installing pre-commit hooks and manually run them

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+ignore =  E501, W503
+max-line-length = 79
+max-complexity = 18
+select = B,C,E,F,W,T4,B9,N
+exclude =
+**/migrations/**

.github/workflows/gh-pages.yaml

@@ -18,7 +18,7 @@ jobs:
         fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
     - name: install theme
       run: |
-            pip3 install sphinx-rtd-theme 
+            pip3 install sphinx-rtd-theme
             pip3 install .
     - name: Build and Commit
       uses: sphinx-notes/pages@master
@@ -28,4 +28,4 @@ jobs:
       uses: ad-m/github-push-action@master
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        branch: gh-pages
+        branch: gh-pages

.github/workflows/pyDataPipeline.yaml

@@ -59,6 +59,3 @@ jobs:
           fail_ci_if_error: false
           verbose: true
         if: matrix.python == '3.9' && matrix.os == 'ubuntu-20.04'
-
-
-

.gitignore

@@ -142,4 +142,4 @@ tmp/
 src/tests/ext/coderuns.txt
 data_store
 
-src/org/fairdatapipeline/simpleModel/ext/test.py
+src/org/fairdatapipeline/simpleModel/ext/test.py

.isort.cfg

@@ -0,0 +1,8 @@
+[settings]
+profile= black
+multi_line_output = 3
+include_trailing_comma = True
+force_grid_wrap = 0
+use_parentheses = True
+ensure_newline_before_comments = True
+line_length = 79

.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: check-ast
+    -   id: check-byte-order-marker
+    -   id: check-case-conflict
+    -   id: check-docstring-first
+    -   id: check-executables-have-shebangs
+    -   id: check-json
+    -   id: check-yaml
+    -   id: detect-aws-credentials
+    -   id: detect-private-key
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: mixed-line-ending
+    -   id: check-merge-conflict
+-   repo: https://github.com/ambv/black
+    rev: 21.5b1
+    hooks:
+    - id: black
+      args: ["--line-length","79"]
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.9.2
+    hooks:
+    - id: flake8
+-   repo: https://github.com/pycqa/isort
+    rev: 5.6.4
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
+-   repo: https://github.com/awslabs/cfn-python-lint
+    rev: v0.54.1 # The version of cfn-lint to use
+    hooks:
+    -   id: cfn-python-lint
+        files: templates/.*\.(json|yml|yaml)$
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v2.25.0
+    hooks:
+    -   id: pyupgrade

.zenodo.json

@@ -28,4 +28,4 @@
       "Python",
       "data"
     ]
-  }
+  }

MANIFEST.in

@@ -1 +1 @@
-recursive-include org fairdatapipeline simpleModel ext *
+recursive-include org fairdatapipeline simpleModel ext *

doc/_build/html/_sources/api/index.rst.txt

@@ -2,4 +2,4 @@ org.fairdatapipeline.api
 ========================
 
 .. automodule:: org.fairdatapipeline.api
-    :members:
+    :members:

doc/_build/html/_sources/examples/SEIRS.rst.txt

@@ -50,7 +50,7 @@ Once the :code:`fair pull` command has been run the following data product shoul
 fair run
 --------
 
-In order to run the script specified in :code:`run_metadata['script']` field of the config.yaml the command :code:`fair run` from the CLI Tools should be used, 
+In order to run the script specified in :code:`run_metadata['script']` field of the config.yaml the command :code:`fair run` from the CLI Tools should be used,
 Once again if the :code:`--ci` flag was used with the :code:`fair init` command then this must be from the :code:`local_repo` directory.
 This should also only be run after activating a poetry shell from the command line and installing the :code:`pyDataPipeline` package within the poetry virtual environment
 following the `Installation <../installation.html>`_ instructions.

doc/_build/html/_sources/index.rst.txt

@@ -13,4 +13,4 @@ Welcome to pyDataPipeline's documentation!
    installation.rst
    examples/SEIRS.rst
    api/index.rst
-   simpleModel/index.rst
+   simpleModel/index.rst

doc/_build/html/_sources/installation.rst.txt

@@ -10,4 +10,4 @@ To install the pyDataPipeline package the following commands should be run from
 
     pip3 install .
 
-**N.B. The pyDataPipeline Package requires Python 3**
+**N.B. The pyDataPipeline Package requires Python 3**

doc/_build/html/_sources/simpleModel/index.rst.txt

@@ -2,4 +2,4 @@ org.fairdatapipeline.simpleModel
 ================================
 
 .. automodule:: org.fairdatapipeline.simpleModel
-    :members:
+    :members:

doc/_build/html/_static/basic.css

@@ -901,4 +901,4 @@ div.math:hover a.headerlink {
     #top-link {
         display: none;
     }
-}
+}

doc/_build/html/_static/css/custom.css

@@ -3,4 +3,4 @@
     display: block;
     height: 500px;
     overflow-y: scroll;
-}
+}