Add plotly option to add_fig_kwargs

.github/workflows/gh-pages.yml

@@ -0,0 +1,50 @@
+name: Deploy documentation with GitHub Pages dependencies preinstalled
+
+on:
+ push:
+ branches: ["develop"]
+ workflow_dispatch: # enable manual workflow execution
+
+# Set permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+ contents: read
+ pages: write
+ id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+ group: "pages"
+ cancel-in-progress: false
+
+jobs:
+ build:
+ # prevent this action from running on forks
+ if: github.repository == 'abinit/abipy'
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v4
+
+ - name: Setup Pages
+ uses: actions/configure-pages@v3
+
+ - name: Build with Jekyll
+ uses: actions/jekyll-build-pages@v1
+ with:
+ source: ./docs
+ destination: ./_site
+
+ - name: Upload artifact
+ uses: actions/upload-pages-artifact@v2
+
+ deploy:
+ environment:
+ name: github-pages
+ url: ${{ steps.deployment.outputs.page_url }}
+ runs-on: ubuntu-latest
+ needs: build
+ steps:
+ - name: Deploy to GitHub Pages
+ id: deployment
+ uses: actions/deploy-pages@v2

.github/workflows/test.yml

@@ -0,0 +1,81 @@
+# Runs the complete test suite. 
+name: Tests
+
+on:
+ push:
+ branches: [develop]
+ paths-ignore: ["**/*.md", docs/**]
+ pull_request:
+ branches: [develop]
+ paths-ignore: ["**/*.md", docs/**]
+ workflow_dispatch:
+ workflow_call: # make this workflow reusable by release.yml
+
+permissions:
+ contents: read
+
+jobs:
+ test:
+ # prevent this action from running on forks
+ if: github.repository == 'abinit/abipy'
+ defaults:
+ run:
+ shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+ strategy:
+ fail-fast: false
+ matrix:
+ # maximize CI coverage of different platforms and python versions while minimizing the
+ # total number of jobs. We run all pytest splits with the oldest supported python
+ # version (currently 3.9) on windows (seems most likely to surface errors) and with
+ # newest version (currently 3.12) on ubuntu (to get complete coverage on unix).
+ config:
+ - os: windows-latest
+ python: "3.9"
+ resolution: highest
+ extras: ci,optional
+ - os: ubuntu-latest
+ python: '>3.9'
+ resolution: lowest-direct
+ extras: ci,optional
+ - os: macos-latest
+ python: '3.10'
+ resolution: lowest-direct
+ extras: ci # test with only required dependencies installed
+
+ # pytest-split automatically distributes work load so parallel jobs finish in similar time
+ # update durations file with `pytest --store-durations --durations-path tests/files/.pytest-split-durations`
+ split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+
+ runs-on: ${{ matrix.config.os }}
+
+ #env:
+ # PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+
+ steps:
+ - name: Check out repo
+ uses: actions/checkout@v4
+
+ - name: Set up micromamba
+ uses: mamba-org/setup-micromamba@main
+
+ - name: Create mamba environment
+ run: |
+ micromamba create -n abipy python=${{ matrix.config.python }} --yes
+
+ - name: Install uv
+ run: micromamba run -n abipy pip install uv
+
+ #- name: Install ubuntu-only conda dependencies
+ # if: matrix.config.os == 'ubuntu-latest'
+ # run: |
+ # micromamba install -n abipy -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
+
+ - name: Install pymatgen and dependencies
+ run: |
+ micromamba activate abipy
+ uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
+
+ - name: pytest split ${{ matrix.split }}
+ run: |
+ micromamba activate abipy
+ pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests

abipy/eph/varpeq.py

@@ -159,9 +159,6 @@ def to_string(self, verbose=0) -> str:
  app(self.structure.to_string(verbose=verbose, title="Structure"))
  app("")
  app(self.ebands.to_string(with_structure=False, verbose=verbose, title="Electronic Bands"))
- #if verbose > 1:
- # app("")
- # app(self.hdr.to_string(verbose=verbose, title="Abinit Header"))
 
  app("")
  app("VARPEQ parameters:")

abipy/ppcodes/oncv_parser.py

@@ -531,7 +531,7 @@ def kin_densities(self) -> dict[str, RadialFunction]:
  @lazy_property
  def vtaus(self) -> dict[str, RadialFunction]:
  """
- Dictionary with Vtau pototentials on the radial mesh.
+ Dictionary with Vtau ptotentials on the radial mesh.
  """
  if not self.is_metapsp:
  raise ValueEror("kin_densities are only available in pseudos generated with metapsp")

abipy/ppcodes/oncv_plotter.py

@@ -327,11 +327,12 @@ def plotly_vtau(self, *args, **kwargs):
  from plotly.tools import mpl_to_plotly
  return mpl_to_plotly(self.plot_vtau(*args, show=False, **kwargs))
 
- def plot_vtau(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
+ def plot_vtau(self, xscale="log", ax=None, fontsize: int = 8, **kwargs) -> Figure:
  """
  Plot v_tau and v_tau(model+pseudo) potentials on axis ax.
 
  Args:
+ xscale: "log" to plot vtau in log scale or "linear". For other options see matplotlib.
  ax: |matplotlib-Axes| or None if a new figure should be created.
  """
  ax, fig, plt = get_ax_fig_plt(ax)
@@ -347,23 +348,26 @@ def plot_vtau(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
  fontsize=fontsize,
  )
  self._add_rc_vlines_ax(ax, with_lloc=True)
+ ax.set_xscale(xscale)
+
+ return fig
 
  def plotly_tau(self, *args, **kwargs):
  """Generate plotly figure from matplotly."""
  from plotly.tools import mpl_to_plotly
  return mpl_to_plotly(self.plot_tau(*args, show=False, **kwargs))
 
- def plot_tau(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
+ def plot_tau(self, ax=None, yscale="log", fontsize: int = 8, **kwargs) -> Figure:
  """
  Plot kinetic energy densities tauPS and tau(M+PS) on axis ax.
 
  Args:
+ yscale: "log" to plot tau in log scale or "linear". For other options see matplotlib.
  ax: |matplotlib-Axes| or None if a new figure should be created.
  """
  ax, fig, plt = get_ax_fig_plt(ax)
 
  for key, den in self.parser.kin_densities.items():
- #mode = "ae" if key == "tau_ps" else "ps"
  ax.plot(den.rmesh, den.values,
  label=den.name)
  #**self._mpl_opts_laeps(0, mode))
@@ -373,6 +377,7 @@ def plot_tau(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
  fontsize=fontsize,
  )
  self._add_rc_vlines_ax(ax, with_lloc=True)
+ ax.set_yscale(yscale)
 
  return fig
 

abipy/ppcodes/tests/test_oncvpsp.py

@@ -474,6 +474,10 @@ def _call_plotter_methods(self, plotter):
  assert plotter.plot_atanlogder_econv(show=False)
  assert plotter.plot_den_formfact(ecut=20, show=False)
 
+ if isinstance(plotter, OncvParser) and plotter.parser.is_metapsp:
+ assert plotter.plot_vtau(show=False)
+ assert plotter.plot_tau(show=False)
+
  #if self.has_plotly():
 
  def test_psp8_get_densities(self):

abipy/tools/plotting.py

@@ -19,12 +19,12 @@
 from collections import namedtuple, OrderedDict
 from typing import Any, Callable, Iterator
 from monty.string import list_strings
-from pymatgen.util.plotting import add_fig_kwargs
+#from pymatgen.util.plotting import add_fig_kwargs
 from abipy.tools import duck
 from abipy.tools.iotools import dataframe_from_filepath
 from abipy.tools.typing import Figure, Axes, VectorLike
 from abipy.tools.numtools import data_from_cplx_mode
-from plotly.tools import mpl_to_plotly
+
 
 __all__ = [
  "set_axlims",
@@ -66,6 +66,115 @@
 )
 
 
+
+def add_fig_kwargs(func):
+ """Decorator that adds keyword arguments for functions returning matplotlib
+ figures.
+
+ The function should return either a matplotlib figure or None to signal
+ some sort of error/unexpected event.
+ See doc string below for the list of supported options.
+ """
+
+ @functools.wraps(func)
+ def wrapper(*args, **kwargs):
+ # pop the kwds used by the decorator.
+ title = kwargs.pop("title", None)
+ size_kwargs = kwargs.pop("size_kwargs", None)
+ show = kwargs.pop("show", True)
+ savefig = kwargs.pop("savefig", None)
+ tight_layout = kwargs.pop("tight_layout", False)
+ ax_grid = kwargs.pop("ax_grid", None)
+ ax_annotate = kwargs.pop("ax_annotate", None)
+ fig_close = kwargs.pop("fig_close", False)
+ plotly = kwargs.pop("fig_close", False)
+
+ # Call func and return immediately if None is returned.
+ fig = func(*args, **kwargs)
+ if fig is None:
+ return fig
+
+ # Operate on matplotlib figure.
+ if title is not None:
+ fig.suptitle(title)
+
+ if size_kwargs is not None:
+ fig.set_size_inches(size_kwargs.pop("w"), size_kwargs.pop("h"), **size_kwargs)
+
+ if ax_grid is not None:
+ for ax in fig.axes:
+ ax.grid(bool(ax_grid))
+
+ if ax_annotate:
+ tags = ascii_letters
+ if len(fig.axes) > len(tags):
+ tags = (1 + len(ascii_letters) // len(fig.axes)) * ascii_letters
+ for ax, tag in zip(fig.axes, tags):
+ ax.annotate(f"({tag})", xy=(0.05, 0.95), xycoords="axes fraction")
+
+ if tight_layout:
+ try:
+ fig.tight_layout()
+ except Exception as exc:
+ # For some unknown reason, this problem shows up only on travis.
+ # https://stackoverflow.com/questions/22708888/valueerror-when-using-matplotlib-tight-layout
+ print("Ignoring Exception raised by fig.tight_layout\n", str(exc))
+
+ if savefig:
+ fig.savefig(savefig)
+
+ if plotly:
+ try:
+ plotly_fig = mpl_to_ply(fig, latex=False)
+ if show: plotly_fig.show()
+ return plotly_fig
+ except Exception as exc:
+ raise
+ #print(str(exc))
+ pass
+
+ import matplotlib.pyplot as plt
+ if show:
+ plt.show()
+
+ if fig_close:
+ plt.close(fig=fig)
+
+ return fig
+
+ # Add docstring to the decorated method.
+ doc_str = """\n\n
+ Keyword arguments controlling the display of the figure:
+
+ ================ ====================================================
+ kwargs Meaning
+ ================ ====================================================
+ title Title of the plot (Default: None).
+ show True to show the figure (default: True).
+ savefig "abc.png" or "abc.eps" to save the figure to a file.
+ size_kwargs Dictionary with options passed to fig.set_size_inches
+ e.g. size_kwargs=dict(w=3, h=4)
+ tight_layout True to call fig.tight_layout (default: False)
+ ax_grid True (False) to add (remove) grid from all axes in fig.
+ Default: None i.e. fig is left unchanged.
+ ax_annotate Add labels to subplots e.g. (a), (b).
+ Default: False
+ fig_close Close figure. Default: False.
+ plotly Try to convert mpl figure to plotly.
+ ================ ====================================================
+
+"""
+
+ if wrapper.__doc__ is not None:
+ # Add s at the end of the docstring.
+ wrapper.__doc__ += f"\n{doc_str}"
+ else:
+ # Use s
+ wrapper.__doc__ = doc_str
+
+ return wrapper
+
+
 class FilesPlotter:
  """
  Use matplotlib to plot multiple png files on a grid.
@@ -1743,9 +1852,7 @@ def add_plotly_fig_kwargs(func: Callable) -> Callable:
  sort of error/unexpected event.
  See doc string below for the list of supported options.
  """
- from functools import wraps
-
- @wraps(func)
+ @functools.wraps(func)
  def wrapper(*args, **kwargs):
  # pop the kwds used by the decorator.
  title = kwargs.pop("title", None)
@@ -2647,6 +2754,8 @@ def add_colorscale_dropwdowns(fig):
  return fig
 
 
+#TODO: Add plotly option to add_fig_kwargs
+
 def mpl_to_ply(fig: Figure, latex: bool= False):
  """
  Nasty workaround for plotly latex rendering in legend/breaking exception
@@ -2699,6 +2808,7 @@ def parse_latex(label):
  text.set_text(new_label)
 
  # Convert to plotly figure
+ from plotly.tools import mpl_to_plotly
  plotly_fig = mpl_to_plotly(fig)
 
  plotly_fig.update_layout(template = "plotly_white", title = {
@@ -2726,7 +2836,6 @@ def parse_latex(label):
  for trace in plotly_fig.data:
  # Retrieve the current label and remove any $ signs
  new_label = trace.name.replace("$", "")
-
  # Update the trace's name (which is used for the legend label)
  trace.name = new_label
 
@@ -2784,3 +2893,5 @@ def plot(self, deg_list: list[int],
 #
 # def extrapolate_to_zero(self, deg: int):
 
+
+