Reorganization to ensure PyCQA Standards

.bandit

@@ -0,0 +1 @@
+skips: ['B101']

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+branch = True
+omit =
+    */.tox/*
+    */.local/*
+    */.cache/*
+    */tests/*

.env-example

@@ -1,4 +1,4 @@
 DATABASE_URL=postgresql://postgres:12345@localhost:5432/epidemiologic
 [email protected]
 MAIL_PASSWORD=ingreseunovalido
-HOST_URL=http://localhost:3000/
+HOST_URL=http://localhost:3000/

.gitignore

@@ -1,5 +1,29 @@
-venv/
-.idea/
-__pycache__/
-*.db
-.env
+.*
+!.bandit
+!.coveragerc
+!.gitignore
+!.isort.cfg
+!.pre-commit-config.yaml
+!.pylintrc*
+!.python-version
+!.remarkrc
+!.travis.yml
+!.tox.ini
+*.py[cod]
+*.ipynb*
+*.egg*
+*.env
+*.sqlite3
+*.pid
+__pycache__
+autogenerated/*
+build
+coverage.*
+dist
+frontend
+legacy
+old.*
+public
+public/*
+
+# File patterns

.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+known_third_party = bcrypt,dotenv,flask,flask_cors,flask_injector,flask_jwt_extended,flask_mail,flask_restful,flask_sqlalchemy,injector,jwt,numpy,scipy,sqlalchemy

.pre-commit-config.yaml

@@ -0,0 +1,57 @@
+repos:
+  - repo: https://github.com/ambv/black
+    rev: 19.10b0
+    hooks:
+      - id: black
+        language_version: python3.8
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v0.761"
+    hooks:
+      - id: mypy
+        language: system
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.2.3
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: flake8
+
+  - repo: https://github.com/asottile/seed-isort-config
+    rev: v1.9.2
+    hooks:
+      - id: seed-isort-config
+
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v4.3.21
+    hooks:
+      - id: isort
+        args: [--filter-files]
+
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 4.0.0
+    hooks:
+      - id: pydocstyle
+        files: ^epical/
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: master
+    hooks:
+      - id: nbstripout
+        files: ".ipynb"
+
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.6.2
+    hooks:
+      - id: bandit
+        args: [-c, .bandit, -r, epical]
+
+  - repo: local
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: system
+        types: [python]
+        args: [--rcfile, .pylintrc.local]

.pylintrc

@@ -0,0 +1,33 @@
+[MASTER]
+load-plugins=pylint.extensions.docparams,pylint.extensions.docstyle,pylint.extensions.bad_builtin,pylint.extensions.mccabe,pylint_flask
+persistent=yes
+profile=no
+cache-size=500
+ignore=migrations
+
+[MESSAGES CONTROL]
+disable=C0103,C0111,C0199,C301,C0303,C0412,C1001,E1004,I0011,R0903,W0232,W0621,W0223,C0301,W0511,F0401,E231
+# disable=C0111,I0011,I0012,W0704,W0142,W0212,W0232,W0613,W0702,R0201,R0903,C1001,C0103,R0901
+
+[DESIGN]
+max-parents=5
+max-complexity=5
+
+[SIMILARITIES]
+min-similarity-lines=8
+ignore-imports=yes
+ignore-comments=yes
+ignore-docstrings=yes
+
+[TYPECHECK]
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E0201 when accessed.
+generated-members=objects,DoesNotExist,id,pk,_meta,base_fields,context
+# List of method names used to declare (i.e. assign) instance attributes
+defining-attr-methods=__init__,__new__
+
+[MISCELLANEOUS]
+notes=FIXME,TODO

.pylintrc.local

@@ -0,0 +1,34 @@
+[MASTER]
+load-plugins=pylint.extensions.docparams,pylint.extensions.docstyle,pylint.extensions.bad_builtin,pylint.extensions.mccabe,pylint_flask
+persistent=yes
+profile=no
+cache-size=500
+ignore=migrations
+
+[MESSAGES CONTROL]
+disable=C0103, C0111, C0330, C0412, C1001, E1004, E1101, I0011, R0903, W0232, W0621
+# disable=C0103,C0111,C0199,C301,C0303,C0412,C1001,E1004,I0011,R0903,W0232,W0621,W0223,C0301,W0511,F0401,E231
+# disable=C0111,I0011,I0012,W0704,W0142,W0212,W0232,W0613,W0702,R0201,R0903,C1001,C0103,R0901
+
+[DESIGN]
+max-parents=5
+max-complexity=5
+
+[SIMILARITIES]
+min-similarity-lines=8
+ignore-imports=yes
+ignore-comments=yes
+ignore-docstrings=yes
+
+[TYPECHECK]
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E0201 when accessed.
+generated-members=objects,DoesNotExist,id,pk,_meta,base_fields,context
+# List of method names used to declare (i.e. assign) instance attributes
+defining-attr-methods=__init__,__new__
+
+[MISCELLANEOUS]
+notes=FIXME,TODO

.python-version

@@ -0,0 +1 @@
+3.8.1

.remarkrc

@@ -0,0 +1,6 @@
+{
+  "plugins": [
+    "remark-preset-lint-recommended",
+    ["remark-lint-list-item-indent", false]
+  ]
+}