Merge pull request #148 from NWChemEx/python_formatting

Python Formatting

.github/workflows/common_pull_request.yaml

@@ -31,7 +31,7 @@ on:
         required: false
         default: '.licenserc.yaml'
       source_dir:
-        description: "Space seperated list of dirs to apply formatting to"
+        description: "Space seperated list of dirs to apply clang-format to"
         type: string
         required: false
         default: 'include src tests'
@@ -55,6 +55,11 @@ on:
         type: boolean
         required: false
         default: true
+      format_python:
+        description: "Whether or not to format python files"
+        type: boolean
+        required: false
+        default: true
     secrets:
       CMAIZE_GITHUB_TOKEN:
         description: "Token passed to CMaize"
@@ -78,6 +83,10 @@ jobs:
           token: ${{ secrets.CMAIZE_GITHUB_TOKEN }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
+      - uses: actions/setup-python@v2
+        if: inputs.format_python == true
+        with:
+          python-version: '3.x'
       - name: Add license
         if: inputs.config_file != ''
         uses: apache/[email protected]
@@ -92,6 +101,12 @@ jobs:
           extensions: 'hpp,cpp,ipp,h,c'
           clangFormatVersion: 12
           inplace: True
+      - name: Apply python formatting
+        if: inputs.format_python == true
+        run: |
+          pip install yapf
+          find . -name '*.py' -print0 | xargs -0 yapf -i
+        shell: bash
       - name: Commit any changes
         id: commit-changes
         uses: EndBug/add-and-commit@v9

docs/source/conf.py

@@ -34,12 +34,8 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
+    'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx',
+    'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax',
     'sphinxcontrib.bibtex'
 ]
 dir_path = os.path.dirname(os.path.realpath(__file__))
@@ -86,9 +82,7 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-html_theme_options = {
-    'vcs_pageview_mode' : 'edit'
-}
+html_theme_options = {'vcs_pageview_mode': 'edit'}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -105,21 +99,19 @@
 #
 # html_sidebars = {}
 
-
 # Allows the edit on GitHub button to make editing the docs easier.
 html_context = {
-  'display_github': True,
-  'github_user': 'NWChemEx',
-  'github_repo': '.github',
-  'github_version': 'master/docs/source/',
+    'display_github': True,
+    'github_user': 'NWChemEx',
+    'github_repo': '.github',
+    'github_version': 'master/docs/source/',
 }
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = project + 'doc'
 
-
 # -- Options for LaTeX output ------------------------------------------------
 
 latex_elements = {
@@ -140,7 +132,6 @@
     # 'figure_align': 'htbp',
 }
 
-
 # -- Extension configuration -------------------------------------------------
 
 # -- Options for intersphinx extension ---------------------------------------
@@ -153,11 +144,8 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
-
 # -- Options for bibtex --------------------------------------------------------
 
-bibtex_bibfiles = [
-    'bibliography/software.bib'
-]
+bibtex_bibfiles = ['bibliography/software.bib']
 bibtex_reference_style = 'super'
 bibtex_default_style = 'plain'

scripts/make_tutorials.py

@@ -23,7 +23,7 @@ def strip_newline(block):
             break
         end -= 1
 
-    return block[start: end]
+    return block[start:end]
 
 
 def write_code(block, lang):
@@ -36,7 +36,7 @@ def write_code(block, lang):
     :param lang: The language of the code snippet
     :return: A string suitable for printing in a reST file
     """
-    a_tab = " "*4
+    a_tab = " " * 4
 
     parsed_block = strip_newline(block)
 
@@ -138,7 +138,7 @@ def parse_file(cc, filename):
             else:  # n-th line outside a comment block
                 if which_first is None:
                     which_first = False
-                if len(code) == 0: # If code came first, there's no array yet
+                if len(code) == 0:  # If code came first, there's no array yet
                     code.append([])
                 code[-1].append(line)
 
@@ -179,9 +179,10 @@ def write_tutorial(name, lang, comments, code, first):
 
     # Write the title of the tutorial
     output = name + '\n'
-    output += '='*len(name) + "\n\n"
+    output += '=' * len(name) + "\n\n"
 
-    for i in range(n_second):  # Loop over second because it is possibly shorter
+    for i in range(
+            n_second):  # Loop over second because it is possibly shorter
         if first:
             output += write_comment(comments[i])
             output += write_code(code[i], lang)
@@ -229,14 +230,8 @@ def make_tutorials(input_dir, output_dir):
     """
 
     # Define the comment characters and name for each language
-    comment_chars = {".py": '#',
-                     ".hpp": "//",
-                     ".cpp" : "//",
-                     ".cmake": '#'}
-    lang = {".py": "python",
-            ".hpp": "c++",
-            ".cpp": "c++",
-            ".cmake": "cmake"}
+    comment_chars = {".py": '#', ".hpp": "//", ".cpp": "//", ".cmake": '#'}
+    lang = {".py": "python", ".hpp": "c++", ".cpp": "c++", ".cmake": "cmake"}
 
     # Make output directory if it does not exist
     if not os.path.exists(output_dir):
@@ -250,7 +245,7 @@ def make_tutorials(input_dir, output_dir):
 
         if os.path.isdir(input_file):
             make_tutorials(input_file, os.path.join(output_dir, file_name))
-            file_names.append(os.path.join(file_name,"index"))
+            file_names.append(os.path.join(file_name, "index"))
             continue
 
         if extension not in lang:  # Not a file we're supposed to parse
@@ -272,7 +267,6 @@ def make_tutorials(input_dir, output_dir):
     #    index_file.write(write_index(file_names))
 
 
-
 # def main():
 #     docs_dir = os.path.dirname(os.path.realpath(__file__))
 #     root_dir = os.path.dirname(docs_dir)