Merge pull request #89 from neutrinoceros/formatting_conf

STY: copy over yt's linting+formatting configuration

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# migrate to black + isort + pyupgrade
+88e8d9e5afd0ca7d20afb0a15383bcede0f1b1cd
+8553023d396182eb2315f3816623f852d2a51dc7

.mailmap

@@ -115,4 +115,4 @@ BW Keller <kellerbw@mcmaster.ca> Ben Keller <malzraa@gmail.com>
 Benjamin Thompson <bthompson2090@gmail.com> Ben Thompson <bthompson2090@gmail.com>
 Alex Lindsay <al007@illinois.edu> Alex Lindsay <alexlindsay239@gmail.com>
 Yi-Hao Chen (ychen@astro.wisc.edu) Yi-Hao Chen (yihaochentw@gmail.com)
-Kacper Kowalik <xarthisius.kk@gmail.com> Kacper Kowalik (Xarthisius) <xarthisius.kk@gmail.com>
+Kacper Kowalik <xarthisius.kk@gmail.com> Kacper Kowalik (Xarthisius) <xarthisius.kk@gmail.com>

.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+# pre-commit 1.1.0 is required for `exclude`
+# however `minimum_pre_commit_version` itself requires 1.15.0
+minimum_pre_commit_version: "1.15.0"
+
+ci:
+    autofix_prs: true
+
+repos:
+#-   repo: https://github.com/asottile/setup-cfg-fmt
+#    rev: v1.17.0
+#    hooks:
+#    -   id: setup-cfg-fmt
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: no-commit-to-branch
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v2.29.0
+    hooks:
+    - id: pyupgrade
+      args: [--py36-plus]
+-   repo: https://github.com/psf/black
+    rev: 21.9b0
+    hooks:
+    - id: black
+-   repo: https://github.com/PyCQA/isort
+    rev: '5.9.3'
+    hooks:
+    - id: isort
+      name: isort (python)
+    - id: isort
+      name: isort (cython)
+      types: [cython]
+-   repo: https://github.com/PyCQA/flake8
+    rev: '3.9.2'
+    hooks:
+    - id: flake8
+      additional_dependencies: [
+        flake8-bugbear==21.9.1,
+        flake8-logging-format==0.6.0,
+        flake8-2020==1.6.0,
+      ]
+-   repo: https://github.com/asottile/blacken-docs
+    rev: v1.11.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies: [black==21.8b0]
+#-   repo: https://github.com/pre-commit/pygrep-hooks
+#    rev: v1.9.0
+#    hooks:
+#    -   id: rst-backticks

COPYING.txt

@@ -53,7 +53,7 @@ The yt Development Team is the set of all contributors to the yt project.  This
 includes all of the yt subprojects.
 
 The core team that coordinates development on BitBucket can be found here:
-http://bitbucket.org/yt_analysis/ 
+http://bitbucket.org/yt_analysis/
 
 
 Our Copyright Policy

README.md

@@ -22,7 +22,7 @@ schedule.
 Full installation documentation can also be found
 [here](https://yt-astro-analysis.readthedocs.io/en/latest/Installation.html).
 
-To install yt_astro_analysis, you will first need to 
+To install yt_astro_analysis, you will first need to
 [install yt](https://github.com/yt-project/yt#installation). Then do,
 
 ```

doc/extensions/config_help.py

@@ -1,34 +1,38 @@
 import re
 import subprocess
+
 from docutils import statemachine
 from sphinx.util.compat import Directive
 
+
 def setup(app):
-    app.add_directive('config_help', GetConfigHelp)
+    app.add_directive("config_help", GetConfigHelp)
     setup.app = app
     setup.config = app.config
     setup.confdir = app.confdir
 
-    retdict = dict(
-        version='1.0',
-        parallel_read_safe=True,
-        parallel_write_safe=True
-    )
+    retdict = dict(version="1.0", parallel_read_safe=True, parallel_write_safe=True)
 
     return retdict
 
+
 class GetConfigHelp(Directive):
     required_arguments = 1
     optional_arguments = 0
     final_argument_whitespace = True
 
     def run(self):
-        rst_file = self.state_machine.document.attributes['source']
-        data = subprocess.check_output(
-            self.arguments[0].split(" ") + ['-h']).decode('utf8').split('\n')
-        ind = next((i for i, val in enumerate(data)
-                    if re.match('\s{0,3}\{.*\}\s*$', val)))
-        lines = ['.. code-block:: none', ''] + data[ind + 1:]
+        rst_file = self.state_machine.document.attributes["source"]
+        data = (
+            subprocess.check_output(self.arguments[0].split(" ") + ["-h"])
+            .decode("utf8")
+            .split("\n")
+        )
+        ind = next(
+            (i for i, val in enumerate(data) if re.match(r"\s{0,3}\{.*\}\s*$", val))
+        )
+        lines = [".. code-block:: none", ""] + data[ind + 1 :]
         self.state_machine.insert_input(
-            statemachine.string2lines("\n".join(lines)), rst_file)
+            statemachine.string2lines("\n".join(lines)), rst_file
+        )
         return []

doc/extensions/pythonscript_sphinxext.py

@@ -1,13 +1,14 @@
-import tempfile
-import time
-import os
+import errno
 import glob
+import os
 import shutil
 import subprocess
+import tempfile
+import time
 import uuid
-import errno
-from sphinx.util.compat import Directive
+
 from docutils import nodes
+from sphinx.util.compat import Directive
 
 
 class PythonScriptDirective(Directive):
@@ -18,6 +19,7 @@ class PythonScriptDirective(Directive):
     along with the script.
 
     """
+
     required_arguments = 0
     optional_arguments = 0
     has_content = True
@@ -27,7 +29,7 @@ def run(self):
         tmpdir = tempfile.mkdtemp()
         os.chdir(tmpdir)
 
-        rst_file = self.state_machine.document.attributes['source']
+        rst_file = self.state_machine.document.attributes["source"]
         rst_dir = os.path.abspath(os.path.dirname(rst_file))
 
         image_dir, image_rel_dir = make_image_dir(setup, rst_dir)
@@ -45,20 +47,19 @@ def run(self):
         print("")
 
         start = time.time()
-        subprocess.call(['python', 'temp.py'])
-        print(">> The execution of the script %s took %f s" %
-              (uid, time.time() - start))
-        text = ''
+        subprocess.call(["python", "temp.py"])
+        print(f">> The execution of the script {uid} took {time.time() - start:f} s")
+        text = ""
         for im in sorted(glob.glob("*.png")):
             text += get_image_tag(im, image_dir, image_rel_dir)
 
         code = content
 
         literal = nodes.literal_block(code, code)
-        literal['language'] = 'python'
+        literal["language"] = "python"
 
-        attributes = {'format': 'html'}
-        img_node = nodes.raw('', text, **attributes)
+        attributes = {"format": "html"}
+        img_node = nodes.raw("", text, **attributes)
 
         # clean up
         os.chdir(cwd)
@@ -68,16 +69,12 @@ def run(self):
 
 
 def setup(app):
-    app.add_directive('python-script', PythonScriptDirective)
+    app.add_directive("python-script", PythonScriptDirective)
     setup.app = app
     setup.config = app.config
     setup.confdir = app.confdir
 
-    retdict = dict(
-        version='0.1',
-        parallel_read_safe=True,
-        parallel_write_safe=True
-    )
+    retdict = dict(version="0.1", parallel_read_safe=True, parallel_write_safe=True)
 
     return retdict
 
@@ -90,9 +87,9 @@ def get_image_tag(filename, image_dir, image_rel_dir):
 
 
 def make_image_dir(setup, rst_dir):
-    image_dir = setup.app.builder.outdir + os.path.sep + '_images'
+    image_dir = setup.app.builder.outdir + os.path.sep + "_images"
     rel_dir = os.path.relpath(setup.confdir, rst_dir)
-    image_rel_dir = rel_dir + os.path.sep + '_images'
+    image_rel_dir = rel_dir + os.path.sep + "_images"
     thread_safe_mkdir(image_dir)
     return image_dir, image_rel_dir
 

doc/extensions/yt_colormaps.py

@@ -3,48 +3,51 @@
 #  2. This script is added to the document in a literalinclude
 #  3. Any _static images found will be added
 
-from sphinx.util.compat import Directive
+import glob
+import os
+import shutil
+
 from docutils.parsers.rst import directives
-import os, glob, shutil
+from sphinx.util.compat import Directive
 
 # Some of this magic comes from the matplotlib plot_directive.
 
+
 def setup(app):
-    app.add_directive('yt_colormaps', ColormapScript)
+    app.add_directive("yt_colormaps", ColormapScript)
     setup.app = app
     setup.config = app.config
     setup.confdir = app.confdir
 
-    retdict = dict(
-        version='0.1',
-        parallel_read_safe=True,
-        parallel_write_safe=True
-    )
+    retdict = dict(version="0.1", parallel_read_safe=True, parallel_write_safe=True)
 
     return retdict
 
+
 class ColormapScript(Directive):
     required_arguments = 1
     optional_arguments = 0
 
     def run(self):
-        rst_file = self.state_machine.document.attributes['source']
+        rst_file = self.state_machine.document.attributes["source"]
         rst_dir = os.path.abspath(os.path.dirname(rst_file))
         script_fn = directives.path(self.arguments[0])
         script_bn = os.path.basename(script_fn)
-        script_name = os.path.basename(self.arguments[0]).split(".")[0]
 
         # This magic is from matplotlib
-        dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir,
-                                                os.path.dirname(script_fn)))
+        dest_dir = os.path.abspath(
+            os.path.join(setup.app.builder.outdir, os.path.dirname(script_fn))
+        )
         if not os.path.exists(dest_dir):
-            os.makedirs(dest_dir) # no problem here for me, but just use built-ins
+            os.makedirs(dest_dir)  # no problem here for me, but just use built-ins
 
         rel_dir = os.path.relpath(rst_dir, setup.confdir)
         place = os.path.join(dest_dir, rel_dir)
-        if not os.path.isdir(place): os.makedirs(place)
-        shutil.copyfile(os.path.join(rst_dir, script_fn),
-                        os.path.join(place, script_bn))
+        if not os.path.isdir(place):
+            os.makedirs(place)
+        shutil.copyfile(
+            os.path.join(rst_dir, script_fn), os.path.join(place, script_bn)
+        )
 
         im_path = os.path.join(rst_dir, "_static")
         images = sorted(glob.glob(os.path.join(im_path, "*.png")))

doc/extensions/yt_cookbook.py

@@ -3,55 +3,60 @@
 #  2. This script is added to the document in a literalinclude
 #  3. Any _static images found will be added
 
-from sphinx.util.compat import Directive
+import glob
+import os
+import shutil
+
 from docutils.parsers.rst import directives
-import os, glob, shutil
+from sphinx.util.compat import Directive
 
 # Some of this magic comes from the matplotlib plot_directive.
 
+
 def setup(app):
-    app.add_directive('yt_cookbook', CookbookScript)
+    app.add_directive("yt_cookbook", CookbookScript)
     setup.app = app
     setup.config = app.config
     setup.confdir = app.confdir
 
-    retdict = dict(
-        version='0.1',
-        parallel_read_safe=True,
-        parallel_write_safe=True
-    )
+    retdict = dict(version="0.1", parallel_read_safe=True, parallel_write_safe=True)
 
     return retdict
 
+
 data_patterns = ["*.h5", "*.out", "*.dat"]
 
+
 class CookbookScript(Directive):
     required_arguments = 1
     optional_arguments = 0
 
     def run(self):
-        rst_file = self.state_machine.document.attributes['source']
+        rst_file = self.state_machine.document.attributes["source"]
         rst_dir = os.path.abspath(os.path.dirname(rst_file))
         script_fn = directives.path(self.arguments[0])
         script_bn = os.path.basename(script_fn)
         script_name = os.path.basename(self.arguments[0]).split(".")[0]
 
         # This magic is from matplotlib
-        dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir,
-                                                os.path.dirname(script_fn)))
+        dest_dir = os.path.abspath(
+            os.path.join(setup.app.builder.outdir, os.path.dirname(script_fn))
+        )
         if not os.path.exists(dest_dir):
-            os.makedirs(dest_dir) # no problem here for me, but just use built-ins
+            os.makedirs(dest_dir)  # no problem here for me, but just use built-ins
 
         rel_dir = os.path.relpath(rst_dir, setup.confdir)
         place = os.path.join(dest_dir, rel_dir)
-        if not os.path.isdir(place): os.makedirs(place)
-        shutil.copyfile(os.path.join(rst_dir, script_fn),
-                        os.path.join(place, script_bn))
+        if not os.path.isdir(place):
+            os.makedirs(place)
+        shutil.copyfile(
+            os.path.join(rst_dir, script_fn), os.path.join(place, script_bn)
+        )
 
         im_path = os.path.join(rst_dir, "_static")
         images = sorted(glob.glob(os.path.join(im_path, "%s__*.png" % script_name)))
         lines = []
-        lines.append("(`%s <%s>`__)" % (script_bn, script_fn))
+        lines.append(f"(`{script_bn} <{script_fn}>`__)")
         lines.append("\n")
         lines.append("\n")
         lines.append(".. literalinclude:: %s" % self.arguments[0])
@@ -65,13 +70,15 @@ def run(self):
             lines.append("\n")
         lines.append("\n")
         for ext in data_patterns:
-            data_files = sorted(glob.glob(os.path.join(
-                im_path, "%s__*.%s" % (script_name, ext))))
+            data_files = sorted(
+                glob.glob(os.path.join(im_path, f"{script_name}__*.{ext}"))
+            )
             for df in data_files:
                 df_bn = os.path.basename(df)
-                shutil.copyfile(os.path.join(rst_dir, df),
-                                os.path.join(dest_dir, rel_dir, df_bn))
-                lines.append(" * Data: `%s <%s>`__)" % (df_bn, df))
+                shutil.copyfile(
+                    os.path.join(rst_dir, df), os.path.join(dest_dir, rel_dir, df_bn)
+                )
+                lines.append(f" * Data: `{df_bn} <{df}>`__)")
             lines.append("\n")
         self.state_machine.insert_input(lines, rst_file)
         return []