deploy: phasorpy/phasorpy@9a81c6b

main/_modules/phasorpy/components.html

@@ -544,7 +544,7 @@ <h1>Source code for phasorpy.components</h1><div class="highlight"><pre>
 <span class="sd">    --------</span>
 <span class="sd">    &gt;&gt;&gt; two_fractions_from_phasor(</span>
 <span class="sd">    ...     [0.6, 0.5, 0.4], [0.4, 0.3, 0.2], [0.2, 0.9], [0.4, 0.3]</span>
-<span class="sd">    ... ) # doctest: +NUMBER</span>
+<span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (array([0.44, 0.56, 0.68]), array([0.56, 0.44, 0.32]))</span>
 
 <span class="sd">    &quot;&quot;&quot;</span>

main/_modules/phasorpy/phasor.html

@@ -668,10 +668,10 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 
 <span class="sd">    &gt;&gt;&gt; sample_phase = numpy.linspace(0, 2 * math.pi, 5, endpoint=False)[::-1]</span>
 <span class="sd">    &gt;&gt;&gt; signal = 1.1 * (</span>
-<span class="sd">    ...     numpy.cos(sample_phase - 0.78539816) * 2 *  0.70710678 + 1</span>
+<span class="sd">    ...     numpy.cos(sample_phase - 0.78539816) * 2 * 0.70710678 + 1</span>
 <span class="sd">    ... )</span>
 <span class="sd">    &gt;&gt;&gt; phasor_from_signal(</span>
-<span class="sd">    ...    signal, sample_phase=sample_phase</span>
+<span class="sd">    ...     signal, sample_phase=sample_phase</span>
 <span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (1.1, 0.5, 0.5)</span>
 
@@ -818,7 +818,7 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 
 <span class="sd">    &gt;&gt;&gt; sample_phase = numpy.linspace(0, 2 * math.pi, 5, endpoint=False)</span>
 <span class="sd">    &gt;&gt;&gt; signal = 1.1 * (</span>
-<span class="sd">    ...     numpy.cos(sample_phase - 0.78539816) * 2 *  0.70710678 + 1</span>
+<span class="sd">    ...     numpy.cos(sample_phase - 0.78539816) * 2 * 0.70710678 + 1</span>
 <span class="sd">    ... )</span>
 <span class="sd">    &gt;&gt;&gt; phasor_from_signal_fft(signal, harmonic=[1, 2])  # doctest: +NUMBER</span>
 <span class="sd">    (1.1, array([0.5, 0.0]), array([0.5, -0]))</span>
@@ -1044,10 +1044,13 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 <span class="sd">    Examples</span>
 <span class="sd">    --------</span>
 <span class="sd">    &gt;&gt;&gt; phasor_calibrate(</span>
-<span class="sd">    ...    [0.1, 0.2, 0.3], [0.4, 0.5, 0.6],</span>
-<span class="sd">    ...    [0.2, 0.3, 0.4], [0.5, 0.6, 0.7],</span>
-<span class="sd">    ...    frequency=80, lifetime=4</span>
-<span class="sd">    ... ) # doctest: +NUMBER</span>
+<span class="sd">    ...     [0.1, 0.2, 0.3],</span>
+<span class="sd">    ...     [0.4, 0.5, 0.6],</span>
+<span class="sd">    ...     [0.2, 0.3, 0.4],</span>
+<span class="sd">    ...     [0.5, 0.6, 0.7],</span>
+<span class="sd">    ...     frequency=80,</span>
+<span class="sd">    ...     lifetime=4,</span>
+<span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (array([0.0658, 0.132, 0.198]), array([0.2657, 0.332, 0.399]))</span>
 
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -1138,18 +1141,15 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 <span class="sd">    Use scalar reference coordinates to rotate and scale phasor coordinates:</span>
 
 <span class="sd">    &gt;&gt;&gt; phasor_transform(</span>
-<span class="sd">    ...     [0.1, 0.2, 0.3],</span>
-<span class="sd">    ...     [0.4, 0.5, 0.6],</span>
-<span class="sd">    ...     0.1,</span>
-<span class="sd">    ...     0.5</span>
-<span class="sd">    ... ) # doctest: +NUMBER</span>
+<span class="sd">    ...     [0.1, 0.2, 0.3], [0.4, 0.5, 0.6], 0.1, 0.5</span>
+<span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (array([0.0298, 0.0745, 0.119]), array([0.204, 0.259, 0.3135]))</span>
 
 <span class="sd">    Use separate reference coordinates for each phasor coordinate:</span>
 
 <span class="sd">    &gt;&gt;&gt; phasor_transform(</span>
 <span class="sd">    ...     [0.1, 0.2, 0.3], [0.4, 0.5, 0.6], [0.2, 0.2, 0.3], [0.5, 0.2, 0.3]</span>
-<span class="sd">    ... ) # doctest: +NUMBER</span>
+<span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (array([0.00927, 0.0193, 0.0328]), array([0.206, 0.106, 0.1986]))</span>
 
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -1213,7 +1213,7 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 
 <span class="sd">        polar_from_reference(</span>
 <span class="sd">            *phasor_to_polar(measured_real, measured_imag),</span>
-<span class="sd">            *phasor_to_polar(known_real, known_imag)</span>
+<span class="sd">            *phasor_to_polar(known_real, known_imag),</span>
 <span class="sd">        )</span>
 
 <span class="sd">    Examples</span>
@@ -1459,7 +1459,7 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 <span class="sd">    only if the phasor coordinates lie on the universal semicircle:</span>
 
 <span class="sd">    &gt;&gt;&gt; phasor_to_apparent_lifetime(</span>
-<span class="sd">    ...    0.5, [0.5, 0.45], frequency=80</span>
+<span class="sd">    ...     0.5, [0.5, 0.45], frequency=80</span>
 <span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (array([1.989, 1.79]), array([1.989, 2.188]))</span>
 
@@ -1894,7 +1894,7 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 <span class="sd">    Phasor coordinates of many single-component lifetimes (fractions omitted):</span>
 
 <span class="sd">    &gt;&gt;&gt; phasor_from_lifetime(</span>
-<span class="sd">    ...     80.0, [3.9788735, 1.9894368, 0.9947183],</span>
+<span class="sd">    ...     80.0, [3.9788735, 1.9894368, 0.9947183]</span>
 <span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (array([0.2, 0.5, 0.8]), array([0.4, 0.5, 0.4]))</span>
 
@@ -1920,7 +1920,7 @@ <h1>Source code for phasorpy.phasor</h1><div class="highlight"><pre>
 <span class="sd">    ...     [40e6, 80e6],</span>
 <span class="sd">    ...     [[1e-9, 0.9947183e-9], [3.9788735e-9, 0.9947183e-9]],</span>
 <span class="sd">    ...     [[0, 1], [0.5, 0.5]],</span>
-<span class="sd">    ...    unit_conversion=1.0</span>
+<span class="sd">    ...     unit_conversion=1.0,</span>
 <span class="sd">    ... )  # doctest: +NUMBER</span>
 <span class="sd">    (array([[0.941, 0.721], [0.8, 0.5]]), array([[0.235, 0.368], [0.4, 0.4]]))</span>
 

main/_sources/contributing.rst.txt

@@ -188,13 +188,15 @@ Configuration settings for pytest and other tools are in the
 Code standards
 ..............
 
-All the PhasorPy source code must conform to the
+All the PhasorPy source code, including tutorials and docstring examples,
+must conform to the
 `PEP8 <https://peps.python.org/pep-0008/>`_
 standard and be formatted with
 `black <https://black.readthedocs.io/en/stable/>`_
 (single quotes and lines up to 79 characters are allowed)::
 
     $ python -m black .
+    $ python -m blackdoc src/phasorpy
 
 User-facing classes and functions must use
 `type hints <https://peps.python.org/pep-0484/>`_

main/_sources/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:27.588** total execution time for 7 files **from all galleries**:
+**00:30.777** total execution time for 7 files **from all galleries**:
 
 .. container::
 
@@ -33,23 +33,23 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_benchmarks_phasorpy_phasor_from_signal.py` (``../tutorials/benchmarks/phasorpy_phasor_from_signal.py``)
-     - 00:13.684
+     - 00:14.354
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_introduction.py` (``../tutorials/phasorpy_introduction.py``)
-     - 00:09.610
+     - 00:12.355
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_fret.py` (``../tutorials/phasorpy_fret.py``)
-     - 00:02.257
+     - 00:02.104
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasorplot.py` (``../tutorials/phasorpy_phasorplot.py``)
-     - 00:00.900
+     - 00:00.868
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasor_from_lifetime.py` (``../tutorials/phasorpy_phasor_from_lifetime.py``)
-     - 00:00.605
+     - 00:00.584
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_components.py` (``../tutorials/phasorpy_components.py``)
-     - 00:00.469
+     - 00:00.450
      - 0.0
    * - :ref:`sphx_glr_tutorials_misc_phasorpy_logo.py` (``../tutorials/misc/phasorpy_logo.py``)
-     - 00:00.063
+     - 00:00.062
      - 0.0

main/_sources/tutorials/benchmarks/phasorpy_phasor_from_signal.rst.txt

@@ -149,34 +149,34 @@ and number of threads:
       axis -1
         phasor_from_signal       0.056s   1.00
           threads 2              0.032s   0.57
-        phasor_from_signal_fft   0.395s   7.08
-          scipy_fft              0.399s   7.15
+        phasor_from_signal_fft   0.410s   7.32
+          scipy_fft              0.438s   7.82
       axis 0
-        phasor_from_signal       0.165s   2.95
+        phasor_from_signal       0.165s   2.94
           threads 2              0.081s   1.44
-        phasor_from_signal_fft   2.661s  47.71
-          scipy_fft              0.488s   8.76
+        phasor_from_signal_fft   3.002s  53.63
+          scipy_fft              0.515s   9.20
       axis 2
         phasor_from_signal       0.056s   1.00
           threads 2              0.032s   0.57
-        phasor_from_signal_fft   0.396s   7.09
-          scipy_fft              0.411s   7.37
+        phasor_from_signal_fft   0.416s   7.43
+          scipy_fft              0.433s   7.73
     harmonics 8
       axis -1
-        phasor_from_signal       0.447s   8.00
-          threads 2              0.246s   4.42
-        phasor_from_signal_fft   0.411s   7.36
-          scipy_fft              0.423s   7.59
+        phasor_from_signal       0.454s   8.11
+          threads 2              0.245s   4.38
+        phasor_from_signal_fft   0.443s   7.91
+          scipy_fft              0.425s   7.59
       axis 0
-        phasor_from_signal       1.315s  23.57
-          threads 2              0.658s  11.80
-        phasor_from_signal_fft   2.663s  47.74
-          scipy_fft              0.490s   8.78
+        phasor_from_signal       1.341s  23.96
+          threads 2              0.656s  11.73
+        phasor_from_signal_fft   2.745s  49.04
+          scipy_fft              0.522s   9.32
       axis 2
-        phasor_from_signal       0.445s   7.98
-          threads 2              0.246s   4.41
-        phasor_from_signal_fft   0.407s   7.29
-          scipy_fft              0.424s   7.60
+        phasor_from_signal       0.444s   7.94
+          threads 2              0.248s   4.42
+        phasor_from_signal_fft   0.417s   7.45
+          scipy_fft              0.433s   7.73
 
 
 
@@ -255,7 +255,7 @@ when computing large number of harmonics with an optimized FFT function.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 13.684 seconds)
+   **Total running time of the script:** (0 minutes 14.354 seconds)
 
 
 .. _sphx_glr_download_tutorials_benchmarks_phasorpy_phasor_from_signal.py:

main/_sources/tutorials/benchmarks/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:13.684** total execution time for 1 file **from tutorials/benchmarks**:
+**00:14.354** total execution time for 1 file **from tutorials/benchmarks**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_benchmarks_phasorpy_phasor_from_signal.py` (``phasorpy_phasor_from_signal.py``)
-     - 00:13.684
+     - 00:14.354
      - 0.0

main/_sources/tutorials/misc/phasorpy_logo.rst.txt

@@ -60,7 +60,7 @@ Create the PhasorPy logo using the PhasorPy library.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.063 seconds)
+   **Total running time of the script:** (0 minutes 0.062 seconds)
 
 
 .. _sphx_glr_download_tutorials_misc_phasorpy_logo.py:

main/_sources/tutorials/misc/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.063** total execution time for 1 file **from tutorials/misc**:
+**00:00.062** total execution time for 1 file **from tutorials/misc**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_misc_phasorpy_logo.py` (``phasorpy_logo.py``)
-     - 00:00.063
+     - 00:00.062
      - 0.0

main/_sources/tutorials/phasorpy_components.rst.txt

@@ -211,7 +211,7 @@ sphinx_gallery_thumbnail_number = 2
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.469 seconds)
+   **Total running time of the script:** (0 minutes 0.450 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_components.py:

main/_sources/tutorials/phasorpy_fret.rst.txt

@@ -407,7 +407,7 @@ mypy: disable-error-code="arg-type"
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 2.257 seconds)
+   **Total running time of the script:** (0 minutes 2.104 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_fret.py:

main/_sources/tutorials/phasorpy_introduction.rst.txt

@@ -424,7 +424,7 @@ Print information about Python interpreter and installed packages:
     Python-3.11.9
     phasorpy-0.1.dev
     numpy-1.26.4
-    tifffile-2024.4.24
+    tifffile-2024.5.3
     imagecodecs-n/a
     lfdfiles-2024.4.24
     sdtfile-2024.4.24
@@ -448,7 +448,7 @@ sphinx_gallery_thumbnail_number = 3
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 9.610 seconds)
+   **Total running time of the script:** (0 minutes 12.355 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_introduction.py:

main/_sources/tutorials/phasorpy_phasor_from_lifetime.rst.txt

@@ -358,7 +358,7 @@ sphinx_gallery_thumbnail_number = -2
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.605 seconds)
+   **Total running time of the script:** (0 minutes 0.584 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_phasor_from_lifetime.py:

main/_sources/tutorials/phasorpy_phasorplot.rst.txt

@@ -461,7 +461,7 @@ sphinx_gallery_thumbnail_number = 10
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.900 seconds)
+   **Total running time of the script:** (0 minutes 0.868 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_phasorplot.py:

main/_sources/tutorials/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:13.841** total execution time for 5 files **from tutorials**:
+**00:16.360** total execution time for 5 files **from tutorials**:
 
 .. container::
 
@@ -33,17 +33,17 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_phasorpy_introduction.py` (``phasorpy_introduction.py``)
-     - 00:09.610
+     - 00:12.355
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_fret.py` (``phasorpy_fret.py``)
-     - 00:02.257
+     - 00:02.104
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasorplot.py` (``phasorpy_phasorplot.py``)
-     - 00:00.900
+     - 00:00.868
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasor_from_lifetime.py` (``phasorpy_phasor_from_lifetime.py``)
-     - 00:00.605
+     - 00:00.584
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_components.py` (``phasorpy_components.py``)
-     - 00:00.469
+     - 00:00.450
      - 0.0

main/api/components.html

@@ -538,7 +538,7 @@
 <p class="rubric">Examples</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">two_fractions_from_phasor</span><span class="p">(</span>
 <span class="gp">... </span>    <span class="p">[</span><span class="mf">0.6</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.9</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">]</span>
-<span class="gp">... </span><span class="p">)</span> 
+<span class="gp">... </span><span class="p">)</span>  
 <span class="go">(array([0.44, 0.56, 0.68]), array([0.56, 0.44, 0.32]))</span>
 </pre></div>
 </div>