xarpes
 import matplotlib.pyplot as plt
 import os
 
+# Default plot configuration from xarpes.plotting.py
 xarpes.plot_settings('default')
 
+# If needed, close figures before running other cells, if figures show up in the wrong places.
+
 script_dir = xarpes.set_script_dir()
 
 dfld = 'data_sets'    # Folder containing the data
@@ -89,6 +93,11 @@ ax = fig.gca()
 
 fig = mdcs.visualize_guess(distributions=guess_dists, energy_value=energy_value, ax=ax)
 
+# #### Note on interactive figures
+# - Operability of the interactive figure is sensitive to configuration of the plotting backend.
+# - With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
+# - As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+
 
 fig = plt.figure(figsize=(7, 5))
 ax = fig.gca()
@@ -98,6 +107,12 @@ mdcs = xarpes.MDCs(*bmap.mdc_set(angle_min, angle_max, energy_range=energy_range
 fig = mdcs.fit_selection(distributions=guess_dists, ax=ax)
 
 
+# fig = plt.figure(figsize=(7, 5))
+# ax = fig.gca()
+
+# mdcs.plot(energy_range=[-0.15, -0.05], ax=ax)
+
+
 self_energy = xarpes.SelfEnergy(*mdcs.expose_parameters(select_label='Linear_test_1',
                                 fermi_velocity=2.85, fermi_wavevector=0.358))
 
@@ -113,6 +128,7 @@ ax.errorbar(self_energy.peak_positions, self_energy.enel_range,
 
 fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
+
 fig = plt.figure(figsize=(7, 5))
 ax = fig.gca()
 
@@ -124,7 +140,8 @@ ax.errorbar(self_energy.enel_range, self_energy.real,
             yerr=stdv * self_energy.real_sigma, label =r"$\Sigma'(E)$")
 ax.set_xlabel(r'$E-\mu$ (eV)'); ax.set_ylabel(r"$\Sigma'(E), -\Sigma''(E)$ (eV)")
 
-plt.legend(); plt.show()
+plt.legend()
+plt.show()
 
 
 angle_min2 = -1e6
@@ -150,26 +167,24 @@ fig = mdc2.fit_selection(distributions=guess_dists2, show=False, fig_close=True)
 self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_1'))
 
 
-fig = plt.figure(figsize=(8, 5))
-ax = fig.gca()
 
-from xarpes.constants import stdv
 
-ax.errorbar(self_left.peak_positions, self_left.enel_range, 
-            xerr=stdv * self_left.peak_positions_sigma,
-           markersize=2, color='tab:red', label=self_left.label)
-
-ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
-            xerr=stdv * self_energy.peak_positions_sigma,
-           markersize=2, color='tab:blue', label=self_energy.label)
-
-fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
 
+# fig = plt.figure(figsize=(8, 5))
+# ax = fig.gca()
 
+# from xarpes.constants import stdv
 
+# ax.errorbar(self_left.peak_positions, self_left.enel_range, 
+#             xerr=stdv * self_left.peak_positions_sigma,
+#            markersize=2, color='tab:red', label=self_left.label)
 
+# ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
+#             xerr=stdv * self_energy.peak_positions_sigma,
+#            markersize=2, color='tab:blue', label=self_energy.label)
 
+# fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
 
 # fig = plt.figure(figsize=(8, 5))
@@ -223,8 +238,6 @@ fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 #      distributions=guess_dists, ax=ax, show=True)
 
 
-
-
 # fig = plt.figure(figsize=(8, 6)); ax = fig.gca()
 
 # guess_dists = xarpes.CreateDistributions([

{xarpes-0.3.0 → xarpes-0.3.1}/examples/srtio3/srtio3.Rmd

@@ -7,7 +7,7 @@ jupyter:
       format_version: '1.2'
       jupytext_version: 1.15.2
   kernelspec:
-    display_name: Python 3 (ipykernel)
+    display_name: 3.7_env
     language: python
     name: python3
 ---
@@ -20,11 +20,16 @@ jupyter:
 # %load_ext autoreload
 # %autoreload 2
 
+# Necessary packages
 import xarpes
 import matplotlib.pyplot as plt
 import os
 
+# Default plot configuration from xarpes.plotting.py
 xarpes.plot_settings('default')
+
+# If needed, close figures before running other cells, if figures show up in the wrong places.
+get_ipython().events.register('pre_run_cell', lambda info: plt.close('all'))
 ```
 
 ```{python}
@@ -98,6 +103,11 @@ fig = mdcs.visualize_guess(distributions=guess_dists, matrix_element=mat_el,
                            matrix_args=mat_args, energy_value=-0.000, ax=ax)
 ```
 
+#### Note on interactive figures
+- Operability of the interactive figure is sensitive to configuration of the plotting backend.
+- With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
+- As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+
 ```{python}
 # %matplotlib widget
 
@@ -140,14 +150,6 @@ ax = fig.gca()
 fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', self_energies=self_energies, ax=ax)
 ```
 
-```{python}
-
-```
-
-```{python}
-
-```
-
 ```{python}
 fig = plt.figure(figsize=(7, 5))
 ax = fig.gca()
@@ -584,3 +586,7 @@ plt.show()
 
 # plt.show()
 ```
+
+```{python}
+
+```

{xarpes-0.3.0 → xarpes-0.3.1}/examples/srtio3/srtio3.py

@@ -7,12 +7,16 @@
 import matplotlib as mpl
 mpl.use('Qt5Agg')
 
+# Necessary packages
 import xarpes
 import matplotlib.pyplot as plt
 import os
 
+# Default plot configuration from xarpes.plotting.py
 xarpes.plot_settings('default')
 
+# If needed, close figures before running other cells, if figures show up in the wrong places.
+
 script_dir = xarpes.set_script_dir()
 
 dfld = 'data_sets' # Folder containing the data
@@ -73,6 +77,11 @@ ax = fig.gca()
 fig = mdcs.visualize_guess(distributions=guess_dists, matrix_element=mat_el,
                            matrix_args=mat_args, energy_value=-0.000, ax=ax)
 
+# #### Note on interactive figures
+# - Operability of the interactive figure is sensitive to configuration of the plotting backend.
+# - With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
+# - As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+
 
 fig = plt.figure(figsize=(7, 5))
 ax = fig.gca()
@@ -105,10 +114,6 @@ ax = fig.gca()
 
 fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', self_energies=self_energies, ax=ax)
 
-
-
-
-
 fig = plt.figure(figsize=(7, 5))
 ax = fig.gca()
 
@@ -475,3 +480,5 @@ plt.show()
 # bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax, zorder=0.5)
 
 # plt.show()
+
+

{xarpes-0.3.0 → xarpes-0.3.1}/pyproject.toml

@@ -25,6 +25,7 @@ dependencies = [
     "lmfit",
     "pyqt5",
     "ipympl",
+    "ipykernel<6.32.0"
 ]
 
 [project.scripts]

{xarpes-0.3.0 → xarpes-0.3.1}/xarpes/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.3.0'
+__version__ = '0.3.1'
 
 from .spectral import *
 from .distributions import *