Fix hidden=True still generating plots in Jupyter notebooks

.gitignore

@@ -21,4 +21,6 @@ docs/build
 docs/source/_build/
 .tox
 .DS_Store
-.coverage*
+.coverage*
+*.ini
+*.bak

docs/source/conf.py

@@ -48,7 +48,7 @@
     "sphinx.ext.coverage",
     "sphinx.ext.mathjax",  # imgmath requires some helpers to be installed
     "sphinx.ext.viewcode",
-    "sphinxcontrib.napoleon",
+    "sphinx.ext.napoleon",
     "nbsphinx",
 ]
 

docs/source/jupyter/qm_explanation.ipynb

@@ -41,7 +41,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from IPython.core.display import display, HTML\n",
+    "from IPython.display import display, HTML\n",
     "display(HTML(\"<style>.container { width:100% !important; }</style>\"))"
    ]
   },
@@ -489,7 +489,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.16"
+   "version": "3.13.2"
   }
  },
  "nbformat": 4,

setup.cfg

@@ -69,7 +69,8 @@ exclude =
     jupyter,
     tests/dnmr_standards.py,
     build,
-    dist
+    dist,
+    .ipynb_checkpoints
 ignore =
     # allowing I for Intensity/Integration *for now*
     E741

src/nmrsim/plt.py

@@ -70,13 +70,12 @@ def mplplot(peaklist, w=1, y_min=-0.01, y_max=1, points=800, limits=None, hidden
         l_limit = peaklist[0][0] - 50
         r_limit = peaklist[-1][0] + 50
     x = np.linspace(l_limit, r_limit, points)
-    plt.ylim(y_min, y_max)
-    plt.gca().invert_xaxis()  # reverses the x axis
     y = add_lorentzians(x, peaklist, w)
     # noinspection PyTypeChecker
-    lines = plt.plot(x, y)
-    print(lines)
     if not hidden:
+        plt.plot(x, y)
+        plt.ylim(y_min, y_max)
+        plt.gca().invert_xaxis()  # reverses the x axis
         plt.show()
     return x, y
 
@@ -102,7 +101,6 @@ def mplplot_stick(peaklist, y_min=-0.01, y_max=1, limits=None, hidden=False):
     numpy.array, numpy.array
         The arrays of x and y coordinates used for the plot.
     """
-    fig, ax = plt.subplots()
     if limits:
         l_limit, r_limit = low_high(limits)
     else:
@@ -115,10 +113,11 @@ def mplplot_stick(peaklist, y_min=-0.01, y_max=1, limits=None, hidden=False):
     # baseline.
     x = np.append(x, [l_limit, r_limit])
     y = np.append(y, [0.001, 0.001])
-    plt.xlim(r_limit, l_limit)
-    plt.ylim(y_min, y_max)
-    ax.stem(x, y, markerfmt=" ", basefmt="C0-", use_line_collection=True)  # suppress warning until mpl 3.3
     if not hidden:
+        fig, ax = plt.subplots()
+        plt.xlim(r_limit, l_limit)
+        plt.ylim(y_min, y_max)
+        ax.stem(x, y, markerfmt=" ", basefmt="C0-")
         plt.show()
     return x, y
     # TODO: or return plt object? Decide behavior.
@@ -159,9 +158,9 @@ def mplplot_lineshape(x, y, y_min=None, y_max=None, limits=None, hidden=False):
             y_min = min(y) - margin
         if y_max is None:
             y_max = max(y) + margin
-    plt.xlim(r_limit, l_limit)  # should invert x axis
-    plt.ylim(y_min, y_max)
-    plt.plot(x, y)
     if not hidden:
+        plt.xlim(r_limit, l_limit)  # should invert x axis
+        plt.ylim(y_min, y_max)
+        plt.plot(x, y)
         plt.show()
     return x, y