Merge pull request #639 from zerothi/black

Black linting

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# Add here the commits that should be ignored
+# when issuing blames
+0ff17210003a85b08f683307e9a73555142c8707

.github/ISSUE_TEMPLATE/005_bug.md

@@ -6,7 +6,7 @@ about: Let us know if something went wrong
 
 **Describe the bug**
 
-**Reproducable code**
+**Code to reproduce problem**
 ```python
 <insert code here>
 ```

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 <!-- Feel free to remove check-list items aren't relevant to your change -->
 
- - [ ] Closes #xxxx
- - [ ] Tests added
- - [ ] Ranned `isort .` at top--level
- - [ ] Documentation for functionality, `docs/`
- - [ ] Changes documented, `CHANGELOG.md`
+ - [ ] Closes #x
+ - [ ] Added tests for new/changed functions?
+ - [ ] Ran `isort .` and `black .` at top-level
+ - [ ] Documentation for functionality in `docs/`
+ - [ ] Changes documented in `CHANGELOG.md`

.github/workflows/linter.yml

@@ -0,0 +1,21 @@
+name: Lint
+
+on:
+  push:
+    paths:
+      - '**.py'
+      - '**.ipynb'
+  pull_request:
+    paths:
+      - '**.py'
+      - '**.ipynb'
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+        with:
+          jupyter: true
+      - uses: isort/isort-action@master

.github/workflows/test.yaml

@@ -10,9 +10,9 @@ env:
 
 
 on:
-  pull_request:
-    # all pull-requests on to main
-    branches: [main]
+  workflow_run:
+    workflows: [Lint]
+    types: [completed]
   schedule:
     # only once every 4 days
     # We can always force run this.
@@ -32,8 +32,11 @@ on:
 jobs:
 
   # Define a few jobs that can be runned
-  check_schedule:
-    if: ${{ github.event_name == 'schedule' }} && ${{ github.actor != 'dependabot[bot]' }}
+  check_if_runnable:
+    if: |
+      github.event_name == 'schedule'
+      && github.actor != 'dependabot[bot]'
+      && github.event.workflow_run.conclusion == 'success'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -42,8 +45,8 @@ jobs:
       - run: test -n $(git rev-list --after="1 week" --max-count=1 ${{ github.sha }})
 
   test_runs:
-    needs: [check_schedule]
-    if: ${{ always() && (contains(needs.*.result, 'success') || contains(needs.*.result, 'skipped')) }}
+    needs: [check_if_runnable]
+    if: ${{ contains(needs.*.result, 'success') || contains(needs.*.result, 'skipped') }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

CHANGELOG.md

@@ -28,6 +28,7 @@ we hit release version 1.0.0.
 - fixed cases where `Geometry.close` would not catch all neighbours, #633
 
 ### Changed
+- sisl now enforces the black style
 - `Lattice` now holds the boundary conditions (not `Grid`), see #626
 - Some siles exposed certain properties containing basic information
   about the content, say number of atoms/orbitals etc.

CONTRIBUTING.md

@@ -15,6 +15,8 @@ you should add this change to your `.git/config`, or in your global `.gitconfig`
     [filter "strip-notebook-output"]
         clean = "jupyter nbconvert --ClearOutputPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR"
 
+We also enforce the black style, please run black before committing.
+
 ## First-time contributors
 Add a comment on the issue and wait for the issue to be assigned before you start working on it. This helps to avoid multiple people working on similar issues.
 

README.md

@@ -3,6 +3,7 @@
 [![Install sisl using PyPI](https://badge.fury.io/py/sisl.svg)](https://pypi.org/project/sisl)
 [![Install sisl using conda](https://anaconda.org/conda-forge/sisl/badges/version.svg)](https://anaconda.org/conda-forge/sisl)
 [![License: MPL 2.0](https://img.shields.io/badge/License-MPL%202.0-brightgreen.svg)](https://www.mozilla.org/en-US/MPL/2.0/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![DOI for citation](https://zenodo.org/badge/doi/10.5281/zenodo.597181.svg)](https://doi.org/10.5281/zenodo.597181)
 <!--- [![Documentation on RTD](https://readthedocs.org/projects/docs/badge/?version=latest)](http://sisl.readthedocs.io/en/latest/) -->
 [![Join discussion on Discord](https://img.shields.io/discord/742636379871379577.svg?label=&logo=discord&logoColor=ffffff&color=green&labelColor=red)](https://discord.gg/5XnFXFdkv2)

benchmarks/bloch.py

@@ -51,6 +51,6 @@
 
 stat = pstats.Stats(pr)
 # We sort against total-time
-stat.sort_stats('tottime')
+stat.sort_stats("tottime")
 # Only print the first 20% of the routines.
-stat.print_stats('sisl', 0.2)
+stat.print_stats("sisl", 0.2)

benchmarks/bz_parallel.py

@@ -52,8 +52,11 @@
     par = bz.apply.renew(eta=True)
 
 E = np.linspace(-2, 2, 200)
+
+
 def wrap_DOS(es):
     return es.DOS(E)
-dos = par.ndarray.eigenstate(wrap=wrap_DOS)
-#dos = par.average.eigenstate(wrap=wrap_DOS)
 
+
+dos = par.ndarray.eigenstate(wrap=wrap_DOS)
+# dos = par.average.eigenstate(wrap=wrap_DOS)

benchmarks/bz_replace.py

@@ -39,12 +39,16 @@
     nks = [50 for _ in range(nlvls)]
 
 if ndim == 1:
+
     def get_nk(nk):
         return [nk, 1, 1]
+
     ns = [2 for _ in range(nlvls)]
 else:
+
     def get_nk(nk):
         return [nk, nk, 1]
+
     if nlvls > 2:
         ns = [50 for _ in range(nlvls)]
     else:
@@ -55,11 +59,12 @@ def get_nk(nk):
 def yield_kpoint(bz, n):
     yield from np.unique(np.random.randint(len(bz), size=n))[::-1]
 
+
 # Replacement function
 
 
 def add_levels(bz, nks, ns, fast=False, as_index=False, debug=False):
-    """ Add different levels according to the length of `ns` """
+    """Add different levels according to the length of `ns`"""
     global nlvls
 
     lvl = nlvls - len(nks)
@@ -72,6 +77,7 @@ def add_levels(bz, nks, ns, fast=False, as_index=False, debug=False):
         bz = bz.copy()
 
     from io import StringIO
+
     s = StringIO()
 
     def print_s(force=True):
@@ -84,12 +90,12 @@ def print_s(force=True):
 
         # reset s
         s = StringIO()
+
     if debug:
         print(f"lvl = {lvl}", file=s)
         print_s()
 
     if len(nks) > 0:
-
         # calculate the size of the current BZ
         dsize = bz._size / bz._diag
 
@@ -115,7 +121,9 @@ def print_s(force=True):
         # create the single monkhorst pack we will use for replacements
         if fast:
             new_bz = sisl.MonkhorstPack(bz.parent, nk, size=dsize, trs=False)
-            new, reps = add_levels(new_bz, nks[:-1], ns[:-1], fast, as_index, debug=debug)
+            new, reps = add_levels(
+                new_bz, nks[:-1], ns[:-1], fast, as_index, debug=debug
+            )
 
             if as_index:
                 bz.replace(iks, new, displacement=True, as_index=True)
@@ -137,8 +145,12 @@ def print_s(force=True):
 
                 # Recursively add a new level
                 # create the single monkhorst pack we will use for replacements
-                new_bz = sisl.MonkhorstPack(bz.parent, nk, size=dsize, trs=False, displacement=k)
-                new, reps = add_levels(new_bz, nks[:-1], ns[:-1], fast, as_index, debug=debug)
+                new_bz = sisl.MonkhorstPack(
+                    bz.parent, nk, size=dsize, trs=False, displacement=k
+                )
+                new, reps = add_levels(
+                    new_bz, nks[:-1], ns[:-1], fast, as_index, debug=debug
+                )
 
                 # calculate number of replaced k-points
                 if debug:
@@ -152,6 +164,7 @@ def print_s(force=True):
 
                 if False:
                     import matplotlib.pyplot as plt
+
                     plt.figure()
                     plt.scatter(bz.k[:, 0], bz.k[:, 1])
                     plt.title(f"{lvl} and {ik}")
@@ -166,7 +179,7 @@ def print_s(force=True):
                     rep_nk = len(new) - (len(bz) - bz_nk)
                     print("replaced k-points ", rep_nk, file=s)
                     print_s()
-                    #print(len(bz)*4 * 8 / 1024**3)
+                    # print(len(bz)*4 * 8 / 1024**3)
 
                 del new
 
@@ -200,6 +213,6 @@ def print_s(force=True):
 
     stat = pstats.Stats(pr)
     # We sort against total-time
-    stat.sort_stats('tottime')
+    stat.sort_stats("tottime")
     # Only print the first 20% of the routines.
-    stat.print_stats('sisl', 0.2)
+    stat.print_stats("sisl", 0.2)

benchmarks/graphene.py

@@ -37,14 +37,14 @@
 gr = sisl.geom.graphene(orthogonal=True).tile(N, 0).tile(N, 1)
 H = sisl.Hamiltonian(gr)
 pr.enable()
-H.construct([(0.1, 1.44), (0., -2.7)], eta=True)
+H.construct([(0.1, 1.44), (0.0, -2.7)], eta=True)
 H.finalize()
 pr.disable()
 pr.dump_stats(f"{sys.argv[0]}.profile")
 
 
 stat = pstats.Stats(pr)
 # We sort against total-time
-stat.sort_stats('tottime')
+stat.sort_stats("tottime")
 # Only print the first 20% of the routines.
-stat.print_stats('sisl', 0.2)
+stat.print_stats("sisl", 0.2)

benchmarks/graphene_io.py

@@ -47,6 +47,6 @@
 
 stat = pstats.Stats(pr)
 # We sort against total-time
-stat.sort_stats('tottime')
+stat.sort_stats("tottime")
 # Only print the first 20% of the routines.
-stat.print_stats('sisl', 0.2)
+stat.print_stats("sisl", 0.2)

benchmarks/graphene_repeat.py

@@ -36,7 +36,7 @@
 
 gr = sisl.geom.graphene(orthogonal=True)
 H = sisl.Hamiltonian(gr)
-H.construct([(0.1, 1.44), (0., -2.7)])
+H.construct([(0.1, 1.44), (0.0, -2.7)])
 pr.enable()
 H.repeat(N, 0).repeat(N, 1)
 H.finalize()
@@ -46,6 +46,6 @@
 
 stat = pstats.Stats(pr)
 # We sort against total-time
-stat.sort_stats('tottime')
+stat.sort_stats("tottime")
 # Only print the first 20% of the routines.
-stat.print_stats('sisl', 0.2)
+stat.print_stats("sisl", 0.2)

benchmarks/graphene_tile.py

@@ -36,7 +36,7 @@
 
 gr = sisl.geom.graphene(orthogonal=True)
 H = sisl.Hamiltonian(gr)
-H.construct([(0.1, 1.44), (0., -2.7)])
+H.construct([(0.1, 1.44), (0.0, -2.7)])
 pr.enable()
 H = H.tile(N, 0).tile(N, 1)
 H.finalize()
@@ -46,6 +46,6 @@
 
 stat = pstats.Stats(pr)
 # We sort against total-time
-stat.sort_stats('tottime')
+stat.sort_stats("tottime")
 # Only print the first 20% of the routines.
-stat.print_stats('sisl', 0.2)
+stat.print_stats("sisl", 0.2)

benchmarks/graphene_within.py

@@ -21,13 +21,13 @@
 
 import sisl
 
-method = 'cube'
-if 'cube' in sys.argv:
-    method = 'cube'
-    sys.argv.remove('cube')
-elif 'sphere' in sys.argv:
-    method = 'sphere'
-    sys.argv.remove('sphere')
+method = "cube"
+if "cube" in sys.argv:
+    method = "cube"
+    sys.argv.remove("cube")
+elif "sphere" in sys.argv:
+    method = "sphere"
+    sys.argv.remove("sphere")
 
 if len(sys.argv) > 1:
     N = int(sys.argv[1])
@@ -37,5 +37,5 @@
 
 gr = sisl.geom.graphene(orthogonal=True).tile(N, 0).tile(N, 1)
 H = sisl.Hamiltonian(gr)
-H.construct([(0.1, 1.44), (0., -2.7)], method=method, eta=True)
+H.construct([(0.1, 1.44), (0.0, -2.7)], method=method, eta=True)
 H.finalize()