Merge pull request #685 from grahamgower/lint

add pre-commit github action
popsim-consortium · Nov 7, 2020 · 78bef56 · 78bef56
2 parents 009235c + 257bf9d
commit 78bef56
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -9,7 +9,7 @@ aliases:
         - image: circleci/python:3.6-stretch
       working_directory: &working_directory /home/circleci/stdpopsim
   - &set_py_circleci_own
-    run: 
+    run:
       name: Set ownership of Python directories
       command: |
         sudo chown -R circleci:circleci /usr/local/bin
@@ -139,20 +139,6 @@ jobs:
       - store_test_results:
           path: xml
 
-  lint:
-    <<: *container_config
-    steps:
-      - checkout
-      - run:
-          name: Lint Python
-          command: |
-            pip install flake8
-            flake8 --version
-      - run:
-          name: Lint Python
-          command: |
-            flake8 --max-line-length 89 stdpopsim setup.py tests docs/_ext maintenance
-
   docs:
     <<: *container_config
     steps:
@@ -178,7 +164,6 @@ workflows:
   version: 2
   build_and_test:
     jobs:
-      - lint
       - build-slim-lib
       - build-deps
       - build-pkg:

diff --git a/.github/ISSUE_TEMPLATE/bug-report-issue-template.md b/.github/ISSUE_TEMPLATE/bug-report-issue-template.md
@@ -1,8 +1,8 @@
 ---
 name: Bug report
 about: A problem with stdpopsim
-title: 
-labels: 
+title:
+labels:
 assignees: ''
 
 ---
@@ -18,4 +18,3 @@ that reproduces the problem.*
 
 **Suggested fixes:**
 *If you have an idea of what's causing the problem or how to fix it, we'd like to hear it!*
-
diff --git a/.github/ISSUE_TEMPLATE/feature-request-issue-template.md b/.github/ISSUE_TEMPLATE/feature-request-issue-template.md
@@ -1,7 +1,7 @@
 ---
 name: Feature request
 about: A suggestion for something to add to stdpopsim.
-title: 
+title:
 labels: enhancement
 assignees: ''
 

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,17 @@
+name: pre-commit
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - uses: pre-commit/action@v2.0.0
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,16 +1,25 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 20.8b1 
+    rev: 20.8b1
     hooks:
       - id: black
         language_version: python3
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.9
+    rev: 3.8.4
     hooks:
       - id: flake8
-        args: [--config=.flake8]
   - repo: https://github.com/asottile/blacken-docs
     rev: v1.8.0
     hooks:
       - id: blacken-docs
-        additional_dependencies: [black==20.8b1] 
+        additional_dependencies: [black==20.8b1]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: mixed-line-ending
+        args: [--fix=lf]
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -65,7 +65,7 @@ Additionally, community organizers are available to help community members engag
 
 ## 8. Addressing Grievances
 
-If you feel you have been falsely or unfairly accused of violating this Code of Conduct, you should notify PopSim Consortium with a concise description of your grievance. Your grievance will be considered by the organizers. 
+If you feel you have been falsely or unfairly accused of violating this Code of Conduct, you should notify PopSim Consortium with a concise description of your grievance. Your grievance will be considered by the organizers.
 
 
 
@@ -81,7 +81,7 @@ Andrew Kern or Jerome Kelleher
 
 ## 11. License and attribution
 
-The Citizen Code of Conduct is distributed by [Stumptown Syndicate](http://stumptownsyndicate.org) under a [Creative Commons Attribution-ShareAlike license](http://creativecommons.org/licenses/by-sa/3.0/). 
+The Citizen Code of Conduct is distributed by [Stumptown Syndicate](http://stumptownsyndicate.org) under a [Creative Commons Attribution-ShareAlike license](http://creativecommons.org/licenses/by-sa/3.0/).
 
 Portions of text derived from the [Django Code of Conduct](https://www.djangoproject.com/conduct/) and the [Geek Feminism Anti-Harassment Policy](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy).
 

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ Please see the [documentation](https://stdpopsim.readthedocs.io/en/latest/) for
 
 Click [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/popsim-consortium/stdpopsim/master?filepath=stdpopsim_example.ipynb) to start an interactive Jupyter Notebook and start playing with `stdpopsim` now!
 
-If you use ``stdpopsim`` in your work, please cite our 
+If you use ``stdpopsim`` in your work, please cite our
 [paper](https://elifesciences.org/articles/54967).
 See [here](https://stdpopsim.readthedocs.io/en/latest/introduction.html#citations) for
 full citation details.
diff --git a/README.rst b/README.rst
@@ -17,4 +17,4 @@ To start an interactive Jupyter Notebook and start playing with ``stdpopsim`` no
 If you use ``stdpopsim`` in your work, please cite our
 `manuscript <https://doi.org/10.1101/2019.12.20.885129>`_ .
 See `here <https://stdpopsim.readthedocs.io/en/latest/introduction.html#citations>`__ for
-full citation details.
+full citation details.
diff --git a/docs/Makefile b/docs/Makefile
@@ -2,13 +2,13 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    = -W 
+SPHINXOPTS    = -W
 SPHINXBUILD   = sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
 
 # JK: added this target so that "make" will build the HTML
-html: 
+html:
 	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 # Put it first so that "make" without argument is like "make help".

diff --git a/docs/_ext/speciescatalog.py b/docs/_ext/speciescatalog.py
@@ -41,7 +41,7 @@ def get_target(self, tid):
         target node and calling note_explicit_target are essential to allow
         us to cross reference these targets from the rest of the documentation.
         """
-        target = nodes.target('', '', ids=[tid], names=[tid])
+        target = nodes.target("", "", ids=[tid], names=[tid])
         self.state.document.note_explicit_target(target)
         return target
 
@@ -59,8 +59,9 @@ def make_field_list(self, data):
                 for i, citation in enumerate(citations):
                     text = f"{citation.author}, {citation.year}"
                     para += nodes.reference(
-                        internal=False, refuri=citation.doi, text=text)
-                    if i != len(citations)-1:
+                        internal=False, refuri=citation.doi, text=text
+                    )
+                    if i != len(citations) - 1:
                         para += nodes.Text("; ")
                 para += nodes.Text(")")
 
@@ -76,10 +77,16 @@ def species_summary(self, species):
             ("ID", species.id, None),
             ("Name", species.name, None),
             ("Common name", species.common_name, None),
-            ("Generation time", species.generation_time,
-                species.generation_time_citations),
-            ("Population size", species.population_size,
-                species.population_size_citations),
+            (
+                "Generation time",
+                species.generation_time,
+                species.generation_time_citations,
+            ),
+            (
+                "Population size",
+                species.population_size,
+                species.population_size_citations,
+            ),
         ]
         return self.make_field_list(data)
 
@@ -98,7 +105,8 @@ def citation_list(self, citable):
 
             para = nodes.paragraph(text=f"{citation.author}, {citation.year}. ")
             para += nodes.reference(
-                internal=False, refuri=citation.doi, text=citation.doi)
+                internal=False, refuri=citation.doi, text=citation.doi
+            )
             list_item += para
             bullet_list += list_item
         return bullet_list
@@ -421,7 +429,7 @@ def setup(app):
     app.add_directive("speciescatalog", SpeciesCatalogDirective)
 
     return {
-        'version': '0.1',
-        'parallel_read_safe': True,
-        'parallel_write_safe': True,
+        "version": "0.1",
+        "parallel_read_safe": True,
+        "parallel_write_safe": True,
     }
diff --git a/docs/catalog.rst b/docs/catalog.rst
@@ -31,7 +31,7 @@ and saves the output to a file called ``test.trees``:
 
     $ stdpopsim HomSap -c chr22 -o test.trees -g HapMapII_GRCh37 -d OutOfAfrica_3G09 2 2 2
 
-(To learn more about using ``stdpopsim`` via the command-line, read our 
+(To learn more about using ``stdpopsim`` via the command-line, read our
 :ref:`tutorial <sec_cli_tute>` about it.)
 
 Are there other well-known organisms, genetic maps or models that

diff --git a/docs/cli_arguments.rst b/docs/cli_arguments.rst
@@ -7,4 +7,4 @@ Command-line options
 .. argparse::
 	:module: stdpopsim.cli
 	:func: stdpopsim_cli_parser
-	:prog: stdpopsim
+	:prog: stdpopsim