Re-style codebase: validphys

.git-blame-ignore-revs

@@ -7,3 +7,8 @@
 fbfd77118d60306d4e0ea84b832088eafb8cb867
 # CAll black and isort on the last commit
 5d9b9e8da6805abd18910cf09314b29a564728a8
+# running black in the root vp folder, closuretest, plotoptions and theorycovariance
+b9084ce695c49b5645b82436b19ec6cc3bd30280
+a5d7385a79ef242e7eb1b1bf7b3746b6ebd6a0d0
+3e8cf70c2d3b36d19fcb764599f6dfa6eb924b77
+27f25d037854caa7e15496e4c6fa9d520f365ac9

doc/sphinx/source/contributing/python-tools.md

@@ -66,6 +66,8 @@ integrated with your editor of choice.
   - The [`black` code formatter](https://github.com/psf/black) runs almost
     without configuration and produces typically good results. It is good to run
     it by default, to avoid spending time on formatting (or arguing about it).
+  - The [`isort`](https://pycqa.github.io/isort/) library sorts imports 
+    alphabetically, and automatically separated into sections and by type.
 
 ## Debugging
 

doc/sphinx/source/contributing/rules.md

@@ -1,6 +1,7 @@
 ```eval_rst
 .. _rules:
 ```
+
 # Code development
 
 Code development is carried out using Github.
@@ -103,11 +104,25 @@ requests:
         configuration](https://github.com/NNPDF/nnpdf/blob/master/.pylintrc) to
         catch common problems with Python code.
 	  * New Python code should come formatted with
-	    [`black` tool](https://github.com/psf/black).
+	    [`black` tool](https://github.com/psf/black) with [our default
+		configuration](https://github.com/NNPDF/nnpdf/blob/master/pyproject.toml) 
+	  * The imports in Python code should be sorted using the 
+	    [`isort`](https://pycqa.github.io/isort/) tool with [our default
+		configuration](https://github.com/NNPDF/nnpdf/blob/master/pyproject.toml) 
 	  * Changes in compiled code should be tested in debug mode, with
 		the address sanitizer enabled. This is done with the
 		`-DCMAKE_BUILD_TYPE=Debug -DENABLE_ASAN=ON` options in `cmake`.
 
+	Some commits corresponding to major cosmetic changes have been collected in
+	[`.git-blame-ignore-revs`](
+	https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
+	). It is possible to configure the local git to ignore these commits when 
+	running `git blame`:
+	``` 
+	git config blame.ignoreRevsFile .git-blame-ignore-revs 
+	```
+
+
   - Regardless of automated tests, always run code with the new changes
     manually. This gives great insight into possible pitfalls and areas of
     improvement.

validphys2/src/validphys/__init__.py

@@ -1,3 +1,4 @@
-#We don't want to import stuff here that could slow down the import times
+# We don't want to import stuff here that could slow down the import times
 from validphys.version import build_version
+
 __version__ = build_version

validphys2/src/validphys/api.py

@@ -17,7 +17,6 @@
 import logging
 
 from reportengine import api
-
 from validphys.app import providers
 from validphys.config import Config, Environment
 

validphys2/src/validphys/app.py

@@ -9,19 +9,16 @@
 The entry point of the validphys application is the ``main`` funcion of this
 module.
 """
-import sys
-import os
-import logging
 import contextlib
-
+import logging
+import os
+import sys
 
 import lhapdf
-from reportengine import app
 
+from reportengine import app
+from validphys import mplstyles, uploadutils
 from validphys.config import Config, Environment
-from validphys import uploadutils
-from validphys import mplstyles
-
 
 providers = [
     "validphys.results",
@@ -37,7 +34,7 @@
     "validphys.correlations",
     "validphys.chi2grids",
     "validphys.eff_exponents",
-    "validphys.asy_exponents",    
+    "validphys.asy_exponents",
     "validphys.paramfits.dataops",
     "validphys.paramfits.plots",
     "validphys.theorycovariance.construction",
@@ -55,14 +52,13 @@
     "validphys.n3fit_data",
     "validphys.mc2hessian",
     "reportengine.report",
-    "validphys.overfit_metric"
+    "validphys.overfit_metric",
 ]
 
 log = logging.getLogger(__name__)
 
 
 class App(app.App):
-
     environment_class = Environment
     config_class = Config
 

validphys2/src/validphys/arclength.py

@@ -12,16 +12,14 @@
 import scipy.integrate as integrate
 
 from reportengine import collect
+from reportengine.checks import check_positive, make_argcheck
 from reportengine.figure import figure
 from reportengine.table import table
-from reportengine.checks import check_positive, make_argcheck
-
+from validphys import plotutils
+from validphys.checks import check_pdf_normalize_to
+from validphys.core import PDF
 from validphys.pdfbases import Basis, check_basis
 from validphys.pdfgrids import xgrid, xplotting_grid
-from validphys.core import PDF
-from validphys.checks import check_pdf_normalize_to
-from validphys import plotutils
-
 
 ArcLengthGrid = namedtuple("ArcLengthGrid", ("pdf", "basis", "flavours", "stats"))
 
@@ -36,22 +34,22 @@ def arc_lengths(
 ):
     """
     Compute arc lengths at scale Q
-    
+
     set up a grid with three segments and
     compute the arclength for each segment.
     Note: the variation of the PDF over the grid
     is computed by computing the forward differences
     between adjacent grid points.
-    
+
 
     Parameters
     ----------
-    
+
     pdf : validphys.core.PDF object
 
     Q : float
         scale at which to evaluate PDF
-    
+
     basis : default = "flavour"
 
     flavours : default = None
@@ -60,9 +58,9 @@ def arc_lengths(
     -------
 
     validphys.arclength.ArcLengthGrid object
-    object that contains the PDF, basis, flavours, and computed 
+    object that contains the PDF, basis, flavours, and computed
     arc length statistics.
-    
+
     """
 
     checked = check_basis(basis, flavours)
@@ -94,12 +92,8 @@ def arc_length_table(arc_lengths):
     """Return a table with the descriptive statistics of the arc lengths
     over members of the PDF."""
     arc_length_data = arc_lengths.stats.error_members()
-    arc_length_columns = [
-        f"${arc_lengths.basis.elementlabel(fl)}$" for fl in arc_lengths.flavours
-    ]
-    return (
-        pd.DataFrame(arc_length_data, columns=arc_length_columns).describe().iloc[1:, :]
-    )
+    arc_length_columns = [f"${arc_lengths.basis.elementlabel(fl)}$" for fl in arc_lengths.flavours]
+    return pd.DataFrame(arc_length_data, columns=arc_length_columns).describe().iloc[1:, :]
 
 
 @figure
@@ -116,27 +110,24 @@ def plot_arc_lengths(
 
     for ipdf, arclengths in enumerate(pdfs_arc_lengths):
         xvalues = np.array(range(len(arclengths.flavours)))
-        xlabels = [
-            "$" + arclengths.basis.elementlabel(fl) + "$" for fl in arclengths.flavours
-        ]
-
+        xlabels = ["$" + arclengths.basis.elementlabel(fl) + "$" for fl in arclengths.flavours]
+
         ylower, yupper = arclengths.stats.errorbar68()
         yvalues = (ylower + yupper) * 0.5
         yerr = np.abs(yupper - ylower) * 0.5
 
-
         if normalize_to is not None:
             norm_cv = pdfs_arc_lengths[normalize_to].stats.central_value()
             yvalues = np.divide(yvalues, norm_cv)
             yerr = np.divide(yerr, norm_cv)
-            
+
         shift = (ipdf - (len(pdfs_arc_lengths) - 1) / 2.0) / 5.0
         ax.errorbar(
             xvalues + shift,
             yvalues,
             yerr=yerr,
             fmt='',
-            linestyle = '',
+            linestyle='',
             label=arclengths.pdf.label,
         )
         ax.set_xticks(xvalues)
@@ -152,8 +143,8 @@ def integrability_number(
     basis: (str, Basis) = "evolution",
     flavours: (list, tuple, type(None)) = None,
 ):
-    """Return \sum_i |x_i*f(x_i)|, x_i = {1e-9, 1e-8, 1e-7} 
-    for selected flavours 
+    """Return \sum_i |x_i*f(x_i)|, x_i = {1e-9, 1e-8, 1e-7}
+    for selected flavours
     """
     checked = check_basis(basis, flavours)
     basis, flavours = checked["basis"], checked["flavours"]