Fixing typos in documentation and tutorials (#229)

* Fix typo in stretch parameter

* Indication to print

* Formatting fixes

* macos-14 tolerance

* Add news

* doc to docs

* Typo fix

Author: Sparks29032

.flake8

@@ -6,7 +6,7 @@ exclude =
     __pycache__,
     build,
     dist,
-    doc/source/conf.py
+    docs/source/conf.py
 max-line-length = 79
 # Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings

.readthedocs.yaml

@@ -10,4 +10,4 @@ python:
     - requirements: requirements/docs.txt
 
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/source/conf.py

docs/source/api/diffpy.morph.morph_helpers.rst

@@ -1,6 +1,6 @@
 :tocdepth: -1
 
-diffpy.morph.morp_helpers package
+diffpy.morph.morph_helpers package
 ==================================
 
 .. automodule:: diffpy.morph.morph_helpers

docs/source/morphpy.rst

@@ -17,7 +17,7 @@ Python Morphing Functions
        morph on the files `darkSub_rh20_C_01.gr` and `darkSub_rh20_C_44.gr` using the command-line
        command ::
 
-          diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.5 --rmin=1.5 --rmax=30 darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
+          diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.005 --rmin=1.5 --rmax=30 darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
 
     2. To do the same on Python, we must first create a new Python script in the same directory as the
        data files `darkSub_rh20_C_01.gr` and `darkSub_rh20_C_44.gr`.
@@ -27,18 +27,19 @@ Python Morphing Functions
 
     3. Finally, we run the ``morph`` function ::
 
-           morph_info, morph_table = morph("darkSub_rh20_C_01.gr", "darkSub_rh20_C_44.gr", scale=0.8, smear=-0.08, stretch=0.5, rmin=1.5, rmax=30)
+           morph_info, morph_table = morph("darkSub_rh20_C_01.gr", "darkSub_rh20_C_44.gr", scale=0.8, smear=-0.08, stretch=0.005, rmin=1.5, rmax=30)
 
-           * The ``morph`` function takes in two file names (or paths). You can also provide various parameters
-             for morphing (see the Full Parameter List below).
-           * If, let's say, the file `darkSub_rh20_C_01.gr` is in a subdirectory `subdir/darkSub_rh20_C_01.gr`,
-             you should replace ``"darkSub_rh20_C_01.gr"`` in the above example with ``"subdir/darkSub_rh20_C_01.gr"``.
+       * The ``morph`` function takes in two file names (or paths). You can also provide various parameters
+         for morphing (see the Full Parameter List below).
+       * If, let's say, the file `darkSub_rh20_C_01.gr` is in a subdirectory `subdir/darkSub_rh20_C_01.gr`,
+         you should replace ``"darkSub_rh20_C_01.gr"`` in the above example with ``"subdir/darkSub_rh20_C_01.gr"``.
 
     4. The ``morph`` function returns a dictionary ``morph_info`` and a numpy array ``morph_table``.
 
        * ``morph_info`` contains all morphs as keys (e.g. ``"scale"``, ``"stretch"``, ``"smear"``) with
          the optimized morphing parameters found by ``diffpy.morph`` as values. ``morph_info`` also contains
-         the Rw and Pearson correlation coefficients found post-morphing.
+         the Rw and Pearson correlation coefficients found post-morphing. Try printing ``print(morph_info)``
+         and compare the values stored in this dictionary to those given by the CLI output!
        * ``morph_table`` is a two-column array of the morphed function interpolated onto the grid of the
          target function (e.g. in our example, it returns the contents of `darkSub_rh20_C_01.gr` after
          the morphs are applied interpolated onto the grid of `darkSub_rh20_C_44.gr`).
@@ -61,7 +62,7 @@ Python Morphing Functions
     9. Notice that the two-column format of the input to ``morph_arrays`` is the same as the
        output of ``morph`` and ``morph_arrays``. It is VERY IMPORTANT that the data is in two-column format
        rather than the traditional two-row format. This is to reflect the file formats conventionally
-       used to store PDFs.
+       used to store PDFs. Again, try printing ``print(morph_info)`` and compare!
     10. For a full list of parameters used by (both) ``morph`` and ``morph_arrays``, see the Full Parameter List
         section below.
 

docs/source/quickstart.rst

@@ -181,7 +181,7 @@ Basic diffpy.morph Workflow
     8. Finally, we will examine the stretch factor. Provide an initial
        guess by typing ::
 
-           diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.5 --rmin=1.5 --rmax=30 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
+           diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.005 --rmin=1.5 --rmax=30 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
 
        And noting that the difference has increased. Before continuing,
        see if you can see which direction (higher or lower) our initial

docs/source/tutorials.rst

@@ -24,17 +24,15 @@ selected directory and plot resulting :math:`R_w` values from each morph.
    <https://global.oup.com/academic/product/
    atomic-pair-distribution-function-analysis-9780198885801>`_.
 
-2. Let us start by getting the Rw of ``SrFe2As2_150K.gr`` compared to
+2. Let us start by getting the :math:`R_w` of ``SrFe2As2_150K.gr`` compared to
    all other files in the directory. Run ::
 
        diffpy.morph SrFe2As2_150K.gr . --multiple-targets
 
    The multiple tag indicates we are comparing PDF file (first input)
    against all PDFs in a directory (second input). Our choice of file
    was ``SeFe2As2_150K.gr`` and directory was the cwd, which should be
-   ``morphsequence``.::
-
-       diffpy.morph SrFe2As2_150K.gr . --multiple-targets --sort-by=temperature
+   ``morphsequence``.
 
 .. figure:: images/ex_tutorial_bar.png
    :align: center
@@ -43,16 +41,16 @@ selected directory and plot resulting :math:`R_w` values from each morph.
    Bar chart of :math:`R_W` values for each target file. Target files are
    listed in ASCII sort order.
 
-3. After running this, we get chart of Rw values for each target file.
+3. After running this, we get chart of :math:`R_w` values for each target file.
    However, this chart can be a bit confusing to interpret. To get a
    more understandable plot, run ::
 
        diffpy.morph SrFe2As2_150K.gr . --multiple-targets --sort-by=temperature
 
-   This plots the Rw against the temperature parameter value provided
+   This plots the :math:`R_w` against the temperature parameter value provided
    at the top of each file. Parameters are entries of the form
    ``<parameter_name> = <parameter_value>`` and are located above
-   the ``r`` versus ``gr`` table in each PDF file.::
+   the ``r`` versus ``gr`` table in each PDF file. ::
 
      # SrFe2As2_150K.gr
      [PDF Parameters]
@@ -77,7 +75,7 @@ selected directory and plot resulting :math:`R_w` values from each morph.
    Note that we are not applying a smear since it takes a long time to
    apply and does not significantly change the Rw values in this example.
 
-5. We should now see a sharper increase in Rw between 192K and 198K.
+5. We should now see a sharper increase in :math:`R_w` between 192K and 198K.
 
 6. Go back to the terminal to see optimized morphing parameters from each morph.
 
@@ -219,27 +217,25 @@ Currently, the supported nanoparticle shapes include: spheres and spheroids.
 
                diffpy.morph Ni_nano_sphere.cgr Ni_nano_sphere.cgr
 
-        3. Nanoparticles tend to have broader peaks at r-values larger
+           Nanoparticles tend to have broader peaks at r-values larger
 	   than the particle size, corresponding to the much weaker
 	   correlations between molecules. On our plot, beyond r=22.5,
 	   peaks are too broad to be visible, indicating our particle
 	   size to be about 22.4. The approximate radius of a sphere
-	   would be half of that, or 11.2.::
-
-               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 -a
+	   would be half of that, or 11.2.
 
 
-        4. Now, we are ready to perform a morph applying spherical
+        3. Now, we are ready to perform a morph applying spherical
 	   effects. To do so, we use the ``--radius`` parameter ::
 
-               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 -a
+               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 -a --rmax=30
 
-        5. We can see that the Rw value has significantly decreased
+        4. We can see that the :math:`Rw` value has significantly decreased
 	   from before. Run without the ``-a`` tag to refine ::
 
-               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2
+               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 --rmax=30
 
-        6. After refining, we see the actual radius of the
+        5. After refining, we see the actual radius of the
 	   nanoparticle was closer to 12.
 
     * Spheroidal Shape
@@ -255,7 +251,7 @@ Currently, the supported nanoparticle shapes include: spheres and spheroids.
 	   enough information to define our spheroid. To apply
 	   spheroid shape effects onto our bulk, run ::
 
-               diffpy.morph Ni_bulk.gr Ni_nano_spheroid.cgr --radius=12 --pradius=6 -a
+               diffpy.morph Ni_bulk.gr Ni_nano_spheroid.cgr --radius=12 --pradius=6 -a --rmax=30
 
            Note that the equatorial radius corresponds to the
 	   ``--radius`` parameter and polar radius to ``--pradius``.

news/doc_review_2.0.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Typo fixes in documentation.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

tests/test_morphio.py

@@ -217,6 +217,14 @@ def quadratic(x, y, a0, a1, a2):
             with open(tmp_path.joinpath("funcy_target.cgr")) as gf:
                 generated = filter(ignore_path, gf)
                 target = filter(ignore_path, tf)
-                for x, y in zip(generated, target):
-                    assert x == y
-                assert all(x == y for x, y in zip(generated, target))
+                for m, t in zip(generated, target):
+                    m_row = m.split()
+                    t_row = t.split()
+                    assert len(m_row) == len(t_row)
+                    for idx, _ in enumerate(m_row):
+                        if isfloat(m_row[idx]) and isfloat(t_row[idx]):
+                            assert np.isclose(
+                                float(m_row[idx]), float(t_row[idx])
+                            )
+                        else:
+                            assert m_row[idx] == t_row[idx]