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01-package-setup.html

@@ -581,19 +581,18 @@ <h3>Running CookieCutter<a class="headerlink" href="#running-cookiecutter" title
 <span class="m">2</span><span class="w"> </span>-<span class="w"> </span>BSD-3-Clause
 <span class="m">3</span><span class="w"> </span>-<span class="w"> </span>LGPLv3
 <span class="m">4</span><span class="w"> </span>-<span class="w"> </span>Not<span class="w"> </span>Open<span class="w"> </span>Source
-Choose<span class="w"> </span>from<span class="w"> </span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span>,<span class="w"> </span><span class="m">3</span>,<span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="o">(</span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span>,<span class="w"> </span><span class="m">3</span>,<span class="w"> </span><span class="m">4</span><span class="o">)</span><span class="w"> </span><span class="o">[</span><span class="m">1</span><span class="o">]</span>:<span class="w"> </span><span class="m">2</span>
+Choose<span class="w"> </span>from<span class="w"> </span><span class="o">[</span><span class="m">1</span>/2/3/4<span class="o">]</span><span class="w"> </span><span class="o">(</span><span class="m">1</span><span class="o">)</span>:
 
 Select<span class="w"> </span>dependency_source:
 <span class="m">1</span><span class="w"> </span>-<span class="w"> </span>Prefer<span class="w"> </span>conda-forge<span class="w"> </span>with<span class="w"> </span>pip<span class="w"> </span>fallback
 <span class="m">2</span><span class="w"> </span>-<span class="w"> </span>Prefer<span class="w"> </span>default<span class="w"> </span>anaconda<span class="w"> </span>channel<span class="w"> </span>with<span class="w"> </span>pip<span class="w"> </span>fallback
 <span class="m">3</span><span class="w"> </span>-<span class="w"> </span>Dependencies<span class="w"> </span>from<span class="w"> </span>pip<span class="w"> </span>only<span class="w"> </span><span class="o">(</span>no<span class="w"> </span>conda<span class="o">)</span>
-
-Choose<span class="w"> </span>from<span class="w"> </span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span>,<span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="o">(</span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span>,<span class="w"> </span><span class="m">3</span><span class="o">)</span><span class="w"> </span><span class="o">[</span><span class="m">1</span><span class="o">]</span>:
+Choose<span class="w"> </span>from<span class="w"> </span><span class="o">[</span><span class="m">1</span>/2/3<span class="o">]</span><span class="w"> </span><span class="o">(</span><span class="m">1</span><span class="o">)</span>:
 
 Select<span class="w"> </span>include_ReadTheDocs:
 <span class="m">1</span><span class="w"> </span>-<span class="w"> </span>y
 <span class="m">2</span><span class="w"> </span>-<span class="w"> </span>n
-Choose<span class="w"> </span>from<span class="w"> </span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="o">(</span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span><span class="o">)</span><span class="w"> </span><span class="o">[</span><span class="m">1</span><span class="o">]</span>:
+Choose<span class="w"> </span>from<span class="w"> </span><span class="o">[</span><span class="m">1</span>/2<span class="o">]</span><span class="w"> </span><span class="o">(</span><span class="m">1</span><span class="o">)</span>:
 </pre></div>
 </div>
 </div>
@@ -824,8 +823,7 @@ <h3>Our first module<a class="headerlink" href="#our-first-module" title="Link t
 View the module (<code class="docutils literal notranslate"><span class="pre">functions.py</span></code>) in a text editor.
 We see a few things about this file.
 The top begins with a description of this module surrounded by three quotations (<code class="docutils literal notranslate"><span class="pre">&quot;&quot;&quot;</span></code>).
-Right now, that is the file name, followed by our short description,
-then the sentence “Handles the primary functions”.
+Right now, that is the sentence “Provides the primary functions”.
 We will change this to be more descriptive later.
 CookieCutter has also created a placeholder function called <code class="docutils literal notranslate"><span class="pre">canvas</span></code>.
 At the start of the <code class="docutils literal notranslate"><span class="pre">canvas</span></code> function, we have a <code class="docutils literal notranslate"><span class="pre">docstring</span></code> (more about this in [documentation]),

04-function-style.html

@@ -555,7 +555,7 @@ <h2>Editing a function in our package<a class="headerlink" href="#editing-a-func
 </div>
 <p>If we want to test our function, we require a pdb file.
 The workshop materials downloaded during the setup include a set of pdb examples.
-These are found in <code class="docutils literal notranslate"><span class="pre">molssi_beter_practices/starting_material/data/pdb/</span></code>.
+These are found in <code class="docutils literal notranslate"><span class="pre">molssi_best_practices/starting_material/data/pdb/</span></code>.
 We want to store these files in our <code class="docutils literal notranslate"><span class="pre">molecool</span></code> directory.
 Luckily, <code class="docutils literal notranslate"><span class="pre">cookiecutter</span></code> created a folder designed specifically for that purpose.
 The folder is in <code class="docutils literal notranslate"><span class="pre">molecool/data/</span></code>.

_sources/01-package-setup.md.txt

@@ -103,19 +103,18 @@ Select open_source_license:
 2 - BSD-3-Clause
 3 - LGPLv3
 4 - Not Open Source
-Choose from 1, 2, 3, 4 (1, 2, 3, 4) [1]: 2
+Choose from [1/2/3/4] (1):
 
 Select dependency_source:
 1 - Prefer conda-forge with pip fallback
 2 - Prefer default anaconda channel with pip fallback
 3 - Dependencies from pip only (no conda)
-
-Choose from 1, 2, 3 (1, 2, 3) [1]:
+Choose from [1/2/3] (1):
 
 Select include_ReadTheDocs:
 1 - y
 2 - n
-Choose from 1, 2 (1, 2) [1]:
+Choose from [1/2] (1):
 ```
 
 ````
@@ -355,8 +354,7 @@ Once inside the `molecool` folder (`molecool/molecool`), examine the files that
 View the module (`functions.py`) in a text editor.
 We see a few things about this file.
 The top begins with a description of this module surrounded by three quotations (`"""`).
-Right now, that is the file name, followed by our short description,
-then the sentence "Handles the primary functions".
+Right now, that is the sentence "Provides the primary functions".
 We will change this to be more descriptive later.
 CookieCutter has also created a placeholder function called `canvas`.
 At the start of the `canvas` function, we have a `docstring` (more about this in [documentation]),

_sources/04-function-style.md.txt

@@ -61,7 +61,7 @@ def open_pdb(f_loc):
 
 If we want to test our function, we require a pdb file.
 The workshop materials downloaded during the setup include a set of pdb examples.
-These are found in `molssi_beter_practices/starting_material/data/pdb/`.
+These are found in `molssi_best_practices/starting_material/data/pdb/`.
 We want to store these files in our `molecool` directory.
 Luckily, `cookiecutter` created a folder designed specifically for that purpose.
 The folder is in `molecool/data/`.